assignmet5_Neerja.ipynb

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  "metadata": {
    "colab": {
      "name": "assignmet5_Neerja.ipynb",
      "provenance": []
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "KK-Ovk_OL8gb"
      },
      "source": [
        "Assignment 5\n",
        "\n",
        "\n",
        "\n",
        "\n",
        "\n",
        "\n",
        "\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "D8T7g_TzC3S5"
      },
      "source": [
        "Konzo is a distinct upper motor neuron disease that is prevalent in sub-Saharan Africa. As part of a pilot study to investigate the relationship of the gutmicrobiome and konzo, individuals with a heavy reliance on cassava, whose consumption without proper detoxification is implicated in konzo, were assessed from regions with varying prevalence of konzo. \n",
        "\n",
        "Samples were taken from the urban capital of Kinshasa (Kin) where no outbreaks of konzo are documented. Additional samples from a rural control, Masimanimba (Mas), where no outbreaks of konzo are historically reported were also taken. Individuals from two regions of high (HPZ) and low prevalence (LPZ) of konzo from the Kahemba region were taken with unaffected (U) and konzo (K) individuals from each. \n",
        "\n",
        "\n",
        "Bacteroides and Prevotella are genus that have known associations with urban and rural lifestyles, respectively. Here we assess using the Kruskal-Wallis test where there is a significant difference in the relative abundance of these genus in the six groups, and the data is visualized using box plots. "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "-5LcQaiSLiVJ"
      },
      "source": [
        "import pandas as pd\n",
        "import numpy as np\n",
        "import scipy\n",
        "import scipy.stats\n",
        "import plotly.express as px"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "KvGQD8EoYJte",
        "outputId": "ecc77f19-1d67-4298-9ad7-2456204093f2"
      },
      "source": [
        "from google.colab import drive\n",
        "drive.mount('/content/drive')"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Mounted at /content/drive\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "tAxzzMGdhIiQ",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 439
        },
        "outputId": "805e4a0f-9d78-4aff-fd25-342d18cd452e"
      },
      "source": [
        "#get csv file that contains read counts for genus for different samples. Header is true\n",
        "#1st column contains genus names. 2nd to 4th column is additional info. Starting at colum 5 is samples read counts for wach genus\n",
        "genus = pd.read_csv(\"/content/drive/My Drive/KinshasaControl_Konzo3_Bacteria_Genus_ReadCounts.csv\")\n",
        "genus"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
              "<div>\n",
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              "\n",
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              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>name</th>\n",
              "      <th>taxRank</th>\n",
              "      <th>taxID</th>\n",
              "      <th>Max</th>\n",
              "      <th>Konzo1</th>\n",
              "      <th>Konzo10</th>\n",
              "      <th>Konzo11</th>\n",
              "      <th>Konzo12</th>\n",
              "      <th>Konzo13</th>\n",
              "      <th>Konzo14</th>\n",
              "      <th>Konzo15</th>\n",
              "      <th>Konzo16</th>\n",
              "      <th>Konzo17</th>\n",
              "      <th>Konzo18</th>\n",
              "      <th>Konzo19</th>\n",
              "      <th>Konzo2</th>\n",
              "      <th>Konzo20</th>\n",
              "      <th>Konzo21</th>\n",
              "      <th>Konzo22</th>\n",
              "      <th>Konzo23</th>\n",
              "      <th>Konzo24</th>\n",
              "      <th>Konzo25</th>\n",
              "      <th>Konzo26</th>\n",
              "      <th>Konzo27</th>\n",
              "      <th>Konzo28</th>\n",
              "      <th>Konzo29</th>\n",
              "      <th>Konzo3</th>\n",
              "      <th>Konzo30</th>\n",
              "      <th>Konzo4</th>\n",
              "      <th>Konzo5</th>\n",
              "      <th>Konzo6</th>\n",
              "      <th>Konzo7</th>\n",
              "      <th>Konzo8</th>\n",
              "      <th>Konzo9</th>\n",
              "      <th>L256</th>\n",
              "      <th>L257</th>\n",
              "      <th>L258</th>\n",
              "      <th>L259</th>\n",
              "      <th>L260</th>\n",
              "      <th>L261</th>\n",
              "      <th>...</th>\n",
              "      <th>L366</th>\n",
              "      <th>L367</th>\n",
              "      <th>L368</th>\n",
              "      <th>L369</th>\n",
              "      <th>L370</th>\n",
              "      <th>L371</th>\n",
              "      <th>L372</th>\n",
              "      <th>L373</th>\n",
              "      <th>L374</th>\n",
              "      <th>L375</th>\n",
              "      <th>L376</th>\n",
              "      <th>L377</th>\n",
              "      <th>L378</th>\n",
              "      <th>L379</th>\n",
              "      <th>L380</th>\n",
              "      <th>L381</th>\n",
              "      <th>L382</th>\n",
              "      <th>L383</th>\n",
              "      <th>L384</th>\n",
              "      <th>L385</th>\n",
              "      <th>L386</th>\n",
              "      <th>L387</th>\n",
              "      <th>L388</th>\n",
              "      <th>L389</th>\n",
              "      <th>L390</th>\n",
              "      <th>L391</th>\n",
              "      <th>L392</th>\n",
              "      <th>L393</th>\n",
              "      <th>L394</th>\n",
              "      <th>L395</th>\n",
              "      <th>L396</th>\n",
              "      <th>L397</th>\n",
              "      <th>L398</th>\n",
              "      <th>L399</th>\n",
              "      <th>L400</th>\n",
              "      <th>L401</th>\n",
              "      <th>L402</th>\n",
              "      <th>L403</th>\n",
              "      <th>L404</th>\n",
              "      <th>L405</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>Faecalibacterium</td>\n",
              "      <td>G</td>\n",
              "      <td>216851</td>\n",
              "      <td>1039600</td>\n",
              "      <td>237552.0</td>\n",
              "      <td>436447.0</td>\n",
              "      <td>41899.0</td>\n",
              "      <td>49418.0</td>\n",
              "      <td>196823.0</td>\n",
              "      <td>56203.0</td>\n",
              "      <td>273675.0</td>\n",
              "      <td>348818.0</td>\n",
              "      <td>135830.0</td>\n",
              "      <td>172076.0</td>\n",
              "      <td>226901.0</td>\n",
              "      <td>319508.0</td>\n",
              "      <td>78705.0</td>\n",
              "      <td>152934.0</td>\n",
              "      <td>106510.0</td>\n",
              "      <td>221411.0</td>\n",
              "      <td>120803.0</td>\n",
              "      <td>258581.0</td>\n",
              "      <td>194292.0</td>\n",
              "      <td>182578.0</td>\n",
              "      <td>119224.0</td>\n",
              "      <td>53910.0</td>\n",
              "      <td>136636.0</td>\n",
              "      <td>79594.0</td>\n",
              "      <td>237466.0</td>\n",
              "      <td>180736.0</td>\n",
              "      <td>257475.0</td>\n",
              "      <td>233646.0</td>\n",
              "      <td>102718.0</td>\n",
              "      <td>297154.0</td>\n",
              "      <td>99767.0</td>\n",
              "      <td>63494.0</td>\n",
              "      <td>310526.0</td>\n",
              "      <td>147088.0</td>\n",
              "      <td>62406.0</td>\n",
              "      <td>213731.0</td>\n",
              "      <td>...</td>\n",
              "      <td>87457.0</td>\n",
              "      <td>169022.0</td>\n",
              "      <td>252772.0</td>\n",
              "      <td>67071.0</td>\n",
              "      <td>154866.0</td>\n",
              "      <td>123966.0</td>\n",
              "      <td>147969.0</td>\n",
              "      <td>87224.0</td>\n",
              "      <td>412471.0</td>\n",
              "      <td>392430.0</td>\n",
              "      <td>68690.0</td>\n",
              "      <td>69037.0</td>\n",
              "      <td>79134.0</td>\n",
              "      <td>41534.0</td>\n",
              "      <td>57960.0</td>\n",
              "      <td>61648.0</td>\n",
              "      <td>79475.0</td>\n",
              "      <td>69929.0</td>\n",
              "      <td>71135.0</td>\n",
              "      <td>98710.0</td>\n",
              "      <td>114945.0</td>\n",
              "      <td>217643.0</td>\n",
              "      <td>84898.0</td>\n",
              "      <td>63051.0</td>\n",
              "      <td>88251.0</td>\n",
              "      <td>76036.0</td>\n",
              "      <td>84981.0</td>\n",
              "      <td>110968.0</td>\n",
              "      <td>100540.0</td>\n",
              "      <td>125155.0</td>\n",
              "      <td>84072.0</td>\n",
              "      <td>50898.0</td>\n",
              "      <td>64280.0</td>\n",
              "      <td>126806.0</td>\n",
              "      <td>88492.0</td>\n",
              "      <td>37992.0</td>\n",
              "      <td>97351.0</td>\n",
              "      <td>64883.0</td>\n",
              "      <td>56363.0</td>\n",
              "      <td>106824.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>Ruminococcus</td>\n",
              "      <td>G</td>\n",
              "      <td>1263</td>\n",
              "      <td>706880</td>\n",
              "      <td>19084.0</td>\n",
              "      <td>11769.0</td>\n",
              "      <td>8667.0</td>\n",
              "      <td>7950.0</td>\n",
              "      <td>10919.0</td>\n",
              "      <td>1875.0</td>\n",
              "      <td>706876.0</td>\n",
              "      <td>14668.0</td>\n",
              "      <td>114060.0</td>\n",
              "      <td>2810.0</td>\n",
              "      <td>6647.0</td>\n",
              "      <td>4887.0</td>\n",
              "      <td>9346.0</td>\n",
              "      <td>20469.0</td>\n",
              "      <td>17325.0</td>\n",
              "      <td>36188.0</td>\n",
              "      <td>21358.0</td>\n",
              "      <td>22670.0</td>\n",
              "      <td>1729.0</td>\n",
              "      <td>19525.0</td>\n",
              "      <td>7267.0</td>\n",
              "      <td>1953.0</td>\n",
              "      <td>31420.0</td>\n",
              "      <td>18361.0</td>\n",
              "      <td>29369.0</td>\n",
              "      <td>10044.0</td>\n",
              "      <td>29057.0</td>\n",
              "      <td>23134.0</td>\n",
              "      <td>6995.0</td>\n",
              "      <td>16986.0</td>\n",
              "      <td>3983.0</td>\n",
              "      <td>3161.0</td>\n",
              "      <td>30267.0</td>\n",
              "      <td>19444.0</td>\n",
              "      <td>1394.0</td>\n",
              "      <td>5306.0</td>\n",
              "      <td>...</td>\n",
              "      <td>7459.0</td>\n",
              "      <td>1437.0</td>\n",
              "      <td>16129.0</td>\n",
              "      <td>2431.0</td>\n",
              "      <td>8095.0</td>\n",
              "      <td>1880.0</td>\n",
              "      <td>5035.0</td>\n",
              "      <td>6042.0</td>\n",
              "      <td>4028.0</td>\n",
              "      <td>5651.0</td>\n",
              "      <td>3144.0</td>\n",
              "      <td>6815.0</td>\n",
              "      <td>1098.0</td>\n",
              "      <td>49956.0</td>\n",
              "      <td>4508.0</td>\n",
              "      <td>18871.0</td>\n",
              "      <td>5900.0</td>\n",
              "      <td>5068.0</td>\n",
              "      <td>6314.0</td>\n",
              "      <td>8399.0</td>\n",
              "      <td>20483.0</td>\n",
              "      <td>3728.0</td>\n",
              "      <td>10738.0</td>\n",
              "      <td>7390.0</td>\n",
              "      <td>4386.0</td>\n",
              "      <td>1293.0</td>\n",
              "      <td>9604.0</td>\n",
              "      <td>15645.0</td>\n",
              "      <td>22208.0</td>\n",
              "      <td>5877.0</td>\n",
              "      <td>3440.0</td>\n",
              "      <td>7991.0</td>\n",
              "      <td>1614.0</td>\n",
              "      <td>23741.0</td>\n",
              "      <td>3251.0</td>\n",
              "      <td>1314.0</td>\n",
              "      <td>5425.0</td>\n",
              "      <td>2741.0</td>\n",
              "      <td>1678.0</td>\n",
              "      <td>3434.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>Flavonifractor</td>\n",
              "      <td>G</td>\n",
              "      <td>946234</td>\n",
              "      <td>15968</td>\n",
              "      <td>11762.0</td>\n",
              "      <td>4310.0</td>\n",
              "      <td>1908.0</td>\n",
              "      <td>1863.0</td>\n",
              "      <td>10275.0</td>\n",
              "      <td>1337.0</td>\n",
              "      <td>4105.0</td>\n",
              "      <td>11588.0</td>\n",
              "      <td>5807.0</td>\n",
              "      <td>2064.0</td>\n",
              "      <td>11334.0</td>\n",
              "      <td>1779.0</td>\n",
              "      <td>15968.0</td>\n",
              "      <td>7628.0</td>\n",
              "      <td>10360.0</td>\n",
              "      <td>6539.0</td>\n",
              "      <td>2969.0</td>\n",
              "      <td>14999.0</td>\n",
              "      <td>9249.0</td>\n",
              "      <td>2606.0</td>\n",
              "      <td>9718.0</td>\n",
              "      <td>1181.0</td>\n",
              "      <td>8202.0</td>\n",
              "      <td>6618.0</td>\n",
              "      <td>4220.0</td>\n",
              "      <td>3191.0</td>\n",
              "      <td>10873.0</td>\n",
              "      <td>2066.0</td>\n",
              "      <td>5276.0</td>\n",
              "      <td>8618.0</td>\n",
              "      <td>1323.0</td>\n",
              "      <td>1035.0</td>\n",
              "      <td>5889.0</td>\n",
              "      <td>7181.0</td>\n",
              "      <td>325.0</td>\n",
              "      <td>1623.0</td>\n",
              "      <td>...</td>\n",
              "      <td>8419.0</td>\n",
              "      <td>507.0</td>\n",
              "      <td>4860.0</td>\n",
              "      <td>658.0</td>\n",
              "      <td>1841.0</td>\n",
              "      <td>536.0</td>\n",
              "      <td>2136.0</td>\n",
              "      <td>10020.0</td>\n",
              "      <td>1741.0</td>\n",
              "      <td>2499.0</td>\n",
              "      <td>9033.0</td>\n",
              "      <td>5076.0</td>\n",
              "      <td>954.0</td>\n",
              "      <td>5853.0</td>\n",
              "      <td>1772.0</td>\n",
              "      <td>6543.0</td>\n",
              "      <td>3542.0</td>\n",
              "      <td>1087.0</td>\n",
              "      <td>1958.0</td>\n",
              "      <td>7029.0</td>\n",
              "      <td>9622.0</td>\n",
              "      <td>4134.0</td>\n",
              "      <td>3805.0</td>\n",
              "      <td>3148.0</td>\n",
              "      <td>4372.0</td>\n",
              "      <td>424.0</td>\n",
              "      <td>6350.0</td>\n",
              "      <td>2571.0</td>\n",
              "      <td>7833.0</td>\n",
              "      <td>5694.0</td>\n",
              "      <td>2049.0</td>\n",
              "      <td>1128.0</td>\n",
              "      <td>836.0</td>\n",
              "      <td>7474.0</td>\n",
              "      <td>734.0</td>\n",
              "      <td>420.0</td>\n",
              "      <td>3920.0</td>\n",
              "      <td>755.0</td>\n",
              "      <td>783.0</td>\n",
              "      <td>804.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>Caproiciproducens</td>\n",
              "      <td>G</td>\n",
              "      <td>1738645</td>\n",
              "      <td>2533</td>\n",
              "      <td>2391.0</td>\n",
              "      <td>860.0</td>\n",
              "      <td>374.0</td>\n",
              "      <td>293.0</td>\n",
              "      <td>1237.0</td>\n",
              "      <td>378.0</td>\n",
              "      <td>877.0</td>\n",
              "      <td>1772.0</td>\n",
              "      <td>625.0</td>\n",
              "      <td>302.0</td>\n",
              "      <td>1490.0</td>\n",
              "      <td>402.0</td>\n",
              "      <td>2122.0</td>\n",
              "      <td>1344.0</td>\n",
              "      <td>1635.0</td>\n",
              "      <td>1846.0</td>\n",
              "      <td>1566.0</td>\n",
              "      <td>1957.0</td>\n",
              "      <td>503.0</td>\n",
              "      <td>2170.0</td>\n",
              "      <td>1189.0</td>\n",
              "      <td>312.0</td>\n",
              "      <td>1488.0</td>\n",
              "      <td>2384.0</td>\n",
              "      <td>1024.0</td>\n",
              "      <td>727.0</td>\n",
              "      <td>1797.0</td>\n",
              "      <td>537.0</td>\n",
              "      <td>937.0</td>\n",
              "      <td>1655.0</td>\n",
              "      <td>373.0</td>\n",
              "      <td>372.0</td>\n",
              "      <td>1171.0</td>\n",
              "      <td>1468.0</td>\n",
              "      <td>121.0</td>\n",
              "      <td>476.0</td>\n",
              "      <td>...</td>\n",
              "      <td>1436.0</td>\n",
              "      <td>250.0</td>\n",
              "      <td>1240.0</td>\n",
              "      <td>172.0</td>\n",
              "      <td>860.0</td>\n",
              "      <td>200.0</td>\n",
              "      <td>555.0</td>\n",
              "      <td>1491.0</td>\n",
              "      <td>450.0</td>\n",
              "      <td>668.0</td>\n",
              "      <td>342.0</td>\n",
              "      <td>853.0</td>\n",
              "      <td>123.0</td>\n",
              "      <td>709.0</td>\n",
              "      <td>400.0</td>\n",
              "      <td>1304.0</td>\n",
              "      <td>702.0</td>\n",
              "      <td>272.0</td>\n",
              "      <td>583.0</td>\n",
              "      <td>1319.0</td>\n",
              "      <td>1722.0</td>\n",
              "      <td>681.0</td>\n",
              "      <td>794.0</td>\n",
              "      <td>586.0</td>\n",
              "      <td>955.0</td>\n",
              "      <td>139.0</td>\n",
              "      <td>1045.0</td>\n",
              "      <td>549.0</td>\n",
              "      <td>1327.0</td>\n",
              "      <td>1086.0</td>\n",
              "      <td>360.0</td>\n",
              "      <td>314.0</td>\n",
              "      <td>132.0</td>\n",
              "      <td>1324.0</td>\n",
              "      <td>142.0</td>\n",
              "      <td>89.0</td>\n",
              "      <td>628.0</td>\n",
              "      <td>135.0</td>\n",
              "      <td>177.0</td>\n",
              "      <td>261.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>Ethanoligenens</td>\n",
              "      <td>G</td>\n",
              "      <td>253238</td>\n",
              "      <td>2388</td>\n",
              "      <td>2011.0</td>\n",
              "      <td>764.0</td>\n",
              "      <td>490.0</td>\n",
              "      <td>292.0</td>\n",
              "      <td>1309.0</td>\n",
              "      <td>482.0</td>\n",
              "      <td>678.0</td>\n",
              "      <td>1877.0</td>\n",
              "      <td>610.0</td>\n",
              "      <td>287.0</td>\n",
              "      <td>1622.0</td>\n",
              "      <td>454.0</td>\n",
              "      <td>2180.0</td>\n",
              "      <td>1014.0</td>\n",
              "      <td>1741.0</td>\n",
              "      <td>1025.0</td>\n",
              "      <td>767.0</td>\n",
              "      <td>2037.0</td>\n",
              "      <td>460.0</td>\n",
              "      <td>880.0</td>\n",
              "      <td>1358.0</td>\n",
              "      <td>261.0</td>\n",
              "      <td>1191.0</td>\n",
              "      <td>1310.0</td>\n",
              "      <td>812.0</td>\n",
              "      <td>627.0</td>\n",
              "      <td>1677.0</td>\n",
              "      <td>468.0</td>\n",
              "      <td>727.0</td>\n",
              "      <td>1439.0</td>\n",
              "      <td>364.0</td>\n",
              "      <td>201.0</td>\n",
              "      <td>1063.0</td>\n",
              "      <td>1302.0</td>\n",
              "      <td>105.0</td>\n",
              "      <td>410.0</td>\n",
              "      <td>...</td>\n",
              "      <td>1291.0</td>\n",
              "      <td>223.0</td>\n",
              "      <td>1022.0</td>\n",
              "      <td>199.0</td>\n",
              "      <td>711.0</td>\n",
              "      <td>170.0</td>\n",
              "      <td>463.0</td>\n",
              "      <td>1648.0</td>\n",
              "      <td>452.0</td>\n",
              "      <td>658.0</td>\n",
              "      <td>304.0</td>\n",
              "      <td>798.0</td>\n",
              "      <td>163.0</td>\n",
              "      <td>744.0</td>\n",
              "      <td>401.0</td>\n",
              "      <td>1304.0</td>\n",
              "      <td>657.0</td>\n",
              "      <td>296.0</td>\n",
              "      <td>583.0</td>\n",
              "      <td>1234.0</td>\n",
              "      <td>1857.0</td>\n",
              "      <td>726.0</td>\n",
              "      <td>743.0</td>\n",
              "      <td>617.0</td>\n",
              "      <td>845.0</td>\n",
              "      <td>116.0</td>\n",
              "      <td>1091.0</td>\n",
              "      <td>499.0</td>\n",
              "      <td>1347.0</td>\n",
              "      <td>1050.0</td>\n",
              "      <td>386.0</td>\n",
              "      <td>366.0</td>\n",
              "      <td>151.0</td>\n",
              "      <td>1313.0</td>\n",
              "      <td>202.0</td>\n",
              "      <td>75.0</td>\n",
              "      <td>658.0</td>\n",
              "      <td>220.0</td>\n",
              "      <td>209.0</td>\n",
              "      <td>259.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1145</th>\n",
              "      <td>Caldimicrobium</td>\n",
              "      <td>G</td>\n",
              "      <td>444090</td>\n",
              "      <td>208</td>\n",
              "      <td>28.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>26.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>71.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>44.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>33.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>52.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>23.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>46.0</td>\n",
              "      <td>82.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>70.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>...</td>\n",
              "      <td>13.0</td>\n",
              "      <td>98.0</td>\n",
              "      <td>105.0</td>\n",
              "      <td>73.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>47.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>99.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>32.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>29.0</td>\n",
              "      <td>26.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>57.0</td>\n",
              "      <td>40.0</td>\n",
              "      <td>50.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>51.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>69.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>64.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>50.0</td>\n",
              "      <td>26.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1146</th>\n",
              "      <td>Thermodesulfatator</td>\n",
              "      <td>G</td>\n",
              "      <td>241192</td>\n",
              "      <td>146</td>\n",
              "      <td>19.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>17.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>65.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>47.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>52.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>57.0</td>\n",
              "      <td>54.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>45.0</td>\n",
              "      <td>26.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>112.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>62.0</td>\n",
              "      <td>146.0</td>\n",
              "      <td>64.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>88.0</td>\n",
              "      <td>44.0</td>\n",
              "      <td>...</td>\n",
              "      <td>32.0</td>\n",
              "      <td>49.0</td>\n",
              "      <td>96.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>46.0</td>\n",
              "      <td>52.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>135.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>55.0</td>\n",
              "      <td>47.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>72.0</td>\n",
              "      <td>36.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>46.0</td>\n",
              "      <td>32.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>50.0</td>\n",
              "      <td>82.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>48.0</td>\n",
              "      <td>34.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>55.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>45.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>70.0</td>\n",
              "      <td>39.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1147</th>\n",
              "      <td>Dictyoglomus</td>\n",
              "      <td>G</td>\n",
              "      <td>13</td>\n",
              "      <td>241</td>\n",
              "      <td>62.0</td>\n",
              "      <td>76.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>73.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>96.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>72.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>58.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>40.0</td>\n",
              "      <td>158.0</td>\n",
              "      <td>36.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>95.0</td>\n",
              "      <td>54.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>95.0</td>\n",
              "      <td>67.0</td>\n",
              "      <td>59.0</td>\n",
              "      <td>84.0</td>\n",
              "      <td>51.0</td>\n",
              "      <td>72.0</td>\n",
              "      <td>55.0</td>\n",
              "      <td>109.0</td>\n",
              "      <td>56.0</td>\n",
              "      <td>114.0</td>\n",
              "      <td>73.0</td>\n",
              "      <td>95.0</td>\n",
              "      <td>74.0</td>\n",
              "      <td>61.0</td>\n",
              "      <td>...</td>\n",
              "      <td>59.0</td>\n",
              "      <td>94.0</td>\n",
              "      <td>142.0</td>\n",
              "      <td>45.0</td>\n",
              "      <td>139.0</td>\n",
              "      <td>92.0</td>\n",
              "      <td>114.0</td>\n",
              "      <td>85.0</td>\n",
              "      <td>206.0</td>\n",
              "      <td>154.0</td>\n",
              "      <td>17.0</td>\n",
              "      <td>241.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>87.0</td>\n",
              "      <td>87.0</td>\n",
              "      <td>103.0</td>\n",
              "      <td>63.0</td>\n",
              "      <td>53.0</td>\n",
              "      <td>75.0</td>\n",
              "      <td>92.0</td>\n",
              "      <td>112.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>66.0</td>\n",
              "      <td>47.0</td>\n",
              "      <td>90.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>40.0</td>\n",
              "      <td>66.0</td>\n",
              "      <td>85.0</td>\n",
              "      <td>60.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>65.0</td>\n",
              "      <td>75.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>64.0</td>\n",
              "      <td>52.0</td>\n",
              "      <td>155.0</td>\n",
              "      <td>35.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1148</th>\n",
              "      <td>Caldisericum</td>\n",
              "      <td>G</td>\n",
              "      <td>693074</td>\n",
              "      <td>78</td>\n",
              "      <td>39.0</td>\n",
              "      <td>32.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>2.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>17.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>29.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>55.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>33.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>23.0</td>\n",
              "      <td>...</td>\n",
              "      <td>15.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>23.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>2.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>29.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>26.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>49.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>54.0</td>\n",
              "      <td>2.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>16.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1149</th>\n",
              "      <td>Coprothermobacter</td>\n",
              "      <td>G</td>\n",
              "      <td>68335</td>\n",
              "      <td>82</td>\n",
              "      <td>14.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>78.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>1.0</td>\n",
              "      <td>17.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>44.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>23.0</td>\n",
              "      <td>...</td>\n",
              "      <td>8.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>63.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>1.0</td>\n",
              "      <td>46.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>34.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>9.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>1150 rows × 184 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                    name taxRank    taxID  ...     L403     L404      L405\n",
              "0       Faecalibacterium       G   216851  ...  64883.0  56363.0  106824.0\n",
              "1           Ruminococcus       G     1263  ...   2741.0   1678.0    3434.0\n",
              "2         Flavonifractor       G   946234  ...    755.0    783.0     804.0\n",
              "3      Caproiciproducens       G  1738645  ...    135.0    177.0     261.0\n",
              "4         Ethanoligenens       G   253238  ...    220.0    209.0     259.0\n",
              "...                  ...     ...      ...  ...      ...      ...       ...\n",
              "1145      Caldimicrobium       G   444090  ...     30.0     50.0      26.0\n",
              "1146  Thermodesulfatator       G   241192  ...     41.0     70.0      39.0\n",
              "1147        Dictyoglomus       G       13  ...     52.0    155.0      35.0\n",
              "1148        Caldisericum       G   693074  ...      8.0      6.0      16.0\n",
              "1149   Coprothermobacter       G    68335  ...     39.0     15.0       9.0\n",
              "\n",
              "[1150 rows x 184 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 58
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "CqINnA5eheXq",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 419
        },
        "outputId": "2d5826fa-8591-47c1-a4cb-1df9cdbfe4ea"
      },
      "source": [
        "#meta file contains sample data (such as which geographical location were the samples collected from)\n",
        "meta = pd.read_csv(\"/content/drive/My Drive/KinshasaControl_Konzo3_sampleData.csv\")\n",
        "meta"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Sample</th>\n",
              "      <th>Name</th>\n",
              "      <th>ID</th>\n",
              "      <th>Region</th>\n",
              "      <th>Status</th>\n",
              "      <th>Disease</th>\n",
              "      <th>Age</th>\n",
              "      <th>Sex</th>\n",
              "      <th>Geography</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>Konzo1</td>\n",
              "      <td>Konzo1</td>\n",
              "      <td>Konzo1_S1</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>8</td>\n",
              "      <td>M</td>\n",
              "      <td>Kinshasa</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>Konzo2</td>\n",
              "      <td>Konzo2</td>\n",
              "      <td>Konzo2_S6</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>6</td>\n",
              "      <td>F</td>\n",
              "      <td>Kinshasa</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>Konzo3</td>\n",
              "      <td>Konzo3</td>\n",
              "      <td>Konzo3_S11</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>10</td>\n",
              "      <td>F</td>\n",
              "      <td>Kinshasa</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>Konzo4</td>\n",
              "      <td>Konzo4</td>\n",
              "      <td>Konzo4_S14</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>9</td>\n",
              "      <td>M</td>\n",
              "      <td>Kinshasa</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>Konzo5</td>\n",
              "      <td>Konzo5</td>\n",
              "      <td>Konzo5_S17</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Kinshasa</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>8</td>\n",
              "      <td>F</td>\n",
              "      <td>Kinshasa</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>175</th>\n",
              "      <td>L401</td>\n",
              "      <td>Konzo401</td>\n",
              "      <td>L401_Mas 22_Vilain_181127</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>8</td>\n",
              "      <td>M</td>\n",
              "      <td>Masimanimba</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>176</th>\n",
              "      <td>L402</td>\n",
              "      <td>Konzo402</td>\n",
              "      <td>L402_Mas 31_Vilain_181127</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>12</td>\n",
              "      <td>F</td>\n",
              "      <td>Masimanimba</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>177</th>\n",
              "      <td>L403</td>\n",
              "      <td>Konzo403</td>\n",
              "      <td>L403_Mas 30_Vilain_181127</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>10</td>\n",
              "      <td>F</td>\n",
              "      <td>Masimanimba</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>178</th>\n",
              "      <td>L404</td>\n",
              "      <td>Konzo404</td>\n",
              "      <td>L404_Mas 35_Vilain_181127</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>13</td>\n",
              "      <td>F</td>\n",
              "      <td>Masimanimba</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>179</th>\n",
              "      <td>L405</td>\n",
              "      <td>Konzo405</td>\n",
              "      <td>L405_Mas 33_Vilain_181127</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Masimanimba</td>\n",
              "      <td>Unaffected</td>\n",
              "      <td>7</td>\n",
              "      <td>F</td>\n",
              "      <td>Masimanimba</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>180 rows × 9 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "     Sample      Name                         ID  ... Age Sex    Geography\n",
              "0    Konzo1    Konzo1                  Konzo1_S1  ...   8   M     Kinshasa\n",
              "1    Konzo2    Konzo2                  Konzo2_S6  ...   6   F     Kinshasa\n",
              "2    Konzo3    Konzo3                 Konzo3_S11  ...  10   F     Kinshasa\n",
              "3    Konzo4    Konzo4                 Konzo4_S14  ...   9   M     Kinshasa\n",
              "4    Konzo5    Konzo5                 Konzo5_S17  ...   8   F     Kinshasa\n",
              "..      ...       ...                        ...  ...  ..  ..          ...\n",
              "175    L401  Konzo401  L401_Mas 22_Vilain_181127  ...   8   M  Masimanimba\n",
              "176    L402  Konzo402  L402_Mas 31_Vilain_181127  ...  12   F  Masimanimba\n",
              "177    L403  Konzo403  L403_Mas 30_Vilain_181127  ...  10   F  Masimanimba\n",
              "178    L404  Konzo404  L404_Mas 35_Vilain_181127  ...  13   F  Masimanimba\n",
              "179    L405  Konzo405  L405_Mas 33_Vilain_181127  ...   7   F  Masimanimba\n",
              "\n",
              "[180 rows x 9 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 49
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "2ARfL38mhs_d",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 439
        },
        "outputId": "9fbfa1ef-c884-46c2-c061-c352941f6f85"
      },
      "source": [
        "#set NA's to 0. Remove the unnecessary colums\n",
        "genus = genus.replace(np.nan,0)\n",
        "genus.pop(\"taxRank\")\n",
        "genus.pop(\"taxID\")\n",
        "genus.pop(\"Max\")\n",
        "genus"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
              "<div>\n",
              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
              "        vertical-align: middle;\n",
              "    }\n",
              "\n",
              "    .dataframe tbody tr th {\n",
              "        vertical-align: top;\n",
              "    }\n",
              "\n",
              "    .dataframe thead th {\n",
              "        text-align: right;\n",
              "    }\n",
              "</style>\n",
              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>name</th>\n",
              "      <th>Konzo1</th>\n",
              "      <th>Konzo10</th>\n",
              "      <th>Konzo11</th>\n",
              "      <th>Konzo12</th>\n",
              "      <th>Konzo13</th>\n",
              "      <th>Konzo14</th>\n",
              "      <th>Konzo15</th>\n",
              "      <th>Konzo16</th>\n",
              "      <th>Konzo17</th>\n",
              "      <th>Konzo18</th>\n",
              "      <th>Konzo19</th>\n",
              "      <th>Konzo2</th>\n",
              "      <th>Konzo20</th>\n",
              "      <th>Konzo21</th>\n",
              "      <th>Konzo22</th>\n",
              "      <th>Konzo23</th>\n",
              "      <th>Konzo24</th>\n",
              "      <th>Konzo25</th>\n",
              "      <th>Konzo26</th>\n",
              "      <th>Konzo27</th>\n",
              "      <th>Konzo28</th>\n",
              "      <th>Konzo29</th>\n",
              "      <th>Konzo3</th>\n",
              "      <th>Konzo30</th>\n",
              "      <th>Konzo4</th>\n",
              "      <th>Konzo5</th>\n",
              "      <th>Konzo6</th>\n",
              "      <th>Konzo7</th>\n",
              "      <th>Konzo8</th>\n",
              "      <th>Konzo9</th>\n",
              "      <th>L256</th>\n",
              "      <th>L257</th>\n",
              "      <th>L258</th>\n",
              "      <th>L259</th>\n",
              "      <th>L260</th>\n",
              "      <th>L261</th>\n",
              "      <th>L262</th>\n",
              "      <th>L263</th>\n",
              "      <th>L264</th>\n",
              "      <th>...</th>\n",
              "      <th>L366</th>\n",
              "      <th>L367</th>\n",
              "      <th>L368</th>\n",
              "      <th>L369</th>\n",
              "      <th>L370</th>\n",
              "      <th>L371</th>\n",
              "      <th>L372</th>\n",
              "      <th>L373</th>\n",
              "      <th>L374</th>\n",
              "      <th>L375</th>\n",
              "      <th>L376</th>\n",
              "      <th>L377</th>\n",
              "      <th>L378</th>\n",
              "      <th>L379</th>\n",
              "      <th>L380</th>\n",
              "      <th>L381</th>\n",
              "      <th>L382</th>\n",
              "      <th>L383</th>\n",
              "      <th>L384</th>\n",
              "      <th>L385</th>\n",
              "      <th>L386</th>\n",
              "      <th>L387</th>\n",
              "      <th>L388</th>\n",
              "      <th>L389</th>\n",
              "      <th>L390</th>\n",
              "      <th>L391</th>\n",
              "      <th>L392</th>\n",
              "      <th>L393</th>\n",
              "      <th>L394</th>\n",
              "      <th>L395</th>\n",
              "      <th>L396</th>\n",
              "      <th>L397</th>\n",
              "      <th>L398</th>\n",
              "      <th>L399</th>\n",
              "      <th>L400</th>\n",
              "      <th>L401</th>\n",
              "      <th>L402</th>\n",
              "      <th>L403</th>\n",
              "      <th>L404</th>\n",
              "      <th>L405</th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>0</th>\n",
              "      <td>Faecalibacterium</td>\n",
              "      <td>237552.0</td>\n",
              "      <td>436447.0</td>\n",
              "      <td>41899.0</td>\n",
              "      <td>49418.0</td>\n",
              "      <td>196823.0</td>\n",
              "      <td>56203.0</td>\n",
              "      <td>273675.0</td>\n",
              "      <td>348818.0</td>\n",
              "      <td>135830.0</td>\n",
              "      <td>172076.0</td>\n",
              "      <td>226901.0</td>\n",
              "      <td>319508.0</td>\n",
              "      <td>78705.0</td>\n",
              "      <td>152934.0</td>\n",
              "      <td>106510.0</td>\n",
              "      <td>221411.0</td>\n",
              "      <td>120803.0</td>\n",
              "      <td>258581.0</td>\n",
              "      <td>194292.0</td>\n",
              "      <td>182578.0</td>\n",
              "      <td>119224.0</td>\n",
              "      <td>53910.0</td>\n",
              "      <td>136636.0</td>\n",
              "      <td>79594.0</td>\n",
              "      <td>237466.0</td>\n",
              "      <td>180736.0</td>\n",
              "      <td>257475.0</td>\n",
              "      <td>233646.0</td>\n",
              "      <td>102718.0</td>\n",
              "      <td>297154.0</td>\n",
              "      <td>99767.0</td>\n",
              "      <td>63494.0</td>\n",
              "      <td>310526.0</td>\n",
              "      <td>147088.0</td>\n",
              "      <td>62406.0</td>\n",
              "      <td>213731.0</td>\n",
              "      <td>141049.0</td>\n",
              "      <td>95251.0</td>\n",
              "      <td>137988.0</td>\n",
              "      <td>...</td>\n",
              "      <td>87457.0</td>\n",
              "      <td>169022.0</td>\n",
              "      <td>252772.0</td>\n",
              "      <td>67071.0</td>\n",
              "      <td>154866.0</td>\n",
              "      <td>123966.0</td>\n",
              "      <td>147969.0</td>\n",
              "      <td>87224.0</td>\n",
              "      <td>412471.0</td>\n",
              "      <td>392430.0</td>\n",
              "      <td>68690.0</td>\n",
              "      <td>69037.0</td>\n",
              "      <td>79134.0</td>\n",
              "      <td>41534.0</td>\n",
              "      <td>57960.0</td>\n",
              "      <td>61648.0</td>\n",
              "      <td>79475.0</td>\n",
              "      <td>69929.0</td>\n",
              "      <td>71135.0</td>\n",
              "      <td>98710.0</td>\n",
              "      <td>114945.0</td>\n",
              "      <td>217643.0</td>\n",
              "      <td>84898.0</td>\n",
              "      <td>63051.0</td>\n",
              "      <td>88251.0</td>\n",
              "      <td>76036.0</td>\n",
              "      <td>84981.0</td>\n",
              "      <td>110968.0</td>\n",
              "      <td>100540.0</td>\n",
              "      <td>125155.0</td>\n",
              "      <td>84072.0</td>\n",
              "      <td>50898.0</td>\n",
              "      <td>64280.0</td>\n",
              "      <td>126806.0</td>\n",
              "      <td>88492.0</td>\n",
              "      <td>37992.0</td>\n",
              "      <td>97351.0</td>\n",
              "      <td>64883.0</td>\n",
              "      <td>56363.0</td>\n",
              "      <td>106824.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>Ruminococcus</td>\n",
              "      <td>19084.0</td>\n",
              "      <td>11769.0</td>\n",
              "      <td>8667.0</td>\n",
              "      <td>7950.0</td>\n",
              "      <td>10919.0</td>\n",
              "      <td>1875.0</td>\n",
              "      <td>706876.0</td>\n",
              "      <td>14668.0</td>\n",
              "      <td>114060.0</td>\n",
              "      <td>2810.0</td>\n",
              "      <td>6647.0</td>\n",
              "      <td>4887.0</td>\n",
              "      <td>9346.0</td>\n",
              "      <td>20469.0</td>\n",
              "      <td>17325.0</td>\n",
              "      <td>36188.0</td>\n",
              "      <td>21358.0</td>\n",
              "      <td>22670.0</td>\n",
              "      <td>1729.0</td>\n",
              "      <td>19525.0</td>\n",
              "      <td>7267.0</td>\n",
              "      <td>1953.0</td>\n",
              "      <td>31420.0</td>\n",
              "      <td>18361.0</td>\n",
              "      <td>29369.0</td>\n",
              "      <td>10044.0</td>\n",
              "      <td>29057.0</td>\n",
              "      <td>23134.0</td>\n",
              "      <td>6995.0</td>\n",
              "      <td>16986.0</td>\n",
              "      <td>3983.0</td>\n",
              "      <td>3161.0</td>\n",
              "      <td>30267.0</td>\n",
              "      <td>19444.0</td>\n",
              "      <td>1394.0</td>\n",
              "      <td>5306.0</td>\n",
              "      <td>9536.0</td>\n",
              "      <td>5263.0</td>\n",
              "      <td>2030.0</td>\n",
              "      <td>...</td>\n",
              "      <td>7459.0</td>\n",
              "      <td>1437.0</td>\n",
              "      <td>16129.0</td>\n",
              "      <td>2431.0</td>\n",
              "      <td>8095.0</td>\n",
              "      <td>1880.0</td>\n",
              "      <td>5035.0</td>\n",
              "      <td>6042.0</td>\n",
              "      <td>4028.0</td>\n",
              "      <td>5651.0</td>\n",
              "      <td>3144.0</td>\n",
              "      <td>6815.0</td>\n",
              "      <td>1098.0</td>\n",
              "      <td>49956.0</td>\n",
              "      <td>4508.0</td>\n",
              "      <td>18871.0</td>\n",
              "      <td>5900.0</td>\n",
              "      <td>5068.0</td>\n",
              "      <td>6314.0</td>\n",
              "      <td>8399.0</td>\n",
              "      <td>20483.0</td>\n",
              "      <td>3728.0</td>\n",
              "      <td>10738.0</td>\n",
              "      <td>7390.0</td>\n",
              "      <td>4386.0</td>\n",
              "      <td>1293.0</td>\n",
              "      <td>9604.0</td>\n",
              "      <td>15645.0</td>\n",
              "      <td>22208.0</td>\n",
              "      <td>5877.0</td>\n",
              "      <td>3440.0</td>\n",
              "      <td>7991.0</td>\n",
              "      <td>1614.0</td>\n",
              "      <td>23741.0</td>\n",
              "      <td>3251.0</td>\n",
              "      <td>1314.0</td>\n",
              "      <td>5425.0</td>\n",
              "      <td>2741.0</td>\n",
              "      <td>1678.0</td>\n",
              "      <td>3434.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>Flavonifractor</td>\n",
              "      <td>11762.0</td>\n",
              "      <td>4310.0</td>\n",
              "      <td>1908.0</td>\n",
              "      <td>1863.0</td>\n",
              "      <td>10275.0</td>\n",
              "      <td>1337.0</td>\n",
              "      <td>4105.0</td>\n",
              "      <td>11588.0</td>\n",
              "      <td>5807.0</td>\n",
              "      <td>2064.0</td>\n",
              "      <td>11334.0</td>\n",
              "      <td>1779.0</td>\n",
              "      <td>15968.0</td>\n",
              "      <td>7628.0</td>\n",
              "      <td>10360.0</td>\n",
              "      <td>6539.0</td>\n",
              "      <td>2969.0</td>\n",
              "      <td>14999.0</td>\n",
              "      <td>9249.0</td>\n",
              "      <td>2606.0</td>\n",
              "      <td>9718.0</td>\n",
              "      <td>1181.0</td>\n",
              "      <td>8202.0</td>\n",
              "      <td>6618.0</td>\n",
              "      <td>4220.0</td>\n",
              "      <td>3191.0</td>\n",
              "      <td>10873.0</td>\n",
              "      <td>2066.0</td>\n",
              "      <td>5276.0</td>\n",
              "      <td>8618.0</td>\n",
              "      <td>1323.0</td>\n",
              "      <td>1035.0</td>\n",
              "      <td>5889.0</td>\n",
              "      <td>7181.0</td>\n",
              "      <td>325.0</td>\n",
              "      <td>1623.0</td>\n",
              "      <td>1322.0</td>\n",
              "      <td>955.0</td>\n",
              "      <td>949.0</td>\n",
              "      <td>...</td>\n",
              "      <td>8419.0</td>\n",
              "      <td>507.0</td>\n",
              "      <td>4860.0</td>\n",
              "      <td>658.0</td>\n",
              "      <td>1841.0</td>\n",
              "      <td>536.0</td>\n",
              "      <td>2136.0</td>\n",
              "      <td>10020.0</td>\n",
              "      <td>1741.0</td>\n",
              "      <td>2499.0</td>\n",
              "      <td>9033.0</td>\n",
              "      <td>5076.0</td>\n",
              "      <td>954.0</td>\n",
              "      <td>5853.0</td>\n",
              "      <td>1772.0</td>\n",
              "      <td>6543.0</td>\n",
              "      <td>3542.0</td>\n",
              "      <td>1087.0</td>\n",
              "      <td>1958.0</td>\n",
              "      <td>7029.0</td>\n",
              "      <td>9622.0</td>\n",
              "      <td>4134.0</td>\n",
              "      <td>3805.0</td>\n",
              "      <td>3148.0</td>\n",
              "      <td>4372.0</td>\n",
              "      <td>424.0</td>\n",
              "      <td>6350.0</td>\n",
              "      <td>2571.0</td>\n",
              "      <td>7833.0</td>\n",
              "      <td>5694.0</td>\n",
              "      <td>2049.0</td>\n",
              "      <td>1128.0</td>\n",
              "      <td>836.0</td>\n",
              "      <td>7474.0</td>\n",
              "      <td>734.0</td>\n",
              "      <td>420.0</td>\n",
              "      <td>3920.0</td>\n",
              "      <td>755.0</td>\n",
              "      <td>783.0</td>\n",
              "      <td>804.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>Caproiciproducens</td>\n",
              "      <td>2391.0</td>\n",
              "      <td>860.0</td>\n",
              "      <td>374.0</td>\n",
              "      <td>293.0</td>\n",
              "      <td>1237.0</td>\n",
              "      <td>378.0</td>\n",
              "      <td>877.0</td>\n",
              "      <td>1772.0</td>\n",
              "      <td>625.0</td>\n",
              "      <td>302.0</td>\n",
              "      <td>1490.0</td>\n",
              "      <td>402.0</td>\n",
              "      <td>2122.0</td>\n",
              "      <td>1344.0</td>\n",
              "      <td>1635.0</td>\n",
              "      <td>1846.0</td>\n",
              "      <td>1566.0</td>\n",
              "      <td>1957.0</td>\n",
              "      <td>503.0</td>\n",
              "      <td>2170.0</td>\n",
              "      <td>1189.0</td>\n",
              "      <td>312.0</td>\n",
              "      <td>1488.0</td>\n",
              "      <td>2384.0</td>\n",
              "      <td>1024.0</td>\n",
              "      <td>727.0</td>\n",
              "      <td>1797.0</td>\n",
              "      <td>537.0</td>\n",
              "      <td>937.0</td>\n",
              "      <td>1655.0</td>\n",
              "      <td>373.0</td>\n",
              "      <td>372.0</td>\n",
              "      <td>1171.0</td>\n",
              "      <td>1468.0</td>\n",
              "      <td>121.0</td>\n",
              "      <td>476.0</td>\n",
              "      <td>456.0</td>\n",
              "      <td>276.0</td>\n",
              "      <td>235.0</td>\n",
              "      <td>...</td>\n",
              "      <td>1436.0</td>\n",
              "      <td>250.0</td>\n",
              "      <td>1240.0</td>\n",
              "      <td>172.0</td>\n",
              "      <td>860.0</td>\n",
              "      <td>200.0</td>\n",
              "      <td>555.0</td>\n",
              "      <td>1491.0</td>\n",
              "      <td>450.0</td>\n",
              "      <td>668.0</td>\n",
              "      <td>342.0</td>\n",
              "      <td>853.0</td>\n",
              "      <td>123.0</td>\n",
              "      <td>709.0</td>\n",
              "      <td>400.0</td>\n",
              "      <td>1304.0</td>\n",
              "      <td>702.0</td>\n",
              "      <td>272.0</td>\n",
              "      <td>583.0</td>\n",
              "      <td>1319.0</td>\n",
              "      <td>1722.0</td>\n",
              "      <td>681.0</td>\n",
              "      <td>794.0</td>\n",
              "      <td>586.0</td>\n",
              "      <td>955.0</td>\n",
              "      <td>139.0</td>\n",
              "      <td>1045.0</td>\n",
              "      <td>549.0</td>\n",
              "      <td>1327.0</td>\n",
              "      <td>1086.0</td>\n",
              "      <td>360.0</td>\n",
              "      <td>314.0</td>\n",
              "      <td>132.0</td>\n",
              "      <td>1324.0</td>\n",
              "      <td>142.0</td>\n",
              "      <td>89.0</td>\n",
              "      <td>628.0</td>\n",
              "      <td>135.0</td>\n",
              "      <td>177.0</td>\n",
              "      <td>261.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>Ethanoligenens</td>\n",
              "      <td>2011.0</td>\n",
              "      <td>764.0</td>\n",
              "      <td>490.0</td>\n",
              "      <td>292.0</td>\n",
              "      <td>1309.0</td>\n",
              "      <td>482.0</td>\n",
              "      <td>678.0</td>\n",
              "      <td>1877.0</td>\n",
              "      <td>610.0</td>\n",
              "      <td>287.0</td>\n",
              "      <td>1622.0</td>\n",
              "      <td>454.0</td>\n",
              "      <td>2180.0</td>\n",
              "      <td>1014.0</td>\n",
              "      <td>1741.0</td>\n",
              "      <td>1025.0</td>\n",
              "      <td>767.0</td>\n",
              "      <td>2037.0</td>\n",
              "      <td>460.0</td>\n",
              "      <td>880.0</td>\n",
              "      <td>1358.0</td>\n",
              "      <td>261.0</td>\n",
              "      <td>1191.0</td>\n",
              "      <td>1310.0</td>\n",
              "      <td>812.0</td>\n",
              "      <td>627.0</td>\n",
              "      <td>1677.0</td>\n",
              "      <td>468.0</td>\n",
              "      <td>727.0</td>\n",
              "      <td>1439.0</td>\n",
              "      <td>364.0</td>\n",
              "      <td>201.0</td>\n",
              "      <td>1063.0</td>\n",
              "      <td>1302.0</td>\n",
              "      <td>105.0</td>\n",
              "      <td>410.0</td>\n",
              "      <td>603.0</td>\n",
              "      <td>292.0</td>\n",
              "      <td>452.0</td>\n",
              "      <td>...</td>\n",
              "      <td>1291.0</td>\n",
              "      <td>223.0</td>\n",
              "      <td>1022.0</td>\n",
              "      <td>199.0</td>\n",
              "      <td>711.0</td>\n",
              "      <td>170.0</td>\n",
              "      <td>463.0</td>\n",
              "      <td>1648.0</td>\n",
              "      <td>452.0</td>\n",
              "      <td>658.0</td>\n",
              "      <td>304.0</td>\n",
              "      <td>798.0</td>\n",
              "      <td>163.0</td>\n",
              "      <td>744.0</td>\n",
              "      <td>401.0</td>\n",
              "      <td>1304.0</td>\n",
              "      <td>657.0</td>\n",
              "      <td>296.0</td>\n",
              "      <td>583.0</td>\n",
              "      <td>1234.0</td>\n",
              "      <td>1857.0</td>\n",
              "      <td>726.0</td>\n",
              "      <td>743.0</td>\n",
              "      <td>617.0</td>\n",
              "      <td>845.0</td>\n",
              "      <td>116.0</td>\n",
              "      <td>1091.0</td>\n",
              "      <td>499.0</td>\n",
              "      <td>1347.0</td>\n",
              "      <td>1050.0</td>\n",
              "      <td>386.0</td>\n",
              "      <td>366.0</td>\n",
              "      <td>151.0</td>\n",
              "      <td>1313.0</td>\n",
              "      <td>202.0</td>\n",
              "      <td>75.0</td>\n",
              "      <td>658.0</td>\n",
              "      <td>220.0</td>\n",
              "      <td>209.0</td>\n",
              "      <td>259.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1145</th>\n",
              "      <td>Caldimicrobium</td>\n",
              "      <td>28.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>26.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>71.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>44.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>33.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>52.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>23.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>46.0</td>\n",
              "      <td>82.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>70.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>...</td>\n",
              "      <td>13.0</td>\n",
              "      <td>98.0</td>\n",
              "      <td>105.0</td>\n",
              "      <td>73.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>47.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>99.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>32.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>29.0</td>\n",
              "      <td>26.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>57.0</td>\n",
              "      <td>40.0</td>\n",
              "      <td>50.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>51.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>69.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>64.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>50.0</td>\n",
              "      <td>26.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1146</th>\n",
              "      <td>Thermodesulfatator</td>\n",
              "      <td>19.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>17.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>65.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>47.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>52.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>57.0</td>\n",
              "      <td>54.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>45.0</td>\n",
              "      <td>26.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>112.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>62.0</td>\n",
              "      <td>146.0</td>\n",
              "      <td>64.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>88.0</td>\n",
              "      <td>44.0</td>\n",
              "      <td>120.0</td>\n",
              "      <td>48.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>...</td>\n",
              "      <td>32.0</td>\n",
              "      <td>49.0</td>\n",
              "      <td>96.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>46.0</td>\n",
              "      <td>52.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>135.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>55.0</td>\n",
              "      <td>47.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>72.0</td>\n",
              "      <td>36.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>46.0</td>\n",
              "      <td>32.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>50.0</td>\n",
              "      <td>82.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>48.0</td>\n",
              "      <td>34.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>55.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>45.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>70.0</td>\n",
              "      <td>39.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1147</th>\n",
              "      <td>Dictyoglomus</td>\n",
              "      <td>62.0</td>\n",
              "      <td>76.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>73.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>38.0</td>\n",
              "      <td>96.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>72.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>58.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>40.0</td>\n",
              "      <td>158.0</td>\n",
              "      <td>36.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>95.0</td>\n",
              "      <td>54.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>95.0</td>\n",
              "      <td>67.0</td>\n",
              "      <td>59.0</td>\n",
              "      <td>84.0</td>\n",
              "      <td>51.0</td>\n",
              "      <td>72.0</td>\n",
              "      <td>55.0</td>\n",
              "      <td>109.0</td>\n",
              "      <td>56.0</td>\n",
              "      <td>114.0</td>\n",
              "      <td>73.0</td>\n",
              "      <td>95.0</td>\n",
              "      <td>74.0</td>\n",
              "      <td>61.0</td>\n",
              "      <td>110.0</td>\n",
              "      <td>71.0</td>\n",
              "      <td>57.0</td>\n",
              "      <td>...</td>\n",
              "      <td>59.0</td>\n",
              "      <td>94.0</td>\n",
              "      <td>142.0</td>\n",
              "      <td>45.0</td>\n",
              "      <td>139.0</td>\n",
              "      <td>92.0</td>\n",
              "      <td>114.0</td>\n",
              "      <td>85.0</td>\n",
              "      <td>206.0</td>\n",
              "      <td>154.0</td>\n",
              "      <td>17.0</td>\n",
              "      <td>241.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>87.0</td>\n",
              "      <td>87.0</td>\n",
              "      <td>103.0</td>\n",
              "      <td>63.0</td>\n",
              "      <td>53.0</td>\n",
              "      <td>75.0</td>\n",
              "      <td>92.0</td>\n",
              "      <td>112.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>66.0</td>\n",
              "      <td>47.0</td>\n",
              "      <td>90.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>40.0</td>\n",
              "      <td>66.0</td>\n",
              "      <td>85.0</td>\n",
              "      <td>60.0</td>\n",
              "      <td>35.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>65.0</td>\n",
              "      <td>75.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>64.0</td>\n",
              "      <td>52.0</td>\n",
              "      <td>155.0</td>\n",
              "      <td>35.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1148</th>\n",
              "      <td>Caldisericum</td>\n",
              "      <td>39.0</td>\n",
              "      <td>32.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>37.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>2.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>17.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>29.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>55.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>33.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>23.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>...</td>\n",
              "      <td>15.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>23.0</td>\n",
              "      <td>43.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>2.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>29.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>26.0</td>\n",
              "      <td>31.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>49.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>54.0</td>\n",
              "      <td>2.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>30.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>16.0</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1149</th>\n",
              "      <td>Coprothermobacter</td>\n",
              "      <td>14.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>19.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>4.0</td>\n",
              "      <td>78.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>1.0</td>\n",
              "      <td>17.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>7.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>44.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>42.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>23.0</td>\n",
              "      <td>20.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>...</td>\n",
              "      <td>8.0</td>\n",
              "      <td>9.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>5.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>13.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>63.0</td>\n",
              "      <td>12.0</td>\n",
              "      <td>1.0</td>\n",
              "      <td>46.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>16.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>22.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>3.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>18.0</td>\n",
              "      <td>21.0</td>\n",
              "      <td>41.0</td>\n",
              "      <td>10.0</td>\n",
              "      <td>27.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>6.0</td>\n",
              "      <td>11.0</td>\n",
              "      <td>8.0</td>\n",
              "      <td>24.0</td>\n",
              "      <td>25.0</td>\n",
              "      <td>28.0</td>\n",
              "      <td>34.0</td>\n",
              "      <td>14.0</td>\n",
              "      <td>39.0</td>\n",
              "      <td>15.0</td>\n",
              "      <td>9.0</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>1150 rows × 181 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                    name    Konzo1   Konzo10  ...     L403     L404      L405\n",
              "0       Faecalibacterium  237552.0  436447.0  ...  64883.0  56363.0  106824.0\n",
              "1           Ruminococcus   19084.0   11769.0  ...   2741.0   1678.0    3434.0\n",
              "2         Flavonifractor   11762.0    4310.0  ...    755.0    783.0     804.0\n",
              "3      Caproiciproducens    2391.0     860.0  ...    135.0    177.0     261.0\n",
              "4         Ethanoligenens    2011.0     764.0  ...    220.0    209.0     259.0\n",
              "...                  ...       ...       ...  ...      ...      ...       ...\n",
              "1145      Caldimicrobium      28.0      41.0  ...     30.0     50.0      26.0\n",
              "1146  Thermodesulfatator      19.0      22.0  ...     41.0     70.0      39.0\n",
              "1147        Dictyoglomus      62.0      76.0  ...     52.0    155.0      35.0\n",
              "1148        Caldisericum      39.0      32.0  ...      8.0      6.0      16.0\n",
              "1149   Coprothermobacter      14.0      12.0  ...     39.0     15.0       9.0\n",
              "\n",
              "[1150 rows x 181 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 59
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "ljRpXdR0cC9h"
      },
      "source": [
        "#Make the column with genus into row names so data structure is only readcounts. \n",
        "genus = genus.set_index('name')"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 640
        },
        "id": "R7lXUX90yRTb",
        "outputId": "adcd120f-0280-49fb-ddb8-366b7d202342"
      },
      "source": [
        "#Conver read counts to relative abundance (done with each column since each sample is one column)\n",
        "genus = genus.apply(lambda x : x / x.sum())\n",
        "genus\n",
        "#genus"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/html": [
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              "<style scoped>\n",
              "    .dataframe tbody tr th:only-of-type {\n",
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              "    }\n",
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              "<table border=\"1\" class=\"dataframe\">\n",
              "  <thead>\n",
              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>Konzo1</th>\n",
              "      <th>Konzo10</th>\n",
              "      <th>Konzo11</th>\n",
              "      <th>Konzo12</th>\n",
              "      <th>Konzo13</th>\n",
              "      <th>Konzo14</th>\n",
              "      <th>Konzo15</th>\n",
              "      <th>Konzo16</th>\n",
              "      <th>Konzo17</th>\n",
              "      <th>Konzo18</th>\n",
              "      <th>Konzo19</th>\n",
              "      <th>Konzo2</th>\n",
              "      <th>Konzo20</th>\n",
              "      <th>Konzo21</th>\n",
              "      <th>Konzo22</th>\n",
              "      <th>Konzo23</th>\n",
              "      <th>Konzo24</th>\n",
              "      <th>Konzo25</th>\n",
              "      <th>Konzo26</th>\n",
              "      <th>Konzo27</th>\n",
              "      <th>Konzo28</th>\n",
              "      <th>Konzo29</th>\n",
              "      <th>Konzo3</th>\n",
              "      <th>Konzo30</th>\n",
              "      <th>Konzo4</th>\n",
              "      <th>Konzo5</th>\n",
              "      <th>Konzo6</th>\n",
              "      <th>Konzo7</th>\n",
              "      <th>Konzo8</th>\n",
              "      <th>Konzo9</th>\n",
              "      <th>L256</th>\n",
              "      <th>L257</th>\n",
              "      <th>L258</th>\n",
              "      <th>L259</th>\n",
              "      <th>L260</th>\n",
              "      <th>L261</th>\n",
              "      <th>L262</th>\n",
              "      <th>L263</th>\n",
              "      <th>L264</th>\n",
              "      <th>L265</th>\n",
              "      <th>...</th>\n",
              "      <th>L366</th>\n",
              "      <th>L367</th>\n",
              "      <th>L368</th>\n",
              "      <th>L369</th>\n",
              "      <th>L370</th>\n",
              "      <th>L371</th>\n",
              "      <th>L372</th>\n",
              "      <th>L373</th>\n",
              "      <th>L374</th>\n",
              "      <th>L375</th>\n",
              "      <th>L376</th>\n",
              "      <th>L377</th>\n",
              "      <th>L378</th>\n",
              "      <th>L379</th>\n",
              "      <th>L380</th>\n",
              "      <th>L381</th>\n",
              "      <th>L382</th>\n",
              "      <th>L383</th>\n",
              "      <th>L384</th>\n",
              "      <th>L385</th>\n",
              "      <th>L386</th>\n",
              "      <th>L387</th>\n",
              "      <th>L388</th>\n",
              "      <th>L389</th>\n",
              "      <th>L390</th>\n",
              "      <th>L391</th>\n",
              "      <th>L392</th>\n",
              "      <th>L393</th>\n",
              "      <th>L394</th>\n",
              "      <th>L395</th>\n",
              "      <th>L396</th>\n",
              "      <th>L397</th>\n",
              "      <th>L398</th>\n",
              "      <th>L399</th>\n",
              "      <th>L400</th>\n",
              "      <th>L401</th>\n",
              "      <th>L402</th>\n",
              "      <th>L403</th>\n",
              "      <th>L404</th>\n",
              "      <th>L405</th>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>name</th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
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              "      <th></th>\n",
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              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "      <th></th>\n",
              "    </tr>\n",
              "  </thead>\n",
              "  <tbody>\n",
              "    <tr>\n",
              "      <th>Faecalibacterium</th>\n",
              "      <td>0.185642</td>\n",
              "      <td>0.251902</td>\n",
              "      <td>0.048876</td>\n",
              "      <td>0.094728</td>\n",
              "      <td>0.101726</td>\n",
              "      <td>0.043729</td>\n",
              "      <td>6.576331e-02</td>\n",
              "      <td>0.270623</td>\n",
              "      <td>0.048622</td>\n",
              "      <td>0.147706</td>\n",
              "      <td>0.110453</td>\n",
              "      <td>2.058402e-01</td>\n",
              "      <td>0.059109</td>\n",
              "      <td>0.089538</td>\n",
              "      <td>0.075446</td>\n",
              "      <td>0.062567</td>\n",
              "      <td>0.089187</td>\n",
              "      <td>0.140631</td>\n",
              "      <td>0.052090</td>\n",
              "      <td>0.061981</td>\n",
              "      <td>0.034840</td>\n",
              "      <td>0.073229</td>\n",
              "      <td>0.150904</td>\n",
              "      <td>0.097817</td>\n",
              "      <td>0.232905</td>\n",
              "      <td>0.133469</td>\n",
              "      <td>0.218602</td>\n",
              "      <td>0.145821</td>\n",
              "      <td>0.156984</td>\n",
              "      <td>0.164458</td>\n",
              "      <td>0.083263</td>\n",
              "      <td>0.054011</td>\n",
              "      <td>0.174972</td>\n",
              "      <td>0.133501</td>\n",
              "      <td>0.054856</td>\n",
              "      <td>0.160470</td>\n",
              "      <td>0.096502</td>\n",
              "      <td>0.091356</td>\n",
              "      <td>0.097847</td>\n",
              "      <td>0.119441</td>\n",
              "      <td>...</td>\n",
              "      <td>0.031793</td>\n",
              "      <td>0.124583</td>\n",
              "      <td>0.090011</td>\n",
              "      <td>0.066417</td>\n",
              "      <td>0.117352</td>\n",
              "      <td>0.103757</td>\n",
              "      <td>0.106558</td>\n",
              "      <td>0.068148</td>\n",
              "      <td>0.203585</td>\n",
              "      <td>0.210625</td>\n",
              "      <td>1.793627e-02</td>\n",
              "      <td>0.051839</td>\n",
              "      <td>0.062586</td>\n",
              "      <td>0.030670</td>\n",
              "      <td>0.041997</td>\n",
              "      <td>0.049060</td>\n",
              "      <td>0.050763</td>\n",
              "      <td>0.050326</td>\n",
              "      <td>0.041368</td>\n",
              "      <td>0.074492</td>\n",
              "      <td>0.082274</td>\n",
              "      <td>0.177635</td>\n",
              "      <td>0.039692</td>\n",
              "      <td>0.038753</td>\n",
              "      <td>0.062070</td>\n",
              "      <td>0.070023</td>\n",
              "      <td>0.039699</td>\n",
              "      <td>0.098889</td>\n",
              "      <td>0.066099</td>\n",
              "      <td>0.116136</td>\n",
              "      <td>0.071292</td>\n",
              "      <td>0.038582</td>\n",
              "      <td>0.060396</td>\n",
              "      <td>0.087744</td>\n",
              "      <td>0.073071</td>\n",
              "      <td>0.037095</td>\n",
              "      <td>0.079247</td>\n",
              "      <td>0.054598</td>\n",
              "      <td>0.053773</td>\n",
              "      <td>0.088187</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Ruminococcus</th>\n",
              "      <td>0.014914</td>\n",
              "      <td>0.006793</td>\n",
              "      <td>0.010110</td>\n",
              "      <td>0.015239</td>\n",
              "      <td>0.005643</td>\n",
              "      <td>0.001459</td>\n",
              "      <td>1.698603e-01</td>\n",
              "      <td>0.011380</td>\n",
              "      <td>0.040829</td>\n",
              "      <td>0.002412</td>\n",
              "      <td>0.003236</td>\n",
              "      <td>3.148406e-03</td>\n",
              "      <td>0.007019</td>\n",
              "      <td>0.011984</td>\n",
              "      <td>0.012272</td>\n",
              "      <td>0.010226</td>\n",
              "      <td>0.015768</td>\n",
              "      <td>0.012329</td>\n",
              "      <td>0.000464</td>\n",
              "      <td>0.006628</td>\n",
              "      <td>0.002124</td>\n",
              "      <td>0.002653</td>\n",
              "      <td>0.034701</td>\n",
              "      <td>0.022565</td>\n",
              "      <td>0.028805</td>\n",
              "      <td>0.007417</td>\n",
              "      <td>0.024670</td>\n",
              "      <td>0.014438</td>\n",
              "      <td>0.010690</td>\n",
              "      <td>0.009401</td>\n",
              "      <td>0.003324</td>\n",
              "      <td>0.002689</td>\n",
              "      <td>0.017055</td>\n",
              "      <td>0.017648</td>\n",
              "      <td>0.001225</td>\n",
              "      <td>0.003984</td>\n",
              "      <td>0.006524</td>\n",
              "      <td>0.005048</td>\n",
              "      <td>0.001439</td>\n",
              "      <td>0.001039</td>\n",
              "      <td>...</td>\n",
              "      <td>0.002712</td>\n",
              "      <td>0.001059</td>\n",
              "      <td>0.005743</td>\n",
              "      <td>0.002407</td>\n",
              "      <td>0.006134</td>\n",
              "      <td>0.001574</td>\n",
              "      <td>0.003626</td>\n",
              "      <td>0.004721</td>\n",
              "      <td>0.001988</td>\n",
              "      <td>0.003033</td>\n",
              "      <td>8.209585e-04</td>\n",
              "      <td>0.005117</td>\n",
              "      <td>0.000868</td>\n",
              "      <td>0.036889</td>\n",
              "      <td>0.003266</td>\n",
              "      <td>0.015018</td>\n",
              "      <td>0.003769</td>\n",
              "      <td>0.003647</td>\n",
              "      <td>0.003672</td>\n",
              "      <td>0.006338</td>\n",
              "      <td>0.014661</td>\n",
              "      <td>0.003043</td>\n",
              "      <td>0.005020</td>\n",
              "      <td>0.004542</td>\n",
              "      <td>0.003085</td>\n",
              "      <td>0.001191</td>\n",
              "      <td>0.004487</td>\n",
              "      <td>0.013942</td>\n",
              "      <td>0.014600</td>\n",
              "      <td>0.005453</td>\n",
              "      <td>0.002917</td>\n",
              "      <td>0.006057</td>\n",
              "      <td>0.001516</td>\n",
              "      <td>0.016428</td>\n",
              "      <td>0.002684</td>\n",
              "      <td>0.001283</td>\n",
              "      <td>0.004416</td>\n",
              "      <td>0.002306</td>\n",
              "      <td>0.001601</td>\n",
              "      <td>0.002835</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Flavonifractor</th>\n",
              "      <td>0.009192</td>\n",
              "      <td>0.002488</td>\n",
              "      <td>0.002226</td>\n",
              "      <td>0.003571</td>\n",
              "      <td>0.005311</td>\n",
              "      <td>0.001040</td>\n",
              "      <td>9.864196e-04</td>\n",
              "      <td>0.008990</td>\n",
              "      <td>0.002079</td>\n",
              "      <td>0.001772</td>\n",
              "      <td>0.005517</td>\n",
              "      <td>1.146105e-03</td>\n",
              "      <td>0.011992</td>\n",
              "      <td>0.004466</td>\n",
              "      <td>0.007338</td>\n",
              "      <td>0.001848</td>\n",
              "      <td>0.002192</td>\n",
              "      <td>0.008157</td>\n",
              "      <td>0.002480</td>\n",
              "      <td>0.000885</td>\n",
              "      <td>0.002840</td>\n",
              "      <td>0.001604</td>\n",
              "      <td>0.009058</td>\n",
              "      <td>0.008133</td>\n",
              "      <td>0.004139</td>\n",
              "      <td>0.002356</td>\n",
              "      <td>0.009231</td>\n",
              "      <td>0.001289</td>\n",
              "      <td>0.008063</td>\n",
              "      <td>0.004770</td>\n",
              "      <td>0.001104</td>\n",
              "      <td>0.000880</td>\n",
              "      <td>0.003318</td>\n",
              "      <td>0.006518</td>\n",
              "      <td>0.000286</td>\n",
              "      <td>0.001219</td>\n",
              "      <td>0.000904</td>\n",
              "      <td>0.000916</td>\n",
              "      <td>0.000673</td>\n",
              "      <td>0.000659</td>\n",
              "      <td>...</td>\n",
              "      <td>0.003061</td>\n",
              "      <td>0.000374</td>\n",
              "      <td>0.001731</td>\n",
              "      <td>0.000652</td>\n",
              "      <td>0.001395</td>\n",
              "      <td>0.000449</td>\n",
              "      <td>0.001538</td>\n",
              "      <td>0.007829</td>\n",
              "      <td>0.000859</td>\n",
              "      <td>0.001341</td>\n",
              "      <td>2.358689e-03</td>\n",
              "      <td>0.003812</td>\n",
              "      <td>0.000755</td>\n",
              "      <td>0.004322</td>\n",
              "      <td>0.001284</td>\n",
              "      <td>0.005207</td>\n",
              "      <td>0.002262</td>\n",
              "      <td>0.000782</td>\n",
              "      <td>0.001139</td>\n",
              "      <td>0.005304</td>\n",
              "      <td>0.006887</td>\n",
              "      <td>0.003374</td>\n",
              "      <td>0.001779</td>\n",
              "      <td>0.001935</td>\n",
              "      <td>0.003075</td>\n",
              "      <td>0.000390</td>\n",
              "      <td>0.002966</td>\n",
              "      <td>0.002291</td>\n",
              "      <td>0.005150</td>\n",
              "      <td>0.005284</td>\n",
              "      <td>0.001738</td>\n",
              "      <td>0.000855</td>\n",
              "      <td>0.000785</td>\n",
              "      <td>0.005172</td>\n",
              "      <td>0.000606</td>\n",
              "      <td>0.000410</td>\n",
              "      <td>0.003191</td>\n",
              "      <td>0.000635</td>\n",
              "      <td>0.000747</td>\n",
              "      <td>0.000664</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Caproiciproducens</th>\n",
              "      <td>0.001869</td>\n",
              "      <td>0.000496</td>\n",
              "      <td>0.000436</td>\n",
              "      <td>0.000562</td>\n",
              "      <td>0.000639</td>\n",
              "      <td>0.000294</td>\n",
              "      <td>2.107406e-04</td>\n",
              "      <td>0.001375</td>\n",
              "      <td>0.000224</td>\n",
              "      <td>0.000259</td>\n",
              "      <td>0.000725</td>\n",
              "      <td>2.589849e-04</td>\n",
              "      <td>0.001594</td>\n",
              "      <td>0.000787</td>\n",
              "      <td>0.001158</td>\n",
              "      <td>0.000522</td>\n",
              "      <td>0.001156</td>\n",
              "      <td>0.001064</td>\n",
              "      <td>0.000135</td>\n",
              "      <td>0.000737</td>\n",
              "      <td>0.000347</td>\n",
              "      <td>0.000424</td>\n",
              "      <td>0.001643</td>\n",
              "      <td>0.002930</td>\n",
              "      <td>0.001004</td>\n",
              "      <td>0.000537</td>\n",
              "      <td>0.001526</td>\n",
              "      <td>0.000335</td>\n",
              "      <td>0.001432</td>\n",
              "      <td>0.000916</td>\n",
              "      <td>0.000311</td>\n",
              "      <td>0.000316</td>\n",
              "      <td>0.000660</td>\n",
              "      <td>0.001332</td>\n",
              "      <td>0.000106</td>\n",
              "      <td>0.000357</td>\n",
              "      <td>0.000312</td>\n",
              "      <td>0.000265</td>\n",
              "      <td>0.000167</td>\n",
              "      <td>0.000154</td>\n",
              "      <td>...</td>\n",
              "      <td>0.000522</td>\n",
              "      <td>0.000184</td>\n",
              "      <td>0.000442</td>\n",
              "      <td>0.000170</td>\n",
              "      <td>0.000652</td>\n",
              "      <td>0.000167</td>\n",
              "      <td>0.000400</td>\n",
              "      <td>0.001165</td>\n",
              "      <td>0.000222</td>\n",
              "      <td>0.000359</td>\n",
              "      <td>8.930273e-05</td>\n",
              "      <td>0.000641</td>\n",
              "      <td>0.000097</td>\n",
              "      <td>0.000524</td>\n",
              "      <td>0.000290</td>\n",
              "      <td>0.001038</td>\n",
              "      <td>0.000448</td>\n",
              "      <td>0.000196</td>\n",
              "      <td>0.000339</td>\n",
              "      <td>0.000995</td>\n",
              "      <td>0.001233</td>\n",
              "      <td>0.000556</td>\n",
              "      <td>0.000371</td>\n",
              "      <td>0.000360</td>\n",
              "      <td>0.000672</td>\n",
              "      <td>0.000128</td>\n",
              "      <td>0.000488</td>\n",
              "      <td>0.000489</td>\n",
              "      <td>0.000872</td>\n",
              "      <td>0.001008</td>\n",
              "      <td>0.000305</td>\n",
              "      <td>0.000238</td>\n",
              "      <td>0.000124</td>\n",
              "      <td>0.000916</td>\n",
              "      <td>0.000117</td>\n",
              "      <td>0.000087</td>\n",
              "      <td>0.000511</td>\n",
              "      <td>0.000114</td>\n",
              "      <td>0.000169</td>\n",
              "      <td>0.000215</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Ethanoligenens</th>\n",
              "      <td>0.001572</td>\n",
              "      <td>0.000441</td>\n",
              "      <td>0.000572</td>\n",
              "      <td>0.000560</td>\n",
              "      <td>0.000677</td>\n",
              "      <td>0.000375</td>\n",
              "      <td>1.629214e-04</td>\n",
              "      <td>0.001456</td>\n",
              "      <td>0.000218</td>\n",
              "      <td>0.000246</td>\n",
              "      <td>0.000790</td>\n",
              "      <td>2.924854e-04</td>\n",
              "      <td>0.001637</td>\n",
              "      <td>0.000594</td>\n",
              "      <td>0.001233</td>\n",
              "      <td>0.000290</td>\n",
              "      <td>0.000566</td>\n",
              "      <td>0.001108</td>\n",
              "      <td>0.000123</td>\n",
              "      <td>0.000299</td>\n",
              "      <td>0.000397</td>\n",
              "      <td>0.000355</td>\n",
              "      <td>0.001315</td>\n",
              "      <td>0.001610</td>\n",
              "      <td>0.000796</td>\n",
              "      <td>0.000463</td>\n",
              "      <td>0.001424</td>\n",
              "      <td>0.000292</td>\n",
              "      <td>0.001111</td>\n",
              "      <td>0.000796</td>\n",
              "      <td>0.000304</td>\n",
              "      <td>0.000171</td>\n",
              "      <td>0.000599</td>\n",
              "      <td>0.001182</td>\n",
              "      <td>0.000092</td>\n",
              "      <td>0.000308</td>\n",
              "      <td>0.000413</td>\n",
              "      <td>0.000280</td>\n",
              "      <td>0.000321</td>\n",
              "      <td>0.000101</td>\n",
              "      <td>...</td>\n",
              "      <td>0.000469</td>\n",
              "      <td>0.000164</td>\n",
              "      <td>0.000364</td>\n",
              "      <td>0.000197</td>\n",
              "      <td>0.000539</td>\n",
              "      <td>0.000142</td>\n",
              "      <td>0.000333</td>\n",
              "      <td>0.001288</td>\n",
              "      <td>0.000223</td>\n",
              "      <td>0.000353</td>\n",
              "      <td>7.938021e-05</td>\n",
              "      <td>0.000599</td>\n",
              "      <td>0.000129</td>\n",
              "      <td>0.000549</td>\n",
              "      <td>0.000291</td>\n",
              "      <td>0.001038</td>\n",
              "      <td>0.000420</td>\n",
              "      <td>0.000213</td>\n",
              "      <td>0.000339</td>\n",
              "      <td>0.000931</td>\n",
              "      <td>0.001329</td>\n",
              "      <td>0.000593</td>\n",
              "      <td>0.000347</td>\n",
              "      <td>0.000379</td>\n",
              "      <td>0.000594</td>\n",
              "      <td>0.000107</td>\n",
              "      <td>0.000510</td>\n",
              "      <td>0.000445</td>\n",
              "      <td>0.000886</td>\n",
              "      <td>0.000974</td>\n",
              "      <td>0.000327</td>\n",
              "      <td>0.000277</td>\n",
              "      <td>0.000142</td>\n",
              "      <td>0.000909</td>\n",
              "      <td>0.000167</td>\n",
              "      <td>0.000073</td>\n",
              "      <td>0.000536</td>\n",
              "      <td>0.000185</td>\n",
              "      <td>0.000199</td>\n",
              "      <td>0.000214</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>...</th>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "      <td>...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Caldimicrobium</th>\n",
              "      <td>0.000022</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000029</td>\n",
              "      <td>0.000025</td>\n",
              "      <td>0.000007</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>9.611884e-07</td>\n",
              "      <td>0.000020</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000061</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>3.221205e-06</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000026</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000048</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000029</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000015</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000022</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000070</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000064</td>\n",
              "      <td>0.000037</td>\n",
              "      <td>0.000020</td>\n",
              "      <td>0.000029</td>\n",
              "      <td>0.000034</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>0.000032</td>\n",
              "      <td>...</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000072</td>\n",
              "      <td>0.000037</td>\n",
              "      <td>0.000072</td>\n",
              "      <td>0.000021</td>\n",
              "      <td>0.000039</td>\n",
              "      <td>0.000031</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000049</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>6.527978e-06</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000033</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000028</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000031</td>\n",
              "      <td>0.000012</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000035</td>\n",
              "      <td>0.000028</td>\n",
              "      <td>0.000046</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000045</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000065</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000021</td>\n",
              "      <td>0.000062</td>\n",
              "      <td>0.000022</td>\n",
              "      <td>0.000025</td>\n",
              "      <td>0.000048</td>\n",
              "      <td>0.000021</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Thermodesulfatator</th>\n",
              "      <td>0.000015</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000043</td>\n",
              "      <td>0.000033</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>2.402971e-06</td>\n",
              "      <td>0.000027</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000056</td>\n",
              "      <td>0.000015</td>\n",
              "      <td>1.610603e-05</td>\n",
              "      <td>0.000029</td>\n",
              "      <td>0.000028</td>\n",
              "      <td>0.000027</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000015</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000055</td>\n",
              "      <td>0.000026</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000016</td>\n",
              "      <td>0.000070</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000034</td>\n",
              "      <td>0.000122</td>\n",
              "      <td>0.000054</td>\n",
              "      <td>0.000021</td>\n",
              "      <td>0.000028</td>\n",
              "      <td>0.000077</td>\n",
              "      <td>0.000033</td>\n",
              "      <td>0.000082</td>\n",
              "      <td>0.000046</td>\n",
              "      <td>0.000021</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>...</td>\n",
              "      <td>0.000012</td>\n",
              "      <td>0.000036</td>\n",
              "      <td>0.000034</td>\n",
              "      <td>0.000020</td>\n",
              "      <td>0.000035</td>\n",
              "      <td>0.000044</td>\n",
              "      <td>0.000027</td>\n",
              "      <td>0.000029</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000020</td>\n",
              "      <td>2.088953e-06</td>\n",
              "      <td>0.000101</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000027</td>\n",
              "      <td>0.000040</td>\n",
              "      <td>0.000037</td>\n",
              "      <td>0.000026</td>\n",
              "      <td>0.000052</td>\n",
              "      <td>0.000021</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>0.000033</td>\n",
              "      <td>0.000026</td>\n",
              "      <td>0.000012</td>\n",
              "      <td>0.000031</td>\n",
              "      <td>0.000058</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000043</td>\n",
              "      <td>0.000022</td>\n",
              "      <td>0.000015</td>\n",
              "      <td>0.000047</td>\n",
              "      <td>0.000020</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000037</td>\n",
              "      <td>0.000036</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000035</td>\n",
              "      <td>0.000067</td>\n",
              "      <td>0.000032</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Dictyoglomus</th>\n",
              "      <td>0.000048</td>\n",
              "      <td>0.000044</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000059</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>9.131290e-06</td>\n",
              "      <td>0.000074</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000032</td>\n",
              "      <td>0.000035</td>\n",
              "      <td>2.770237e-05</td>\n",
              "      <td>0.000028</td>\n",
              "      <td>0.000034</td>\n",
              "      <td>0.000029</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000117</td>\n",
              "      <td>0.000020</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000032</td>\n",
              "      <td>0.000016</td>\n",
              "      <td>0.000053</td>\n",
              "      <td>0.000105</td>\n",
              "      <td>0.000082</td>\n",
              "      <td>0.000058</td>\n",
              "      <td>0.000062</td>\n",
              "      <td>0.000043</td>\n",
              "      <td>0.000045</td>\n",
              "      <td>0.000084</td>\n",
              "      <td>0.000060</td>\n",
              "      <td>0.000047</td>\n",
              "      <td>0.000097</td>\n",
              "      <td>0.000041</td>\n",
              "      <td>0.000086</td>\n",
              "      <td>0.000065</td>\n",
              "      <td>0.000046</td>\n",
              "      <td>0.000075</td>\n",
              "      <td>0.000068</td>\n",
              "      <td>0.000040</td>\n",
              "      <td>0.000032</td>\n",
              "      <td>...</td>\n",
              "      <td>0.000021</td>\n",
              "      <td>0.000069</td>\n",
              "      <td>0.000051</td>\n",
              "      <td>0.000045</td>\n",
              "      <td>0.000105</td>\n",
              "      <td>0.000077</td>\n",
              "      <td>0.000082</td>\n",
              "      <td>0.000066</td>\n",
              "      <td>0.000102</td>\n",
              "      <td>0.000083</td>\n",
              "      <td>4.439025e-06</td>\n",
              "      <td>0.000181</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000064</td>\n",
              "      <td>0.000063</td>\n",
              "      <td>0.000082</td>\n",
              "      <td>0.000040</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000044</td>\n",
              "      <td>0.000069</td>\n",
              "      <td>0.000080</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000031</td>\n",
              "      <td>0.000029</td>\n",
              "      <td>0.000063</td>\n",
              "      <td>0.000040</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>0.000059</td>\n",
              "      <td>0.000056</td>\n",
              "      <td>0.000056</td>\n",
              "      <td>0.000030</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000061</td>\n",
              "      <td>0.000052</td>\n",
              "      <td>0.000032</td>\n",
              "      <td>0.000041</td>\n",
              "      <td>0.000052</td>\n",
              "      <td>0.000044</td>\n",
              "      <td>0.000148</td>\n",
              "      <td>0.000029</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Caldisericum</th>\n",
              "      <td>0.000030</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000007</td>\n",
              "      <td>0.000071</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>3.364159e-06</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>4.509687e-06</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000016</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000001</td>\n",
              "      <td>0.000004</td>\n",
              "      <td>0.000004</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000022</td>\n",
              "      <td>0.000016</td>\n",
              "      <td>0.000027</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000004</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000031</td>\n",
              "      <td>0.000030</td>\n",
              "      <td>0.000016</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>0.000012</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000021</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>...</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000020</td>\n",
              "      <td>0.000004</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000034</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>2.611191e-06</td>\n",
              "      <td>0.000031</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000008</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000028</td>\n",
              "      <td>0.000008</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000032</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000008</td>\n",
              "      <td>0.000008</td>\n",
              "      <td>0.000037</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000007</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000013</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>Coprothermobacter</th>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000007</td>\n",
              "      <td>0.000022</td>\n",
              "      <td>0.000008</td>\n",
              "      <td>0.000008</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>9.611884e-07</td>\n",
              "      <td>0.000061</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000019</td>\n",
              "      <td>6.442411e-07</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000008</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>0.000015</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000012</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000007</td>\n",
              "      <td>0.000004</td>\n",
              "      <td>0.000012</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000037</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000022</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000013</td>\n",
              "      <td>0.000018</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>...</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000007</td>\n",
              "      <td>0.000007</td>\n",
              "      <td>0.000016</td>\n",
              "      <td>0.000004</td>\n",
              "      <td>0.000003</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000031</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>2.611191e-07</td>\n",
              "      <td>0.000035</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000004</td>\n",
              "      <td>0.000012</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000016</td>\n",
              "      <td>0.000008</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000015</td>\n",
              "      <td>0.000002</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000015</td>\n",
              "      <td>0.000038</td>\n",
              "      <td>0.000005</td>\n",
              "      <td>0.000024</td>\n",
              "      <td>0.000010</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000009</td>\n",
              "      <td>0.000006</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000017</td>\n",
              "      <td>0.000023</td>\n",
              "      <td>0.000033</td>\n",
              "      <td>0.000011</td>\n",
              "      <td>0.000033</td>\n",
              "      <td>0.000014</td>\n",
              "      <td>0.000007</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "<p>1150 rows × 180 columns</p>\n",
              "</div>"
            ],
            "text/plain": [
              "                      Konzo1   Konzo10   Konzo11  ...      L403      L404      L405\n",
              "name                                              ...                              \n",
              "Faecalibacterium    0.185642  0.251902  0.048876  ...  0.054598  0.053773  0.088187\n",
              "Ruminococcus        0.014914  0.006793  0.010110  ...  0.002306  0.001601  0.002835\n",
              "Flavonifractor      0.009192  0.002488  0.002226  ...  0.000635  0.000747  0.000664\n",
              "Caproiciproducens   0.001869  0.000496  0.000436  ...  0.000114  0.000169  0.000215\n",
              "Ethanoligenens      0.001572  0.000441  0.000572  ...  0.000185  0.000199  0.000214\n",
              "...                      ...       ...       ...  ...       ...       ...       ...\n",
              "Caldimicrobium      0.000022  0.000024  0.000029  ...  0.000025  0.000048  0.000021\n",
              "Thermodesulfatator  0.000015  0.000013  0.000043  ...  0.000035  0.000067  0.000032\n",
              "Dictyoglomus        0.000048  0.000044  0.000024  ...  0.000044  0.000148  0.000029\n",
              "Caldisericum        0.000030  0.000018  0.000007  ...  0.000007  0.000006  0.000013\n",
              "Coprothermobacter   0.000011  0.000007  0.000022  ...  0.000033  0.000014  0.000007\n",
              "\n",
              "[1150 rows x 180 columns]"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 61
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "C7NdfsMn1efx"
      },
      "source": [
        "#transpose data frame so samples are rows. \n",
        "#Also remove NA's since those got introduces for genus whose sum was 0 (making denominator 0 for relative abundance calculation)\n",
        "genus_t = genus.transpose()\n",
        "genus_t = genus_t.replace(np.nan,0)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "w1C_ygL02WYN"
      },
      "source": [
        "#might be a better way to do this, but convert rownames back to column so we can merge the meta file with sample name \n",
        "genus_t.index.name = 'name'\n",
        "genus_t.reset_index(inplace=True)"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "RpC6HouT3f-w"
      },
      "source": [
        "#name column Sample to match meta file\n",
        "genus_t = genus_t.rename(columns=str).rename(columns={'name':'Sample'})"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "GRTiufY84N7-"
      },
      "source": [
        "#Merge meta data with genus_t\n",
        "genus_tj = pd.merge(genus_t, meta, on=['Sample'])\n",
        "genus_tj"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "cH0Se-WGiM3a"
      },
      "source": [
        "genus_tj = genus_tj.set_index('Sample')"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "vY5Y_9VA40mY",
        "outputId": "44644011-88fd-4661-9b5c-9787db7f1994"
      },
      "source": [
        "#Do Kruskal Wallis test to see if there is a sig difference in the relative abundance of Prevotella genus between the six groups\n",
        "#microbiome data tends to not be normally distributed so a non-parametric test is appropriate\n",
        "#Bacteroides has been previously shown to be enriched in urban populations\n",
        "bact_kw = scipy.stats.kruskal(*[group[\"Bacteroides\"].values for name, group in genus_tj.groupby(\"Status\")])\n",
        "bact_kw\n",
        "#KruskalResult(statistic=2.0190546347452027, pvalue=0.8465022320762265)"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "KruskalResult(statistic=2.0190546347452027, pvalue=0.8465022320762265)"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 106
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "fvhtwyFk-dYu",
        "outputId": "addaa87b-6275-4521-ee9a-d8c35cf983b2"
      },
      "source": [
        "#Prevotella genus has previously been shown to be enriched in in rural populations \n",
        "\n",
        "prev_kw = scipy.stats.kruskal(*[group[\"Prevotella\"].values for name, group in genus_tj.groupby(\"Status\")])\n",
        "prev_kw\n",
        "#KruskalResult(statistic=39.928496009821856, pvalue=1.5437782911043988e-07)"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "KruskalResult(statistic=39.928496009821856, pvalue=1.5437782911043988e-07)"
            ]
          },
          "metadata": {
            "tags": []
          },
          "execution_count": 107
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 542
        },
        "id": "z_hDba1i91nU",
        "outputId": "f9ab057b-041c-4798-ce2f-14d637dff781"
      },
      "source": [
        "Bact = px.box(genus_tj, x=\"Status\", y=\"Bacteroides\", color = \"Status\", category_orders={ \"Status\" :\n",
        "                     [\"Kinshasa\",\n",
        "                     \"Masimanimba\",\n",
        "                     \"Unaffected_Low_Prevalence_Zone\",\n",
        "                     \"Konzo_Low_Prevalence_Zone\",\n",
        "                     \"Unaffected_High_Prevalence_Zone\",\n",
        "                     \"Konzo_High_Prevalence_Zone\"]}, boxmode=\"overlay\")\n",
        "Bact.update_layout(\n",
        "    xaxis = dict(\n",
        "        tickvals = [\"Kinshasa\",\n",
        "                     \"Masimanimba\",\n",
        "                     \"Unaffected_Low_Prevalence_Zone\",\n",
        "                     \"Konzo_Low_Prevalence_Zone\",\n",
        "                     \"Unaffected_High_Prevalence_Zone\",\n",
        "                     \"Konzo_High_Prevalence_Zone\"],\n",
        "        ticktext = [\"Kin\", \"Mas\", \"ULPZ\", \"KLPZ\", \"UHPZ\", \"KHPZ\"]\n",
        "          ),\n",
        "          showlegend=False\n",
        ")\n",
        "Bact.show()\n",
        "#Although Kruskal-Wallis test resulted in a p-value > 0.05, a post-hoc test may be considered to see if there is an enrichment of Bacteroides in urban population in this dataset."
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "text/html": [
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              "        <script src=\"https://cdn.plot.ly/plotly-latest.min.js\"></script>    \n",
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          "metadata": {
            "tags": []
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    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 542
        },
        "id": "HdM3mwq0-Qz8",
        "outputId": "7469d536-cdfb-486e-a5a1-0d05b670f3fa"
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      "source": [
        "Prev = px.box(genus_tj, x=\"Status\", y=\"Prevotella\", color = \"Status\", category_orders={ \"Status\" :\n",
        "                     [\"Kinshasa\",\n",
        "                     \"Masimanimba\",\n",
        "                     \"Unaffected_Low_Prevalence_Zone\",\n",
        "                     \"Konzo_Low_Prevalence_Zone\",\n",
        "                     \"Unaffected_High_Prevalence_Zone\",\n",
        "                     \"Konzo_High_Prevalence_Zone\"]}, boxmode=\"overlay\")\n",
        "Prev.update_layout(\n",
        "    xaxis = dict(\n",
        "        tickvals = [\"Kinshasa\",\n",
        "                     \"Masimanimba\",\n",
        "                     \"Unaffected_Low_Prevalence_Zone\",\n",
        "                     \"Konzo_Low_Prevalence_Zone\",\n",
        "                     \"Unaffected_High_Prevalence_Zone\",\n",
        "                     \"Konzo_High_Prevalence_Zone\"],\n",
        "        ticktext = [\"Kin\", \"Mas\", \"ULPZ\", \"KLPZ\", \"UHPZ\", \"KHPZ\"]\n",
        "          ),\n",
        "          showlegend=False\n",
        ")\n",
        "Prev.show()\n",
        "#The Kruskal-Wallis test resulted in a p-value < 0.01, a post-hoc test is necessary to see if there is an enrichment of Prevotella in rural population in specific pairwise comparisons"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
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