# Metagenomic data from gutter water in the city of Pointe-Noire, Republic of Congo

Bouziane Moumen, Céline Samba-Louaka, Victoire Aubierge Matondo

Kimpamboudi, Anicet Magloire Boumba, Hervé Sabin Ngoma, Ascel

Samba-Louaka

► To cite this version:

Bouziane Moumen, Céline Samba-Louaka, Victoire Aubierge Matondo Kimpamboudi, Anicet Magloire Boumba, Hervé Sabin Ngoma, et al.. Metagenomic data from gutter water in the city of Pointe-Noire, Republic of Congo. Data in Brief, 2024, 55, pp.110655. 10.1016/j.dib.2024.110655. hal-04632769

HAL Id: hal-04632769

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Data Article

# Metagenomic data from gutter water in the city of Pointe-Noire, Republic of Congo

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Bouziane Moumen<sup>a</sup>, Céline Samba-Louaka<sup>b</sup>,
Victoire Aubierge Matondo Kimpamboudi<sup>c</sup>,
Anicet Magloire Boumba<sup>c</sup>, Hervé Sabin Ngoma<sup>c</sup>,
Ascel Samba-Louaka<sup>a,*</sup>

ARTICLE INFO

Article history:
Received 2 February 2024
Revised 13 June 2024
Accepted 13 June 2024
Available online 27 June 2024

Dataset link: Metagenome from sample collected from water stream in Pointe-Noire city (Republic of Congo) (Original data)

Keywords:
Antibiotic-resistance genes
Shotgun metagenomics
Gutter water
Central Africa

ABSTRACT

After Amazonia, the Congo Basin represents the second-largest tropical rainforest area in the world. This basin harbours remarkable biodiversity, yet much of its microbiological diversity within its waters, soils, and populations remains largely unexplored and undiscovered. While many initiatives to characterize global biodiversity are being undertaken, few are conducted in Africa and none of them concern the Congo Basin specifically in urban areas. In this context, we assessed the microbial diversity present in gutter water in the city of Pointe-Noire, Congo. This town has interesting characteristics as the population density is high and it is located between the Atlantic Ocean and the forest of Mayombe in Central Africa. The findings illuminate the microbial composition of surface water in Pointe-Noire. The dataset allows the identification of putative new bacteria through the assembly of 81 meta-genome-assembled genomes. It also serves as a valuable primary resource for assessing the presence of

<figure><img src="image_2.png" /></figure>

<footnote><sup>a</sup>Université de Poitiers, UMR CNRS 7267, Laboratoire Ecologie et Biologie des Interactions, Poitiers, France</footnote>

<footnote><sup>b</sup>Centre Médical CMC Medico, Pointe-Noire, Congo</footnote>

<footnote><sup>c</sup>Direction Départementale des Soins et Services de Santé de Pointe Noire, Pointe-Noire, Congo</footnote>

<footnote>* Corresponding author.</footnote>

<footnote>E-mail address: ascel.samba@univ-poitiers.fr (A. Samba-Louaka).</footnote>

<footnote>Social media: 👄 @pythseq (B. Moumen), 👄 @ascel_samba (A. Samba-Louaka)</footnote>
antibiotic-resistant genes, offering a useful tool for monitoring risks by public health authorities.

© 2024 The Author(s). Published by Elsevier Inc.

This is an open access article under the CC BY license

(http://creativecommons.org/licenses/by/4.0/)

<table><caption>Specifications Table</caption><tr><td>Subject</td><td>Environmental Genomics and Metagenomics</td></tr><tr><td>Specific subject area</td><td>Metagenomics</td></tr><tr><td>Type of data</td><td>Tables, Images, Figures<br/>Raw, Analyzed, Filtered, Processed, and analyzed DNA sequencing data.</td></tr><tr><td>Data collection</td><td>One liter of water was sampled within a gutter along houses. Four hundred milliliters were successively filtered through two mixed cellulose ester filters of 5 µm, one of 1.2 µm, and three of 0.22 µm to recover the maximum of microorganisms. Total DNA was extracted using the DNeasy PowerWater kit. DNA library sequencing was performed on an Illumina HiSeq 4000 machine with paired-end 150 base sequencing reads.</td></tr><tr><td>Data source location</td><td>Water was sampled in the city of Pointe-Noire, Republic of Congo (precise coordinates: 4°48'43.1"S 11°52'27.8"E) under the supervision of the Direction Départementale des Soins et Services de Santé de Pointe Noire.</td></tr><tr><td>Data accessibility</td><td>The raw data files were deposited in the NCBI database under the study entitled "Metagenome from sample collected from water stream in Pointe-Noire city (Republic of Congo)", BioProject No. PRJNA1021800. Supplementary tables (S1-S5) and refined and dereplicated (not assemblies paired) bins are available in the Zenodo data repository: https://zenodo.org/records/11278913<br/>All the tools and command lines used in the present study are detailed and made public in a Github repository available at the following address: https://github.com/UMR-CNRS-7267/Metacongo_Paper</td></tr></table>

## 1. Value of the Data

* The dataset provides the first insights into the microbial diversity of gutter water from the city of Pointe-Noire, Republic of Congo.

* The discovery of pathogenic microorganisms could help local authorities anticipate epidemics' emergence.

* The dataset allows the identification of new metagenome-assembled genomes (MAGs) that are of interest to environmental microbiologists.

* The dataset serves as a valuable primary resource for assessing the presence of antibiotic-resistance genes, offering a useful tool for monitoring risks by public health authorities as already done in Kenya, Uganda, and Tanzania.

## 2. Background

The city prevents flood damage by digging gutters to drain excessive water. Sometimes people use these gutters to discharge numerous wastes including domestic wastewater. Thus, we selected one gutter point with a mix of water (rainwater and waste) to perform a preliminary study of the microbial composition useful for both environmental microbial ecology and public health authorities (Fig. 1). Results of such a project could convince public health authorities to extend the current analysis to different seasons or areas in the city of Pointe-Noire.
a

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b

<figure><img src="image_4.png" /><figcaption>**Fig. 1.** Geographical overview and location of the sampling site in Pointe-Noire. (a) The sampling was performed within the red circle area and the map was obtained from the website https://www.mapnall.com/en/. (b) photo of the gutter where water was sampled. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>

**3. Data Description**

The dataset is based on raw Illumina paired-end reads obtained through shotgun metagenomics sequencing of DNA isolated from gutter water collected in the city of Pointe-Noire. The raw data contain 84,886,827 paired-end reads of 150 bp (25,466 Mbases). The raw data used in this analysis and associated data analyses are available under NCBI BioProject No. PRJNA1021800.

Regarding the taxonomic distribution, using the Kaiju profiler, we identified Bacteria, viruses, Archea, and Eukaryota. The list of the microbial taxonomy of identified organisms is provided in supplementary tables S1, S2, and S3. Unclassified reads were analysed with a second profiler (kraken 2) to extract the maximum information from the data. However, although some reads were assigned to bacteria, most of them remained unassigned (supplementary table S4). Furthermore, de novo assembly of the whole dataset allowed the identification of
81 metagenome-assembled genomes (Fig. 2, supplementary table S5) with an associated taxonomy described in Table 1.

Table 1. List and taxonomy of MAGs.

Our study also included a screening of antibiotic-resistance genes in the whole assembly,
with 27 antibiotic-resistance genes identified and listed in Table 2.

Table 2. Identification and characterization of antibiotic-resistance genes.

<figure><img src="image_5.png" /><figcaption>**Fig. 2.** Phylogeny of identified bins (MAGs) using the FastTree software on the multi-alignment files generated by the pipeline. These MAGs belong to several phyla: Actinobacteriota (red); Bacteroidota (aqua); Bdellovibrio nota (pink); Hydrogenentota (gray); Myxococcota (brown); Planctomycetota (green); Proteobacteria (orange) and Verrucomicrobiota (blue). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>
<table><caption>**Table 1**
Taxonomic categories of the 81 MAGs identified.</caption><thead><tr><th>BIN</th><th>DIVISION</th><th>PHYLUM</th><th>CLASS</th><th>ORDER</th><th>FAMILY</th><th>GENUS</th><th>SPECIES</th><th>Others</th></tr></thead><tbody><tr><td>mghit_bin.1</td><td>d_Bacteria</td><td>p_Verrucom<br>icrobiota</td><td>c_Verrucom<br>icrobiae</td><td>o_Verrucom<br>icrobiales</td><td>f_Verrucom<br>icrobiaceae</td><td>g_Prosthec<br>obacter</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.11</td><td>d_Bacteria</td><td>p_Actinob<br>acteriota</td><td>c_Actinom<br>ycetia</td><td>o_Actinom<br>ycetales</td><td>f_Microba<br>cteriaceae</td><td>g_Schumannella</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.12</td><td>d_Bacteria</td><td>p_Actinob<br>acteriota</td><td>c_Actino<br>mycetia</td><td>o_Nanope<br>lagicales</td><td>f_S36-B12</td><td>g_UBA6154</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.13</td><td>d_Bacteria</td><td>p_Proteo<br>bacteria</td><td>c_Gammapr<br>oteobacteria</td><td>o_Burkhol<br>deriales</td><td>f_Rhodocy<br>claceae</td><td>g_Paddy-1</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.16</td><td>d_Bacteria</td><td>p_Actinob<br>acteriota</td><td>c_Actinom<br>ycetia</td><td>o_Actinom<br>ycetales</td><td>f_Microba<br>cteriaceae</td><td>g_Rhodoluna</td><td>s_Rhodoluna</td><td>planktonica</td></tr><tr><td>mghit_bin.17</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Gammaprote<br>obacteria</td><td>o_Burkhold<br>eriales</td><td>f_Burkhold<br>eriaceae</td><td>g_SCGC-AAA<br>027-K21</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.19</td><td>d_Bacteria</td><td>p_Proteo<br>bacteria</td><td>c_Alphapro<br>teobacteria</td><td>o_Rhizobiales</td><td>f_Beijeri<br>nckiaceae</td><td>g_Alsobacter</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.2</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Alphaprot<br>eobacteria</td><td>o_Rhodobac<br>terales</td><td>f_Rhodobac<br>teraceae</td><td>g_TH137</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.20</td><td>d_Bacteria</td><td>p_Actinoba<br>cteriota</td><td>c_Actinom<br>ycetia</td><td>o_Actinom<br>ycetales</td><td>f_Microbact<br>eriaceae</td><td>g_Rhodoluna</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.21</td><td>d_Bacteria</td><td>p_Bdellov<br>ibrionota</td><td>c_Bacteri<br>ovoracia</td><td>o_Bacterio<br>vorales</td><td>f_Bacterio<br>voracaceae</td><td>g_UBA4096</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.22</td><td>d_Bacteria</td><td>p_Bacter<br>oidota</td><td>c_Bacter<br>oidia</td><td>o_Chitino<br>phagales</td><td>f_Chitinop<br>hagaceae</td><td>g_RDXD01</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.23</td><td>d_Bacteria</td><td>p_Actinob<br>acteriota</td><td>c_Actinom<br>ycetia</td><td>o_Nanopel<br>agicales</td><td>f_Nanopel<br>agicaceae</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.25</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Gammapr<br>oteobacteria</td><td>o_Burkhol<br>deriales</td><td>f_Burkhol<br>deriaceae</td><td>g_Polynuc<br>leobacter</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.26</td><td>d_Bacteria</td><td>p_Bacte<br>roidota</td><td>c_Bacteroidia</td><td>o_Chit<br>nophagales</td><td>f_Chitino<br>phagaceae</td><td>g_SXYR01</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.29</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_AKYH767</td><td>f_Palsa-965</td><td>g_GCA-2737665</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.32</td><td>d_Bacteria</td><td>p_Verruc<br>omicrobiota</td><td>c_Verruc<br>omicrobiae</td><td>o_Opitutales</td><td>f_Opitutaceae</td><td>g_Opitutus</td><td>s_</td><td>N/A</td></tr></tbody></table>

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<table><caption>**Table 1 (continued)**</caption><thead><tr><th>BIN</th><th>DIVISION</th><th>PHYLUM</th><th>CLASS</th><th>ORDER</th><th>FAMILY</th><th>GENUS</th><th>SPECIES</th><th>Others</th></tr></thead><tbody><tr><td>mghit_bin.33</td><td>d_Bacteria</td><td>p_Myxococcota</td><td>c_UBA9042</td><td>o_UBA9042</td><td>f_UBA9042</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.34</td><td>d_Bacteria</td><td>p_Hydroge<br>nedentota</td><td>c_Hydroge<br>nedentia</td><td>o_Hydroge<br>nedentiales</td><td>f_SCBR16-9</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.35</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_Flavoba<br>chteriales</td><td>f_Flavoba<br>chteriaceae</td><td>g_Flavoba<br>chterium</td><td>s_Flavoba<br>chterium</td><td>sp002422095</td></tr><tr><td>mghit_bin.36</td><td>d_Bacteria</td><td>p_Verruco<br>microbiota</td><td>c_Verruco<br>microbiae</td><td>o_Verruco<br>microbiales</td><td>f_Akkerman<br>nsiaceae</td><td>g_UBA1315</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.37</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Gammapr<br>oteobacteria</td><td>o_Burkhol<br>deriales</td><td>f_Burkhol<br>deriaceae</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.38</td><td>d_Bacteria</td><td>p_Actino<br>bacteriota</td><td>c_Actino<br>mycetia</td><td>o_Nanope<br>lagicales</td><td>f_UBA5976</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.39</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_NS11-12g</td><td>f_UBA955</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.4</td><td>d_Bacteria</td><td>p_Plancto<br>mycetota</td><td>c_Plancto<br>mycetes</td><td>o_Isospha<br>erales</td><td>f_Isospha<br>eraceae</td><td>g_QWQI01</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.40</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Gammapr<br>oteobacteria</td><td>o_Burkhol<br>deriales</td><td>f_Burkhol<br>deriaceae</td><td>g_Limnoha<br>bitans</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.41</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Gammapr<br>oteobacteria</td><td>o_Methylo<br>coccales</td><td>f_Methylo<br>coccaceae</td><td>g_UBA6136</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.42</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Alphapr<br>oteobacteria</td><td>o_Rickett<br>siales</td><td>f_Midichl<br>oriaceae</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.43</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Gammapr<br>oteobacteria</td><td>o_Burkhol<br>deriales</td><td>f_Methylo<br>philaceae</td><td>g_Methylo<br>pumilus_A</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.44</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Alphapr<br>oteobacteria</td><td>o_Acetoba<br>chterales</td><td>f_Acetoba<br>chteraceae</td><td>g_Ga0074136</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.45</td><td>d_Bacteria</td><td>p_Actinob<br>acteriota</td><td>c_Actinom<br>ycetia</td><td>o_Actinom<br>ycetales</td><td>f_Microba<br>chteriaceae</td><td>g_Auranti<br>microbium</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.46</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Gammapro<br>teobacteria</td><td>o_Burkhold<br>eriales</td><td>f_Burkhold<br>eriaceae</td><td>g_SCGC-AAA<br>027-K21</td><td>s_SCGC-AAA<br>027-K21</td><td>sp003507735</td></tr><tr><td>mghit_bin.47</td><td>d_Bacteria</td><td>p_Proteob<br>acteria</td><td>c_Gammapro<br>teobacteria</td><td>o_Burkhold<br>eriales</td><td>f_Burkhold<br>eriaceae</td><td>g_Limnoha<br>bitans</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.48</td><td>d_Bacteria</td><td>p_Bacter<br>oidota</td><td>c_Bacter<br>oidia</td><td>o_Chitino<br>phagales</td><td>f_Chitinop<br>hagaceae</td><td>g_JJ008</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.49</td><td>d_Bacteria</td><td>p_Verruco<br>icrobiota</td><td>c_Verrucom<br>icrobiae</td><td>o_Pedosp<br>aerales</td><td>f_UBA9464</td><td>g_SXXZ01</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.5</td><td>d_Bacteria</td><td>p_Actinob<br>acteriota</td><td>c_Actinom<br>ycetia</td><td>o_Nanopel<br>agicales</td><td>f_S36-B12</td><td>g_UBA10649</td><td>s_</td><td>N/A</td></tr></tbody></table>

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<table><caption>**Table 1 (continued)**</caption><thead><tr><th>BIN</th><th>DIVISION</th><th>PHYLUM</th><th>CLASS</th><th>ORDER</th><th>FAMILY</th><th>GENUS</th><th>SPECIES</th><th>Others</th></tr></thead><tbody><tr><td>mghit_bin.50</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_Flavobacteriales</td><td>f_UA16</td><td>g_UBA4660</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.51</td><td>d_Bacteria</td><td>p_Proteobacteria</td><td>c_Alphaproteobacteria</td><td>o_Reyrane llales</td><td>f_Reyrane llaceae</td><td>g_Reyranella</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.52</td><td>d_Bacteria</td><td>p_Proteobacteria</td><td>c_Alphaproteobacteria</td><td>o_Sphingom onadales</td><td>f_Sphingom onadaceae</td><td>g_Novosphi ngobium</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.53</td><td>d_Bacteria</td><td>p_Verrucomicrobiota</td><td>c_Verrucomicrobiae</td><td>o_Verrucomicrobiae</td><td>f_Verrucomicrobiaceae</td><td>g_Prosthe obacter</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.54</td><td>d_Bacteria</td><td>p_Bdellovi brionota</td><td>c_Bacteriovoracia</td><td>o_Bacteriovoracales</td><td>f_Bacteriovoracaceae</td><td>g_UBA4096</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.55</td><td>d_Bacteria</td><td>p_Proteobacteria</td><td>c_Alphaproteobacteria</td><td>o_Rhizobiales</td><td>f_Beijerinckciaceae</td><td>g_Allobacter</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.56</td><td>d_Bacteria</td><td>p_Actinobacteriota</td><td>c_Actidimicrobii</td><td>o_Actidimicrobiales</td><td>f_Llumatobacteraceae</td><td>g_UBA668</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.57</td><td>d_Bacteria</td><td>p_Actinobacteriota</td><td>c_Actinomycetia</td><td>o_Actinomycetales</td><td>f_Microbacteriaceae</td><td>g_Auranti microbium</td><td>s_Auranti microbium</td><td>minutum</td></tr><tr><td>mghit_bin.58</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_Sphingobacteriales</td><td>f_</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.59</td><td>d_Bacteria</td><td>p_Verruco microbiota</td><td>c_Verruco microbiae</td><td>o_Verruco microbiales</td><td>f_Verruco microbiaceae</td><td>g_Prosthe cobacter</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.6</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacterooidia</td><td>o_Chitin ophagales</td><td>f_Chitinop hagaceae</td><td>g_UBA3961</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.7</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_Chitin ophagales</td><td>f_Saprosp iraceae</td><td>g_M3007</td><td>s_</td><td>N/A</td></tr><tr><td>mghit_bin.9</td><td>d_Bacteria</td><td>p_Verruco microbiota</td><td>c_Verruco microbiae</td><td>o_Verruco microbiales</td><td>f_Verruco microbiaceae</td><td>g_Prosthe cobacter</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.1</td><td>d_Bacteria</td><td>p_Verruco microbiota</td><td>c_Verruco microbiae</td><td>o_Verruco microbiales</td><td>f_Verruco microbiaceae</td><td>g_Prosthe cobacter</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.10</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_Chitino phagales</td><td>f_Chitino phagaceae</td><td>g_SXYR01</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.11</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacterooidia</td><td>o_NS11-12g</td><td>f_UBA955</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.12</td><td>d_Bacteria</td><td>p_Planctomycetota</td><td>c_Planctomycetes</td><td>o_Isosphaeriales</td><td>f_Isosphaeraceae</td><td>g_QWQI01</td><td>s_</td><td>N/A</td></tr></tbody></table>

(continued on next page)
<table><caption>**Table 1 (continued)**</caption><thead><tr><th>BIN</th><th>DIVISION</th><th>PHYLUM</th><th>CLASS</th><th>ORDER</th><th>FAMILY</th><th>GENUS</th><th>SPECIES</th><th>Others</th></tr></thead><tbody><tr><td>mtspades_bin.13</td><td>d_Bacteria</td><td>p_Myxococcota</td><td>c_Myxococcia</td><td>o_Myxococcales</td><td>f_Myxococcaceae</td><td>g_Archangium_A</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.14</td><td>d_Bacteria</td><td>p_Proteob_acteria</td><td>c_Alphapr_oteobacteria</td><td>o_Sphingo_monadales</td><td>f_Sphingom_onadaceae</td><td>g_Novosphi ngobium</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.15</td><td>d_Bacteria</td><td>p_Proteob_acteria</td><td>c_Gammapro teobacteria</td><td>o_Burkhold eriales</td><td>f_Rhodocyc laceae</td><td>g_Paddy-1</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.16</td><td>d_Bacteria</td><td>p_Proteob_acteria</td><td>c_Gammapro teobacteria</td><td>o_Burkhold eriales</td><td>f_Burkhold eriaceae</td><td>g_Limnohab itans</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.17</td><td>d_Bacteria</td><td>p_Verruco microbiota</td><td>c_Verruco microbiae</td><td>o_Opitutales</td><td>f_Opitutaceae</td><td>g_Opitutus</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.18</td><td>d_Bacteria</td><td>p_Bdellov ibrionota</td><td>c_Bacteri ovoracia</td><td>o_Sphingo ovoracales</td><td>f_Bacteri ovoracaceae</td><td>g_UBA4096</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.19</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_Sphingo bacteriales</td><td>f_</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.2</td><td>d_Bacteria</td><td>p_Actinob_acteriota</td><td>c_Actinom ycetia</td><td>o_Actinom ycetales</td><td>f_Microba cteriaceae</td><td>g_Schumannella</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.20</td><td>d_Bacteria</td><td>p_Actinob_acteriota</td><td>c_Actinom ycetia</td><td>o_Actinom ycetales</td><td>f_Microba cteriaceae</td><td>g_Auranti microbium</td><td>s_Auranti microbium</td><td>minutum</td></tr><tr><td>mtspades_bin.21</td><td>d_Bacteria</td><td>p_Verruco microbiota</td><td>c_Verruco microbiae</td><td>o_Verruco microbiales</td><td>f_Verrucom icrobiaceae</td><td>g_Prosthec obacter</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.22</td><td>d_Bacteria</td><td>p_Verruco microbiota</td><td>c_Verruco microbiae</td><td>o_Verruco microbiales</td><td>f_Verruco microbiaceae</td><td>g_Prosthe cobacter</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.23</td><td>d_Bacteria</td><td>p_Bacteroidota</td><td>c_Bacteroidia</td><td>o_Cytophagales</td><td>f_Spirosomaceae</td><td>g_UBA6715</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.24</td><td>d_Bacteria</td><td>p_Bdellov ibrionota</td><td>c_Bacteri ovoracia</td><td>o_Bacteri ovoracales</td><td>f_Bacteri ovoracaceae</td><td>g_UBA4096</td><td>s_</td><td>N/A</td></tr><tr><td>mtspades_bin.25</td><td>d_Bacteria</td><td>p_Proteob_acteria</td><td>c_Gammapr_oteobacteria</td><td>o_Burkhol deriales</td><td>f_Burkhol deriaceae</td><td>g_JOSHI-001</td><td>s_</td><td>N/A</td></tr></tbody></table>

(continued on next page)
<table><caption>**Table 1 (continued)**</caption><thead><tr><th>BIN</th><th>DIVISION</th><th>PHYLUM</th><th>CLASS</th><th>ORDER</th><th>FAMILY</th><th>GENUS</th><th>SPECIES</th><th>Others</th></tr></thead><tbody><tr><td>mtspades_</td><td>d_Bacteria</td><td>p-Proteob</td><td>c-Alphapr</td><td>o_Rhodoba</td><td>f_Rhodoba</td><td>g_TH137</td><td>s_</td><td>N/A</td></tr><tr><td>bin.26</td><td></td><td>acteria</td><td>oteobacteria</td><td>cterales</td><td>cteraceae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p-Proteob</td><td>c-Alphapr</td><td>o_Reyrane</td><td>f_Reyrane</td><td>g_Reyranella</td><td>s_</td><td>N/A</td></tr><tr><td>bin.27</td><td></td><td>acteria</td><td>oteobacteria</td><td>llales</td><td>llaceae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p-Proteob</td><td>c-Alphapr</td><td>o_Rickett</td><td>f_Midichl</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>bin.28</td><td></td><td>acteria</td><td>oteobacteria</td><td>siales</td><td>oriaceae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p-Proteob</td><td>c_Gammapr</td><td>o_Burkhol</td><td>f_Burkhol</td><td>g_Limnoha</td><td>s_</td><td>N/A</td></tr><tr><td>bin.29</td><td></td><td>acteria</td><td>oteobacteria</td><td>deriales</td><td>deriaceae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p_Verruco</td><td>c_Verruco</td><td>o_Verruco</td><td>f_Akkerma</td><td>g_UBA1315</td><td>s_</td><td>N/A</td></tr><tr><td>bin.3</td><td></td><td>microbiota</td><td>microbiae</td><td>microbiales</td><td>nsiacae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p_Actinob</td><td>c_Actino</td><td>o_Nanope</td><td>f_UBA5976</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>bin.30</td><td></td><td>acteriota</td><td>mycetia</td><td>lagicales</td><td></td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p_Bacter</td><td>c_Bacter</td><td>o_Chitino</td><td>f_Chitino</td><td>g_JJ008</td><td>s_</td><td>N/A</td></tr><tr><td>bin.31</td><td></td><td>oidota</td><td>oidia</td><td>phagales</td><td>phagaceae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p_Hydroge</td><td>c_Hydroge</td><td>o_Hydrogen</td><td>f_</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>bin.32</td><td></td><td>nedentota</td><td>nedentia</td><td>edentiales</td><td></td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p_Actinob</td><td>c_Actino</td><td>o_Actinom</td><td>f_Microbac</td><td>g_Rhodoluna</td><td>s_</td><td>N/A</td></tr><tr><td>bin.33</td><td></td><td>acteriota</td><td>mycetia</td><td>ycetales</td><td>teriaceae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p_Bacter</td><td>c_Bacteroidia</td><td>o_Flavob</td><td>f_Flavoba</td><td>g_Flavoba</td><td>s_Flavoba</td><td>sp002422095</td></tr><tr><td>bin.4</td><td></td><td>oidota</td><td></td><td>acteriales</td><td>cteriaceae</td><td>cterium</td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p_Actinob</td><td>c_Actinom</td><td>o_Nanopel</td><td>f_Nanopel</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>bin.5</td><td></td><td>acteriota</td><td>ycetia</td><td>agicales</td><td>agicaceae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p_Myxococcota</td><td>c_UBA9042</td><td>o_UBA9042</td><td>f_UBA9042</td><td>g_</td><td>s_</td><td>N/A</td></tr><tr><td>bin.6</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p-Proteob</td><td>c_Alphapro</td><td>o_Rhizobiales</td><td>f_Beijerin</td><td>g_Allobacter</td><td>s_</td><td>N/A</td></tr><tr><td>bin.7</td><td></td><td>acteria</td><td>oteobacteria</td><td></td><td>ckiacae</td><td></td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p-Proteob</td><td>c_Gammapro</td><td>o_Burkhold</td><td>f_Methylop</td><td>g_Methylop</td><td>s_</td><td>N/A</td></tr><tr><td>bin.8</td><td></td><td>acteria</td><td>oteobacteria</td><td>eriales</td><td>hilaceae</td><td>umilus_A</td><td></td><td></td></tr><tr><td>mtspades_</td><td>d_Bacteria</td><td>p-Proteob</td><td>c_Gammapro</td><td>o_Burkhold</td><td>f_Burkhold</td><td>g_Limnohab</td><td>s_</td><td>N/A</td></tr><tr><td>bin.9</td><td></td><td>acteria</td><td>oteobacteria</td><td>eriales</td><td>eriaceae</td><td>itans</td><td></td><td></td></tr></tbody></table>
<table><caption>**Table 2**

Accession number, gene functions and antibiotic resistance.</caption><thead><tr><th>%COVERAGE</th><th>%IDENTITY</th><th>ACCESSION</th><th>PRODUCT</th><th>RESISTANCE</th></tr></thead><tbody><tr><td>100.00</td><td>100.00</td><td>NG_049393.1</td><td>oxacillin-hydrolyzing class D beta-lactamase OXA-10</td><td>CEPHALOSPORIN</td></tr><tr><td>100.00</td><td>99.87</td><td>NG_052266.1</td><td>ANT(3')-la family aminoglycoside nucleotidyltransferase AadA1</td><td>STREPTOMYCIN</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_047702.1</td><td>trimethoprim-resistant dihydrofolate reductase DfrA15</td><td>TRIMETHOPRIM</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_051852.1</td><td>sulfonamide-resistant dihydropteroate synthase Sul2</td><td>SULFONAMIDE</td></tr><tr><td>100.00</td><td>95.49</td><td>NG_051907.1</td><td>tetracycline efflux MFS transporter Tet(G)</td><td>TETRACYCLINE</td></tr><tr><td>100.00</td><td>95.77</td><td>NG_047380.1</td><td>aminoglycoside 6-adenylyltransferase AadS</td><td>STREPTOMYCIN</td></tr><tr><td>100.00</td><td>99.64</td><td>NG_051844.1</td><td>aminoglycoside N-acetyltransferase AAC(6')-Ib4</td><td>GENTAMICIN</td></tr><tr><td>100.00</td><td>80.62</td><td>NG_049735.1</td><td>oxacillin-hydrolyzing class D extended-spectrum beta-lactamase OXA-45</td><td>CEPHALOSPORIN</td></tr><tr><td>100.00</td><td>99.75</td><td>NG_049343.1</td><td>oxacillin-hydrolyzing class D beta-lactamase NPS-1</td><td>BETA-LACTAM</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_056174.1</td><td>sulfonamide-resistant dihydropteroate synthase Sul4</td><td>SULFONAMIDE</td></tr><tr><td>100.00</td><td>99.92</td><td>NG_047979.1</td><td>macrolide efflux MFS transporter Mef(C)</td><td>MACROLIDE</td></tr><tr><td>100.00</td><td>99.77</td><td>NG_047998.1</td><td>Mph(G) family macrolide 2'-phosphotransferase</td><td>MACROLIDE</td></tr><tr><td>100.00</td><td>96.60</td><td>NG_065882.1</td><td>class A beta-lactamase PAU-1</td><td>BETA-LACTAM</td></tr><tr><td>100.00</td><td>99.16</td><td>NG_047746.1</td><td>trimethoprim-resistant dihydrofolate reductase DfrB2</td><td>TRIMETHOPRIM</td></tr><tr><td>89.03</td><td>99.53</td><td>NG_052353.1</td><td>trimethoprim-resistant dihydrofolate reductase DfrA1</td><td>TRIMETHOPRIM</td></tr><tr><td>100.00</td><td>99.92</td><td>NG_047875.1</td><td>chloramphenicol/florfenicol efflux MFS transporter FlorR2</td><td>CHLORAMPHENICOL; FLORFENICOL</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_051699.1</td><td>trimethoprim-resistant dihydrofolate reductase DfrA5</td><td>TRIMETHOPRIM</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_048581.1</td><td>NAD(+)-rampin ADP-ribosyltransferase Arr-3</td><td>RIFAMYCIN</td></tr><tr><td>84.48</td><td>99.86</td><td>NG_049639.1</td><td>class D beta-lactamase OXA-347</td><td>BETA-LACTAM</td></tr><tr><td>100.00</td><td>99.65</td><td>NG_047380.1</td><td>aminoglycoside 6-adenylyltransferase AadS</td><td>STREPTOMYCIN</td></tr><tr><td>85.34</td><td>98.27</td><td>NG_052426.1</td><td>EraA family erythromycin esterase</td><td>MACROLIDE</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_048082.1</td><td>sulfonamide-resistant dihydropteroate synthase Sul1</td><td>SULFONAMIDE</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_047464.1</td><td>aminoglycoside O-phosphotransferase APH(6)-Id</td><td>STREPTOMYCIN</td></tr><tr><td>100.00</td><td>99.92</td><td>NG_048177.1</td><td>tetracycline efflux MFS transporter Tet(C)</td><td>TETRACYCLINE</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_056035.1</td><td>trimethoprim-resistant dihydrofolate reductase DfrA14</td><td>TRIMETHOPRIM</td></tr><tr><td>100.00</td><td>99.68</td><td>NG_047647.1</td><td>chloramphenicol efflux MFS transporter CmlA1</td><td>CHLORAMPHENICOL</td></tr><tr><td>100.00</td><td>100.00</td><td>NG_049115.1</td><td>class A beta-lactamase GES-13</td><td>CEPHALOSPORIN</td></tr></tbody></table>

# 4. Experimental Design, Materials and Methods

## 4.1. Sample collection

For this preliminary study, one liter of water was sampled once on September 19th, 2019 within a gutter along houses in the city of Pointe-Noire (latitude and longitude 4°48′43.1″S 11°52′27.8″E) in the Republic of Congo. Water was transported in a bottle with an iced pack and stored at 4 °C for six days until DNA extraction.

## 4.2. DNA isolation, library preparation, and shotgun sequencing

Four hundred milliliter of water were successively filtered through two mixed cellulose esters filters of 5 µm, one of 1.2 µm, and three of 0.22 µm (MCE membrane; 47 mm; MF-Millipore). DNA was extracted and pooled from the six filters using the DN easy PowerWater kit (Qiagen) according to the manufacturer's instructions. Library preparation and sequencing were performed by GENEWIZ, from Azenta Life Sciences company®. DNA library sequencing was performed on an Illumina HiSeq 4000 machine in paired-end mode producing reads of 150 base pairs length. The raw data contain 2 × 84,886,827 paired-end reads of 150 bp (25,466 Mbases).

## 4.3. Data preprocessing and cleaning

The quality of sequencing data was assessed and visualized using the fastqc tool v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). To filter out adapters, undetermined bases, and poor-quality sequences, reads were subjected to a cleaning process using Fastp tool v0.23.2 [1]. Only sequences with a length greater than or equal to 50 bp were kept for analysis. Possible human sequences were filtered by a mapping approach using bowtie2 v2.3.4.3 [2]
on the GRCh38 version of the human genome index available here (https://benlangmead.github.ioaws-indexes/bowtie). To extract unmapped reads, samtools v1.9 tool was used [3].

## 4.4. Metagenomics profiling

Two profilers were used Kaiju [4] and kraken2 [5]. The latter was used on reads that were not classified by the first profiler in order to minimize false positives. We used three available databases for Kaiju, nr_euk (version 2022-03-10) a database like NR (Non-Redundant Protein database but includes fungi and microbial eukaryotes), rvdb, (version 2022-04-07) which is Reference Viral Database [6] and finally a plasmids database (version 2022-04-10). All these databases are available on Kaiju homepage. All the classifications were merged into one file at the end of the analyses.

For these classifications reads that were not classified in the first database, were used in the second, and so on. Seqtk v 1.3-r106 (https://github.com/lh3/seqtk) tool extracted non-assigned reads in each step and prepared the input to the next one.

All reads unclassified by Kaiju were employed as inputs for profiling with Kraken2, a nucleic-based classifier utilizing a k-mer-based similarity approach. The database used in conjunction with Kraken2 is the PlusPF database, encompassing the standard Kraken2 database (RefSeq archaea, bacteria, viral, plasmid, human, UniVec_Core) along with Ref-Seq protozoa and fungi. The indexes of this database and others are freely available at https://benlangmead.github.io/aws-indexes/k2.

## 4.5. Metagenome assembled genomes (MAGs) reconstruction, taxonomic assignment, and functional annotation

Filtered and decontaminated reads were assembled by MEGAHIT [7] using kmer values ranging from 21 to 127 with a step of 2. Contigs with lengths inferior to 200 base pairs were discarded. In the same way and with the same kmer parameters, the metaSPAdes assembler [8] was used to generate the second assembly. The two binners used on each assembly (the so-called megahit assembly and the metaSPAdes assembly) are MaxBin2 [9] and Metabat2 [10]. They are widely used in binning and routinely are integrated into many metagenomic data analysis pipelines. They work in much the same way but with different sensitivities. The only notable difference between the two tools is the minimum length of contigs accepted by the binner. For metabat2, all contigs with a length < 1500 base pairs are filtered and not binned.

We then used two assemblers and two binners, resulting in four binned assemblies. The goal was to refine these assemblies to extract the maximum information from our dataset, particularly given the limitation of having only one sample. Subsequently, four modules from the MetaWRAP v1.1.2 [11] pipeline were applied to the bins. The bin refinement stage was performed using a MetaWRAP module (bin refinement module), where dereplication is performed. This module combines bins to create hybrid bins after evaluating the quality of each bin using CheckM. It then removes duplicate contigs appearing in multiple bins to ultimately identify the best version of each bin. For taxonomic assignment, we used also gtdbtk v 1.4.1 [12–16], using the whole pipeline to place contigs/bins in the GTDB reference tree. Contigs of each bin were annotated using prokka annotation pipeline v1.12 [17].

## 4.6. Screening of antibiotic resistance genes

MMseqs2 (release 14-7e284) [18] was employed to cluster the two assemblies (mega-hit and metaspades). Subsequently, the clustered assembly was used for the search for antimicrobial resistance genes. For this purpose, we used ABRicate (release 12), which can be found at https://github.com/tseemann/abricate.
**Limitations**

The sampled water was stored at 4 °C for 6 days. Thus, organisms with a greater tolerance to cold temperatures may have taken advantage of the nutrients in the water and less competition to bloom which affects the relative abundance of bins.

**Ethics Statement**

The authors have read and follow the ethical requirements for publication in Data in Brief and confirming that the current work does not involve human subjects, animal experiments, or any data collected from social media platforms.

**CRediT Author Statement**

**Ascel Samba-Louaka:** Conceptualization, Supervision, Project administration, Resources, Funding acquisition, Writing - original draft; **Bouziane Moumen:** Formal analysis, Writing - original draft; **Céline Samba-Louaka:** Methodology, Resources, review & editing; Anicet Magloire Boumba and Hervé Sabin Ngoma: review & editing; Aubierge Kimpamboudi: Project administration, Formal analysis, Writing - review & editing.

**Data Availability**

Metagenome from sample collected from water stream in Pointe-Noire city (Republic of Congo) (Original data) (NCBI).

**Acknowledgments**

We thank Yann Dussert for the critical reading of the manuscript. We acknowledge the Ebioinfo facility at the UMR CNRS 7267, University of Poitiers, for supplying the necessary computing infrastructure.

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

**Declaration of Competing Interest**

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

**Supplementary Materials**

Supplementary material associated with this article can be found, in the online version, at doi:10.1016/j.dib.2024.110655.

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