| collection date | 2011-01-01 |
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| broad-scale environmental context | Host-associated |
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| local-scale environmental context | Human |
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| environmental medium | Digestive system |
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| geographic location | Bangladesh |
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| investigation type | metagenome-assembled genome |
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| isolation source | human gut metagenome |
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| project name | Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these communities respond to diarrheal disease and its treatment. Here, we report that after V. cholerae infection, human gut microbiota undergo an orderly and reproducible succession featuring transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli (ETEC) infection. Our metagenomic analyses suggest multiple mechanisms driving microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure, but driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea. |
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| sample name | ERR866566_bin.49_CONCOCT_v1.1_MAG |
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| ENA-CHECKLIST | ERC000047 |
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| ENA-FIRST-PUBLIC | 2023-01-03 |
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| ENA-LAST-UPDATE | 2023-01-03 |
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| External Id | SAMEA14085131 |
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| INSDC center alias | EBI |
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| INSDC center name | European Bioinformatics Institute |
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| INSDC first public | 2023-01-03T00:33:18Z |
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| INSDC last update | 2023-01-03T00:33:18Z |
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| INSDC status | public |
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| Submitter Id | ERR866566_bin.49_CONCOCT_v1.1_MAG |
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| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics |
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| assembly software | spadesv3.11.1 |
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| binning parameters | Default |
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| binning software | CONCOCT v1.1 |
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| broker name | EMG broker account, EMBL-EBI |
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| completeness score | 94.88 |
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| completeness software | CheckM |
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| contamination score | 0.81 |
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| geographic location (latitude) | 23.7 |
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| geographic location (longitude) | 90.3667 |
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| metagenomic source | human gut metagenome |
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| sample derived from | SAMEA3360662 |
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| scientific_name | uncultured Mobiluncus sp. |
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| sequencing method | Illumina HiSeq 2000 |
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| taxonomic identity marker | multi-marker approach |
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