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A recent study used 16S ribosomal RNA amplicon sequencing to quantify the composition of the gut microbiome and identify predictive biomarkers of infection with limited taxonomic resolution.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>To achieve increased resolution of gut microbial factors associated with V. cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Using machine learning, we resolved species, strains, gene families, and cellular pathways in the microbiome at the time of exposure to V. cholerae to identify markers that predict infection and symptoms. Use of metagenomic features improved the precision and accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although with greater uncertainty than our infection prediction. Species within the genera Prevotella and Bifidobacterium predicted protection from infection, and genes involved in iron metabolism were also correlated with protection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/infdis\/jiaa358","type":"journal-article","created":{"date-parts":[[2020,6,18]],"date-time":"2020-06-18T07:10:10Z","timestamp":1592464210000},"page":"342-351","source":"Crossref","is-referenced-by-count":36,"title":["Predicting\n                    <i>Vibrio cholerae<\/i>\n                    Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study"],"prefix":"10.1093","volume":"223","author":[{"given":"In\u00e8s","family":"Levade","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morteza M","family":"Saber","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Firas S","family":"Midani","sequence":"additional","affiliation":[{"name":"Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, USA"},{"name":"Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA"},{"name":"Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fahima","family":"Chowdhury","sequence":"additional","affiliation":[{"name":"Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashraful I","family":"Khan","sequence":"additional","affiliation":[{"name":"Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasmin A","family":"Begum","sequence":"additional","affiliation":[{"name":"Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward T","family":"Ryan","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA"},{"name":"Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. 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USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason B","family":"Harris","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Regina C","family":"LaRocque","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Firdausi","family":"Qadri","sequence":"additional","affiliation":[{"name":"Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6819-8699","authenticated-orcid":false,"given":"B 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