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Here, we assessed the growth of 92 representative human gut bacterial strains spanning 28 families across multiple pH values and osmolalities\n                    <jats:italic>in vitro<\/jats:italic>\n                    . The ability to grow in extreme pH or osmolality conditions correlated with the availability of known stress response genes in many cases, but not all, indicating that novel pathways may participate in protecting against acid or osmotic stresses. Machine learning analysis uncovered genes or subsystems that are predictive of differential tolerance in either acid or osmotic stress. For osmotic stress, we corroborated the increased abundance of these genes\n                    <jats:italic>in vivo<\/jats:italic>\n                    during osmotic perturbation. The growth of specific taxa in limiting conditions in isolation\n                    <jats:italic>in vitro<\/jats:italic>\n                    correlated with survival in complex communities\n                    <jats:italic>in vitro<\/jats:italic>\n                    and in an\n                    <jats:italic>in vivo<\/jats:italic>\n                    mouse model of diet-induced intestinal acidification. Our data show that\n                    <jats:italic>in vitro<\/jats:italic>\n                    stress tolerance results are generalizable and that physical parameters may supersede interspecies interactions in determining the relative abundance of community members. This study provides insight into the ability of the microbiota to respond to common perturbations that may be encountered in the gut and provides a list of genes that correlate with increased ability to survive in these conditions.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>To achieve greater predictability in microbiota studies, it is crucial to consider physical environmental factors such as pH and particle concentration, as they play a pivotal role in influencing bacterial function and survival. For example, pH is significantly altered in various diseases, including cancers, inflammatory bowel disease, as well in the case of over-the-counter drug use. Additionally, conditions like malabsorption can affect particle concentration. In our study, we investigate how changes in environmental pH and osmolality can serve as predictive indicators of bacterial growth and abundance. Our research provides a comprehensive resource for anticipating shifts in microbial composition and gene abundance during complex perturbations. Moreover, our findings underscore the significance of the physical environment as a major driver of bacterial composition. Finally, this work emphasizes the necessity of incorporating physical measurements into animal and clinical studies to better understand the factors influencing shifts in microbiota abundance.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.00753-23","type":"journal-article","created":{"date-parts":[[2023,7,11]],"date-time":"2023-07-11T09:11:15Z","timestamp":1689066675000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":34,"title":["Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3494-5697","authenticated-orcid":true,"given":"Katharine M.","family":"Ng","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"},{"name":"School of Biomedical Engineering, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9201-7621","authenticated-orcid":true,"given":"Sagar","family":"Pannu","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sijie","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan C.","family":"Burckhardt","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thad","family":"Hughes","sequence":"additional","affiliation":[{"name":"Independent Researcher, Vancouver, British Columbia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Will","family":"Van Treuren","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jen","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kisa","family":"Naqvi","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bachviet","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte A.","family":"Clayton","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deanna M.","family":"Pepin","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel R.","family":"Collins","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7542-1577","authenticated-orcid":true,"given":"Carolina","family":"Tropini","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada"},{"name":"School of Biomedical Engineering, University of British Columbia, Vancouver, Canada"},{"name":"Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2023,7,11]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3552"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.micinf.2021.104815"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2017.03.010"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2009.01931.x"},{"key":"e_1_3_5_6_2","first-page":"49","article-title":"A role of hydrogen peroxide producing commensal bacteria present in colon of adolescents with inflammatory bowel disease in perpetuation of the inflammatory process","volume":"60","author":"Strus M","year":"2009","unstructured":"Strus M, Gosiewski T, Fyderek K, Wedrychowicz A, Kowalska-Duplaga K, Kochan P, Adamski P, Heczko PB. 2009. 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