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Here, using topological data analysis, we identify states and dynamical features relevant to macroscopic processes. We show that gut disease processes and marine geochemical events are associated with transitions between community states, defined as topological features of the data density. We find a reproducible two-state succession during recovery from cholera in the gut microbiomes of multiple patients, evidence of dynamic stability in the gut microbiome of a healthy human after experiencing diarrhea during travel, and periodic state transitions in a marine\n                    <jats:italic>Prochlorococcus<\/jats:italic>\n                    community driven by water column cycling. Our approach bridges small-scale fluctuations in microbiome composition and large-scale changes in phenotype without details of underlying mechanisms, and provides an assessment of microbiome stability and its relation to human and environmental health.\n                  <\/jats:p>","DOI":"10.1038\/s41522-020-00145-9","type":"journal-article","created":{"date-parts":[[2020,10,14]],"date-time":"2020-10-14T06:04:11Z","timestamp":1602655451000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Topological analysis reveals state transitions in human gut and marine bacterial communities"],"prefix":"10.1038","volume":"6","author":[{"given":"William K.","family":"Chang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"VanInsberghe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1933-8103","authenticated-orcid":false,"given":"Libusha","family":"Kelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,10,14]]},"reference":[{"key":"145_CR1","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1038\/nrmicro1750","volume":"5","author":"CA Suttle","year":"2007","unstructured":"Suttle, C. 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