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Here we analyzed metagenome-assembled genomes of the \u201cGenomes from Earth\u2019s Microbiomes\u201d initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.<\/jats:p>","DOI":"10.1038\/s41467-021-24294-3","type":"journal-article","created":{"date-parts":[[2021,6,29]],"date-time":"2021-06-29T10:06:39Z","timestamp":1624961199000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":51,"title":["Pangenomics reveals alternative environmental lifestyles among chlamydiae"],"prefix":"10.1038","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6710-7572","authenticated-orcid":false,"given":"Stephan","family":"K\u00f6stlbacher","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4100-832X","authenticated-orcid":false,"given":"Astrid","family":"Collingro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5678-1366","authenticated-orcid":false,"given":"Tamara","family":"Halter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4932-4677","authenticated-orcid":false,"given":"Frederik","family":"Schulz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9265-8341","authenticated-orcid":false,"given":"Sean P.","family":"Jungbluth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8309-5855","authenticated-orcid":false,"given":"Matthias","family":"Horn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,6,29]]},"reference":[{"key":"24294_CR1","doi-asserted-by":"publisher","first-page":"3229","DOI":"10.1073\/pnas.1218525110","volume":"110","author":"M McFall-Ngai","year":"2013","unstructured":"McFall-Ngai, M. et al. 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