Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota

Cale O. Seymour, Marike Palmer, Eric D. Becraft, Ramunas Stepanauskas, Ariel D. Friel, Frederik Schulz, Tanja Woyke, Emiley Eloe-Fadrosh, Dengxun Lai, Jian Yu Jiao, Zheng Shuang Hua, Lan Liu, Zheng Han Lian, Wen Jun Li, Maria Chuvochina, Brianna K. Finley, Benjamin J. Koch, Egbert Schwartz, Paul Dijkstra, Duane P. MoserBruce A. Hungate, Brian P. Hedlund

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.

Original languageEnglish (US)
Pages (from-to)727-744
Number of pages18
JournalNature Microbiology
Issue number4
StatePublished - Apr 2023

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Applied Microbiology and Biotechnology
  • Genetics
  • Microbiology (medical)
  • Cell Biology


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