Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria

mBio

Jillian F. Banfield¹  Ray Keren²  Keith Bouma-Gregson³  Alex D. Thomas⁴  Patrick T. West⁵  Luis E. Valentin-Alvarado⁶  Alexander L. Jaffe⁶  Rohan Sachdeva⁷  Christine He⁷  Patrick Munk⁸  Yuki Amano⁹  Ibrahim F. Farag^1,10 

[1] Blood and Marrow Transplantation), Stanford University, Stanford, California, USA;Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California, USA;Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, USA;Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA;;Department of Medicine (Hematology &Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA;Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA;National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark;Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Ibaraki, Japan;School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA;

关键词: CPR bacteria;    animal microbiome;    bacterial evolution;    comparative genomics;    habitat transition;   

DOI  :  10.1128/mBio.00521-21

来源: DOAJ

【 摘 要 】

ABSTRACT Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth’s ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions among these habitats remain unclear. Here, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain Saccharibacteria have broad bacterial host ranges and constrain possible host relationships for Absconditabacteria and Gracilibacteria. Full-proteome analyses show that animal-associated Saccharibacteria have smaller gene repertoires than their environmental counterparts and are enriched in numerous protein families, including those likely functioning in amino acid metabolism, phage defense, and detoxification of peroxide. In contrast, some freshwater Saccharibacteria encode a putative rhodopsin. For protein families exhibiting the clearest patterns of differential habitat distribution, we compared protein and species phylogenies to estimate the incidence of lateral gene transfer and genomic loss occurring over the species tree. These analyses suggest that habitat transitions were likely not accompanied by large transfer or loss events but rather were associated with continuous proteome remodeling. Thus, we speculate that CPR habitat transitions were driven largely by availability of suitable host taxa and were reinforced by acquisition and loss of some capacities. IMPORTANCE Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts. We found that shifts of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.

【 授权许可】

Unknown