Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria.
Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria.
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DOI：
10.1128/mbio.00521-21
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发表时间：
2021-08-31
期刊：
影响因子：
6.4
通讯作者：
Banfield JF
中科院分区：
文献类型：
--
作者：
Jaffe AL;Thomas AD;He C;Keren R;Valentin-Alvarado LE;Munk P;Bouma-Gregson K;Farag IF;Amano Y;Sachdeva R;West PT;Banfield JF
候选的门辐射（CPR）细菌是小的，可能是在地球生态系统中发现的外共生生物。尽管它们的流行，CPR谱系在栖息地和这些栖息地之间的过渡的基因组签名的分布仍然不清楚。在这里，我们扩展了Absconditabacteria（SR1），Gracilibacteria和Saccharomyces bacteria（TM7）的基因组库存，CPR细菌已知发生在动物相关和环境微生物组中，并调查了基因含量随原产地的变化。通过将微生物发生与栖息地信息叠加，我们发现这三个谱系的细菌经历了从环境栖息地到动物微生物组的多次转变。基于数百个宏基因组的共现分析，我们扩展了先前的建议，即某些Saccharomyces细菌具有广泛的细菌宿主范围，并限制了Absconditabacteria和Gracilibacteria的可能宿主关系。全蛋白质组分析表明，与动物相关的Saccharomyces细菌的基因库比环境中的细菌小，并且富含许多蛋白质家族，包括那些可能在氨基酸代谢、噬菌体防御和过氧化物解毒中起作用的蛋白质家族。相反，一些淡水Saccharomyces细菌编码一种假定的视紫红质。对于蛋白质家族表现出最清晰的差异栖息地分布模式，我们比较了蛋白质和物种的遗传，以估计发生横向基因转移和基因组丢失的物种树。这些分析表明，栖息地的转变可能并不伴随着大的转移或损失事件，而是与持续的蛋白质组重塑。因此，我们推测，CPR栖息地的转变主要是由合适的主机类群的可用性，并加强收购和损失的一些能力。
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.