ArticleBMC biology2020
The rise of diversity in metabolic platforms across the Candidate Phyla Radiation.
Article in BMC biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Divergent evolution of the PRPS enzymes across the tree of life.bioRxiv : the preprint server for biology · 2026Article
- Ultrasmall oral Saccharibacteria modulate gingival immunoactivation through type IV pili and TLR2-dependent endocytosis.Nature communications · 2026Article
- Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean.Genome biology · 2025Article
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.eLife · 2025Article
- Categorization of Bacteria That Leak from Activated Sludge to Secondary Treated Water: Year-round Observations.Microbes and environments · 2025Article
- Proposal ofISME communications · 2025Article
- Beyond genomics in Patescibacteria: A trove of unexplored biology packed into ultrasmall bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Comprehensive analysis of insertion sequences within rRNA genes of CPR bacteria and biochemical characterization of a homing endonuclease encoded by these sequences.Journal of bacteriology · 2024Article
- A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex.Protein science : a publication of the Protein Society · 2024Article
- More than the sum of its parts: uncovering emerging effects of microbial interactions in complex communities.FEMS microbiology ecology · 2024Article
- MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life.Bioinformatics (Oxford, England) · 2024Article
- Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism.Microbiome · 2024Article
- Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.The ISME journal · 2024Review
- Genome characterization and taxonomy of Actinomyces acetigenes sp. nov., and Actinomyces stomatis sp. nov., previously isolated from the human oral cavity.BMC genomics · 2023Article
- Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil.World journal of microbiology & biotechnology · 2023Article
- "Applied and environmental microbiology · 2023Article
- Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin.Microbiome · 2023Article
- Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment.Frontiers in microbiology · 2023Article
- Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome.Microbiome · 2022Article
- In vitro study of the modulatory effects of heat-killed bacterial biomass on aquaculture bacterioplankton communities.Scientific reports · 2022Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved.
resultsHere, we selected ~ 1000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Mapping of glycolysis, the pentose phosphate pathway, and pyruvate metabolism onto the tree showed that some components of these pathways are sparsely distributed and that similarity between metabolic platforms is only partially predicted by phylogenetic relationships. To evaluate the extent to which gene loss and lateral gene transfer have shaped trait distribution, we analyzed the patchiness of gene presence in a phylogenetic context, examined the phylogenetic depth of clades with shared traits, and compared the reference tree topology with those of specific metabolic proteins. While the central glycolytic pathway in CPR is widely conserved and has likely been shaped primarily by vertical transmission, there is evidence for both gene loss and transfer especially in steps that convert glucose into fructose 1,6-bisphosphate and glycerate 3P into pyruvate. Additionally, the distribution of Group 3 and Group 4-related NiFe hydrogenases is patchy and suggests multiple events of ancient gene transfer.
conclusionsWe infer that patterns of gene gain and loss in CPR, including acquisition of accessory traits in independent transfer events, could have been driven by shifts in host-derived resources and led to sparse but varied genetic inventories.
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