ArticlemBio2013
Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla.
Article in mBio, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 159 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
159 citing papers in PubMed, 321 citations in OpenAlex.
- Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant.Scientific reports · 2017Trial
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- Encapsulation of Exosomal Volatile Organic Compounds for Modulating the NF-κB Pathway in Monocytes.ACS bio & med chem Au · 2026Article
- Ecological and evolutionary dynamics of the oral microbiome across childhood.bioRxiv : the preprint server for biology · 2026Article
- Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem.The ISME journal · 2026Article
- Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota.Microbes and environments · 2026Review
- Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge.Environmental microbiology reports · 2025Article
- Diverse Patescibacteria assemblages and prevalence of ultra-small free-living Parcubacteria along a subterranean estuary.mSystems · 2025Article
- Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.Microbiome · 2025Article
- Article
- Carbon source diversity shapes bacterial interspecies interactions.The ISME journal · 2025Article
- Revealing an unprecedented diversity of episymbiotic Saccharibacteria in a high-quality genome collection.NPJ biofilms and microbiomes · 2024Article
- Investigation of pure lung microbiota in patients with lung cancer after eliminating upper airway contamination: a prospective cohort study.Journal of thoracic disease · 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
- Article
- Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing.Communications biology · 2024Article
- Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.ISME communications · 2024Article
- Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique.ISME communications · 2024Article
- Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality.Microorganisms · 2023Article
- Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.Applied and environmental microbiology · 2023Article
99 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledCultivation-independent surveys of microbial diversity have revealed many bacterial phyla that lack cultured representatives. These lineages, referred to as candidate phyla, have been detected across many environments. Here, we deeply sequenced microbial communities from acetate-stimulated aquifer sediment to recover the complete and essentially complete genomes of single representatives of the candidate phyla SR1, WWE3, TM7, and OD1. All four of these genomes are very small, 0.7 to 1.2 Mbp, and have large inventories of novel proteins. Additionally, all lack identifiable biosynthetic pathways for several key metabolites. The SR1 genome uses the UGA codon to encode glycine, and the same codon is very rare in the OD1 genome, suggesting that the OD1 organism could also transition to alternate coding. Interestingly, the relative abundance of the members of SR1 increased with the appearance of sulfide in groundwater, a pattern mirrored by a member of the phylum Tenericutes. All four genomes encode type IV pili, which may be involved in interorganism interaction. On the basis of these results and other recently published research, metabolic dependence on other organisms may be widely distributed across multiple bacterial candidate phyla. IMPORTANCE: Few or no genomic sequences exist for members of the numerous bacterial phyla lacking cultivated representatives, making it difficult to assess their roles in the environment. This paper presents three complete and one essentially complete genomes of members of four candidate phyla, documents consistently small genome size, and predicts metabolic capabilities on the basis of gene content. These metagenomic analyses expand our view of a lifestyle apparently common across these candidate phyla.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.