ArticleApplied and environmental microbiology2016
Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia.
Article in Applied and environmental microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 50 citations in OpenAlex.
- Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter.Environmental microbiology · 2022Article
- The survivor strain: isolation and characterization ofFrontiers in bioengineering and biotechnology · 2022Article
- Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration.Frontiers in microbiology · 2022Article
- Proteome and strain analysis of cyanobacteriumiScience · 2021Article
- Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems.Applied microbiology and biotechnology · 2021Review
- Genera specific distribution of DEAD-box RNA helicases in cyanobacteria.Microbial genomics · 2021Article
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- Nitrogen Source Governs Community Carbon Metabolism in a Model Hypersaline Benthic Phototrophic Biofilm.mSystems · 2020Article
- Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater GenusApplied and environmental microbiology · 2020Article
- Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes.Microbiome · 2020Article
- MhpA Is a Hydroxylase Catalyzing the Initial Reaction of 3-(3-Hydroxyphenyl)Propionate Catabolism inApplied and environmental microbiology · 2020Article
- Article
- A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.Microbiome · 2018Article
- Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake.Microbiome · 2018Article
- ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes.BMC genomics · 2018Article
- Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture.Scientific reports · 2018Article
- Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.Nature biotechnology · 2017Article
- Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities.The ISME journal · 2017Article
- Non-autotrophic methanogens dominate in anaerobic digesters.Scientific reports · 2017Article
- Trade-offs between microbiome diversity and productivity in a stratified microbial mat.The ISME journal · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set.
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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.