ArticleApplied and environmental microbiology2016
Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota.Nature communications · 2024Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- A network approach to elucidate and prioritize microbial dark matter in microbial communities.The ISME journal · 2021Article
- Microbial single-cell omics: the crux of the matter.Applied microbiology and biotechnology · 2020Review
- Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs.The ISME journal · 2020Article
- Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics.Frontiers in microbiology · 2020Article
- Single cell ecology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes.Genome biology and evolution · 2019Review
- Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures.Frontiers in microbiology · 2019Article
- Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.Microbiome · 2018Article
- Single-cell metagenomics: challenges and applications.Protein & cell · 2018Review
- Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle.Microbes and environments · 2018Article
- ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes.BMC genomics · 2018Article
- Assembling metagenomes, one community at a time.BMC genomics · 2017Article
- Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla.Frontiers in microbiology · 2017Article
- Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs.Frontiers in microbiology · 2017Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "Calescamantes" (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs.
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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.