ArticleScientific reports2016
Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed.
- An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov.Microbial ecology · 2025Review
- Article
- Bacterial Microbiota ofMicroorganisms · 2023Article
- Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota.Nature microbiology · 2023Article
- Physiological changes during torpor favor association withFrontiers in microbiology · 2023Article
- Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking.BMC genomics · 2022Article
- Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle.The ISME journal · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Non-essential ribosomal proteins in bacteria and archaea identified using COGs.Journal of bacteriology · 2021Article
- First evidence of virus-like particles in the bacterial symbionts of Bryozoa.Scientific reports · 2021Article
- Review
- Accurate and complete genomes from metagenomes.Genome research · 2020Review
- Article
- Computational Modeling of the Human Microbiome.Microorganisms · 2020Review
- Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.Nucleic acids research · 2019Article
- Diversity and Dynamics of "Candidatus Endobugula" and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.Microbial ecology · 2019Article
- Microbial-derived products as potential new antimicrobials.Veterinary research · 2018Review
- Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity.Genome biology and evolution · 2018Article
- Chemoenzymatic Dissection of Polyketide β-Branching in the Bryostatin Pathway.Methods in enzymology · 2018Article
- Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations.Marine drugs · 2017Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain "universal" 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of "microbial dark matter," or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.
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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.