ArticlePloS one2019
Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It has been retracted, and should not be counted. Cited by 35 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.
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Who cites it
35 citing papers in PubMed.
- Isolation and characterization of microalgal growth-enhancing bacteria from a wastewater treatment facility.World journal of microbiology & biotechnology · 2026Article
- Beyond metagenomics: culturomics uncovers aerobic and facultative anaerobic bacterial diversity in the camel gut.Animal microbiome · 2026Article
- From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.World journal of microbiology & biotechnology · 2026Article
- Review
- Comparative analysis of three experimental methods for revealing human fecal microbial diversity.BMC microbiology · 2025Article
- Editorial Note: Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.PloS one · 2025Article
- Retraction: Among live and dead bacteria, the optimization of sample collection and processing remains essential in recovering gut microbiota components.Frontiers in microbiology · 2025Article
- Retraction: Deciphering the urinary microbiota repertoire by culturomics reveals mostly anaerobic bacteria from the gut.Frontiers in microbiology · 2025Article
- Retraction: Tobacco smoking affects the salivary gram-positive bacterial population.Frontiers in public health · 2025Article
- Bacterial profiling of colorectal cancer biopsies: a culture-based study in Indian patients.Frontiers in cellular and infection microbiology · 2025Article
- Culture-based characterization of gut microbiota in inflammatory bowel disease.Frontiers in microbiology · 2025Article
- A streamlined culturomics case study for the human gut microbiota research.Scientific reports · 2024Article
- Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont.FEMS microbiology ecology · 2024Review
- Bisphenol A exposure affects specific gut taxa and drives microbiota dynamics in childhood obesity.mSystems · 2024Article
- MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies.Cell reports methods · 2023Article
- The pivotal roles of gut microbiota in insect plant interactions for sustainable pest management.NPJ biofilms and microbiomes · 2023Review
- Description of Agathobaculum massiliense sp. nov., a new bacterial species prevalent in the human gut and predicted to produce indole and tryptophan based on genomic analysis.Antonie van Leeuwenhoek · 2023Article
- Maliibacterium massiliense gen. nov. sp. nov., Isolated from Human Feces and Proposal of Maliibacteriaceae fam. nov.Current microbiology · 2023Article
- Preliminary landscape ofFrontiers in cellular and infection microbiology · 2023Article
- Description of Ornithinibacillus massiliensis sp. nov., Isolated from a Child with Marasmus.Current microbiology · 2022Article
Corrections and comments
- Expression of concern · 2022-12-13Investigation by Journal/Publisher ·
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular approaches have long led to the assumption that the human gut microbiota is dominated by uncultivable bacteria. The recent advent of large-scale culturing methods, and in particular that of culturomics have demonstrated that these prokaryotes can in fact be cultured. This is increasing in a dramatic manner the repertoire of commensal microbes inhabiting the human gut. Following eight years of culturomics approach applied on more than 900 samples, we propose herein a remake of the pioneering study applying a dual approach including culturomics and metagenomics on a cohort of 8 healthy specimen. Here we show that culturomics enable a 20% higher richness when compared to molecular approaches by culturing 1 archaeal species and 494 bacterial species of which 19 were new taxa. Species discovered as a part of previous culturomics studies represent 30% of the cultivated isolates, while sequences derived from these new taxa enabled to increase by 22% the bacterial richness retrieved by metagenomics. Overall, 67% of the total reads generated were covered by cultured isolates, significantly reducing the hidden content of sequencing methods compared to the pioneering study. By redefining culture conditions to recover microbes previously considered fastidious, there are greater opportunities than ever to eradicate metagenomics dark matter.
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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.