ArticleBMC microbiology2021
Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota.
Article in BMC microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome.Nature medicine · 2025Article
- A droplet microfluidic strategy for cultivation, investigation, and high-throughput isolation of mouse gut microbiome bacteria.Applied and environmental microbiology · 2025Article
- Article
- BioMapAI: Artificial Intelligence Multi-Omics Modeling of Myalgic Encephalomyelitis / Chronic Fatigue Syndrome.bioRxiv : the preprint server for biology · 2025Article
- Article
- The Application of Culturomics to Explore African Skin Microbiota.The American journal of tropical medicine and hygiene · 2024Article
- Diversity of Neurotransmitter-Producing Human Skin Commensals.International journal of molecular sciences · 2024Article
- Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery.Journal of microbiology and biotechnology · 2024Review
- Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat-Specific Microbiome Diversity and Function.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Seminars in immunology special issue: Nutrition, microbiota and immunity The unexplored microbes in health and disease.Seminars in immunology · 2023Review
- Screening and evaluation of skin potential probiotic from high-altitude Tibetans to repair ultraviolet radiation damage.Frontiers in microbiology · 2023Article
- Review
- Strains to go: interactions of the skin microbiome beyond its species.Current opinion in microbiology · 2022Review
- New research frontiers pertaining to the infant gut microbiota.Microbiome research reports · 2022Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
backgroundGenomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exists at the subspecies, or strain, level. High-resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. High-throughput approaches are needed to acquire and identify the significant species- and strain-level diversity present in the oral, skin, and gut microbiome. Here, we describe and validate a streamlined workflow for cultivating dominant bacterial species and strains from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling.
resultsOf total genera discovered by either metagenomic sequencing or culturomics, our cultivation pipeline recovered between 18.1-44.4% of total genera identified. These represented a high proportion of the community composition reconstructed with metagenomic sequencing, ranging from 66.2-95.8% of the relative abundance of the overall community. Fourier-Transform Infrared spectroscopy (FT-IR) was effective in differentiating genetically distinct strains compared with whole-genome sequencing, but was less effective as a proxy for genetic distance.
conclusionsUse of a streamlined set of conditions selected for cultivation of skin, oral, and gut microbiota facilitates recovery of dominant microbes and their strain variants from a relatively large sample set. FT-IR spectroscopy allows rapid differentiation of strain variants, but these differences are limited in recapitulating genetic distance. Our data highlights the strength of our cultivation and characterization pipeline, which is in throughput, comparisons with high-resolution genomic data, and rapid identification of strain variation.
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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.