Diversity of the human gastrointestinal tract microbiota revisited
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Summary: Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation‐based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species‐level phylogenetic types (phylotypes). Such knowledge is essential for the design of high‐throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.
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Comparisons of sequence-based versus culture-based studies of the microbiota have shown that sequence-based approaches completely failed to detect some species that were only recovered using traditional culturing methods.
“Comparisons of sequence-based versus culture-based studies of the microbiota have shown that sequence-based approaches completely failed to detect some species that were only recovered using traditional culturing methods 34 .”
From Human microbiome myths and misconceptions (2023) · cites this paper as [34]
Gut microbiota analysis is challenging because estimates suggest over 1000 bacterial species.
“It should also be taken into account that analysing intestinal microbiota is in general tremendously challenging, as current estimates are that the microbiota comprises more than 1000 bacterial species. 36”
From Clinical trial: multispecies probiotic supplementation alleviates the symptoms of irritable bowel syndrome and stabilizes intestinal microbiota (2008) · cites this paper as [36]
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Gut microbiota in health and disease: an overview focused on metabolic inflammation
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- Authors
- Rajilić‐Stojanović, M., Smidt, H., & De Vos, W. M.
- Affiliations
- Wageningen University & Research (NL)
- ORCID
- Smidt, Hauke
- Venue
- Environmental Microbiology
- Publisher
- Wiley
- Published
- 2007-07-17
- Volume
- 9
- Issue
- 9
- Pages
- 2125-2136
- ISSN
- 1462-2912 (ISSN-L)
- 1462-2920
- OpenAlex
- W1987992874
- Cited by
- 559
- References
- 92
- Citations by year
- 2026: 7 · 2025: 11 · 2024: 19 · 2023: 13 · 2022: 27 · 2021: 13 · 2020: 27 · 2019: 28 · 2018: 27 · 2017: 32 · 2016: 35 · 2015: 41 · 2014: 39 · 2013: 54 · 2012: 40
- FWCI
- 2.64
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Environmental Microbiology (publishedVersion)
- PubMed (publishedVersion)
- TechnoRep (University of Belgrade – Faculty of Technology and Metallurgy) (publishedVersion, other-oa)
- Socio-Environmental Systems Modeling (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- microbial diversity, small subunit rRNA, phylotypes, molecular ecology, taxonomic resolution
- MeSH terms
- Animals, Bacteria, Humans, Phylogeny, Ecosystem, Gastrointestinal Tract, Biodiversity
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