Diversity of the Human Intestinal Microbial Flora
Open accessAbstract
The human endogenous intestinal microflora is an essential “organ” in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features remain poorly described. We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity. A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms. We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease.
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The gut hosts a diverse population of microorganisms including yeasts, archaea, parasites such as helminths, viruses, and protozoa, but the bacterial population is currently the most well characterized.
“The gut hosts a diverse population of microorganisms including yeasts, archaea, parasites such as helminths, viruses, and protozoa, but the bacterial population is currently the most well characterized (Eckburg et al., 2005;Gaci et al., 2014;Lankelma et al., 2015;Scarpellini et al., 2015;Williamson et al., 2016).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Eckburg et al., 2005
The Abstract reports diverse intestinal bacteria and detects archaeal sequences, supporting those parts of the claim. It does not address yeasts, helminths, viruses, or protozoa, or compare how well bacteria are characterized with those groups. (LLM, conf=0.88)
Experimental — accuracy not yet measuredFusobacteria and Verrucomicrobia phyla are present in low abundance.
“while Fusobacteria and Verrucomicrobia phyla are present in low abundance (Eckburg et al., 2005).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Eckburg et al., 2005
With age, there is a decrease in beneficial microorganisms and an accumulation of potentially pro-inflammatory microorganisms in the gut, leading to a change in microbial composition and a decrease in microbial diversity.
“However, with age, there is a decrease in beneficial microorganisms216,217 and an accumulation of potentially pro-inflammatory microorganisms in the gut,218 leading to a change in microbial composition and a decrease in microbial diversity.”
From Inflammation and aging: signaling pathways and intervention therapies (2023) · cites this paper as [217]
The Abstract describes gut microbial diversity and differences between subjects and between stool and mucosal communities, but not changes with age. Searches for aging, beneficial microorganisms, pro-inflammatory microorganisms, and declining diversity found no passage addressing the claimed age-related pattern. (LLM, conf=0.75)
Experimental — accuracy not yet measuredThe taxonomic composition of the gut microbiota changes throughout the gastrointestinal tract according to nutrient availability, mucus structure, pH and oxygen availability.
“The taxonomic composition of the gut microbiota changes throughout the gastrointestinal tract, according to nutrient availability, mucus structure, pH and oxygen availability [1–6].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [5]
Increasing culture-independent omic-based technologies have facilitated the discovery of novel functional dynamics of microbiota and their relationship with host pathophysiology.
“Increasing culture-independent omic-based technologies such as biomarker sequencing, metagenomics, metatranscriptomics, metaproteomics, and metabolomics have facilitated the discovery of novel functional dynamics of microbiota2, 3, 4, 5 and their relationship with host pathophysiology.6, 7, 8, 9”
From Regulation of Intestinal Barrier Function by Microbial Metabolites (2021) · cites this paper as [5]
Human gut microbial composition differs substantially among individuals and depends on age, genetic background, physiological state, microbial interactions, environmental factors, and diet.
“Human studies have unveiled substantial differences in the gut microbial composition among individuals139–141 that depend on age, genetic background, physiological state, microbial interactions, environmental factors, and diet.142–144”
From The Gut Microbiome and the Brain (2014) · cites this paper as [140]
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- Authors
- Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A.
- Affiliations
- Stanford Medicine (US)
- Corresponding author
- Eckburg, Paul B.
- Relman, David A.
- ORCID
- Venue
- Science
- Published
- 2005-06-10
- Volume
- 308
- Issue
- 5728
- Pages
- 1635-1638
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC1395357
- OpenAlex
- W2169330513
- Cited by
- 7,913
- References
- 21
- Citations by year
- 2026: 165 · 2025: 275 · 2024: 402 · 2023: 454 · 2022: 564 · 2021: 523 · 2020: 483 · 2019: 516 · 2018: 453 · 2017: 411 · 2016: 417 · 2015: 433 · 2014: 492 · 2013: 442 · 2012: 392
- FWCI
- 70.15
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases (AI51259, R01AI051259)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiota, intestinal microbial diversity, colonic mucosa, fecal microbiota, interindividual variability, novel microorganisms, innate immunity, epithelial development
- MeSH terms
- Adult, Bacteria, Colon, DNA, Ribosomal, Feces, Genes, Bacterial, Humans, Intestinal Mucosa, Middle Aged, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Genetic Variation, Polymerase Chain Reaction, Ecosystem, Genes, Archaeal, Genes, rRNA, Methanobrevibacter, Bacteroidetes, Biodiversity
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