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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 (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
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“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
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“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]
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“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]
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“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]
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“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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Staudacher, H. M., Lomer, M. C. E., Anderson, J. L., Barrett, J. S., Muir, J. G., Irving, P. M., & Whelan, K. (2012) · The Journal of Nutrition · doi:10.3945/jn.112.159285 · Cited by 590
Secreted bioactive factors from Bifidobacterium infantis enhance epithelial cell barrier function
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Mucin-bacterial interactions in the human oral cavity and digestive tract
Derrien, M., van Passel, M. W. J., van de Bovenkamp, J. H. B., Schipper, R., de Vos, W., & Dekker, J. (2010) · Gut Microbes · doi:10.4161/gmic.1.4.12778 · Cited by 556
Collective unconscious: How gut microbes shape human behavior
Dinan, T. G., Stilling, R. M., Stanton, C., & Cryan, J. F. (2015) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2015.02.021 · Cited by 571
Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection
Ducarmon, Q. R., Zwittink, R. D., Hornung, B. V. H., van Schaik, W., Young, V. B., & Kuijper, E. J. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00007-19 · Cited by 566
Nod2 is required for the regulation of commensal microbiota in the intestine
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Diversity of the human gastrointestinal tract microbiota revisited
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The gut microbiome in human neurological disease: A review
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Towards the Human Colorectal Cancer Microbiome
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Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut
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Gut microbiota, obesity and diabetes
Patterson, E., Ryan, P. M., Cryan, J. F., Dinan, T. G., Ross, R. P., Fitzgerald, G. F., & Stanton, C. (2016) · Postgraduate Medical Journal · doi:10.1136/postgradmedj-2015-133285 · Cited by 552
High Prevalence of Mucosa-Associated E. coli Producing Cyclomodulin and Genotoxin in Colon Cancer
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Bergström, A., Skov, T. H., Bahl, M. I., Roager, H. M., Christensen, L. B., Ejlerskov, K. T., Mølgaard, C., Michaelsen, K. F., & Licht, T. R. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00342-14 · Cited by 532
Gut microbiota and dysbiosis in Alzheimer's disease: Implications for pathogenesis and treatment
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“Firmicutes and Bacteroidetes constitute the most abundant phyla in human intestinal microbiota [23].”
BackgroundThe microbiome: a key regulator of stress and neuroinflammation
Rea, K., Dinan, T. G., & Cryan, J. F. (2016) · Neurobiology of Stress · doi:10.1016/j.ynstr.2016.03.001 · Cited by 508
Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome
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Gut microbiome and liver diseases
Tilg, H., Cani, P. D., & Mayer, E. A. (2016) · Gut · doi:10.1136/gutjnl-2016-312729 · Cited by 525
Assembly of the human intestinal microbiota
Dethlefsen, L., Eckburg, P. B., Bik, E. M., & Relman, D. A. (2006) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.06.013 · Cited by 509
Self-citationMetagenomic approaches for defining the pathogenesis of inflammatory bowel diseases
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Gut microbiota modulation with norfloxacin and ampicillin enhances glucose tolerance in mice
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The role of inflammation and the gut microbiome in depression and anxiety
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Microbiota-gut-brain axis: Modulator of host metabolism and appetite
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Microbiome–microglia connections via the gut–brain axis
Abdel-Haq, R., Schlachetzki, J. C. M., Glass, C. K., & Mazmanian, S. K. (2019) · Journal of Experimental Medicine · doi:10.1084/jem.20180794 · Cited by 471
“By the age of 5, the gut microbiota stabilizes and begins to resemble that of an adult, with members of Bacteroidetes and Firmicutes becoming most abundant (Eckburg et al., 2005).”
BackgroundRajilić‐Stojanović, M., Heilig, H. G. H. J., Molenaar, D., Kajander, K., Surakka, A., Smidt, H., & De Vos, W. M. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01900.x · Cited by 484
Metadata
- 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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