A core gut microbiome in obese and lean twins
Open accessAbstract
The human distal gut harbours a vast ensemble of microbes (the microbiota) that provide important metabolic capabilities, including the ability to extract energy from otherwise indigestible dietary polysaccharides. Studies of a few unrelated, healthy adults have revealed substantial diversity in their gut communities, as measured by sequencing 16S rRNA genes, yet how this diversity relates to function and to the rest of the genes in the collective genomes of the microbiota (the gut microbiome) remains obscure. Studies of lean and obese mice suggest that the gut microbiota affects energy balance by influencing the efficiency of calorie harvest from the diet, and how this harvested energy is used and stored. Here we characterize the faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers, to address how host genotype, environmental exposure and host adiposity influence the gut microbiome. Analysis of 154 individuals yielded 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences, plus 2.14 gigabases from their microbiomes. The results reveal that the human gut microbiome is shared among family members, but that each person's gut microbial community varies in the specific bacterial lineages present, with a comparable degree of co-variation between adult monozygotic and dizygotic twin pairs. However, there was a wide array of shared microbial genes among sampled individuals, comprising an extensive, identifiable 'core microbiome' at the gene, rather than at the organismal lineage, level. Obesity is associated with phylum-level changes in the microbiota, reduced bacterial diversity and altered representation of bacterial genes and metabolic pathways. These results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiological states (obese compared with lean).
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The composition of the gut microbiota is altered in animal models of obesity and subjects with prediabetes or type 2 diabetes compared with controls.
“Compelling evidence have shown that the composition of the gut microbiota is altered in animal models of obesity and subjects with prediabetes or type 2 diabetes compared with controls (182–186).”
From The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication (2020) · cites this paper as [182]
The passage labeled Abstract (page unavailable) reports altered gut microbiota in obese versus lean people and says the findings agree with previous work in mice. It does not address subjects with prediabetes or type 2 diabetes, so it supports only the obesity-related part of the citing sentence. (LLM, conf=0.88)
Experimental — accuracy not yet measuredAltered microbiota composition may contribute to obesity and T2DM, and correction by antibiotics, probiotics or prebiotics may improve the disease condition.
“An altered microbiota composition may also contribute to obesity243, 244 as well as to T2DM245, 246, 247 and ‘correction' by antibiotics,248 probiotics249 or prebiotics, the last of which causing a short-chain FFA-stimulated increase in GLP-1,250 may improve the disease condition.251”
From Pancreatic regulation of glucose homeostasis. (2016) · cites this paper as [244]
Chronic autoimmune inflammatory diseases such as celiac disease, type 2 diabetes, and obesity are associated with intestinal dysbiosis.
“Chronic autoimmune inflammatory diseases, including celiac disease,17 type 2 diabetes18 and obesity19 are associated with intestinal dysbiosis.”
From Probiotics and the gut microbiota in intestinal health and disease (2010) · cites this paper as [19]
Body fat percentage and mass are highly associated with gut microbiota composition.
“In addition, in the study of Bressa et al. the sedentary group had significantly higher body fat percentage and mass (Bressa et al., 2017), traits known to be highly associated with gut microbiota composition (Turnbaugh et al., 2009).”
From Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women (2018) · cites this paper as Turnbaugh et al., 2009
Gut microbiota composition is highly associated with weight and body composition.
“Due to that the gut microbiota composition is known to be highly associated with weight and body composition (Turnbaugh et al., 2009)”
From Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women (2018) · cites this paper as Turnbaugh et al., 2009
Obesity is associated with a significant decrease in gut microbiota diversity.
“Obesity has been associated with a significant decrease in the diversity of the gut microbiota.81, 82”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [81]
Some but not all cross-sectional studies found enrichment of Firmicutes and depletion of Bacteroidetes in obese compared with lean individuals.
“Some83 but not all81, 84 cross-sectional studies found an enrichment of the phylum Firmicutes and depletion of the phylum Bacteroidetes in obese individuals compared with lean individuals.”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [81]
Emerging evidence has shown associations of gut microbiota with obesity.
“Emerging evidence has shown associations of gut microbiota with obesity.48, 49, 50, 51”
From Gut Microbiota Metabolites and Risk of Major Adverse Cardiovascular Disease Events and Death: A Systematic Review and Meta‐Analysis of Prospective Studies (2017) · cites this paper as [48]
The gut microbiota of obese individuals is more efficient at energy extraction and contributes to obesity.
“Metagenomic and microbiota transplantation studies have shown that the gut microbiota from obese individuals is more efficient at energy extraction and thereby contributes to obesity53,54.”
From The gut microbiome and liver cancer: mechanisms and clinical translation (2017) · cites this paper as [54]
Obese individuals share a functionally similar gut microbiome, with reduced but still considerable species diversity.
“Obese individuals share a functionally similar gut microbiome between them, with reduced but still considerable species diversity (Human Microbiome Project Consortium, 2012; Kurokawa et al., 2007; Qin et al., 2010; Turnbaugh et al., 2009).”
From Understanding the Holobiont: How Microbial Metabolites Affect Human Health and Shape the Immune System (2017) · cites this paper as Turnbaugh et al., 2009
Obesity has been associated with altered gut microbiota composition, reduced microbial diversity, and reduced gene richness.
“Indeed, obesity has been associated with altered gut microbiota composition, reduced microbial diversity, and reduced gene richness (Le Chatelier et al., 2013; Ley et al., 2005; Turnbaugh et al., 2009).”
From Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation (2015) · cites this paper as Turnbaugh et al., 2009
Obesity is associated with reduced diversity of the gut microbiota.
“The picture that is emerging suggests that obesity is associated with reduced diversity of the gut microbiota13,17.”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [17]
Improved metabolic health is associated with relatively high microbiota gene content and increased microbial diversity in three metagenomic studies.
“Three metagenomic studies13,21,51 have shown that improved metabolic health is associated with a relatively high microbiota gene content and with an increased microbial diversity.”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [51]
Similar findings (decreased diversity and altered metabolic pathways) have been reported in relation to gene richness in obese individuals.
“Similar findings have been reported in relation to gene richness and altered metabolic pathways [155].”
From The athletic gut microbiota (2020) · cites this paper as [155]
Particular population changes in the oral microbiota are associated with pathologies that confer an increased risk of developing PH and other vascular disease, including obesity, diabetes, and insulin resistance.
“there is evidence that particular population changes are associated with pathologies that confer an increased risk of developing PH and other vascular disease, including obesity[273–275], diabetes[276], and insulin resistance[277].”
From Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health (2017) · cites this paper as [274]
Numerous facets of GI microbial community composition and metabolism have been associated with various disease states, including CVD, obesity, diabetes, and features of metabolic syndrome.
“Numerous facets of GI microbial community composition and metabolism have been associated with various disease states, including CVD, obesity, diabetes, and features of metabolic syndrome[274,310–313].”
From Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health (2017) · cites this paper as [274]
Elevations in the Firmicutes:Bacteroidetes ratio have been associated with a high-fat diet and obesity, irritable bowel syndrome, hypertension, type 1 diabetes, and HIV.
“Elevations in the Firmicutes:Bacteroidetes ratio have been associated with a high-fat diet and obesity[274,328,329], irritable bowel syndrome[330], hypertension[331], type 1 diabetes[276], and HIV[332].”
From Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health (2017) · cites this paper as [274]
Excess nutrient uptake and storage (obesity) is associated with low microbial diversity and changes in the relative abundance of Bacteroidetes and Firmicutes.
“excess nutrient uptake and storage (i.e., obesity) is associated with low microbial diversity and changes in the relative abundance of the major bacterial phyla (Bacteroidetes and Firmicutes) [27–29].”
From Gut Microbiota Contribute to Age-Related Changes in Skeletal Muscle Size, Composition, and Function: Biological Basis for a Gut-Muscle Axis (2018) · cites this paper as [28]
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Self-citationGut immune maturation depends on colonization with a host-specific microbiota
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Self-citationGut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor
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“However, the lower proportion of Bacteroides/Prevotella in obese subjects before RYGB and their increase after weight loss are in agreement with landmark studies in less obese populations (11,20).”
ResultDiet dominates host genotype in shaping the murine gut microbiota
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Self-citationCharacterization of the oral fungal microbiome (mycobiome) in healthy individuals
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Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
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- Authors
- Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., Egholm, M., Henrissat, B., Heath, A. C., Knight, R., & Gordon, J. I.
- Affiliations
- Washington University in St. Louis (US)
- Centre National de la Recherche Scientifique (FR)
- Marine Biological Laboratory (US)
- University of South Carolina (US)
- University of Oklahoma (US)
- University of Colorado Boulder (US)
- Corresponding author
- Gordon, Jeffrey I.
- ORCID
- Venue
- Nature
- Published
- 2008-11-30
- Volume
- 457
- Issue
- 7228
- Pages
- 480-484
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2677729
- OpenAlex
- W2149573313
- Cited by
- 7,823
- References
- 35
- Citations by year
- 2026: 186 · 2025: 277 · 2024: 400 · 2023: 417 · 2022: 507 · 2021: 601 · 2020: 628 · 2019: 612 · 2018: 570 · 2017: 527 · 2016: 553 · 2015: 511 · 2014: 491 · 2013: 444 · 2012: 388
- FWCI
- 96.01
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Science Foundation (0430724)
- W. M. Keck Foundation
- Crohn's and Colitis Foundation of America
- University of Oklahoma
- Crohn's and Colitis Foundation
- National Institutes of Health (UL1TR000448)
- National Institute on Alcohol Abuse and Alcoholism (K05AA017688, R01AA009022, AA 09022)
- National Human Genome Research Institute
- National Institute of General Medical Sciences (T32GM065103)
- National Institute of Diabetes and Digestive and Kidney Diseases (P01DK078669, DK78669, P30DK056341)
- National Institute of Environmental Health Sciences (P50ES012742, ES012742)
- National Center for Advancing Translational Sciences
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD049024, R01HD049024)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- gut microbiota, core microbiome, obesity, monozygotic twins, dizygotic twins, fecal microbiota, carbohydrate metabolism, host genotype, maternal microbiota, 16S rRNA gene sequencing, microbial diversity, energy balance, host-microbe interactions, host-microbe coevolution
- MeSH terms
- Adult, Africa, Environment, Europe, Feces, Female, Genotype, Humans, Missouri, Molecular Sequence Data, Mothers, Obesity, RNA, Ribosomal, 16S, Thinness, Twins, Dizygotic, Twins, Monozygotic, Gastrointestinal Tract, Biodiversity, Metagenome
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