The Core Gut Microbiome, Energy Balance and Obesity

Overview

Journal J Physiol

Specialty Physiology

Date 2009 Jun 4

PMID 19491241

Citations 468

Authors

Peter J Turnbaugh

Jeffrey I Gordon

Affiliations

Soon will be listed here.

Abstract

Metagenomics is an emerging field focused on characterizing the structures, functions and dynamic operations of microbial communities sampled in their native habitats without the need for culture. Here, we present findings from a 16S rRNA gene sequence- and whole community DNA shotgun sequencing-based analysis of the adult human gut microbiomes of lean and obese mono- and dizygotic twins. Our findings indicate that a core microbiome can be found at the gene level, despite large variation in community membership, and that variations from the core are associated with obesity. These findings have implications for ongoing Human Microbiome Project(s), and highlight important challenges to the field of metagenomics.

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References

Collado M, Isolauri E, Laitinen K, Salminen S . Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr. 2008; 88(4):894-9. DOI: 10.1093/ajcn/88.4.894. View

Ley R, Lozupone C, Hamady M, Knight R, Gordon J . Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008; 6(10):776-88. PMC: 2664199. DOI: 10.1038/nrmicro1978. View

Backhed F, Manchester J, Semenkovich C, Gordon J . Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A. 2007; 104(3):979-84. PMC: 1764762. DOI: 10.1073/pnas.0605374104. View

Ram R, VerBerkmoes N, Thelen M, Tyson G, Baker B, Blake 2nd R . Community proteomics of a natural microbial biofilm. Science. 2005; 308(5730):1915-20. DOI: 10.1126/science. 1109070. View

Ley R, Knight R, Gordon J . The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology. Environ Microbiol. 2007; 9(1):3-4. DOI: 10.1111/j.1462-2920.2006.01222_3.x. View

Poretsky R, Hewson I, Sun S, Allen A, Zehr J, Moran M . Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol. 2009; 11(6):1358-75. DOI: 10.1111/j.1462-2920.2008.01863.x. View

Guo X, Xia X, Tang R, Zhou J, Zhao H, Wang K . Development of a real-time PCR method for Firmicutes and Bacteroidetes in faeces and its application to quantify intestinal population of obese and lean pigs. Lett Appl Microbiol. 2009; 47(5):367-73. DOI: 10.1111/j.1472-765X.2008.02408.x. View

Tringe S, von Mering C, Kobayashi A, Salamov A, Chen K, Chang H . Comparative metagenomics of microbial communities. Science. 2005; 308(5721):554-7. DOI: 10.1126/science.1107851. View

Duncan S, Lobley G, Holtrop G, Ince J, Johnstone A, Louis P . Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond). 2008; 32(11):1720-4. DOI: 10.1038/ijo.2008.155. View

10.

Dinsdale E, Edwards R, Hall D, Angly F, Breitbart M, Brulc J . Functional metagenomic profiling of nine biomes. Nature. 2008; 452(7187):629-32. DOI: 10.1038/nature06810. View

11.

Turnbaugh P, Ley R, Mahowald M, Magrini V, Mardis E, Gordon J . An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006; 444(7122):1027-31. DOI: 10.1038/nature05414. View

12.

Nadal I, Santacruz A, Marcos A, Warnberg J, Garagorri J, Garagorri M . Shifts in clostridia, bacteroides and immunoglobulin-coating fecal bacteria associated with weight loss in obese adolescents. Int J Obes (Lond). 2008; 33(7):758-67. DOI: 10.1038/ijo.2008.260. View

13.

Lo I, Denef V, VerBerkmoes N, Shah M, Goltsman D, DiBartolo G . Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature. 2007; 446(7135):537-41. DOI: 10.1038/nature05624. View

14.

Waldram A, Holmes E, Wang Y, Rantalainen M, Wilson I, Tuohy K . Top-down systems biology modeling of host metabotype-microbiome associations in obese rodents. J Proteome Res. 2009; 8(5):2361-75. DOI: 10.1021/pr8009885. View

15.

Kalliomaki M, Collado M, Salminen S, Isolauri E . Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr. 2008; 87(3):534-8. DOI: 10.1093/ajcn/87.3.534. View

16.

Backhed F, Ding H, Wang T, Hooper L, Koh G, Nagy A . The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 2004; 101(44):15718-23. PMC: 524219. DOI: 10.1073/pnas.0407076101. View

17.

Marcy Y, Ouverney C, Bik E, Losekann T, Ivanova N, Garcia Martin H . Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A. 2007; 104(29):11889-94. PMC: 1924555. DOI: 10.1073/pnas.0704662104. View

18.

Hugenholtz P, Tyson G . Microbiology: metagenomics. Nature. 2008; 455(7212):481-3. DOI: 10.1038/455481a. View

19.

Frias-Lopez J, Shi Y, Tyson G, Coleman M, Schuster S, Chisholm S . Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A. 2008; 105(10):3805-10. PMC: 2268829. DOI: 10.1073/pnas.0708897105. View

20.

Wu D, Daugherty S, Van Aken S, Pai G, Watkins K, Khouri H . Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 2006; 4(6):e188. PMC: 1472245. DOI: 10.1371/journal.pbio.0040188. View