Home LiteratureArticle Details
PMID: 25647347 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities.

The ISME journal ·Vol. 9 ·No. 9 ·2015-09-00 ·Pages 1979-90

Zhang J, Guo Z, Xue Z, Sun Z, Zhang M, Wang L, Wang G, Wang F, Xu J, Cao H, Xu H, Lv Q, Zhong Z, Chen Y, Qimuge S, Menghe B, Zheng Y, Zhao L, Chen W, Zhang H

Abstract

Structural profiling of healthy human gut microbiota across heterogeneous populations is necessary for benchmarking and characterizing the potential ecosystem services provided by particular gut symbionts for maintaining the health of their hosts. Here we performed a large structural survey of fecal microbiota in 314 healthy young adults, covering 20 rural and urban cohorts from 7 ethnic groups living in 9 provinces throughout China. Canonical analysis of unweighted UniFrac principal coordinates clustered the subjects mainly by their ethnicities/geography and less so by lifestyles. Nine predominant genera, all of which are known to contain short-chain fatty acid producers, co-occurred in all individuals and collectively represented nearly half of the total sequences. Interestingly, species-level compositional profiles within these nine genera still discriminated the subjects according to their ethnicities/geography and lifestyles. Therefore, a phylogenetically diverse core of gut microbiota at the genus level may be commonly shared by distinctive healthy populations as functionally indispensable ecosystem service providers for the hosts.

MeSH Terms
Adolescent Adult Bacteria/genetics China Cluster Analysis Cohort Studies Ecosystem Ethnicity Fatty Acids, Volatile/chemistry Feces Female Gastrointestinal Microbiome Geography Humans Intestines/microbiology Life Style Male Microbiota/genetics Phylogeny RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA Young Adult
Chemicals
Fatty Acids, Volatile RNA, Ribosomal, 16S
Authors & Affiliations
20 authors, click to expand affiliations / ORCID
Zhang Jiachao
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Guo Zhuang
State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China.
Xue Zhengsheng
State Key Laboratory of Microbial Metabolism, Department of Biological Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Sun Zhihong
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Zhang Menghui
State Key Laboratory of Microbial Metabolism, Department of Biological Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Wang Lifeng
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Wang Guoyang
State Key Laboratory of Microbial Metabolism, Department of Biological Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Wang Fang
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Xu Jie
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Cao Hongfang
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Xu Haiyan
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Lv Qiang
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Zhong Zhi
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Chen Yongfu
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Qimuge Sudu
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Menghe Bilige
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Zheng Yi
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
Zhao Liping
1] State Key Laboratory of Microbial Metabolism, Department of Biological Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China [2] Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai, China.
Chen Wei
State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China.
Zhang Heping
Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Inner Mongolia, China.
References (52)
52 references, click to expand
  1. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43.
    Nature. 2009 Oct 29;461(7268):1282-6 PMID: 19865172
  2. Linking long-term dietary patterns with gut microbial enterotypes.
    Science. 2011 Oct 7;334(6052):105-8 PMID: 21885731
  3. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers.
    J Nutr. 2009 Sep;139(9):1619-25 PMID: 19625695
  4. Towards the human intestinal microbiota phylogenetic core.
    Environ Microbiol. 2009 Oct;11(10):2574-84 PMID: 19601958
  5. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges.
    Genome Res. 2009 Jul;19(7):1141-52 PMID: 19383763
  6. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol.
    PLoS One. 2009;4(9):e7063 PMID: 19759898
  7. A metagenome-wide association study of gut microbiota in type 2 diabetes.
    Nature. 2012 Oct 4;490(7418):55-60 PMID: 23023125
  8. Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces.
    Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):423-8 PMID: 11931151
  9. Enterotypes of the human gut microbiome.
    Nature. 2011 May 12;473(7346):174-80 PMID: 21508958
  10. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.
    Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6 PMID: 20679230
  11. Genetic relationship of populations in China.
    Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11763-8 PMID: 9751739
  12. Butyrate production from dietary fibre and protection against large bowel cancer in a rat model.
    Gut. 1993 Mar;34(3):386-91 PMID: 8386131
  13. Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces.
    Int J Syst Evol Microbiol. 2002 Sep;52(Pt 5):1615-20 PMID: 12361264
  14. Metagenomic analysis of the human distal gut microbiome.
    Science. 2006 Jun 2;312(5778):1355-9 PMID: 16741115
  15. Composition, variability, and temporal stability of the intestinal microbiota of the elderly.
    Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4586-91 PMID: 20571116
  16. A core human microbiome as viewed through 16S rRNA sequence clusters.
    PLoS One. 2012;7(6):e34242 PMID: 22719824
  17. Blautia stercoris sp. nov., isolated from human faeces.
    Int J Syst Evol Microbiol. 2012 Apr;62(Pt 4):776-9 PMID: 21571940
  18. Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing.
    PLoS One. 2011;6(7):e22109 PMID: 21829445
  19. The role of the gut microbiota in nutrition and health.
    Nat Rev Gastroenterol Hepatol. 2012 Oct;9(10):577-89 PMID: 22945443
  20. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides.
    Int J Syst Bacteriol. 1990 Apr;40(2):205-8 PMID: 2223612
  21. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.
    Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4554-61 PMID: 20847294
  22. Evolution of mammals and their gut microbes.
    Science. 2008 Jun 20;320(5883):1647-51 PMID: 18497261
  23. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts.
    Genome Res. 2012 Oct;22(10):1974-84 PMID: 22665442
  24. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.
    PLoS One. 2012;7(6):e26284 PMID: 22719818
  25. Human gut microbiome viewed across age and geography.
    Nature. 2012 Jun 14;486(7402):222-7 PMID: 22699611
  26. Carbohydrate fermentation in the human colon and its relation to acetate concentrations in venous blood.
    J Clin Invest. 1985 May;75(5):1448-54 PMID: 3998144
  27. QIIME allows analysis of high-throughput community sequencing data.
    Nat Methods. 2010 May;7(5):335-6 PMID: 20383131
  28. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice.
    ISME J. 2013 Apr;7(4):880-4 PMID: 23235292
  29. Isolation and preliminary probiotic selection of lactobacilli from koumiss in Inner Mongolia.
    J Basic Microbiol. 2009 Jun;49(3):318-26 PMID: 19219898
  30. Diversity of the human intestinal microbial flora.
    Science. 2005 Jun 10;308(5728):1635-8 PMID: 15831718
  31. A human gut microbial gene catalogue established by metagenomic sequencing.
    Nature. 2010 Mar 4;464(7285):59-65 PMID: 20203603
  32. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea.
    ISME J. 2011 Apr;5(4):650-64 PMID: 21085196
  33. Ecological and evolutionary forces shaping microbial diversity in the human intestine.
    Cell. 2006 Feb 24;124(4):837-48 PMID: 16497592
  34. UniFrac: a new phylogenetic method for comparing microbial communities.
    Appl Environ Microbiol. 2005 Dec;71(12):8228-35 PMID: 16332807
  35. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.
    PLoS One. 2013;8(6):e66019 PMID: 23799070
  36. The impact of the gut microbiota on human health: an integrative view.
    Cell. 2012 Mar 16;148(6):1258-70 PMID: 22424233
  37. Microbial co-occurrence relationships in the human microbiome.
    PLoS Comput Biol. 2012;8(7):e1002606 PMID: 22807668
  38. The application of ecological theory toward an understanding of the human microbiome.
    Science. 2012 Jun 8;336(6086):1255-62 PMID: 22674335
  39. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers.
    ISME J. 2012 Feb;6(2):320-9 PMID: 21850056
  40. Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome.
    PLoS One. 2012;7(8):e43052 PMID: 22905200
  41. Butyrate inhibits inflammatory responses through NFkappaB inhibition: implications for Crohn's disease.
    Gut. 2000 Sep;47(3):397-403 PMID: 10940278
  42. Subdoligranulum variabile gen. nov., sp. nov. from human feces.
    Anaerobe. 2004 Jun;10(3):197-203 PMID: 16701519
  43. The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43.
    Nat Commun. 2013;4:1829 PMID: 23652017
  44. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases.
    PLoS One. 2014;9(2):e87734 PMID: 24498365
  45. Genome sequencing in microfabricated high-density picolitre reactors.
    Nature. 2005 Sep 15;437(7057):376-80 PMID: 16056220
  46. Bifidobacteria can protect from enteropathogenic infection through production of acetate.
    Nature. 2011 Jan 27;469(7331):543-7 PMID: 21270894
  47. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.
    Appl Environ Microbiol. 2007 Mar;73(5):1576-85 PMID: 17220268
  48. Human gut microbiota community structures in urban and rural populations in Russia.
    Nat Commun. 2013;4:2469 PMID: 24036685
  49. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients.
    Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16731-6 PMID: 18936492
  50. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov.
    Int J Syst Evol Microbiol. 2002 Nov;52(Pt 6):2141-6 PMID: 12508881
  51. A core gut microbiome in obese and lean twins.
    Nature. 2009 Jan 22;457(7228):480-4 PMID: 19043404
  52. Structure, function and diversity of the healthy human microbiome.
    Nature. 2012 Jun 14;486(7402):207-14 PMID: 22699609
Article Info
Journal
The ISME journal
Abbr.
ISME J
ISSN
1751-7370
DOI
10.1038/ismej.2015.11
Published
2015-09-00
Epub
2015-00-03
Pages
1979-90
Language
English
Region
England
NLM ID
101301086
PMCID
PMC4542028
Subset
IM
External Links
PubMed source DOI: 10.1038/ismej.2015.11 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2