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Effect of dietary interventions on the intestinal microbiota of Mongolian hosts

Abstract

The gut microbiota of Mongolian hosts has distinctive characteristics due to their meat- and dairy-oriented daily diets and unique genotype. The aim of the present study was to investigate the effect of switching from the typical high protein and fat Mongolian diets to carbohydrate-rich meals composed principally of wheat, rice and naked oats on the host gut microbiota within 3 weeks. Our study took the advantage of the long sequence reads produced by the PacBio single molecule real-time sequencing technology to enable the profiling of subjects’ gut microbiota communities along the diet intervention to the species precision. We found that the bacterial richness and diversity decreased apparently along the diet intervention. During the diet intervention, the gut microbiota composition displayed no significant difference at phylum level (with major phyla of Firmicutes, Bacteroidetes, Tenericutes and Proteobacteria). The relative abundances of some genera such as Bacteroidetes, Faecalibacterium, Roseburia, Alistipes, Streptococcus, and Oscillospira were significantly altered after the diet switching started. Notably, significant changes were also observed in the proportions of the species Bacteroides dorei, Bacteroides fragilis, Bacteroides thetaiotaomicron, Ruminococcus albus, Ruminococcus faecis, Roseburia faecis and Eubacterium ventriosum. These results have demonstrated that diet and host gut microbiota is closely linked.

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References

  1. 1.

    Hentges DJ (1983) Human intestinal microflora in health and disease. Academic Press, New York

    Google Scholar 

  2. 2.

    Khachatryan ZA, Ktsoyan ZA, Manukyan GP et al (2008) Predominant role of host genetics in controlling the composition of gut microbiota. PLoS ONE 3:e3064

    ADS  Article  PubMed  PubMed Central  Google Scholar 

  3. 3.

    De Filippo C, Cavalieri D, Di Paola M et al (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural africa. Proc Natl Acad Sci USA 107:14691–14696

    ADS  Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837–848

    CAS  Article  PubMed  Google Scholar 

  5. 5.

    David LA, Maurice CF, Carmody RN et al (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563

    ADS  CAS  Article  PubMed  Google Scholar 

  6. 6.

    Turnbaugh PJ, Ley RE, Mahowald MA et al (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031

    ADS  Article  PubMed  Google Scholar 

  7. 7.

    Christian D (1998) A history of Russia, Central Asia and Mongolia: V. 1 inner Eurasia from prehistory to the Mongol Empire. Blackwell, Oxford

    Google Scholar 

  8. 8.

    Bai HH, Guo XS, Zhang D et al (2014) The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. Genome Biol Evol 6:3122–3136

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Nam YD, Jung MJ, Roh SW et al (2011) Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS ONE 6:e22109

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Yatsunenko T, Rey FE, Manary MJ et al (2012) Human gut microbiome viewed across age and geography. Nature 486:222–227

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Zhang J, Zheng Y, Guo Z et al (2013) The diversity of intestinal microbiota of Mongolians living in Inner Mongolia, China. Benef Microbes 4:319–328

    CAS  Article  PubMed  Google Scholar 

  12. 12.

    Zhang J, Guo Z, Lim AA et al (2014) Mongolians core gut microbiota and its correlation with seasonal dietary changes. Sci Rep 4:5001

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Turnbaugh PJ, Hamady M, Yatsunenko T et al (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484

    ADS  CAS  Article  PubMed  Google Scholar 

  14. 14.

    Turnbaugh PJ, Ley RE, Hamady M et al (2007) The human microbiome project. Nature 449:804–810

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    ADS  CAS  Article  PubMed  Google Scholar 

  16. 16.

    Amir A, Zeisel A, Zuk O et al (2013) High-resolution microbial community reconstruction by integrating short reads from multiple 16s rRNA regions. Nucleic Acids Res 41:391–404

    Article  Google Scholar 

  17. 17.

    Hou Q, Xu H, Zheng Y et al (2015) Evaluation of bacterial contamination in raw milk, ultra-high temperature milk and infant formula using single molecule, real-time sequencing technology. J Dairy Sci 98:8464–8472

    CAS  Article  PubMed  Google Scholar 

  18. 18.

    Mosher JJ, Bernberg EL, Shevchenko O et al (2013) Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16s rRNA genes from environmental samples. J Microbiol Methods 95:175–181

    CAS  Article  PubMed  Google Scholar 

  19. 19.

    Tanaka S, Kobayashi T, Songjinda P et al (2009) Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota. FEMS Immunol Med Microbiol 56:80–87

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Liu W, Zheng Y, Kwok LY et al (2015) High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow’s milk in Russia. BMC Microbiol 15:1–12

    Article  Google Scholar 

  21. 21.

    Caporaso JG, Bittinger K, Bushman FD et al (2009) Pynast: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267

    Article  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Edgar RC (2010) Search and clustering orders of magnitude faster than blast. Bioinformatics 26:2460–2461

    CAS  Article  PubMed  Google Scholar 

  23. 23.

    Kim M, Oh HS, Park SC et al (2014) Towards a taxonomic coherence between average nucleotide identity and 16s rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    CAS  Article  PubMed  Google Scholar 

  24. 24.

    Haas BJ, Gevers D, Earl AM et al (2011) Chimeric 16s rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Cole JR, Chai B, Farris RJ et al (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35:D169–D172

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Price MN, Dehal PS, Arkin AP (2009) Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Hammer Ø, Harper DA, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:1–9

    Google Scholar 

  29. 29.

    Cotillard A, Kennedy SP, Kong LC et al (2013) Dietary intervention impact on gut microbial gene richness. Nature 500:585–588

    CAS  Article  PubMed  Google Scholar 

  30. 30.

    Angelis MD, Montemurno E, Vannini L et al (2015) The role of whole-grain barley on human fecal microbiota and metabolome. Appl Environ Microbiol 81:7945–7956

    Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Martinez I, Lattimer JM, Hubach KL et al (2013) Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J 7:269–280

    CAS  Article  PubMed  Google Scholar 

  32. 32.

    Tap J, Furet JP, Bensaada M et al (2015) Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol 17:4954–4964

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    O’Keefe SJ, Li JV, Lahti L et al (2015) Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun 6:6342

    Article  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Carmody RN, Gerber GK, Luevano JM et al (2015) Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe 17:72–84

    CAS  Article  PubMed  Google Scholar 

  35. 35.

    German JB, Dillard CJ (2004) Saturated fats: what dietary intake? Am J Clin Nutr 80:550–559

    CAS  PubMed  Google Scholar 

  36. 36.

    Hu FB (2005) Protein, body weight, and cardiovascular health. Am J Clin Nutr 82:242S–247S

    CAS  PubMed  Google Scholar 

  37. 37.

    Zhang CH, Zhang MH, Pang XY et al (2012) Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations. ISME J 6:1848–1857

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Brown K, DeCoffe D, Molcan E et al (2012) Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients 4:1095

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Duncan SH, Belenguer A, Holtrop G et al (2007) Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 73:1073–1078

    CAS  Article  PubMed  Google Scholar 

  40. 40.

    Faber F, Baumler AJ (2014) The impact of intestinal inflammation on the nutritional environment of the gut microbiota. Immunol Lett 162:48–53

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Kohl KD, Amaya J, Passement CA et al (2014) Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts. FEMS Microbiol Ecol 90:883–894

    CAS  Article  PubMed  Google Scholar 

  42. 42.

    Qin JJ, Li RQ, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:U59–U70

    Article  Google Scholar 

  43. 43.

    Zhong YD, Marungruang N, Fak F et al (2015) Effects of two whole-grain barley varieties on caecal SCFA, gut microbiota and plasma inflammatory markers in rats consuming low- and high-fat diets. Br J Nutr 113:1558–1570

    CAS  Article  PubMed  Google Scholar 

  44. 44.

    Chassard C, Delmas E, Robert C et al (2010) The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens. FEMS Microbiol Ecol 74:205–213

    CAS  Article  PubMed  Google Scholar 

  45. 45.

    Etxeberria U, Arias N, Boque N et al (2015) Shifts in microbiota species and fermentation products in a dietary model enriched in fat and sucrose. Benef Microbes 6:97–111

    CAS  Article  PubMed  Google Scholar 

  46. 46.

    Anderson JW, Deakins DA, Floore TL et al (1990) Dietary fiber and coronary heart disease. Crit Rev Food Sci Nutr 29:95–147

    CAS  Article  PubMed  Google Scholar 

  47. 47.

    Jaskari J, Kontula P, Siitonen A et al (1998) Oat β-glucan and xylan hydrolysates as selective substrates for bifidobacterium and lactobacillus strains. Appl Microbiol Biotechnol 49:175–181

    CAS  Article  PubMed  Google Scholar 

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Correspondence to Heping Zhang.

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The authors declare that they have no conflict of interest.

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Jing Li and Haiyan Xu contributed equally to this work.

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Li, J., Xu, H., Sun, Z. et al. Effect of dietary interventions on the intestinal microbiota of Mongolian hosts. Sci. Bull. 61, 1605–1614 (2016). https://doi.org/10.1007/s11434-016-1173-0

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Keywords

  • Gut microbiota
  • Diet intervention
  • Mongolian
  • PacBio single molecule real-time sequencing technology (SMRT sequencing)