Changes in human gut microbiota influenced by probiotic fermented milk ingestion

Journal of Dairy Science

Volumn 98, Issue 6, 2015, Pages 3568-3576

  Unno, Tatsuya ^a   Choi, Jung Hye ^b   Hur, Hor Gil ^c   Sadowsky, Michael J ^d   Ahn, Young Tae ^e   Huh, Chul Sung ^f   Kim, Geun Bae ^b   Cha, Chang Jun ^b  

^a Jeju National University   (South Korea)

^b Chung Ang University   (South Korea)

^c Gwangju Institute of Science and Technology (GIST)   (South Korea)

^d UNIVERSITY OF MINNESOTA   (United States)

^e Korea Yakult Co   (South Korea)

^f Seoul National University   (South Korea)

Author keywords

Gut microbiota; Probiotic fermented milk; Pyrosequencing

Indexed keywords

BACTEROIDACEAE; BACTEROIDETES; PREVOTELLACEAE;

PROBIOTIC AGENT; RNA 16S;

ADULT; ANIMAL; BACTERIUM; CHEMISTRY; CLASSIFICATION; DAIRY PRODUCT; FECES; GASTROINTESTINAL TRACT; GENETICS; HUMAN; INTESTINE; INTESTINE FLORA; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY;

ADULT; ANIMALS; BACTERIA; CULTURED MILK PRODUCTS; FECES; GASTROINTESTINAL MICROBIOME; GASTROINTESTINAL TRACT; HUMANS; INTESTINES; PROBIOTICS; RNA, RIBOSOMAL, 16S;

EID: 84929514929     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2014-8943     Document Type: Article

References (53)

1. Adolfsson O., Meydani S.N., Russell R.M. Yogurt and gut function. Am. J. Clin. Nutr. 2004, 80:245-256.
2. Anukam K.C., Osazuwa E.O., Osadolor H.B., Bruce A.W., Reid G. Yogurt containing probiotic Lactobacillus rhamnosus GR-1 and L. reuteri RC-14 helps resolve moderate diarrhea and increases CD4 count in HIV/AIDS patients. J. Clin. Gastroenterol. 2008, 42:239-243.
3. Bisanz J.E., Reid G. Unraveling how probiotic yogurt works. Sci. Transl. Med. 2011, 3:106ps41.
4. Caporaso J.G., Lauber C.L., Costello E.K., Berg-Lyons D., Gonzalez A., Stombaugh J., Knights D., Gajer P., Ravel J., Fierer N., Gordon J.I., Knight R. Moving pictures of the human microbiome. Genome Biol. 2011, 12:R50.
5. Claesson M.J., O'Sullivan O., Wang Q., Nikkila J., Marchesi J.R., Smidt H., de Vos W.M., Ross R.P., O'Toole P.W. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 2009, 4:e6669.
6. Claus S.P., Ellero S.L., Berger B., Krause L., Bruttin A., Molina J., Paris A., Want E.J., de Waziers I., Cloarec O., Richards S.E., Wang Y., Dumas M.E., Ross A., Rezzi S., Kochhar S., Van Bladeren P., Lindon J.C., Holmes E., Nicholson J.K. Colonization-induced host-gut microbial metabolic interaction. MBio 2011, 2. e00271-10.
7. Diepvens K., Soenen S., Steijns J., Arnold M., Westerterp-Plantenga M. Long-term effects of consumption of a novel fat emulsion in relation to body-weight management. Int. J. Obes. (Lond.) 2007, 31:942-949.
8. Elli M., Callegari M.L., Ferrari S., Bessi E., Cattivelli D., Soldi S., Morelli L., Goupil Feuillerat N., Antoine J.M. Survival of yogurt bacteria in the human gut. Appl. Environ. Microbiol. 2006, 72:5113-5117.
9. Flores R., Shi J., Gail M.H., Gajer P., Ravel J., Goedert J.J. Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences. Eur. J. Clin. Invest. 2012, 42:855-863.
10. García-Albiach R., Pozuelo de Felipe M.J., Angulo S., Morosini M.I., Bravo D., Baquero F., del Campo R. Molecular analysis of yogurt containing Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus in human intestinal microbiota. Am. J. Clin. Nutr. 2008, 87:91-96.
11. Gerritsen J., Smidt H., Rijkers G.T., de Vos W.M. Intestinal microbiota in human health and disease: The impact of probiotics. Genes Nutr. 2011, 6:209-240.
12. Gill S.R., Pop M., Deboy R.T., Eckburg P.B., Turnbaugh P.J., Samuel B.S., Gordon J.I., Relman D.A., Fraser-Liggett C.M., Nelson K.E. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312:1355-1359.
13. Griffen A.L., Beall C.J., Campbell J.H., Firestone N.D., Kumar P.S., Yang Z.K., Podar M., Leys E.J. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J. 2012, 6:1176-1185.
14. Hamady M., Lozupone C., Knight R. Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010, 4:17-27.
15. Hammer Ø., Harper D.A.T., Ryan P.D. PAST: Paleontological statistics software package for education and data analysis. Paleontol. Electron. 2001, 4:1-9.
16. Han S.Y., Huh C.-S., Ahn Y.-T., Lim K.-S., Baek Y.-J., Kim D.-H. Hepatoprotective effect of lactic acid bacteria. J. Microbiol. Biotechnol. 2005, 15:887-890. a.
17. Han S.Y., Huh C.-S., Ahn Y.-T., Lim K.-S., Baek Y.-J., Kim D.-H. Hepatoprotective effect of lactic acid bacteria, inhibitors of β-glucuronidase production against intestinal microflora. Arch. Pharm. Res. 2005, 28:325-329. b.
18. Hildebrandt M.A., Hoffmann C., Sherrill-Mix S.A., Keilbaugh S.A., Hamady M., Chen Y.Y., Knight R., Ahima R.S., Bushman F., Wu G.D. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 2009, 137:1716-1724.
19. Hunt K.M., Foster J.A., Forney L.J., Schutte U.M., Beck D.L., Abdo Z., Fox L.K., Williams J.E., McGuire M.K., McGuire M.A. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS ONE 2011, 6:e21313.
20. Kim B.S., Kim J.N., Yoon S.H., Chun J., Cerniglia C.E. Impact of enrofloxacin on the human intestinal microbiota revealed by comparative molecular analysis. Anaerobe 2012, 18:310-320.
21. Kullen M.J., Amann M.M., O'Shaughnessy M.J., O'Sullivan D.J., Busta F.F., Brady L.J. Differentiation of ingested and endogenous bifidobacteria by DNA fingerprinting demonstrates the survival of an unmodified strain in the gastrointestinal tract of humans. J. Nutr. 1997, 127:89-94.
22. Larsen N., Vogensen F.K., van den Berg F.W., Nielsen D.S., Andreasen A.S., Pedersen B.K., Al-Soud W.A., Sorensen S.J., Hansen L.H., Jakobsen M. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE 2010, 5:e9085.
23. Lee H.-S., Han S.-Y., Bae E.-A., Huh C.-S., Ahn Y.-T., Lee J.-H., Kim D.-H. Lactic acid bacteria inhibit proinflammatory cytokine expression and bacteial glycosaminoglycan degradation activity in dextran sulfate sodium-induced colitic mice. Int. Immunopharmacol. 2008, 8:574-580.
24. Levy R., Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc. Natl. Acad. Sci. USA 2013, 110:12804-12809.
25. Ley R.E., Backhed F., Turnbaugh P., Lozupone C.A., Knight R.D., Gordon J.I. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 2005, 102:11070-11075.
26. Ley R.E., Turnbaugh P.J., Klein S., Gordon J.I. Microbial ecology: human gut microbes associated with obesity. Nature 2006, 444:1022-1023.
27. Lozupone C.A., Hamady M., Kelley S.T., Knight R. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 2007, 73:1576-1585.
28. Martínez I., Muller C.E., Walter J. Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species. PLoS ONE 2013, 8:e69621.
29. McNulty N.P., Yatsunenko T., Hsiao A., Faith J.J., Muegge B.D., Goodman A.L., Henrissat B., Oozeer R., Cools-Portier S., Gobert G., Chervaux C., Knights D., Lozupone C.A., Knight R., Duncan A.E., Bain J.R., Muehlbauer M.J., Newgard C.B., Heath A.C., Gordon J.I. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci. Transl. Med. 2011, 3:106ra106.
30. Momozawa Y., Deffontaine V., Louis E., Medrano J.F. Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human. PLoS ONE 2011, 6:e16952.
31. Nam Y.D., Jung M.J., Roh S.W., Kim M.S., Bae J.W. Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS ONE 2011, 6:e22109.
32. Nawrocki E.P., Kolbe D.L., Eddy S.R. Infernal 1.0: Inference of RNA alignments. Bioinformatics 2009, 25:1335-1337.
33. Nikooyeh B., Neyestani T.R., Farvid M., Alavi-Majd H., Houshiarrad A., Kalayi A., Shariatzadeh N., Gharavi A., Heravifard S., Tayebinejad N., Salekzamani S., Zahedirad M. Daily consumption of vitamin D- or vitamin D + calcium-fortified yogurt drink improved glycemic control in patients with type 2 diabetes: a randomized clinical trial. Am. J. Clin. Nutr. 2011, 93:764-771.
34. Osei-Poku J., Mbogo C.M., Palmer W.J., Jiggins F.M. Deep sequencing reveals extensive variation in the gut microbiota of wild mosquitoes from Kenya. Mol. Ecol. 2012, 21:5138-5150.
35. Palaria A., Johnson-Kanda I., O'Sullivan D.J. Effect of a synbiotic yogurt on levels of fecal bifidobacteria, clostridia, and enterobacteria. Appl. Environ. Microbiol. 2012, 78:933-940.
36. Pepper J.W., Rosenfeld S. The emerging medical ecology of the human gut microbiome. Trends Ecol. Evol. 2012, 27:381-384.
37. Price M.N., Dehal P.S., Arkin A.P. FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 2009, 26:1641-1650.
38. Quince C., Lanzen A., Davenport R.J., Turnbaugh P.J. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 2011, 12:38.
39. Rolfe R.D. The role of probiotic cultures in the control of gastrointestinal health. J. Nutr. 2000, 130(2S Suppl.):396S-402S.
40. Sanz Y., Santacruz A., De Palma G. Insights into the roles of gut microbes in obesity. Interdiscip. Perspect. Infect. Dis. 2008, 2008:829101.
41. Saxelin M., Lassig A., Karjalainen H., Tynkkynen S., Surakka A., Vapaatalo H., Jarvenpaa S., Korpela R., Mutanen M., Hatakka K. Persistence of probiotic strains in the gastrointestinal tract when administered as capsules, yoghurt, or cheese. Int. J. Food Microbiol. 2010, 144:293-300.
42. Schiffrin E.J., Parlesak A., Bode C., Bode J.C., van't Hof M.A., Grathwohl D., Guigoz Y. Probiotic yogurt in the elderly with intestinal bacterial overgrowth: endotoxaemia and innate immune functions. Br. J. Nutr. 2009, 101:961-966.
43. Schloss P.D., Gevers D., Westcott S.L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 2011, 6:e27310.
44. Schloss P.D., Westcott S.L. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl. Environ. Microbiol. 2011, 77:3219-3226.
45. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing Mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
46. Shin H.S., Park S.Y., Lee Do K., Kim S.A., An H.M., Kim J.R., Kim M.J., Cha M.G., Lee S.W., Kim K.J., Lee K.O., Ha N.J. Hypocholesterolemic effect of sonication-killed Bifidobacterium longum isolated from healthy adult Koreans in high cholesterol fed rats. Arch. Pharm. Res. 2010, 33:1425-1431.
47. Sim K., Cox M.J., Wopereis H., Martin R., Knol J., Li M.S., Cookson W.O., Moffatt M.F., Kroll J.S. Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing. PLoS ONE 2012, 7:e32543.
48. Sun X., Zemel M.B. Calcium and dairy products inhibit weight and fat regain during ad libitum consumption following energy restriction in Ap2-agouti transgenic mice. J. Nutr. 2004, 134:3054-3060.
49. Tremaroli V., Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature 2012, 489:242-249.
50. Unno T., Jang J., Han D., Kim J.H., Sadowsky M.J., Kim O.S., Chun J., Hur H.G. Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ. Sci. Technol. 2010, 44:7777-7782.
51. Vintiñi E.O., Medina M.S. Host immunity in the protective response to nasal immunization with a pneumococcal antigen associated to live and heat-killed Lactobacillus casei. BMC Immunol. 2011, 12:46.
52. Wang T., Cai G., Qiu Y., Fei N., Zhang M., Pang X., Jia W., Cai S., Zhao L. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 2012, 6:320-329.
53. White K.M., Bauer S.J., Hartz K.K., Baldridge M. Changes in body composition with yogurt consumption during resistance training in women. Int. J. Sport Nutr. Exerc. Metab. 2009, 19:18-33.