Bang SJ, Kim G, Mi YL, Song EJ, Jung DH, Kum JS, Nam YD, Park CS, Seo DH (2018) The influence of in vitro pectin fermentation on the human fecal microbiome. Amb Express 8(1):98. https://doi.org/10.1186/s13568-018-0629-9
Article
CAS
PubMed
PubMed Central
Google Scholar
Barberan A, Bates ST, Casamayor EO, Fierer N (2012) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 6(2):343–351. https://doi.org/10.1038/ismej.2011.119
Article
CAS
PubMed
Google Scholar
Brisse S, Grimont F, Grimont PAD (2006) The genus Klebsiella. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, vol 6. Proteobacteria: gamma subclass. Springer, New York, pp 159–196
Chapter
Google Scholar
Callahan BJ, Mcmurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13(7):581–583. https://doi.org/10.1038/nmeth.3869
Article
CAS
PubMed
PubMed Central
Google Scholar
Carlson JL, Erickson JM, Hess JM, Gould TJ, Slavin JL (2017) Prebiotic dietary fiber and gut health: comparing the in vitro fermentations of beta-glucan, inulin and xylooligosaccharide. Nutrients. https://doi.org/10.3390/nu9121361
Article
PubMed
PubMed Central
Google Scholar
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635. https://doi.org/10.1126/science.1110591
Article
PubMed
PubMed Central
Google Scholar
Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 8(7):e1002606. https://doi.org/10.1371/journal.pcbi.1002606
Article
CAS
PubMed
PubMed Central
Google Scholar
Fusco A, Savio V, Cammarota M, Alfano A, Schiraldi C, Donnarumma G (2017) Beta-defensin-2 and beta-defensin-3 reduce intestinal damage caused by salmonella typhimurium modulating the expression of cytokines and enhancing the probiotic activity of Enterococcus faecium. J Immunol Res 2017:6976935. https://doi.org/10.1155/2017/6976935
Article
CAS
PubMed
PubMed Central
Google Scholar
Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, Gordon JI (2011) Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci USA 108(15):6252–6257. https://doi.org/10.1073/pnas.1102938108
Article
PubMed
PubMed Central
Google Scholar
Gupta A, Khanna S (2017) Fecal microbiota transplantation. Jama 318(1):102. https://doi.org/10.1001/jama.2017.6466
Article
PubMed
Google Scholar
Jin W, Han K, Dong S, Yang Y, Mao Z, Su M, Zeng M (2018) Modifications in gut microbiota and fermentation metabolites in the hindgut of rats after the consumption of galactooligosaccharide glycated with fish peptide. Food Funct. https://doi.org/10.1039/C7FO02002C
Article
PubMed
Google Scholar
Kassinen A, Krogius-Kurikka L, Makivuokko H, Rinttila T, Paulin L, Corander J, Malinen E, Apajalahti J, Palva A (2007) The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133(1):24–33. https://doi.org/10.1053/j.gastro.2007.04.005
Article
CAS
PubMed
Google Scholar
Kovatcheva-Datchary P, Nilsson A, Akrami R, Lee YS, De Vadder F, Arora T, Hallen A, Martens E, Bjorck I, Backhed F (2015) Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab 22(6):971–982. https://doi.org/10.1016/j.cmet.2015.10.001
Article
CAS
PubMed
Google Scholar
Lagier JC, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, Levasseur A, Rolain JM, Fournier PE, Raoult D (2018) Culturing the human microbiota and culturomics. Nat Rev Microbiol. https://doi.org/10.1038/s41579-018-0041-0
Article
PubMed
Google Scholar
Lau JT, Whelan FJ, Herath I, Lee CH, Collins SM, Bercik P, Surette MG (2016) Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling. Genome Med 8(1):72. https://doi.org/10.1186/s13073-016-0327-7
Article
CAS
PubMed
PubMed Central
Google Scholar
Macfarlane GT, Allison C, Gibson SA, Cummings JH (1988) Contribution of the microflora to proteolysis in the human large intestine. J Appl Microbiol 64(1):37–46. https://doi.org/10.1111/j.1365-2672.1988.tb02427.x
Article
CAS
Google Scholar
Makki K, Deehan EC, Walter J, Backhed F (2018) The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe 23(6):705–715. https://doi.org/10.1016/j.chom.2018.05.012
Article
CAS
PubMed
Google Scholar
Mcdonald JAK, Schroeter K, Fuentes S, Heikamp-Dejong I, Khursigara CM, Vos WMD, Allen-Vercoe E (2013) Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model. J Microbiol Methods 95(2):167–174. https://doi.org/10.1016/j.mimet.2013.08.008
Article
CAS
PubMed
Google Scholar
Nakano V, Ignacio A, Fernandes MR, Fugukaiti MH, Avila-Campos MJ (2013) Intestinal Bacteroides and Parabacteroides species producing antagonistic substances. Curr Trends Immunol 1:1–4
Google Scholar
Pham VT, Mohajeri MH (2018) The application of in vitro human intestinal models on the screening and development of pre- and probiotics. Benef Microb. https://doi.org/10.3920/BM2017.0164
Article
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41(Database issue):D590–D596. https://doi.org/10.1093/nar/gks1219
Article
CAS
PubMed
Google Scholar
Reese AT, Dunn RR (2018) Drivers of microbiome biodiversity: a review of general rules, feces, and ignorance. Mbio. https://doi.org/10.1128/mbio.01294-18
Article
PubMed
PubMed Central
Google Scholar
Ren YD, Ye ZS, Yang LZ, Jin LX, Wei WJ, Deng YY, Chen XX, Xiao CX, Yu XF, Xu HZ (2017) Fecal microbiota transplantation induces hepatitis B virus e-antigen (HBeAg) clearance in patients with positive HBeAg after long-term antiviral therapy. Hepatology 65(5):1765. https://doi.org/10.1002/hep.29008
Article
PubMed
Google Scholar
Routy B, Gopalakrishnan V, Daillere R, Zitvogel L, Wargo JA, Kroemer G (2018) The gut microbiota influences anticancer immunosurveillance and general health. Nat Rev Clin Oncol 15(6):382–396. https://doi.org/10.1038/s41571-018-0006-2
Article
CAS
PubMed
Google Scholar
Schneeberger M, Everard A, Gomez-Valades AG, Matamoros S, Ramirez S, Delzenne NM, Gomis R, Claret M, Cani PD (2015) Akkermansia muciniphila inversely correlates with the onset of inflammation, altered adipose tissue metabolism and metabolic disorders during obesity in mice. Sci Rep 5:16643. https://doi.org/10.1038/srep16643
Article
CAS
PubMed
PubMed Central
Google Scholar
Sekirov I, Russell SL, Antunes LC, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90(3):859–904. https://doi.org/10.1152/physrev.00045.2009
Article
CAS
PubMed
Google Scholar
Seo M, Heo J, Yoon J, Kim SY, Kang YM, Yu J, Cho S, Kim H (2017) Methanobrevibacter attenuation via probiotic intervention reduces flatulence in adult human: a non-randomised paired-design clinical trial of efficacy. PLoS ONE 12(9):e0184547. https://doi.org/10.1371/journal.pone.0184547
Article
CAS
PubMed
PubMed Central
Google Scholar
Soto M, Herzog C, Pacheco JA, Fujisaka S, Bullock K, Clish CB, Kahn CR (2018) Gut microbiota modulate neurobehavior through changes in brain insulin sensitivity and metabolism. Mol Psychiatry. https://doi.org/10.1038/s41380-018-0086-5
Article
PubMed
PubMed Central
Google Scholar
Staley C, Kaiser T, Vaughn BP, Graiziger CT, Hamilton MJ, Rehman Tu, Song K, Khoruts A, Sadowsky MJ (2018) Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation. Microbiome 6(1):166. https://doi.org/10.1186/s40168-018-0549-6
Article
PubMed
PubMed Central
Google Scholar
Surawicz CM, Brandt LJ, Binion DG, Ananthakrishnan AN, Curry SR, Gilligan PH, Mcfarland LV, Mark M, Zuckerbraun BS (2013) Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections. Am J Gastroenterol 108(4):478–494. https://doi.org/10.1038/ajg.2013.4
Article
CAS
PubMed
Google Scholar
Thomson P, Medina DA, Ortuzar V, Gotteland M, Garrido D (2018) Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides. Food Res Int 109:14–23. https://doi.org/10.1016/j.foodres.2018.04.008
Article
CAS
PubMed
Google Scholar
Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P (2018) Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nature Microbiology. https://doi.org/10.1038/nature07540
Article
PubMed
Google Scholar
Tremaroli V, Bäckhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 71(7415):242–249. https://doi.org/10.1038/nature11552
Article
CAS
Google Scholar
Wang X, Wang X, Jiang H, Cai C, Li G, Hao J, Yu G (2018) Marine polysaccharides attenuate metabolic syndrome by fermentation products and altering gut microbiota: an overview. Carbohydr Polym 195:601–612. https://doi.org/10.1016/j.carbpol.2018.05.003
Article
CAS
PubMed
Google Scholar
Williams CF, Walton GE, Jiang L, Plummer S, Garaiova I, Gibson GR (2015) Comparative analysis of intestinal tract models. Ann Rev Food Sci Technol 6(1):329–350. https://doi.org/10.1146/annurev-food-022814-015429
Article
CAS
Google Scholar
Yan D, Zhang T, Su J, Zhao LL, Wang H, Fang XM, Zhang YQ, Liu HY, Yu LY (2018) Structural variation in the bacterial community associated with airborne particulate matter in Beijing, China, during hazy and nonhazy days. Appl Environ Microbiol. https://doi.org/10.1128/aem.00004-18
Article
PubMed
PubMed Central
Google Scholar
Zadehtahmasebi M, Duca FA, Rasmussen BA, Bauer PV, Côté CD, Filippi BM, Lam TKT (2016) Activation of short and long chain fatty acid sensing machinery in the ileum lowers glucose production in vivo. J Biol Chem 291(16):8816–8882. https://doi.org/10.1074/jbc.M116.718460
Article
CAS
Google Scholar
Zhou W, Yan Y, Mi J, Zhang H, Lu L, Luo Q, Li X, Zeng X, Cao Y (2018) Simulated digestion and fermentation in vitro by human gut microbiota of polysaccharides from bee collected pollen of Chinese Wolfberry. J Agric Food Chem. https://doi.org/10.1021/acs.jafc.7b05546
Article
PubMed
Google Scholar