Irrazábal T, Belcheva A, Girardin SE, Martin A, Philpott DJ. The multifaceted role of the intestinal microbiota in colon cancer. Mol Cell. 2014;54:309–20.
Article
PubMed
CAS
Google Scholar
El Mouzan MI, Winter HS, Assiri AA, Korolev KS, Al Sarkhy AA, Dowd SE, et al. Microbiota profile in new-onset pediatric Crohn’s disease: data from a non-Western population. Gut Pathog. 2018;10:49.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lv LX, Fang DQ, Shi D, Chen DY, Yan R, Zhu YX, et al. Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis. Environ Microbiol. 2016;18:2272–86.
Article
CAS
PubMed
Google Scholar
Jayasudha R, Kalyana Chakravarthy S, Sai Prashanthi G, Sharma S, Garg P, Murthy SI, et al. Alterations in gut bacterial and fungal microbiomes are associated with bacterial keratitis, an inflammatory disease of the human eye. J Biosci. 2018;43:835–56.
Article
CAS
PubMed
Google Scholar
Gorkiewicz G, Moschen A. Gut microbiome: a new player in gastrointestinal disease. Virchows Arch. 2018;472:159–72.
Article
CAS
PubMed
Google Scholar
Rajagopala SV, Vashee S, Oldfield LM, Suzuki Y, Venter JC, Telenti A, et al. The human microbiome and cancer. Cancer Prev Res. 2017;10:226–34.
Article
Google Scholar
Marchesi JR, Dutilh BE, Hall N, Peters WHM, Roelofs R, Boleij A, et al. Towards the human colorectal cancer microbiome. PLoS One. 2011;6:e20447.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, et al. Altered fecal microbiota composition in patients with major depressive disorder. Brain Behav Immun. 2015;48:186–94.
Article
PubMed
Google Scholar
Sabatino A, Regolisti G, Cosola C, Gesualdo L, Fiaccadori E. Intestinal microbiota in type 2 diabetes and chronic kidney disease. Current Diabetes Reports. 2017;17:16.
Article
PubMed
CAS
Google Scholar
Garrett WS. The gut microbiota and colon cancer. Science. 2019;364:1133–5.
Article
CAS
PubMed
Google Scholar
Bullman S, Pedamallu CS, Sicinska E, Clancy TE, Zhang X, Cai D, et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science. 2017;358:1443–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brennan CA, Garrett WS. Fusobacterium nucleatum — symbiont, opportunist and oncobacterium. Nat Rev Microbiol. 2019;17:156–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dejea CM, Fathi P, Craig JM, Boleij A, Taddese R, Geis AL, et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science. 2018;359:592–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arthur JC, Perez-Chanona E, Mühlbauer M, Tomkovich S, Uronis JM, Fan TJ, et al. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science. 2012;338:120–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thakur BK, Malaisé Y, Martin A. Unveiling the mutational mechanism of the bacterial Genotoxin Colibactin in colorectal Cancer. Mol Cell. 2019;74:227–9.
Article
CAS
PubMed
Google Scholar
Miller KD, Siegel RL, Lin CC, Mariotto AB, Kramer JL, Rowland JH, et al. Cancer treatment and survivorship statistics, 2016. CA Cancer J Clin. 2016;66:271–89.
Article
PubMed
Google Scholar
Fearon ER. Molecular genetics of colorectal Cancer. Annu Rev Pathol Mech Dis. 2011;6:479–507.
Article
CAS
Google Scholar
Saito H. An immunological fecal occult blood test for mass screening of colorectal cancer by reversed passive hemagglutination (RPHA). Japanese J Gastroenterol. 1984;81:2831.
Google Scholar
Gouvernement du Québec. Immunochemical Fecal Occult Blood Test (iFOBT) | Gouvernement du Québec. https://www.quebec.ca/en/health/advice-and-prevention/screening-and-carrier-testing-offer/colorectal-cancer-screening/immunochemical-fecal-occult-blood-test-ifobt/. .
Fraser CG, Mathew CM, Mowat NAG, Wilson JA, Carey FA, Steele RJC. Evaluation of a card collection-based faecal immunochemical test in screening for colorectal cancer using a two-tier reflex approach. Gut. 2007;56:1415–8.
Article
PubMed
PubMed Central
Google Scholar
Sun J, Kato I. Gut microbiota, inflammation and colorectal cancer. Genes and Diseases. 2016;3:130–43.
Article
PubMed
PubMed Central
Google Scholar
Flemer B, Lynch DB, Brown JMR, Jeffery IB, Ryan FJ, Claesson MJ, et al. Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut. 2017;66:633–43.
Article
CAS
PubMed
Google Scholar
Zackular JP, Rogers MAM, Ruffin MT, Schloss PD. The human gut microbiome as a screening tool for colorectal Cancer. Cancer Prev Res. 2014;7:1112–21.
Article
CAS
Google Scholar
Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, De Kievit T, et al. A comparative study of the gut microbiota in immune-mediated inflammatory diseases - does a common dysbiosis exist? Microbiome. 2018;6:221.
Article
PubMed
PubMed Central
Google Scholar
Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15:382–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shannon CE. A mathematical theory of communication. Bell Syst Tech J. 1948;27:379–423.
Article
Google Scholar
Simpson EH. Measurement of diversity. Nature. 1949;163:688.
Article
Google Scholar
Bray JR, Curtis JT. An ordination of the upland Forest communities of southern Wisconsin. Source Ecol Monogr. 1957;27:325–49.
Article
Google Scholar
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.
Article
PubMed
PubMed Central
Google Scholar
Gauffin Cano P, Santacruz A, Moya Á, Sanz Y. Bacteroides uniformis CECT 7771 ameliorates metabolic and immunological dysfunction in mice with high-fat-diet induced obesity. PLoS One. 2012;7:e41079.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fernández-Murga ML, Sanz Y. Safety assessment of Bacteroides uniformis CECT 7771 isolated from stools of healthy breast-fed infants. PLoS One. 2016;11:e0145503.
Article
PubMed
PubMed Central
CAS
Google Scholar
Benítez-Páez A, Gómez del Pulgar EM, Sanz Y. The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides. Front Cell Infect Microbiol. 2017;7:383.
Article
PubMed
PubMed Central
CAS
Google Scholar
Baxter NT, Schmidt AW, Venkataraman A, Kim KS, Waldron C, Schmidt TM. Dynamics of human gut microbiota and short-chain fatty acids in response to dietary interventions with three fermentable fibers. MBio. 2019;10:e02566–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mittal R, Debs LH, Patel AP, Nguyen D, Patel K, O’Connor G, et al. Neurotransmitters: the critical modulators regulating gut-brain Axis. J Cell Physiol. 2017;232:2359–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qin P, Zou Y, Dai Y, Luo G, Zhang X, Xiao L. Characterization a novel butyric acid-producing bacterium Collinsella aerofaciens Subsp. Shenzhenensis Subsp Nov. Microorganisms. 2019;7:E78.
Article
PubMed
CAS
Google Scholar
Kalinkovich A, Livshits G. A cross talk between dysbiosis and gut-associated immune system governs the development of inflammatory arthropathies. Semin Arthritis Rheum. 2019;49:474–84.
Article
CAS
PubMed
Google Scholar
Balakrishnan B, Luckey D, Taneja V. Autoimmunity-associated gut commensals modulate gut permeability and immunity in humanized mice. Mil Med. 2019;184:529–36.
Article
PubMed
Google Scholar
Woerther PL, Antoun S, Chachaty E, Merad M. Eggerthella lenta bacteremia in solid tumor cancer patients: pathogen or witness of frailty? Anaerobe. 2017;47:70–2.
Article
PubMed
Google Scholar
Harris SC, Devendran S, Méndez-García C, Mythen SM, Wright CL, Fields CJ, et al. Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243 T. Gut Microbes. 2018;9:523–39.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xie YH, Gao QY, Cai GX, Sun XM, Zou TH, Chen HM, et al. Fecal Clostridium symbiosum for noninvasive detection of early and advanced colorectal Cancer: test and validation studies. EBioMedicine. 2017;25:32–40.
Article
PubMed
PubMed Central
Google Scholar
Elsayed S, Zhang K. Bacteraemia caused by Clostridium symbiosum. J Clin Microbiol. 2004;42:4390–2.
Article
PubMed
PubMed Central
Google Scholar
Toprak N, Özcan E, Pekin T, Yumuk P, Soyletir G. Bacteraemia caused by Clostridium symbiosum: case report and review of the literature. Indian J Med Microbiol. 2014;32:92–4.
Article
CAS
PubMed
Google Scholar
Franke T, Deppenmeier U. Physiology and central carbon metabolism of the gut bacterium Prevotella copri. Mol Microbiol. 2018;109:528–40.
Article
CAS
PubMed
Google Scholar
Kovatcheva-Datchary P, Nilsson A, Akrami R, Lee YS, De Vadder F, Arora T, et al. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab. 2015;22:971–82.
Article
CAS
PubMed
Google Scholar
Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife. 2013;2:e01202.
Article
PubMed
PubMed Central
CAS
Google Scholar
Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ. 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;52:2141–6.
CAS
PubMed
Google Scholar
Munukka E, Rintala A, Toivonen R, Nylund M, Yang B, Takanen A, et al. Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice. ISME J. 2017;11:1667–79.
Article
PubMed
PubMed Central
Google Scholar
Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J. 2017;11:841–52.
Article
PubMed
PubMed Central
Google Scholar
Reichardt N, Duncan SH, Young P, Belenguer A, McWilliam Leitch C, Scott KP, et al. Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. ISME J. 2014;8:1323–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Malinen E, Krogius-Kurikka L, Lyra A, Nikkilä J, Jääskeläinen A, Rinttilä T, et al. Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World J Gastroenterol. 2010;16:4532–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petrov VA, Saltykova IV, Zhukova IA, Alifirova VM, Zhukova NG, Dorofeeva YB, et al. Analysis of gut microbiota in patients with Parkinson’s disease. Bull Exp Biol Med. 2017;162:734–7.
Article
CAS
PubMed
Google Scholar
Hatziioanou D, Mayer MJ, Duncan SH, Flint HJ, Narbad A. A representative of the dominant human colonic Firmicutes, Roseburia faecis M72/1, forms a novel bacteriocin-like substance. Anaerobe. 2013;23:5–8.
Article
CAS
PubMed
Google Scholar
Mullish BH, McDonald JAK, Pechlivanis A, Allegretti JR, Kao D, Barker GF, et al. Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection. Gut. 2019;68:1791–800.
Article
CAS
PubMed
Google Scholar
Hatziioanou D, Gherghisan-Filip C, Saalbach G, Horn N, Wegmann U, Duncan SH, et al. Discovery of a novel lantibiotic nisin O from Blautia obeum A2–162, isolated from the human gastrointestinal tract. Microbiol (United Kingdom). 2017;163:1292–305.
CAS
Google Scholar
Gherghisan-Filip C, Saalbach G, Hatziioanou D, Narbad A, Mayer MJ. Processing and structure of the lantibiotic peptide Nso from the human gut bacterium Blautia obeum A2-162 analysed by mass spectrometry. Sci Rep. 2018;8:10077.
Article
PubMed
PubMed Central
CAS
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013;79:5112–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotech. 2019;37:852–7.
Article
CAS
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.
Article
PubMed
PubMed Central
Google Scholar
McDonald D, Price MN, Goodrich J, Nawrocki EP, Desantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.
Article
CAS
PubMed
Google Scholar
Oksanen J, Blanchet G, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. 2018. https://cran.r-project.org/package=vegan.
McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.
Article
CAS
PubMed
PubMed Central
Google Scholar
The R Core Team. R: A language and environment for statistical computing. R foundation for Statistical Computing, Vienne, Austria. 2018. https://www.R-project.org/.
Kruskal JB. Nonmetric multidimensional scaling: a numerical method. Psychometrika. 1964;29:115–29.
Article
Google Scholar
Kruskal WH, Wallis WA. Use of ranks in one-criterion variance analysis. J Am Stat Assoc. 1952;47:583–621.
Article
Google Scholar
Wilcoxon F. Individual comparisons by ranking methods. Biom Bull. 1945;1:80.
Article
Google Scholar
Xanthopoulos P, Pardalos PM, Trafalis TB. Linear Discriminant Analysis. In: In Robust Data Mining. New York: Springer; 2013. p. 27–33.
Chapter
Google Scholar