The opportunistic nature of gut commensal microbiota

References

• Abreu MT, Vora P, Faure E, Thomas LS, Arnold ET, Arditi M. 2001. Decreased expression of Toll-like receptor-4 and MD-2 correlates with intestinal epithelial cell protection against dysregulated proinflammatory gene expression in response to bacterial lipopolysaccharide. J Immunol. 167(3):1609–1616.
   PubMed Web of Science ®Google Scholar
• Abt MC, Artis D. 2013. The dynamic influence of commensal bacteria on the immune response to pathogens. Curr Opin Microbiol. 16(1):4–9.
   PubMed Web of Science ®Google Scholar
• Ailloud F, Didelot X, Woltemate S, Pfaffinger G, Overmann J, Bader RC, Schulz C, Malfertheiner P, Suerbaum S. 2019. Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps. Nat Commun. 10(1):1–13.
   PubMedGoogle Scholar
• Anhê FF, Barra NG, Cavallari JF, Henriksbo BD, Schertzer JD. 2021. Metabolic endotoxemia is dictated by the type of lipopolysaccharide. Cell Rep. 36(11):109691.
   PubMed Web of Science ®Google Scholar
• Assimakopoulos SF, Triantos C, Maroulis I, Gogos C. 2018. The role of the gut barrier function in health and disease. Gastroenterology Res. 11(4):261–263.
   PubMed Web of Science ®Google Scholar
• Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, Stotland A, Wolkowicz R, Cutting AS, Doran KS, et al. 2013. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A. 110(26):10771–10776.
   PubMed Web of Science ®Google Scholar
• Barraud D, Bollaert P-E, Gibot S. 2013. Impact of the administration of probiotics on mortality in critically ill adult patients: a meta-analysis of randomized controlled trials. Chest. 143(3):646–655.
   PubMed Web of Science ®Google Scholar
• Becattini S, Littmann ER, Carter RA, Kim SG, Morjaria SM, Ling L, Gyaltshen Y, Fontana E, Taur Y, Leiner IM, et al. 2017. Commensal microbes provide first line defense against Listeria monocytogenes infection. J Exp Med. 214(7):1973–1989.
   PubMed Web of Science ®Google Scholar
• Belkaid Y, Hand TW. 2014. Role of the microbiota in immunity and inflammation. Cell. 157(1):121–141.
   PubMed Web of Science ®Google Scholar
• Bhar S, Bose T, Mande SS. 2020. Can pathogenic and nonpathogenic bacteria be distinguished by sensory protein abundance? Appl Environ Microbiol. 86(14):e00478–20.
   PubMed Web of Science ®Google Scholar
• Bischoff SC. 2011. ‘Gut health’: a new objective in medicine? BMC Med. 9(1):1–14.
   PubMedGoogle Scholar
• Boldock E, Surewaard BGJ, Shamarina D, Na M, Fei Y, Ali A, Williams A, Pollitt EJG, Szkuta P, Morris P, et al. 2018. Human skin commensals augment Staphylococcus aureus pathogenesis. Nat Microbiol. 3(8):881–890.
   PubMed Web of Science ®Google Scholar
• Brevi A, Cogrossi LL, Grazia G, Masciovecchio D, Impellizzieri D, Lacanfora L, Grioni M, Bellone M. 2020. Much more than IL-17A: cytokines of the IL-17 family between microbiota and cancer. Front Immunol. 11:565470.
   PubMed Web of Science ®Google Scholar
• Brown RL, Larkinson ML, Clarke TB. 2021. Immunological design of commensal communities to treat intestinal infection and inflammation. PLoS Pathog. 17(1):e1009191.
   PubMed Web of Science ®Google Scholar
• Brugger SD, Bomar L, Lemon KP. 2016. Commensal-pathogen interactions along the human nasal passages. PLoS Pathog. 12(7):e1005633.
   PubMed Web of Science ®Google Scholar
• Butta H, Sardana R, Vaishya R, Singh KN, Mendiratta L. 2017. Bifidobacterium: an emerging clinically significant metronidazole-resistant anaerobe of mixed pyogenic infections. Cureus. 9(4):e1134.
   PubMedGoogle Scholar
• Cai R, Cheng C, Chen J, Xu X, Ding C, Gu B. 2020. Interactions of commensal and pathogenic microorganisms with the mucus layer in the colon. Gut Microbes. 11(4):680–690.
   PubMed Web of Science ®Google Scholar
• Casadevall A, Pirofski LA. 1999. Host-pathogen interactions: redefining the basic concepts of virulence and pathogenicity. Infect Immun. 67(8):3703–3713.
   PubMed Web of Science ®Google Scholar
• Casadevall A, Pirofski LA. 2000. Host-pathogen interactions: basic concepts of microbial commensalism, colonization, infection, and disease. Infect Immun. 68(12):6511–6518.
   PubMed Web of Science ®Google Scholar
• Casadevall A, Pirofski L-A. 2014. Microbiology: ditch the term pathogen. Nature News. 516(7530):165–166.
   PubMed Web of Science ®Google Scholar
• Cash HL, Whitham CV, Behrendt CL, Hooper LV. 2006. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science. 313(5790):1126–1130.
   PubMed Web of Science ®Google Scholar
• Chang PV, Hao L, Offermanns S, Medzhitov R. 2014. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc Natl Acad Sci U S A. 111(6):2247–2252.
   PubMed Web of Science ®Google Scholar
• Chassaing B, Ley RE, Gewirtz AT. 2014. Intestinal epithelial cell toll-like receptor 5 regulates the intestinal microbiota to prevent low-grade inflammation and metabolic syndrome in mice. Gastroenterology. 147(6):1363–1377.e17.
   PubMed Web of Science ®Google Scholar
• Cirrincione S, Neumann B, Zühlke D, Riedel K, Pessione E. 2019. Detailed soluble proteome analyses of a dairy-isolated Enterococcus faecalis: a possible approach to assess food safety and potential probiotic value. Front Nutr. 6:71.
   PubMed Web of Science ®Google Scholar
• Conway T, Cohen PS. 2015. Commensal and pathogenic Escherichia coli metabolism in the gut. Microbiol Spectr. 3(3):3–24.
   Google Scholar
• Cornuault JK, Moncaut E, Loux V, Mathieu A, Sokol H, Petit M-A, De Paepe M. 2020. The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition. Isme J. 14(3):771–787.
   PubMed Web of Science ®Google Scholar
• Corrêa RO, Vieira A, Sernaglia EM, Lancellotti M, Vieira AT, Avila-Campos MJ, Rodrigues HG, Vinolo MAR. 2017. Bacterial short‐chain fatty acid metabolites modulate the inflammatory response against infectious bacteria. Cell Microbiol. 19(7):e12720.
   Web of Science ®Google Scholar
• Costa RL, Moreira J, Lorenzo A, Lamas CC. 2018. Infectious complications following probiotic ingestion: a potentially underestimated problem? A systematic review of reports and case series. BMC Complement Altern Med. 18(1):1–8.
   PubMedGoogle Scholar
• Cross SA, Callaway CW. 1984. D-Lactic acidosis and selected cerebellar ataxias. Mayo Clin Proc. 59(3):202–205.
   PubMed Web of Science ®Google Scholar
• Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, Cunningham AF, Petty NK, Mahon V, Brinkley C, Hobman JL, et al. 2010. A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. J Bacteriol. 192(21):5822–5831.
   PubMed Web of Science ®Google Scholar
• Datta P, Gupta V, Mohi GK, Chander J, Janmeja AK. 2017. Lactobacillus coryniformis causing pulmonary infection in a patient with metastatic small cell carcinoma: case report and review of literature on lactobacillus pleuro-pulmonary infections. J Clin Diagn Res. 11(2):DE01–DE05.
   PubMedGoogle Scholar
• David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 505(7484):559–563.
   PubMed Web of Science ®Google Scholar
• de Jong MF, Alto NM. 2018. Cooperative immune suppression by Escherichia coli and shigella effector proteins. Infect Immun. 86(4):e00560-17.
   PubMed Web of Science ®Google Scholar
• Denamur E, Matic I. 2006. Evolution of mutation rates in bacteria. Mol Microbiol. 60(4):820–827.
   PubMed Web of Science ®Google Scholar
• Dey P, Chaudhuri SR, Efferth T, Pal S. 2021. The intestinal 3M (microbiota, metabolism, metabolome) Zeitgeist–from fundamentals to future challenges. Free Radic Biol Med. 176:265–285.
   PubMed Web of Science ®Google Scholar
• Dey P, Ray Chaudhuri S. 2022. Cancer-associated microbiota: from mechanisms of disease causation to microbiota-centric anti-cancer approaches. Biology. 11(5):757.
   PubMedGoogle Scholar
• Dey P, Sasaki GY, Wei P, Li J, Wang L, Zhu J, McTigue D, Yu Z, Bruno RS. 2019. Green tea extract prevents obesity in male mice by alleviating gut dysbiosis in association with improved intestinal barrier function that limits endotoxin translocation and adipose inflammation. J Nutr Biochem. 67:78–89.
   PubMed Web of Science ®Google Scholar
• Dey P. 2019. Gut microbiota in phytopharmacology: a comprehensive overview of concepts, reciprocal interactions, biotransformations and mode of actions. Pharmacol Res. 147:104367.
   PubMed Web of Science ®Google Scholar
• Dey P. 2020a. Targeting gut barrier dysfunction with phytotherapies: effective strategy against chronic diseases. Pharmacol Res. 161(11):105135.
   PubMedGoogle Scholar
• Dey P. 2020b. The role of gut microbiome in chemical-induced metabolic and toxicological murine disease models. Life Sci. 258:118172.
   PubMed Web of Science ®Google Scholar
• Diard M, Hardt W-D. 2017. Evolution of bacterial virulence. FEMS Microbiol Rev. 41(5):679–697.
   PubMed Web of Science ®Google Scholar
• Dingemanse C, Belzer C, van Hijum SA, Günthel M, Salvatori D, Dunnen JTd, Kuijper EJ, Devilee P, de Vos WM, van Ommen GB, et al. 2015. Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice. CARCIN. 36(11):1388–1396.
   PubMed Web of Science ®Google Scholar
• Duarte SMB, Stefano JT, Miele L, Ponziani FR, Souza-Basqueira M, Okada LSRR, de Barros Costa FG, Toda K, Mazo DFC, Sabino EC, et al. 2018. Gut microbiome composition in lean patients with NASH is associated with liver damage independent of caloric intake: a prospective pilot study. Nutr Metab Cardiovasc Dis. 28(4):369–384.
   PubMed Web of Science ®Google Scholar
• Duscha A, Gisevius B, Hirschberg S, Yissachar N, Stangl GI, Eilers E, Bader V, Haase S, Kaisler J, David C, et al. 2020. Propionic acid shapes the multiple sclerosis disease course by an immunomodulatory mechanism. Cell. 180(6):1067–1080. e16.
   PubMed Web of Science ®Google Scholar
• Egervärn M, Lindmark H, Olsson J, Roos S. 2010. Transferability of a tetracycline resistance gene from probiotic Lactobacillus reuteri to bacteria in the gastrointestinal tract of humans. Antonie Van Leeuwenhoek. 97(2):189–200.
   PubMed Web of Science ®Google Scholar
• Elomaa E, Aho K. 1990. The colon, the rumen, and D-lactic acidosis. Lancet. 336:599–600.
   PubMed Web of Science ®Google Scholar
• Fast D, Kostiuk B, Foley E, Pukatzki S. 2018. Commensal pathogen competition impacts host viability. Proc Natl Acad Sci U S A. 115(27):7099–7104.
   PubMed Web of Science ®Google Scholar
• FDA. Fecal microbiota for transplantation: safety alert - risk of serious adverse events likely due to transmission of pathogenic organisms. 2020. https://www.fda.gov/safety/medical-product-safety-information/fecal-microbiota-transplantation-safety-alert-risk-serious-adverse-events-likely-due-transmission
   Google Scholar
• Franz CM, Holzapfel WH, Stiles ME. 1999. Enterococci at the crossroads of food safety? Int J Food Microbiol. 47(1–2):1–24.
   PubMed Web of Science ®Google Scholar
• Franz CM, Muscholl-Silberhorn AB, Yousif NM, Vancanneyt M, Swings J, Holzapfel WH. 2001. Incidence of virulence factors and antibiotic resistance among Enterococci isolated from food. Appl Environ Microbiol. 67(9):4385–4389.
   PubMed Web of Science ®Google Scholar
• Freter R. 1992. Factors affecting the microecology of the gut. In: Probiotics. Dordrecht: Springer; p. 111–144.
   Google Scholar
• Fritts RK, McCully AL, McKinlay JB. 2021. Extracellular metabolism sets the table for microbial cross-feeding. Microbiol Mol Biol Rev. 85(1):e00135–20.
   PubMed Web of Science ®Google Scholar
• Fuchs TM, Eisenreich W, Heesemann J, Goebel W. 2012. Metabolic adaptation of human pathogenic and related nonpathogenic bacteria to extra-and intracellular habitats. FEMS Microbiol Rev. 36(2):435–462.
   PubMed Web of Science ®Google Scholar
• Furuya-Kanamori L, Marquess J, Yakob L, Riley TV, Paterson DL, Foster NF, Huber CA, Clements ACA. 2015. Asymptomatic Clostridium difficile colonization: epidemiology and clinical implications. BMC Infect Dis. 15:516.
   PubMed Web of Science ®Google Scholar
• Gaboriau-Routhiau V, Rakotobe S, Lécuyer E, Mulder I, Lan A, Bridonneau C, Rochet V, Pisi A, De Paepe M, Brandi G, et al. 2009. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity. 31(4):677–689.
   PubMed Web of Science ®Google Scholar
• Gewirtz AT, Simon PO, Schmitt CK, Taylor LJ, Hagedorn CH, O'Brien AD, Neish AS, Madara JL. 2001. Salmonella typhimurium translocates flagellin across intestinal epithelia, inducing a proinflammatory response. J Clin Invest. 107(1):99–109.
   PubMed Web of Science ®Google Scholar
• Ghosh AR. 2013. Appraisal of microbial evolution to commensalism and pathogenicity in humans. Clin Med Insights Gastroenterol. 6:1–12.
   PubMedGoogle Scholar
• Giannakis M, Chen SL, Karam SM, Engstrand L, Gordon JI. 2008. Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells. Proc Natl Acad Sci U S A. 105(11):4358–4363.
   PubMed Web of Science ®Google Scholar
• Gibson JF, Pidwill GR, Carnell OT, Surewaard BGJ, Shamarina D, Sutton JAF, Jeffery C, Derré-Bobillot A, Archambaud C, Siggins MK, et al. 2021. Commensal bacteria augment Staphylococcus aureus infection by inactivation of phagocyte-derived reactive oxygen species. PLoS Pathog. 17(9):e1009880.
   PubMed Web of Science ®Google Scholar
• Graver MA, Wade JJ. 2011. The role of acidification in the inhibition of Neisseria gonorrhoeae by vaginal lactobacilli during anaerobic growth. Ann Clin Microbiol Antimicrob. 10:8.
   PubMed Web of Science ®Google Scholar
• Gray MJ, Escalante-Semerena JC. 2010. A new pathway for the synthesis of α‐ribazole‐phosphate in Listeria innocua. Mol Microbiol. 77(6):1429–1438.
   PubMed Web of Science ®Google Scholar
• Gren C, Spiegelhauer MR, Rotbain EC, Ehmsen BK, Kampmann P, Andersen LP. 2019. Ruminococcus gnavus bacteraemia in a patient with multiple haematological malignancies. Access Microbiol. 1(8):e000048.
   PubMedGoogle Scholar
• Gronbach K, Eberle U, Müller M, Ölschläger TA, Dobrindt U, Leithäuser F, Niess JH, Döring G, Reimann J, Autenrieth IB, et al. 2010. Safety of probiotic Escherichia coli strain Nissle 1917 depends on intestinal microbiota and adaptive immunity of the host. Infect Immun. 78(7):3036–3046.
   PubMed Web of Science ®Google Scholar
• Gurung M, Li Z, You H, Rodrigues R, Jump DB, Morgun A, Shulzhenko N. 2020. Role of gut microbiota in type 2 diabetes pathophysiology. EBioMedicine. 51:102590.
   PubMed Web of Science ®Google Scholar
• Gustafsson I, Sjölund M, Torell E, Johannesson M, Engstrand L, Cars O, Andersson DI. 2003. Bacteria with increased mutation frequency and antibiotic resistance are enriched in the commensal flora of patients with high antibiotic usage. J Antimicrob Chemother. 52(4):645–650.
   PubMed Web of Science ®Google Scholar
• Hadjisymeou S, Loizou P, Kothari P. 2013. Lactococcus lactis cremoris infection: not rare anymore? BMJ Case Rep. 2013(may09 1):bcr2012008479.
   PubMedGoogle Scholar
• Han YW. 2015. Fusobacterium nucleatum: a commensal-turned pathogen. Curr Opin Microbiol. 23:141–147.
   PubMed Web of Science ®Google Scholar
• Hanchi H, Mottawea W, Sebei K, Hammami R. 2018. The genus Enterococcus: between probiotic potential and safety concerns—an update. Front Microbiol. 9:1791.
   PubMed Web of Science ®Google Scholar
• Hansen SGK, Skov MN, Justesen US. 2013. Two cases of Ruminococcus gnavus bacteremia associated with diverticulitis. J Clin Microbiol. 51(4):1334–1336.
   PubMed Web of Science ®Google Scholar
• Hassall J, Cheng JK, Unnikrishnan M. 2021. Dissecting individual interactions between pathogenic and commensal bacteria within a multispecies gut microbial community. Msphere. 6(2):e00013–21.
   PubMed Web of Science ®Google Scholar
• Heeney DD, Gareau MG, Marco ML. 2018. Intestinal Lactobacillus in health and disease, a driver or just along for the ride? Curr Opin Biotechnol. 49:140–147.
   PubMed Web of Science ®Google Scholar
• Henriques SF, Dhakan DB, Serra L, Francisco AP, Carvalho-Santos Z, Baltazar C, Elias AP, Anjos M, Zhang T, Maddocks ODK, et al. 2020. Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour. Nat Commun. 11(1):1–15.
   PubMed Web of Science ®Google Scholar
• Honda K, Moto M, Uchida N, He F, Hashizume N. 2012. Anti-diabetic effects of lactic acid bacteria in normal and type 2 diabetic mice. J Clin Biochem Nutr. 51(2):96–101.
   PubMed Web of Science ®Google Scholar
• Honeycutt TC, El Khashab M, Wardrop RM, III, McNeal-Trice K, Honeycutt AL, Christy CG, et al. 2007. Probiotic administration and the incidence of nosocomial infection in pediatric intensive care: a randomized placebo-controlled trial. Pediatric Crit Care Med. 8(5):452–458.
   PubMed Web of Science ®Google Scholar
• Howe C, Kim SJ, Mitchell J, Im E, Kim YS, Kim YS, Rhee SH. 2018. Differential expression of tumor-associated genes and altered gut microbiome with decreased Akkermansia muciniphila confer a tumor-preventive microenvironment in intestinal epithelial Pten-deficient mice. Biochim Biophys Acta Mol Basis Dis. 1864(12):3746–3758.
   PubMed Web of Science ®Google Scholar
• Huang P-Y, Yang Y-C, Wang C-I, Hsiao P-W, Chiang H-I, Chen T-W. 2021. Increase in akkermansiaceae in gut microbiota of prostate cancer-bearing mice. IJMS. 22(17):9626.
   Google Scholar
• Hummel A, Holzapfel WH, Franz CM. 2007. Characterisation and transfer of antibiotic resistance genes from enterococci isolated from food. Syst Appl Microbiol. 30(1):1–7.
   PubMed Web of Science ®Google Scholar
• Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch SV, et al. 2009. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 139(3):485–498.
   PubMed Web of Science ®Google Scholar
• Jacobsen L, Wilcks A, Hammer K, Huys G, Gevers D, Andersen SR. 2007. Horizontal transfer of tet (M) and erm (B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats. FEMS Microbiol Ecol. 59(1):158–166.
   PubMed Web of Science ®Google Scholar
• Jellbauer S, Perez Lopez A, Behnsen J, Gao N, Nguyen T, Murphy C, Edwards RA, Raffatellu M. 2016. Beneficial effects of sodium phenylbutyrate administration during infection with Salmonella enterica serovar typhimurium. Infect Immun. 84(9):2639–2652.
   PubMed Web of Science ®Google Scholar
• Jiang F, Meng D, Weng M, Zhu W, Wu W, Kasper D, Walker WA. 2017. The symbiotic bacterial surface factor polysaccharide A on Bacteroides fragilis inhibits IL-1β-induced inflammation in human fetal enterocytes via toll receptors 2 and 4. PLoS One. 12(3):e0172738.
   PubMed Web of Science ®Google Scholar
• Jiminez JA, Uwiera TC, Abbott DW, Uwiera RRE, Inglis GD. 2017. Butyrate supplementation at high concentrations alters enteric bacterial communities and reduces intestinal inflammation in mice infected with Citrobacter rodentium. mSphere. 2(4):e00243-17.
   PubMed Web of Science ®Google Scholar
• Jochum L, Stecher B. 2020. Label or concept–what is a pathobiont? Trends Microbiol. 28(10):789–792.
   PubMed Web of Science ®Google Scholar
• Johnson JL, Jones MB, Cobb BA. 2015. Polysaccharide A from the capsule of Bacteroides fragilis induces clonal CD4+ T cell expansion. J Biol Chem. 290(8):5007–5014.
   PubMed Web of Science ®Google Scholar
• Johnson TJ, Nolan LK. 2009. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol Rev. 73(4):750–774.
   PubMed Web of Science ®Google Scholar
• Kamada N, Kim Y-G, Sham HP, Vallance BA, Puente JL, Martens EC, Núñez G. 2012. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science. 336(6086):1325–1329.
   PubMed Web of Science ®Google Scholar
• Khalesi S, Bellissimo N, Vandelanotte C, Williams S, Stanley D, Irwin C. 2019. A review of probiotic supplementation in healthy adults: helpful or hype? Eur J Clin Nutr. 73(1):24–37.
   PubMed Web of Science ®Google Scholar
• Kim YJ, Kang HY, Han Y, Lee MS, Lee HJ. 2017. A bloodstream infection by Ruminococcus gnavus in a patient with a gall bladder perforation. Anaerobe. 47:129–131.
   PubMed Web of Science ®Google Scholar
• Köhler C-D, Dobrindt U. 2011. What defines extraintestinal pathogenic Escherichia coli? Int J Med Microbiol. 301(8):642–647.
   PubMed Web of Science ®Google Scholar
• Koli P, Sudan S, Fitzgerald D, Adhya S, Kar S. 2011. Conversion of commensal Escherichia coli K-12 to an invasive form via expression of a mutant histone-like protein. mBio. 2(6):e00182–11.
   PubMed Web of Science ®Google Scholar
• Kothari D, Patel S, Kim S-K. 2019. Probiotic supplements might not be universally-effective and safe: a review. Biomed Pharmacother. 111:537–547.
   PubMed Web of Science ®Google Scholar
• Kowlgi NG, Chhabra L. 2015. D-lactic acidosis: an underrecognized complication of short bowel syndrome. Gastroenterol Res Pract. 2015:476215.
   PubMed Web of Science ®Google Scholar
• Kumar P, Monin L, Castillo P, Elsegeiny W, Horne W, Eddens T, Vikram A, Good M, Schoenborn AA, Bibby K, et al. 2016. Intestinal interleukin-17 receptor signaling mediates reciprocal control of the gut microbiota and autoimmune inflammation. Immunity. 44(3):659–671.
   PubMed Web of Science ®Google Scholar
• LeClerc JE, Li B, Payne WL, Cebula TA. 1996. High mutation frequencies among Escherichia coli and Salmonella pathogens. Science. 274(5290):1208–1211.
   PubMed Web of Science ®Google Scholar
• Lertpiriyapong K, Whary MT, Muthupalani S, Lofgren JL, Gamazon ER, Feng Y, Ge Z, Wang TC, Fox JG. 2014. Gastric colonisation with a restricted commensal microbiota replicates the promotion of neoplastic lesions by diverse intestinal microbiota in the Helicobacter pylori INS-GAS mouse model of gastric carcinogenesis. Gut. 63(1):54–63.
   PubMed Web of Science ®Google Scholar
• Li X-Q, Zhu Y-H, Zhang H-F, Yue Y, Cai Z-X, Lu Q-P, Zhang L, Weng XG, Zhang FJ, Zhou D, et al. 2012. Risks associated with high-dose Lactobacillus rhamnosus in an Escherichia coli model of piglet diarrhoea: intestinal microbiota and immune imbalances. PLoS One. 7:e40666.
   PubMed Web of Science ®Google Scholar
• Li Z-P, Liu J-X, Lu L-L, Wang L-L, Xu L, Guo Z-H, Dong Q-J. 2021. Overgrowth of Lactobacillus in gastric cancer. World J Gastrointest Oncol. 13(9):1099–1108.
   PubMed Web of Science ®Google Scholar
• Lood R, Waldetoft KW, Nordenfelt P. 2015. Localization-triggered bacterial pathogenesis. Future Microbiol. 10(10):1659–1668.
   PubMed Web of Science ®Google Scholar
• Madan R, Kolter R, Mahadevan S. 2005. Mutations that activate the silent bgl operon of Escherichia coli confer a growth advantage in stationary phase. J Bacteriol. 187(23):7912–7917.
   PubMed Web of Science ®Google Scholar
• Magne F, Gotteland M, Gauthier L, Zazueta A, Pesoa S, Navarrete P, Balamurugan R. 2020. The firmicutes/bacteroidetes ratio: a relevant marker of gut dysbiosis in obese patients? Nutrients. 12(5):1474.
   PubMed Web of Science ®Google Scholar
• Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, et al. 2009. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci USA. 106(14):5859–5864.
   PubMed Web of Science ®Google Scholar
• Malek A, De la Hoz A, Gomez-Villegas SI, Nowbakht C, Arias CA. 2019. Lactococcus garvieae, an unusual pathogen in infective endocarditis: case report and review of the literature. BMC Infect Dis. 19(1):1–10.
   PubMedGoogle Scholar
• Maltby R, Leatham-Jensen MP, Gibson T, Cohen PS, Conway T. 2013. Nutritional basis for colonization resistance by human commensal Escherichia coli strains HS and Nissle 1917 against E. coli O157: H7 in the mouse intestine. PLoS One. 8(1):e53957.
   PubMed Web of Science ®Google Scholar
• Martens EC, Neumann M, Desai MS. 2018. Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier. Nat Rev Microbiol. 16(8):457–470.
   PubMed Web of Science ®Google Scholar
• Maurelli AT, Fernández RE, Bloch CA, Rode CK, Fasano A. 1998. “Black holes” and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci U S A. 95(7):3943–3948.
   PubMed Web of Science ®Google Scholar
• Mazmanian SK, Round JL, Kasper DL. 2008. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature. 453(7195):620–625.
   PubMed Web of Science ®Google Scholar
• McLaren MR, Callahan BJ. 2020. Pathogen resistance may be the principal evolutionary advantage provided by the microbiome. Philos Trans R Soc Lond B Biol Sci. 375(1808):20190592.
   PubMed Web of Science ®Google Scholar
• Metcalf CJE, Koskella B. 2019. Protective microbiomes can limit the evolution of host pathogen defense. Evol Lett. 3(5):534–543.
   PubMed Web of Science ®Google Scholar
• Million M, Lagier J-C, Yahav D, Paul M. 2013. Gut bacterial microbiota and obesity. Clin Microbiol Infect. 19(4):305–313.
   PubMed Web of Science ®Google Scholar
• Morris BE, Henneberger R, Huber H, Moissl-Eichinger C. 2013. Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev. 37(3):384–406.
   PubMed Web of Science ®Google Scholar
• Mosca A, Leclerc M, Hugot JP. 2016. Gut microbiota diversity and human diseases: should we reintroduce key predators in our ecosystem? Front Microbiol. 7:455.
   PubMed Web of Science ®Google Scholar
• Moxon ER, Murphy PA. 1978. Haemophilus influenzae bacteremia and meningitis resulting from survival of a single organism. Proc Natl Acad Sci USA. 75(3):1534–1536.
   PubMed Web of Science ®Google Scholar
• Murray G, Balmer AJ, Herbert J, Hadijirn NF, Kemp CL, Matuszewska M, Bruchmann S, Hossain ASMM, Gottschalk M, Tucker AW et al. 2021. Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen. PLoS Genet. 17:e1009864.
   PubMed Web of Science ®Google Scholar
• Najdenski H, Iteman I, Carniel E. 1995. The genome of Yersinia enterocolitica is the most stable of the three pathogenic species. Contrib Microbiol Immunol. 13:281–284.
   PubMedGoogle Scholar
• Nascimento LCS, Casarotti SN, Todorov SD, Penna ALB. 2019. Probiotic potential and safety of enterococci strains. Ann Microbiol. 69(3):241–252.
   Web of Science ®Google Scholar
• Neish AS, Gewirtz AT, Zeng H, Young AN, Hobert ME, Karmali V, Rao AS, Madara JL. 2000. Prokaryotic regulation of epithelial responses by inhibition of IkappaB-alpha ubiquitination. Science. 289(5484):1560–1563.
   PubMed Web of Science ®Google Scholar
• Ng KM, Ferreyra JA, Higginbottom SK, Lynch JB, Kashyap PC, Gopinath S, Naidu N, Choudhury B, Weimer BC, Monack DM, et al. 2013. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature. 502(7469):96–99.
   PubMed Web of Science ®Google Scholar
• Nguyen M-T, Uebele J, Kumari N, Nakayama H, Peter L, Ticha O, Woischnig A-K, Schmaler M, Khanna N, Dohmae N, et al. 2017. Lipid moieties on lipoproteins of commensal and non-commensal staphylococci induce differential immune responses. Nat Commun. 8(1):1–12.
   PubMedGoogle Scholar
• Noh CK, Lee KJ. 2020. Fecal microbiota alterations and small intestinal bacterial overgrowth in functional abdominal bloating/distention. J Neurogastroenterol Motil. 26(4):539–549.
   PubMed Web of Science ®Google Scholar
• Okubo H, Sakoda H, Kushiyama A, Fujishiro M, Nakatsu Y, Fukushima T, Matsunaga Y, Kamata H, Asahara T, Yoshida Y, et al. 2013. Lactobacillus casei strain Shirota protects against nonalcoholic steatohepatitis development in a rodent model. Am J Physiol Gastrointest Liver Physiol. 305(12):G911–G918.
   PubMed Web of Science ®Google Scholar
• Ortega-Cava CF, Ishihara S, Rumi MAK, Kawashima K, Ishimura N, Kazumori H, Udagawa J, Kadowaki Y, Kinoshita Y. 2003. Strategic compartmentalization of Toll-like receptor 4 in the mouse gut. J Immunol. 170(8):3977–3985.
   PubMed Web of Science ®Google Scholar
• Ottman N, Reunanen J, Meijerink M, Pietilä TE, Kainulainen V, Klievink J, Huuskonen L, Aalvink S, Skurnik M, Boeren S, et al. 2017. Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function. PLoS One. 12(3):e0173004–e.
   PubMed Web of Science ®Google Scholar
• Paczosa MK, Mecsas J. 2016. Klebsiella pneumoniae: going on the offense with a strong defense. Microbiol Mol Biol Rev. 80(3):629–661.
   PubMed Web of Science ®Google Scholar
• Park D-Y, Ahn Y-T, Park S-H, Huh C-S, Yoo S-R, Yu R, Sung M-K, McGregor RA, Choi M-S. 2013. Supplementation of Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 in diet-induced obese mice is associated with gut microbial changes and reduction in obesity. PLoS One. 8(3):e59470.
   PubMed Web of Science ®Google Scholar
• Pathak P, Trilligan C, Rapose A. 2014. Bifidobacterium–friend or foe? A case of urinary tract infection with Bifidobacterium species. BMJ Case Rep. 2014(sep24 1):bcr2014205122.
   PubMedGoogle Scholar
• Pearson T, Sahl JW, Hepp CM, Handady K, Hornstra H, Vazquez AJ, Settles E, Mayo M, Kaestli M, Williamson CHD, et al. 2020. Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic > 16-year Burkholderia pseudomallei infection. PLoS Pathog. 16(3):e1008298.
   PubMed Web of Science ®Google Scholar
• Pessione E. 2020. The Russian doll model: how bacteria shape successful and sustainable inter-kingdom relationships. Front Microbiol. 11:573759.
   PubMed Web of Science ®Google Scholar
• Peterson DA, McNulty NP, Guruge JL, Gordon JI. 2007. IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe. 2(5):328–339.
   PubMed Web of Science ®Google Scholar
• Png CW, Lindén SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI, McGuckin MA, Florin THJ. 2010. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol. 105(11):2420–2428.
   PubMed Web of Science ®Google Scholar
• Postler TS, Ghosh S. 2017. Understanding the holobiont: how microbial metabolites affect human health and shape the immune system. Cell Metab. 26(1):110–130.
   PubMed Web of Science ®Google Scholar
• Pray L. 2008. Antibiotic resistance, mutation rates and MRSA. Nat Educ. 1(1):30.
   Google Scholar
• Proença JT, Barral DC, Gordo I. 2017. Commensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli-macrophage interaction. Sci Rep. 7(1):1–12.
   PubMedGoogle Scholar
• Qiang X, Liotta AS, Shiloach J, Gutierrez JC, Wang H, Ochani M, Ochani K, Yang H, Rabin A, LeRoith D, et al. 2017. New melanocortin-like peptide of E. coli can suppress inflammation via the mammalian melanocortin-1 receptor (MC1R): possible endocrine-like function for microbes of the gut. NPJ Biofilms Microbiomes. 3:31.
   PubMed Web of Science ®Google Scholar
• Quigley EMM, Murray JA, Pimentel M. 2020. AGA clinical practice update on small intestinal bacterial overgrowth: expert review. Gastroenterology. 159(4):1526–1532.
   PubMed Web of Science ®Google Scholar
• Ramakrishnan SK, Zhang H, Ma X, Jung I, Schwartz AJ, Triner D, Devenport SN, Das NK, Xue X, Zeng MY, et al. 2019. Intestinal non-canonical NFκB signaling shapes the local and systemic immune response. Nat Commun. 10(1):660.
   PubMedGoogle Scholar
• Rath S, Rud T, Karch A, Pieper DH, Vital M. 2018. Pathogenic functions of host microbiota. Microbiome. 6(1):1–13.
   PubMedGoogle Scholar
• Revitt-Mills SA, Robinson A. 2020. Antibiotic-induced mutagenesis: under the microscope. Front Microbiol. 11:585175.
   PubMed Web of Science ®Google Scholar
• Rezaïki L, Lamberet G, Derré A, Gruss A, Gaudu P. 2008. Lactococcus lactis produces short‐chain quinones that cross‐feed Group B Streptococcus to activate respiration growth. Mol Microbiol. 67(5):947–957.
   PubMed Web of Science ®Google Scholar
• Ribet D, Cossart P. 2015. How bacterial pathogens colonize their hosts and invade deeper tissues. Microbes Infect. 17(3):173–183.
   PubMed Web of Science ®Google Scholar
• Rocca MF, Aguerre L, Cipolla L, Martínez C, Armitano R, Dangiolo G, Prieto M. 2018. Lactobacillus spp. invasive infections in Argentina. Int J Infect Dis. 73:163.
   Web of Science ®Google Scholar
• Rolhion N, Chassaing B, Nahori M-A, de Bodt J, Moura A, Lecuit M, Dussurget O, Bérard M, Marzorati M, Fehlner-Peach H, et al. 2019. A Listeria monocytogenes bacteriocin can target the commensal Prevotella copri and modulate intestinal infection. Cell Host Microbe. 26(5):691–701. e5.
   PubMed Web of Science ®Google Scholar
• Rooks MG, Garrett WS. 2016. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 16(6):341–352.
   PubMed Web of Science ®Google Scholar
• Rosenberg E, Zilber-Rosenberg I. 2018. The hologenome concept of evolution after 10 years. Microbiome. 6(1):1–14.
   PubMedGoogle Scholar
• Rossi F, Amadoro C, Colavita G. 2019. Members of the Lactobacillus Genus Complex (LGC) as opportunistic pathogens: a review. Microorganisms. 7(5):126.
   PubMed Web of Science ®Google Scholar
• Salminen MK, Rautelin H, Tynkkynen S, Poussa T, Saxelin M, Valtonen V, Järvinen A. 2004. Lactobacillus bacteremia, clinical significance, and patient outcome, with special focus on probiotic L. rhamnosus GG. Clin Infect Dis. 38(1):62–69.
   PubMed Web of Science ®Google Scholar
• Sarker P, Ahmed S, Tiash S, Rekha RS, Stromberg R, Andersson J, Bergman P, Gudmundsson GH, Agerberth B, Raqib R, et al. 2011. Phenylbutyrate counteracts Shigella mediated downregulation of cathelicidin in rabbit lung and intestinal epithelia: a potential therapeutic strategy. PLoS One. 6(6):e20637.
   PubMed Web of Science ®Google Scholar
• Seth EC, Taga ME. 2014. Nutrient cross-feeding in the microbial world. Front Microbiol. 5:350.
   PubMed Web of Science ®Google Scholar
• Shah SC, Day LW, Somsouk M, Sewell JL. 2013. Meta-analysis: antibiotic therapy for small intestinal bacterial overgrowth. Aliment Pharmacol Ther. 38(8):925–934.
   PubMed Web of Science ®Google Scholar
• Sharma V, Rodionov DA, Leyn SA, Tran D, Iablokov SN, Ding H, Peterson DA, Osterman AL, Peterson SN. 2019. B-vitamin sharing promotes stability of gut microbial communities. Front Microbiol. 10:1485.
   PubMed Web of Science ®Google Scholar
• Shekhar S, Schenck K, Petersen FC. 2017. Exploring host–commensal interactions in the respiratory tract. Front Immunol. 8:1971.
   PubMed Web of Science ®Google Scholar
• Sherid M, Samo S, Sulaiman S, Husein H, Sifuentes H, Sridhar S. 2016. Liver abscess and bacteremia caused by lactobacillus: role of probiotics? Case report and review of the literature. BMC Gastroenterol. 16(1):1–6.
   PubMedGoogle Scholar
• Shin CM, Kim N, Kim YS, Nam RH, Park JH, Lee DH, Seok Y-J, Kim Y-R, Kim J-H, Kim JM, et al. 2016. Impact of long-term proton pump inhibitor therapy on gut microbiota in F344 rats: pilot study. Gut Liver. 10(6):896–901.
   PubMed Web of Science ®Google Scholar
• Singh N, Gurav A, Sivaprakasam S, Brady E, Padia R, Shi H, Thangaraju M, Prasad PD, Manicassamy S, Munn DH, et al. 2014. Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity. 40(1):128–139.
   PubMed Web of Science ®Google Scholar
• Skov Sørensen UB, Yao K, Yang Y, Tettelin H, Kilian M. 2016. Capsular polysaccharide expression in commensal Streptococcus species: genetic and antigenic similarities to Streptococcus pneumoniae. mBio. 7(6):e01844–16.
   PubMed Web of Science ®Google Scholar
• Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. 2019. The classification and evolution of bacterial cross-feeding. Front Ecol Evol. 7:153.
   Web of Science ®Google Scholar
• Sokurenko EV, Hasty DL, Dykhuizen DE. 1999. Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends Microbiol. 7(5):191–195.
   PubMed Web of Science ®Google Scholar
• Srinivasan N. 2010. Telling apart friend from foe: discriminating between commensals and pathogens at mucosal sites. Innate Immun. 16(6):391–404.
   PubMed Web of Science ®Google Scholar
• Stacy A, Fleming D, Lamont RJ, Rumbaugh KP, Whiteley M. 2016. A commensal bacterium promotes virulence of an opportunistic pathogen via cross-respiration. mBio. 7(3):e00782–16.
   PubMed Web of Science ®Google Scholar
• Steimle A, Autenrieth IB, Frick J-S. 2016. Structure and function: lipid A modifications in commensals and pathogens. Int J Med Microbiol. 306(5):290–301.
   PubMed Web of Science ®Google Scholar
• Stella GJ. 1980. Peptococcla urinary tract infection with bacteremia: a case report. J Urol. 124(1):158–159.
   PubMed Web of Science ®Google Scholar
• Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, et al. 2018. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell. 174(6):1406–1423. e16.
   PubMed Web of Science ®Google Scholar
• Suresh A, Rajesh A, Bhat RM, Rai Y. 2009. Cytolytic vaginosis: a review. Indian J Sex Transm Dis AIDS. 30(1):48–50.
   PubMedGoogle Scholar
• Sydenham TV, Arpi M, Klein K, Justesen US. 2014. Four cases of bacteremia caused by Oscillibacter ruminantium, a newly described species. J Clin Microbiol. 52(4):1304–1307.
   PubMed Web of Science ®Google Scholar
• Szajewska H. 2016. What are the indications for using probiotics in children? Arch Dis Child. 101(4):398–403.
   PubMed Web of Science ®Google Scholar
• Tanoue T, Umesaki Y, Honda K. 2010. Immune responses to gut microbiota-commensals and pathogens. Gut Microbes. 1(4):224–233.
   PubMed Web of Science ®Google Scholar
• Tropini C. 2021. How the physical environment shapes the microbiota. mSystems. 6(4):e00675.
   PubMed Web of Science ®Google Scholar
• Usami M, Kishimoto K, Ohata A, Miyoshi M, Aoyama M, Fueda Y, Kotani J. 2008. Butyrate and trichostatin A attenuate nuclear factor kappaB activation and tumor necrosis factor alpha secretion and increase prostaglandin E2 secretion in human peripheral blood mononuclear cells. Nutr Res. 28(5):321–328.
   PubMed Web of Science ®Google Scholar
• Vancamelbeke M, Vermeire S. 2017. The intestinal barrier: a fundamental role in health and disease. Expert Rev Gastroenterol Hepatol. 11(9):821–834.
   PubMed Web of Science ®Google Scholar
• Vinolo MA, Rodrigues HG, Hatanaka E, Sato FT, Sampaio SC, Curi R. 2011. Suppressive effect of short-chain fatty acids on production of proinflammatory mediators by neutrophils. J Nutr Biochem. 22(9):849–855.
   PubMed Web of Science ®Google Scholar
• von Eiff C, Becker K, Machka K, Stammer H, Peters G. 2001. Nasal carriage as a source of Staphylococcus aureus bacteremia. Study Group. N Engl J Med. 344(1):11–16.
   PubMed Web of Science ®Google Scholar
• Wang L, Tang L, Feng Y, Zhao S, Han M, Zhang C, Yuan G, Zhu J, Cao S, Wu Q, et al. 2020. A purified membrane protein from Akkermansia muciniphila or the pasteurised bacterium blunts colitis associated tumourigenesis by modulation of CD8(+) T cells in mice. Gut. 69(11):1988–1997.
   PubMed Web of Science ®Google Scholar
• Wang S, Xu M, Wang W, Cao X, Piao M, Khan S, Yan F, Cao H, Wang B. 2016. Systematic review: adverse events of fecal microbiota transplantation. PLoS One. 11(8):e0161174.
   PubMed Web of Science ®Google Scholar
• Wang Z, Zhang X, Zhu L, Yang X, He F, Wang T, Bao T, Lu H, Wang H, Yang S, et al. 2020. Inulin alleviates inflammation of alcoholic liver disease via SCFAs-inducing suppression of M1 and facilitation of M2 macrophages in mice. Int Immunopharmacol. 78:106062.
   PubMed Web of Science ®Google Scholar
• Weber E, Reynaud Q, Suy F, Gagneux-Brunon A, Carricajo A, Guillot A, Botelho-Nevers E. 2015. Bifidobacterium species bacteremia: risk factors in adults and infants. Clin Infect Dis. 61(3):482–484.
   PubMed Web of Science ®Google Scholar
• Webster GF, Ruggieri MR, McGinley KJ. 1981. Correlation of Propionibacterium acnes populations with the presence of triglycerides on nonhuman skin. Appl Environ Microbiol. 41(5):1269–1270.
   PubMed Web of Science ®Google Scholar
• Wei W, Cao Z, Zhu Y-L, Wang X, Ding G, Xu H, Jia P, Qu D, Danchin A, Li Y. 2006. Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228. BMC Genomics. 7(1):1–12.
   PubMedGoogle Scholar
• Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL, Ryan EP. 2013. Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS One. 8(8):e70803.
   PubMed Web of Science ®Google Scholar
• Werner G, Coque TM, Franz CMAP, Grohmann E, Hegstad K, Jensen L, van Schaik W, Weaver K. 2013. Antibiotic resistant enterococci-tales of a drug resistance gene trafficker. Int J Med Microbiol. 303(6–7):360–379.
   PubMed Web of Science ®Google Scholar
• Wilks J, Beilinson H, Golovkina TV. 2013. Dual role of commensal bacteria in viral infections. Immunol Rev. 255(1):222–229.
   PubMed Web of Science ®Google Scholar
• Winter SE, Winter MG, Xavier MN, Thiennimitr P, Poon V, Keestra AM, Laughlin RC, Gomez G, Wu J, Lawhon SD, et al. 2013. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science. 339(6120):708–711.
   PubMed Web of Science ®Google Scholar
• World Health Organization. 2020. Global report on the epidemiology and burden of sepsis: Current evidence, identifying gaps and future directions. Geneva: WHO.
   Google Scholar
• Wu KQ, Sun WJ, Li N, Chen YQ, Wei YL, Chen DF. 2019. Small intestinal bacterial overgrowth is associated with Diarrhea-predominant irritable bowel syndrome by increasing mainly Prevotella abundance. Scand J Gastroenterol. 54(12):1419–1425.
   PubMed Web of Science ®Google Scholar
• Wu Y, Wang Y, Yang H, Li Q, Gong X, Zhang G, Zhu K. 2021. Resident bacteria contribute to opportunistic infections of the respiratory tract. PLoS Pathog. 17(3):e1009436.
   PubMed Web of Science ®Google Scholar
• Wurtzel O, Sesto N, Mellin JR, Karunker I, Edelheit S, Bécavin C, Archambaud C, Cossart P, Sorek R. 2012. Comparative transcriptomics of pathogenic and non‐pathogenic Listeria species. Mol Syst Biol. 8(1):583.
   PubMedGoogle Scholar
• Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, et al. 2020. The cancer microbiome: distinguishing direct and indirect effects requires a systemic view. Trends Cancer. 6(3):192–204.
   PubMed Web of Science ®Google Scholar
• Yang K, Niu J, Zuo T, Sun Y, Xu Z, Tang W, Liu Q, Zhang J, Ng EK, Wong SK, et al. 2021. Alterations in the gut virome in obesity and type 2 diabetes mellitus. Gastroenterology. 161(4):1257–1269.e13.
   PubMed Web of Science ®Google Scholar
• Young BC, Wu C-H, Gordon NC, Cole K, Price JR, Liu E, Sheppard AE, Perera S, Charlesworth J, Golubchik T, et al. 2017. Severe infections emerge from commensal bacteria by adaptive evolution. elife. 6:e30637.
   PubMed Web of Science ®Google Scholar
• Yu Z-T, Chen C, Kling DE, Liu B, McCoy JM, Merighi M, Heidtman M, Newburg DS. 2013. The principal fucosylated oligosaccharides of human milk exhibit prebiotic properties on cultured infant microbiota. Glycobiology. 23(2):169–177.
   PubMed Web of Science ®Google Scholar
• Zaborin A, Penalver Bernabe B, Keskey R, Sangwan N, Hyoju S, Gottel N, Gilbert JA, Zaborina O, Alverdy JC. 2020. Spatial compartmentalization of the microbiome between the lumen and crypts is lost in the murine cecum following the process of surgery, including overnight fasting and exposure to antibiotics. mSystems. 5(3):e00377–20.
   PubMed Web of Science ®Google Scholar
• Załuga J, Stragier P, Baeyen S, Haegeman A, Van Vaerenbergh J, Maes M, De Vos P. 2014. Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle. BMC Genomics. 15(1):314–392.
   PubMedGoogle Scholar
• Zhang H, Du M, Yang Q, Zhu MJ. 2016. Butyrate suppresses murine mast cell proliferation and cytokine production through inhibiting histone deacetylase. J Nutr Biochem. 27:299–306.
   PubMed Web of Science ®Google Scholar