The human gut microbiota protects the host from invading pathogens and the overgrowth of indigenous opportunistic species via a process called colonization resistance. Here, we investigated the antagonistic activity of human gut bacteria towards Candida albicans, an opportunistic fungal pathogen that can cause severe infections in susceptible individuals. Coculture batch incubations of C. albicans in the presence of faecal microbiota from six healthy individuals revealed varying levels of inhibitory activity against C. albicans. 16S rRNA gene amplicon profiling of these faecal coculture bacterial communities showed that the Bifidobacteriaceae family, and Bifidobacterium adolescentis in particular, were most correlated with antagonistic activity against C. albicans. Follow-up mechanistic studies performed under anaerobic conditions confirmed that culture supernatants of Bifidobacterium species, particularly B. adolescentis, inhibited C. albicans in vitro. Fermentation acids (FA), including acetate and lactate, present in the bifidobacterial supernatants were important contributors to inhibitory activity. However, increasing the pH of both bacterial supernatants and mixtures of FA reduced their anti-Candida effects, indicating a combinatorial effect of prevailing pH and FA. This work, therefore, demonstrates potential mechanisms underpinning gut microbiome-mediated colonization resistance against C. albicans, and identifies particularly inhibitory components such as bifidobacteria and FA as targets for further study.

Aberdeen Fungal Group Institute of Medical Sciences University of Aberdeen Aberdeen AB25 2ZD United Kingdom

CIBIO Department of Cellular Computational and Integrative Biology University of Trento Trento 38123 Italy

Department of Microbiology Faculty of Medicine and Dentistry Palacký University Olomouc Olomouc 77515 Czech Republic

MRC Centre for Medical Mycology University of Exeter Exeter EX4 4QD United Kingdom

Rowett Institute University of Aberdeen Aberdeen AB25 2ZD United Kingdom

School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW 2052 Australia

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Axe D, Bailey J. Transport of lactate and acetate through the energized cytoplasmic membrane of Escherichiacoli. Biotechnol Bioeng. 1995;47:8–19. PubMed

Bohnhoff M, Miller CP, Martin WR. Resistance of the mouse's intestinal tract to experimental Salmonella infection. Factors which interfere with the initiation of infection by oral inoculation. J Exp Med. 1964;120:805–16. PubMed PMC

Brown GD, Denning DW, Gow NAR. et al. . Hidden killers: human fungal infections. Sci Transl Med. 2012;4:165–78. PubMed

Bryant MP. Commentary on the hungate technique for culture of anaerobic bacteria. Am J Clin Nutr. 1972;25:1324–8. PubMed

Buffie CG, Bucci V, Stein RR. et al. . Precision microbiome reconstitution restores bile acid mediated resistance to Clostridiumdifficile. Nature. 2015;517:205–8. PubMed PMC

Carroll IM, Ringel-Kulka T, Siddle JP. et al. . Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Neurogastroenterol Mot. 2012;24:521–30. PubMed PMC

Cash HL, Whitham C V, Behrendt CL. et al. . Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science. 2006;313:1126–30. PubMed PMC

Cherrington CA, Hinton M, Pearson GR. et al. . Short-chain organic acids at ph 5.0 kill Escherichiacoli and Salmonella spp. without causing membrane perturbation. J Appl Bacteriol. 1991;70:161–5. PubMed

Cole JR, Wang Q, Fish JA. et al. . Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633–42. PubMed PMC

Cottier F, Tan ASM, Chen J. et al. . The transcriptional stress response of Candidaalbicans to weak organic acids. G3 Genes Genomes Genet. 2015;5:497–505. PubMed PMC

Cummings JH, Macfarlane GT. The control and consequences of bacterial fermentation in the human colon. J Appl Bacteriol. 1991;70:443–59. PubMed

Cummings JH. Short chain fatty acids in the human colon. Gut. 1981;22:763–79. PubMed PMC

d'Enfert C, Kaune A-K, Alaban L-R. et al. . The impact of the fungus-host-microbiota interplay upon Candidaalbicans infections: current knowledge and new perspectives. FEMS Microbiol Rev. 2020;45:fuaa060. PubMed PMC

Deriu E, Liu JZ, Pezeshki M. et al. . Probiotic bacteria reduce Salmonella Typhimurium intestinal colonization by competing for iron. Cell Host Microbe. 2013;14:26–37. PubMed PMC

Donia MS, Fischbach MA. Small molecules from the human microbiota. Science. 2015;116:1477–90. PubMed PMC

Duncan SH, Belenguer A, Holtrop G. et al. . Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol. 2007;73:1073–8. PubMed PMC

Ene IV, Adya AK, Wehmeier S. et al. . Host carbon sources modulate cell wall architecture, drug resistance and virulence in a fungal pathogen. Cell Microbiol. 2012a;14:1319–35. PubMed PMC

Ene IV, Heilmann CJ, Sorgo AG. et al. . Carbon source-induced reprogramming of the cell wall proteome and secretome modulates the adherence and drug resistance of the fungal pathogen Candidaalbicans. Proteomics. 2012b;12:3164–79. PubMed PMC

Ene IV, Walker LA, Schiavone M. et al. . Cell wall remodeling enzymes modulate fungal cell wall elasticity and osmotic stress resistance. MBio. 2015;6:e00986. PubMed PMC

Fan D, Coughlin LA, Neubauer MM. et al. . Activation of HIF-1α and LL-37 by commensal bacteria inhibits Candidaalbicans colonization. Nat Med. 2015;21:808–14. PubMed PMC

Flint HJ, Duncan SH, Scott KP. et al. . Links between diet, gut microbiota composition and gut metabolism. Proc Nutr Soc. 2015;74:13–22. PubMed

Freter R, Brickner H, Botney M. et al. . Mechanisms that control bacterial populations in continuous-flow culture models of mouse large intestinal flora. Infect Immun. 1983;39:676–85. PubMed PMC

Fukuda S, Toh H, Hase Ket al. . Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature. 2011;469:543–7. PubMed

Geirnaert A, Calatayud M, Grootaert C. et al. . Butyrate-producing bacteria supplemented in vitro to Crohn's disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity. Nature. 2017;7:11450. PubMed PMC

Gillum A, Tsay E, Kirsch D. Isolation of the Candidaalbicans gene for orotidine-5′-phosphate decarboxylase by complementation of S. cerevisiae ura3 and E. coli pyrF mutations. Mol Gen Genet. 1984;198:179–82. PubMed

Guinan J, Wang S, Hazbun TR. et al. . Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candidaalbicans. Sci Rep. 2019;9:1–11. PubMed PMC

Guinea J. Global trends in the distribution of Candida species causing candidemia. Clin Microbiol Infect. 2014;20:5–10. PubMed

Gulati M, Nobile CJ. Candida albicans biofilms: development, regulation, and molecular mechanisms. Microbes Infect. 2016;18:310–21. PubMed PMC

Harnett J, Myers SP, Rolfe M. Significantly higher faecal counts of the yeasts Candida and Saccharomyces identified in people with coeliac disease. Gut Pathog. 2017;9:28484520. PubMed PMC

Heaney H, Laing J, Paterson L. et al. . The environmental stress sensitivities of pathogenic Candida species, including Candidaauris, and implications for their spread in the hospital setting. Med Mycol. 2020;58:744–55. PubMed PMC

Henriques M, Quintas C, Loureiro-Dias M. Extrusion of benzoic acid in Saccharomycescerevisiae by an energy-dependent mechanism. Microbiology. 1997;143:1877–83. PubMed

Hobson PN. Rumen bacteria. Methods Microbiol. 1969;3B:133–49.

Hove H, Norgard Andersen I, Mortensen PB. Fecal DL-lactate concentrations in 100 gastrointestinal patients. Scand J Gastroenterol. 1994;29:255–9. PubMed

Huang CB, Alimova Y, Myers TM. et al. . Short- and medium-chain fatty acids exhibit antimicrobial activity for oral microorganisms. Arch Oral Biol. 2011;56:650–4. PubMed PMC

Hube B. From commensal to pathogen: stage- and tissue-specific gene expression of Candidaalbicans. Curr Opin Microbiol. 2004;7:336–41. PubMed

Jacobson A, Lam L, Rajendram M. et al. . A gut commensal-produced metabolite mediates colonization resistance to Salmonella infection. Cell Host Microbe. 2018;24:296–307.e7. PubMed PMC

Johnson M, Zaretskaya I, Raytselis Y. et al. . NCBI BLAST: a better web interface. Nucleic Acids Res. 2008;36:W5–9. PubMed PMC

Junick J, Blaut M. Quantification of human fecal Bifidobacterium species by use of quantitative real-time PCR analysis targeting the groEL gene. Appl Environ Microbiol. 2012;78:2613–22. PubMed PMC

Kau AL, Ahern PP, Griffin NW. et al. . Human nutrition, the gut microbiome and the immune system. Nature. 2011;474:327–36. PubMed PMC

Kennedy MJ, Volz PA. Ecology of Candidaalbicans gut colonization: inhibition of Candida adhesion, colonization, and dissemination from the gastrointestinal tract by bacterial antagonism. Infect Immun. 1985a;49:654–63. PubMed PMC

Kennedy MJ, Volz PA. Effect of various antibiotics on gastrointestinal colonization and dissemination by Candidaalbicans. Med Mycol. 1985b;23:265–73. PubMed

Khonsari S, Suganthy M, Burczynska B. et al. . A comparative study of bifidobacteria in human babies and adults. Biosci Microbiota Food Heal. 2016;35:97–103. PubMed PMC

Koh A, De Vadder F, Kovatcheva-Datchary P. et al. . From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell. 2016;165:1332–45. PubMed

Köhler GA, Assefa S, Reid G. Probiotic interference of Lactobacillusrhamnosus GR-1 and Lactobacillusreuteri RC-14 with the opportunistic fungal pathogen Candidaalbicans. Infect Dis Obstet Gynecol. 2012;2012:636474. PubMed PMC

Lammers KM, Brigidi P, Vitali B. et al. . Immunomodulatory effects of probiotic bacteria DNA: IL-1 and IL-10 response in human peripheral blood mononuclear cells. FEMS Immunol Med Microbiol. 2003;38:165–72. PubMed

León C, Ruiz-Santana S, Saavedra Pet al. . Usefulness of the "Candida score" for discriminating between Candida colonization and invasive candidiasis in non-neutropenic critically ill patients: a prospective multicenter study. Crit Care Med. 2009;37:1624–33. PubMed

Lourenço A, Pedro NA, Salazar SB. et al. . Effect of acetic acid and lactic acid at low pH in growth and azole resistance of Candidaalbicans and Candidaglabrata. Front Microbiol. 2018;9:3265. PubMed PMC

Low CY, Rotstein C. Emerging fungal infections in immunocompromised patients. F1000 Med Rep. 2011;3:14. PubMed PMC

MacCallum DM, Findon H, Kenny CC. et al. . Different consequences of ACE2 and SWI5 gene disruptions for virulence of pathogenic and nonpathogenic yeasts. Infect Immun. 2006;74:5244–8. PubMed PMC

Makras L, De Vuyst L. The in vitro inhibition of Gram-negative pathogenic bacteria by bifidobacteria is caused by the production of organic acids. Int Dairy J. 2006;16:1049–57.

Maldonado-Gómez MX, Martínez I, Bottacini F. et al. . Stable engraftment of Bifidobacteriumlongum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host Microbe. 2016;20:515–26. PubMed

Maltby R, Leatham-Jensen MP, Gibson T. et al. . Nutritional basis for colonization resistance by human commensal Escherichiacoli strains HS and nissle 1917 against E. coli O157:H7 in the mouse intestine. PLoS ONE. 2013;8:e53957. PubMed PMC

Marteyn B, Scorza FB, Sansonetti PJ. et al. . Breathing life into pathogens: the influence of oxygen on bacterial virulence and host responses in the gastrointestinal tract. Cell Microbiol. 2011;13:171–6. PubMed

Martinez-Medina M, Denizot J, Dreux N. et al. . Western diet induces dysbiosis with increased E. coli in CEABAC10 mice, alters host barrier function favouring AIEC colonisation. Gut. 2014;63:116–24. PubMed

Mason KL, Downward JRE, Mason KD. et al. Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infect Immun. 2012;80:3371–80. PubMed PMC

Matsuki T, Watanabe K, Fujimoto J. et al. . Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria. Appl Environ Microbiol. 2004;70:167–73. PubMed PMC

Matsuki T, Watanabe K, Tanaka R. et al. . Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers. Appl Environ Microbiol. 1999;65:4506–12. PubMed PMC

Meng D, Zhu W, Ganguli K. et al. . Anti-inflammatory effects of Bifidobacteriumlongum subsp infantis secretions on fetal human enterocytes are mediated by TLR-4 receptors. Am J Physiol Liver Physiol. 2016;311:G744–53. PubMed PMC

Miranda LN, van der Heijden IM, Costa SF. et al. Candida colonisation as a source for candidaemia. J Hosp Infect. 2009;72:9–16. PubMed

Mirhakkak MH, Schäuble S, Klassert TE. et al. . Metabolic modeling predicts specific gut bacteria as key determinants for Candidaalbicans colonization levels. ISME J. 2020;15:1257–70. PubMed PMC

Miyazaki K, Martin J., Marinsek-Logar R. et al. . Degradation and utilization of xylans by the rumen anaerobe Prevotellabryantii (formerly P. ruminicola subsp. brevis) B14. Anaerobe. 1997;3:373–81. PubMed

Mortensen PB, Clausen MR. Short-chain fatty acids in the human colon: relation to gastrointestinal health and disease. Scand J Gastroenterol. 1996;31:132–48. PubMed

Nash AK, Auchtung TA, Wong MC. et al. . The gut mycobiome of the human microbiome project healthy cohort. Microbiome. 2017;5:153. PubMed PMC

Neville BA, d'Enfert C, Bougnoux M-E. Candida albicans commensalism in the gastrointestinal tract. Munroe C (ed.), FEMS Yeast Res. 2015;15:fov081. PubMed

Odds FC, Kibbler CC, Walker E. et al. . Carriage of Candida species and C. albicans biotypes in patients undergoing chemotherapy or bone marrow transplantation for haematological disease. J Clin Pathol. 1989;42:1259–66. PubMed PMC

Odds FC. Molecular phylogenetics and epidemiology of Candidaalbicans. Fut Microbiol. 2010;5:67–79. PubMed

Pasolli E, Asnicar F, Manara S. et al. . Extensive unexplored human microbiome diversity revealed by over 150 000 genomes from metagenomes spanning age, geography, and lifestyle. Cell. 2019;176:1–14. PubMed PMC

Pfaller MA, Jones RN, Doern G V. et al. . Bloodstream infections due to Candida species: SENTRY antimicrobial surveillance program in North America and Latin America, 1997-1998. Antimicrob Agents Chemother. 2000;44:747–51. PubMed PMC

Pittet D, Monod M, Suter PM. et al. Candida colonization and subsequent infections in critically ill surgical patients. Ann Surg. 1994;220:751–8. PubMed PMC

Quast C, Pruesse E, Yilmaz P. et al. . The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013:D590–6. PubMed PMC

Rea MC, Sit CS, Clayton E. et al. . Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridiumdifficile. Proc Natl Acad Sci. 2010;107:9352–7. PubMed PMC

Reuter G. Comparative studies on the bifidus flora in the feces of infants and adults. Zentralbl Bakteriol Orig. 1963;191:486–507. PubMed

Richardson AJ, Calder AG, Stewart CS. et al. . Simultaneous determination of volatile and non-volatile acidic fermentation products of anaerobes by capillary gas chromatography. Lett Appl Microbiol. 1989;9:5–8.

Rivera-Chávez F, Zhang LF, Faber F. et al. . Depletion of butyrate-producing Clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella. Cell Host Microbe. 2016;19:443–54. PubMed PMC

Rivière A, Moens F, Selak M. et al. . The ability of bifidobacteria to degrade arabinoxylan oligosaccharide constituents and derived oligosaccharides is strain dependent. Appl Environ Microbiol. 2014;80:204–17. PubMed PMC

Roe AJ, O'Byrne C, McLaggan D. et al. . Inhibition of Escherichiacoli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity. Microbiology. 2002;148:2215–22. PubMed

Romeo MG, Romeo DM, Trovato L. et al. . Role of probiotics in the prevention of the enteric colonization by Candida in preterm newborns: incidence of late-onset sepsis and neurological outcome. J Perinatol. 2011;31:63–9. PubMed PMC

Rossi M, Corradini C, Amaretti A. et al. . Fermentation of fructooligosaccharides and inulin by bifidobacteria: a comparative study of pure and fecal cultures. Appl Environ Microbiol. 2005;71:6150–8. PubMed PMC

Rossi O, Khan MT, Schwarzer M. et al. Faecalibacterium prausnitzii strain HTF-F and its extracellular polymeric matrix attenuate clinical parameters in DSS-induced colitis. Riedel CU (ed.), PLoS ONE. 2015;10:e0123013. PubMed PMC

Roy A, Chaudhuri J, Sarkar D. et al. . Role of enteric supplementation of probiotics on late-onset sepsis by Candida species in preterm low birth weight neonates: a randomized, double blind, placebo-controlled trial. N Am J Med Sci. 2014;6:50–7. PubMed PMC

Samonis G, Anastassiadou H, Dassiou Met al. . Effects of broad-spectrum antibiotics on colonization of gastrointestinal tracts of mice by Candida albicans. Antimicrob Agents Chemother. 1994;38:602–3. PubMed PMC

Satokari RM, Vaughan EE, Akkermans ADL. et al. . Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl Environ Microbiol. 2001;67:504–13. PubMed PMC

Schloss PD, Westcott SL, Ryabin T. et al. . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41. PubMed PMC

Segata N, Izard J, Waldron L. et al. . Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60. PubMed PMC

Stecher B, Robbiani R, Walker AW. et al. Salmonella enterica serovar Typhimurium exploits inflammation to compete with the intestinal microbiota. Waldor M (ed.), PLoS Biol. 2007;5:e244. PubMed PMC

Suez J, Zmora N, Zilberman-Schapira G. et al. . Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell. 2018;174:1406–23.e16. PubMed

Tan TG, Sefik E, Geva-Zatorsky N. et al. . Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice. Proc Natl Acad Sci. 2016;113:E8141–50. PubMed PMC

Thaiss CA, Zmora N, Levy M. et al. . The microbiome and innate immunity. Nature. 2016;535:65–74. PubMed

Ventura M, Montes SA, Ruiz L. et al. . High iron-sequestrating bifidobacteria inhibit enteropathogen growth and adhesion to intestinal epithelial cells in vitro. Front Microbiol. 2016;7:1480. PubMed PMC

Vollaard EJ, Clasener HAL, Janssen AJHM. Co-trimoxazole impairs colonization resistance in healthy volunteers. J Antimicrob Chemother. 1992;30:685–91. PubMed

Wagner RD, Warner T, Pierson C. et al. . Biotherapeutic effects of Bifidobacterium spp. on orogastric and systemic candidiasis in immunodeficient mice. Rev Iberoam Micol. 1998;15:265–70. PubMed

Whaley SG, Berkow EL, Rybak JM. et al. . Azole antifungal resistance in Candidaalbicans and emerging non-albicansCandida species. Front Microbiol. 2016;7:2173. PubMed PMC

Whitman WB, Coleman DC, Wiebe WJ. Perspective prokaryotes: the unseen majority. Proc Natl Acad Sci. 1998;95:6578–83. PubMed PMC

Wilson KH, Perini F. Role of competition for nutrients in suppression of Clostridiumdifficile by the colonic microflora. Infect Immun. 1988;56:2610–4. PubMed PMC

Yatsunenko T, Rey FE, Manary MJ. et al. . Human gut microbiome viewed across age and geography. Nature. 2012;486:222–7. PubMed PMC

Zangl I, Pap IJ, Aspöck C. et al. . The role of Lactobacillus species in the control of Candida via biotrophic interactions. Microbial Cell. 2020;7:1–14. PubMed PMC

Ze X, Duncan SH, Louis P. et al. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 2012;6:1535–43. PubMed PMC

Zhai B, Ola M, Rolling T. et al. . High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis. Nat Med. 2020;26:59–64. PubMed PMC

Bifidobacteria in disease: from head to toe