A pilot study of dietary fibres on pathogen growth in an ex vivo colonic model reveals their potential ability to limit vancomycin-resistant Enterococcus expansion

Abstract

Aim: Dietary fibre is important for shaping gut microbiota. The aim of this pilot study was to investigate the impact of dietary fibres on pathogen performance in the presence of gut microbiota.

Methods: In an ex vivo gut model, pooled faecal samples were spiked with a cocktail of representative gastrointestinal pathogens and fermented with yeast β-glucan for 24 hours, after which 16S rRNA amplicon sequencing and short-chain and branched-chain fatty acid (SCFA and BCFA) analyses were performed. In addition, oat β-glucan, arabinoxylan, yeast β-glucan, and galactooligosaccharides were each tested against individual representative pathogens and pathogen growth was assessed via qPCR. Glucose served as a control carbon source.

Results: Based on 16S rRNA amplicon sequencing, yeast β-glucan selected for higher proportions of Bacteroides (P = 0.0005, ~6 fold) and Clostridia (P = 0.005, ~3.6 fold) while species of Escherichia/Shigella (P = 0.021, ~2.8 fold) and Lactobacillus (P = 0.007, ~ 15.7-fold) were higher in glucose. Pathogen relative abundance did not differ between glucose and yeast β-glucan. In the absence of pathogens, higher production of BCFAs (P = 0.002) and SCFAs (P = 0.002) fatty acids was observed for fibre group(s). For individual pathogens, yeast β-glucan increased growth of Escherichia coli, Salmonella typhimurium, and Listeria monocytogenes (P < 0.05), arabinoxylan increased S. typhimurium (P < 0.05). Tested fibres decreased vancomycin-resistant Enterococcus faecium (P < 0.05), with yeast β-glucan causing a 1-log reduction (P < 0.01), while galactooligosaccharides decreased L. monocytogenes (P < 0.05).

Conclusion: Tested fibres differentially influenced the growth of pathogens, but yeast β-glucan could represent a dietary strategy to help limit vancomycin-resistant enterococci (VRE) expansion in the gut.

Keywords

Dietary fibre / gut microbiota / pathogens / colonisation resistance

References

[1] Sender R,Milo R.Revised estimates for the number of human and bacteria cells in the body.PLoS Biol2016;14:e1002533 PMCID:PMC4991899

[2] Jandhyala SM,Subramanyam C,Sasikala M.Role of the normal gut microbiota.World J Gastroenterol2015;21:8787-803 PMCID:PMC4528021

[3] Gill SR,Deboy RT.Metagenomic analysis of the human distal gut microbiome.Science2006;312:1355-9 PMCID:PMC3027896

[4] Chung WSF,Vermeiren J.Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota.FEMS Microbiol Ecol2019;95:1 PMCID:PMC6238074

[5] Jones JM.CODEX-aligned dietary fiber definitions help to bridge the ‘fiber gap’.Nutr J2014;13:34 PMCID:PMC4007020

[6] Russell WR,Flint HJ.Colonic bacterial metabolites and human health.Curr Opin Microbiol2013;16:246-54

[7] Heiman ML.A healthy gastrointestinal microbiome is dependent on dietary diversity.Mol Metab2016;5:317-20 PMCID:PMC4837298

[8] Rakoff-Nahoum S,Comstock LE.The evolution of cooperation within the gut microbiota.Nature2016;533:255-9 PMCID:PMC4978124

[9] Bohnhoff M,Miller CP.Effect of streptomycin on susceptibility of intestinal tract to experimental salmonella infection.Proc Soc Exp Biol Med1954;86:132-7

[10] Slimings C.Antibiotics and hospital-acquired clostridium difficile infection: update of systematic review and meta-analysis.J Antimicrob Chemother2014;69:881-91

[11] Martinez-Medina M,Dreux N.Western diet induces dysbiosis with increased E coli in CEABAC10 mice, alters host barrier function favouring AIEC colonisation.Gut2014;63:116-24

[12] Sonnenburg ED,Tikhonov M,Wingreen NS.Diet-induced extinctions in the gut microbiota compound over generations.Nature2016;529:212-5 PMCID:PMC4850918

[13] Desai MS,Koropatkin NM.A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility.Cell2016;167:1339-1353.e21 PMCID:PMC5131798

[14] Hryckowian AJ,Smits SA.Microbiota-accessible carbohydrates suppress clostridium difficile infection in a murine model.Nat Microbiol2018;3:662-9 PMCID:PMC6126909

[15] Ebersbach T,Heegaard PM.Certain dietary carbohydrates promote listeria infection in a guinea pig model, while others prevent it.Int J Food Microbiol2010;140:218-24

[16] Strain R. 2021. Novel insights into the influence of fibre and lipid substrates on the microbiome. A thesis presented to the National University of Ireland for the Degree of Doctor of Philosophy. University College Cork, Ireland. Available from: https://cora.ucc.ie/server/api/core/bitstreams/38efc6ff-b272-4c5b-9c02-b8b901fbf61a/content [Last accessed on 12 Jun 2023]

[17] Minekus M,Alvito P.A standardised static in vitro digestion method suitable for food - an international consensus.Food Funct2014;5:1113-24

[18] O’Donnell MM,O’Sullivan Ó.Preparation of a standardised faecal slurry for ex-vivo microbiota studies which reduces inter-individual donor bias.J Microbiol Methods2016;129:109-16

[19] Fooks LJ.Mixed culture fermentation studies on the effects of synbiotics on the human intestinal pathogens campylobacter jejuni and escherichia coli.Anaerobe2003;9:231-42

[20] O’Donnell MM,Shanahan F.The use of a mini-bioreactor fermentation system as a reproducible, high-throughput ex vivo batch model of the distal colon.Front Microbiol2018;9:1844 PMCID:PMC6096000

[21] Yu Z.Improved extraction of PCR-quality community DNA from digesta and fecal samples.Biotechniques2004;36:808-12

[22] Klindworth A,Schweer T.Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies.Nucleic Acids Res2013;41:e1 PMCID:PMC3592464

[23] Tran TTT,Kellingray L.APOE genotype influences the gut microbiome structure and function in humans and mice: relevance for Alzheimer’s disease pathophysiology.FASEB J2019;33:8221-31 PMCID:PMC6593891

[24] Ye J,Zaretskaya I,Rozen S.Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction.BMC Bioinformatics2012;13:134 PMCID:PMC3412702

[25] Bustin SA,Garson JA.The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.Clin Chem2009;55:611-22

[26] Pfaffl MW.A new mathematical model for relative quantification in real-time RT-PCR.Nucleic Acids Res2001;29:e45 PMCID:PMC55695

[27] Cussotto S,Fouhy F.Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function.Psychopharmacology2019;236:1671-85

[28] McRorie JW Jr.Evidence-based approach to fiber supplements and clinically meaningful health benefits, part 1: what to look for and how to recommend an effective fiber therapy.Nutr Today2015;50:82-9 PMCID:PMC4415962

[29] Henrion M,Lê KA.Cereal B-Glucans: the impact of processing and how it affects physiological responses.Nutrients2019;11:1729 PMCID:PMC6722849

[30] Yarza P,Pruesse E.Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.Nat Rev Microbiol2014;12:635-45

[31] Luo Y,Li H.Different types of dietary fibers trigger specific alterations in composition and predicted functions of colonic bacterial communities in BALB/c mice.Front Microbiol2017;8:966 PMCID:PMC5447771

[32] Tamura K,Déjean G.Molecular mechanism by which prominent human gut bacteroidetes utilize mixed-linkage beta-glucans, major health-promoting cereal polysaccharides.Cell Rep2017;21:417-30 PMCID:PMC5656003

[33] Pereira FC.Microbial nutrient niches in the gut.Environ Microbiol2017;19:1366-78 PMCID:PMC5412925

[34] Lopetuso LR,Petito V.Commensal clostridia: leading players in the maintenance of gut homeostasis.Gut Pathog2013;5:23 PMCID:PMC3751348

[35] Dols M,Remaud-Simeon M,Monsan PF.Growth and energetics of leuconostoc mesenteroides NRRL B-1299 during metabolism of various sugars and their consequences for dextransucrase production.Appl Environ Microbiol1997;63:2159-65 PMCID:PMC168507

[36] Greetham HL,Gibson GR,Falsen E.Sutterella stercoricanis sp. nov., isolated from canine faeces.Int J Syst Evol Microbiol2004;54:1581-4

[37] Hiippala K,Kalliomäki M,Satokari R.Mucosal prevalence and interactions with the epithelium indicate commensalism of sutterella spp.Front Microbiol2016;7:1706 PMCID:PMC5080374

[38] Bukin YS,Morozov IV,Zakharenko AS.The effect of 16S rRNA region choice on bacterial community metabarcoding results.Sci Data2019;6:190007 PMCID:PMC6362892

[39] Jacobson A,Rajendram M.A gut commensal-produced metabolite mediates colonization resistance to salmonella infection.Cell Host Microbe2018;24:296-307.e7 PMCID:PMC6223613

[40] Hockenberry AM,Takács G,Hardt WD.Microbiota-derived metabolites inhibit salmonella virulent subpopulation development by acting on single-cell behaviors.Proc Natl Acad Sci U S A2021;118:e2103027118 PMCID:PMC8346864

[41] Wotzka SY,Maier L.Escherichia coli limits salmonella typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice.Nat Microbiol2019;4:2164-74 PMCID:PMC6881180

[42] Makki K,Walter J.The impact of dietary fiber on gut microbiota in host health and disease.Cell Host Microbe2018;23:705-15

[43] Kodali S,Lin F.A vaccine approach for the prevention of infections by multidrug-resistant enterococcus faecium.J Biol Chem2015;290:19512-26 PMCID:PMC4528116

[44] Seong H,Cheon JH.Fecal microbiota transplantation for multidrug-resistant organism: efficacy and response prediction.J Infect2020;81:719-25

[45] Cossart P.Illuminating the landscape of host-pathogen interactions with the bacterium listeria monocytogenes.Proc Natl Acad Sci U S A2011;108:19484-91 PMCID:PMC3241796

[46] Ruiz-Herrera J.Cell wall glucans of fungi. A review.Cell Surf2019;5:100022 PMCID:PMC7389562

[47] Becattini S,Carter RA.Commensal microbes provide first line defense against Listeria monocytogenes infection.J Exp Med2017;214:1973-89 PMCID:PMC5502438

[48] Aguirre M,Koenen ME.To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies.J Microbiol Methods2014;107:1-7

[49] Fletcher SM,Ellis JT.Prevalence of gastrointestinal pathogens in developed and developing countries: systematic review and meta-analysis.J Public Health Res2013;2:42-53 PMCID:PMC4140330

[50] Gannon VP,Graham T,Rahn K.Use of the flagellar H7 gene as a target in multiplex PCR assays and improved specificity in identification of enterohemorrhagic escherichia coli strains.J Clin Microbiol1997;35:656-62 PMCID:PMC229645

[51] Shanmugasundaram M,Murali HS.Detection of salmonella enterica serovar typhimurium by selective amplification of fliC, fljB, iroB, invA, rfbJ, STM2755, STM4497 genes by polymerase chain reaction in a monoplex and multiplex format.World J Microbiol Biotechnol2009;25:1385-94

[52] D’Agostino M,Vazquez-Boland JA.A validated PCR-based method to detect listeria monocytogenes using raw milk as a food model - towards an international standard.J Food Prot2004;67:1646-55