The worldwide incidence of many immune-mediated and metabolic diseases, initially affecting only the wealthy Western countries, is increasing rapidly. Many of these diseases are associated with the compositional and functional alterations of gut microbiota, i.e., dysbiosis. The most consistent markers of the dysbiosis are a decrease in microbiota diversity and an expansion of Proteobacteria. The role of food preservatives as potential triggers of gut microbiota dysbiosis has been long overlooked. Using a human microbiota-associated mouse model, we demonstrate that a mixture of common antimicrobial food additives induces dysbiosis characterised by an overgrowth of Proteobacteria phylum and a decrease in the Clostridiales order. Remarkably, human gut microbiota in a Nod2-deficient genetic background is even more susceptible to the induction of Proteobacteria dysbiosis by additives than the microbiota in a wild-type background. To conclude, our data demonstrate that antimicrobial food additives trigger gut microbiota dysbiosis in both wild-type and Nod2-deficient backgrounds and at the exposure levels reached in European populations. Whether this additive-modified gut microbiota plays a significant role in the pathogenesis of immune-mediated and metabolic diseases remains to be elucidated.

Charles University Prague The Faculty of Medicine in Hradec Kralove 500 03 Hradec Kralove Czech Republic

The Institute of Microbiology The Czech Academy of Sciences 549 22 Novy Hradek Czech Republic

See more in PubMed

Mosca A., Leclerc M., Hugot J.P. Gut microbiota diversity and human diseases: Should we reintroduce key predators in our ecosystem? Front. Microbiol. 2016;7:455. doi: 10.3389/fmicb.2016.00455. PubMed DOI PMC

Walters W.A., Xu Z., Knight R. Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 2014;588:4223–4233. doi: 10.1016/j.febslet.2014.09.039. PubMed DOI PMC

Zhou Y., Xu Z.Z., He Y., Yang Y., Liu L., Lin Q., Nie Y., Li M., Zhi F., Liu S., et al. Gut microbiota offers universal biomarkers across ethnicity in inflammatory bowel disease diagnosis and infliximab response prediction. mSystems. 2018;3:1063. doi: 10.1128/mSystems.00188-17. PubMed DOI PMC

Frank D.N., St Amand A.L., Feldman R.A., Boedeker E.C., Harpaz N., Pace N.R. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA. 2007;104:13780–13785. doi: 10.1073/pnas.0706625104. PubMed DOI PMC

Garrett W.S., Lord G.M., Punit S., Lugo-Villarino G., Mazmanian S.K., Ito S., Glickman J.N., Glimcher L.H. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell. 2007;131:33–45. doi: 10.1016/j.cell.2007.08.017. PubMed DOI PMC

Shin N.-R., Whon T.W., Bae J.-W. Proteobacteria: Microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015;33:496–503. doi: 10.1016/j.tibtech.2015.06.011. PubMed DOI

Levy M., Kolodziejczyk A.A., Thaiss C.A., Elinav E. Dysbiosis and the immune system. Nat. Rev. Immunol. 2017;17:219–232. doi: 10.1038/nri.2017.7. PubMed DOI

Kostic A.D., Gevers D., Siljander H., Vatanen T., Hyotylainen T., Hämäläinen A.-M., Peet A., Tillmann V., Pöhö P., Mattila I., et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17:260–273. doi: 10.1016/j.chom.2015.01.001. PubMed DOI PMC

Scheperjans F., Aho V., Pereira P.A.B., Koskinen K., Paulin L., Pekkonen E., Haapaniemi E., Kaakkola S., Eerola-Rautio J., Pohja M., et al. Gut microbiota are related to Parkinson’s disease and clinical phenotype. Mov. Disord. 2015;30:350–358. doi: 10.1002/mds.26069. PubMed DOI

Schaubeck M., Clavel T., Calasan J., Lagkouvardos I., Haange S.B., Jehmlich N., Basic M., Dupont A., Hornef M., von Bergen M., et al. Dysbiotic gut microbiota causes transmissible Crohn’s disease-like ileitis independent of failure in antimicrobial defence. Gut. 2016;65:225–237. doi: 10.1136/gutjnl-2015-309333. PubMed DOI PMC

Turnbaugh P.J., Ley R.E., Mahowald M.A., Magrini V., Mardis E.R., Gordon J.I. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027131. doi: 10.1038/nature05414. PubMed DOI

Chassaing B., Van de Wiele T., De Bodt J., Marzorati M., Gewirtz A.T. Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation. Gut. 2017;66:1414–1427. doi: 10.1136/gutjnl-2016-313099. PubMed DOI PMC

Rodriguez-Palacios A., Harding A., Menghini P., Himmelman C., Retuerto M., Nickerson K.P., Lam M., Croniger C.M., McLean M.H., Durum S.K., et al. The artificial sweetener Splenda promotes gut Proteobacteria, dysbiosis, and myeloperoxidase reactivity in Crohn’s disease-like ileitis. Inflamm. Bowel. Dis. 2018;24:1005–1020. doi: 10.1093/ibd/izy060. PubMed DOI PMC

Irwin S.V., Fisher P., Graham E., Malek A., Robidoux A. Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food. PLoS ONE. 2017;12:e0186629. doi: 10.1371/journal.pone.0186629. PubMed DOI PMC

You X., Einson J.E., Lopez-Pena C.L., Song M., Xiao H., McClements D.J., Sela D.A. Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice. NPJ Sci. Food. 2017;1:8. doi: 10.1038/s41538-017-0006-0. PubMed DOI PMC

Hrncirova L., Hudcovic T., Sukova E., Machova V., Trckova E., Krejsek J., Hrncir T. Human gut microbes are susceptible to antimicrobial food additives in vitro. Folia Microbiol. 2019:1–12. doi: 10.1007/s12223-018-00674-z. PubMed DOI

Turnbaugh P.J., Ridaura V.K., Faith J.J., Rey F.E., Knight R., Gordon J.I. The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 2009;1:6ra14. doi: 10.1126/scitranslmed.3000322. PubMed DOI PMC

Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Huntley J., Fierer N., Owens S.M., Betley J., Fraser L., Bauer M., et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–1624. doi: 10.1038/ismej.2012.8. PubMed DOI PMC

Bolyen E., Rideout J.R., Dillon M.R., Bokulich N.A., Abnet C., Al-Ghalith G.A., Alexander H. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Prepr. 2018;6:e27295v2. doi: 10.1038/s41587-019-0209-9. PubMed DOI PMC

Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J.A., Holmes S.P. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods. 2016;13:581–583. doi: 10.1038/nmeth.3869. PubMed DOI PMC

Katoh K., Misawa K., Kuma K.I., Miyata T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–3066. doi: 10.1093/nar/gkf436. PubMed DOI PMC

Price M.N., Dehal P.S., Arkin A.P. FastTree 2—Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE. 2010;5:e9490. doi: 10.1371/journal.pone.0009490. PubMed DOI PMC

Faith D.P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 1992;61:1–10. doi: 10.1016/0006-3207(92)91201-3. DOI

Bokulich N.A., Kaehler B.D., Rideout J.R., Dillon M., Bolyen E., Knight R., Huttley G.A., Gregory Caporaso J. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6:90. doi: 10.1186/s40168-018-0470-z. PubMed DOI PMC

McDonald D., Price M.N., Goodrich J., Nawrocki E.P., DeSantis T.Z., Probst A., Andersen G.L., Knight R., Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–618. doi: 10.1038/ismej.2011.139. PubMed DOI PMC

Anderson M.J. Permutational Multivariate Analysis of Variance (PERMANOVA) John Wiley & Sons, Ltd.; Hoboken, NJ, USA: 2014.

Petnicki-Ocwieja T., Hrncir T., Liu Y.-J., Biswas A., Hudcovic T., Tlaskalova-Hogenova H., Kobayashi K.S. Nod2 is required for the regulation of commensal microbiota in the intestine. Proc. Natl. Acad. Sci. USA. 2009;106:15813–15818. doi: 10.1073/pnas.0907722106. PubMed DOI PMC

Synergistic Effects of Fructose and Food Preservatives on Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): From Gut Microbiome Alterations to Hepatic Gene Expression

Gut Microbiota Dysbiosis: Triggers, Consequences, Diagnostic and Therapeutic Options

Gut Microbiota and NAFLD: Pathogenetic Mechanisms, Microbiota Signatures, and Therapeutic Interventions