There are extensive differences in the caecal microbiota of chicks from hatcheries and those inoculated with faecal material from adult hens. Besides differences in microbial composition, the latter chickens are highly resistant to Salmonella Enteritidis challenges, while the former are susceptible. In this study, we tested whether strains from genera Bacteroides, Megamonas, or Megasphaera can increase chicken resistance to Salmonella and Campylobacter jejuni when defined microbial mixtures consisting of these bacterial genera are administered. Mixtures consisting of different species and strains from the above-mentioned genera efficiently colonised the chicken caecum and increased chicken resistance to Salmonella by a factor of 50. The tested mixtures were even more effective in protecting chickens from Salmonella in a seeder model of infection (3-5 log reduction). The tested mixtures partially protected chickens from C. jejuni infection, though the effect was lower than that against Salmonella. The obtained data represent a first step for the development of a new type of probiotics for poultry.

Veterinary Research Institute 621 00 Brno Czech Republic

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Varmuzova K., Kubasova T., Davidova-Gerzova L., Sisak F., Havlickova H., Sebkova A., Faldynova M., Rychlik I. Composition of Gut Microbiota Influences Resistance of Newly Hatched Chickens to Salmonella Enteritidis Infection. Front. Microbiol. 2016;7:957. doi: 10.3389/fmicb.2016.00957. PubMed DOI PMC

Kubasova T., Kollarcikova M., Crhanova M., Karasova D., Cejkova D., Sebkova A., Matiasovicova J., Faldynova M., Pokorna A., Cizek A., et al. Contact with adult hen affects development of caecal microbiota in newly hatched chicks. PLoS ONE. 2019;14:e0212446. doi: 10.1371/journal.pone.0212446. PubMed DOI PMC

Marcolla C.S., Ju T., Willing B.P. Cecal Microbiota Development and Physiological Responses of Broilers Following Early Life Microbial Inoculation Using Different Delivery Methods and Microbial Sources. Appl. Environ. Microbiol. 2023;89:e0027123. doi: 10.1128/aem.00271-23. PubMed DOI PMC

Videnska P., Sedlar K., Lukac M., Faldynova M., Gerzova L., Cejkova D., Sisak F., Rychlik I. Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life. PLoS ONE. 2014;9:e115142. doi: 10.1371/journal.pone.0115142. PubMed DOI PMC

Stanley D., Geier M.S., Hughes R.J., Denman S.E., Moore R.J. Highly variable microbiota development in the chicken gastrointestinal tract. PLoS ONE. 2013;8:e84290. doi: 10.1371/journal.pone.0084290. PubMed DOI PMC

Xi Y., Shuling N., Kunyuan T., Qiuyang Z., Hewen D., ChenCheng G., Tianhe Y., Liancheng L., Xin F. Characteristics of the intestinal flora of specific pathogen free chickens with age. Microb. Pathog. 2019;132:325–334. doi: 10.1016/j.micpath.2019.05.014. PubMed DOI

Sergeant M.J., Constantinidou C., Cogan T.A., Bedford M.R., Penn C.W., Pallen M.J. Extensive microbial and functional diversity within the chicken cecal microbiome. PLoS ONE. 2014;9:e91941. doi: 10.1371/journal.pone.0091941. PubMed DOI PMC

Beal R.K., Wigley P., Powers C., Hulme S.D., Barrow P.A., Smith A.L. Age at primary infection with Salmonella enterica serovar Typhimurium in the chicken influences persistence of infection and subsequent immunity to re-challenge. Vet. Immunol. Immunopathol. 2004;100:151–164. doi: 10.1016/j.vetimm.2004.04.005. PubMed DOI

Juricova H., Matiasovicova J., Faldynova M., Sebkova A., Kubasova T., Prikrylova H., Karasova D., Crhanova M., Havlickova H., Rychlik I. Probiotic Lactobacilli Do Not Protect Chickens against Salmonella Enteritidis Infection by Competitive Exclusion in the Intestinal Tract but in Feed, Outside the Chicken Host. Microorganisms. 2022;10:219. doi: 10.3390/microorganisms10020219. PubMed DOI PMC

Rantala M., Nurmi E. Prevention of the growth of Salmonella infantis in chicks by the flora of the alimentary tract of chickens. Br. Poult. Sci. 1973;14:627–630. doi: 10.1080/00071667308416073. PubMed DOI

Methner U., Barrow P.A., Martin G., Meyer H. Comparative study of the protective effect against Salmonella colonisation in newly hatched SPF chickens using live, attenuated Salmonella vaccine strains, wild-type Salmonella strains or a competitive exclusion product. Int. J. Food Microbiol. 1997;35:223–230. doi: 10.1016/S0168-1605(96)01236-6. PubMed DOI

Faldynova M., Prikrylova H., Sebkova A., Volf J., Karasova D., Crhanova M., Babak V., Rychlik I. Contact with adult hens affects the composition of skin and respiratory tract microbiota in newly hatched chicks. Poult. Sci. 2024;103:103302. doi: 10.1016/j.psj.2023.103302. PubMed DOI PMC

Kubasova T., Seidlerova Z., Rychlik I. Ecological Adaptations of Gut Microbiota Members and Their Consequences for Use as a New Generation of Probiotics. Int. J. Mol. Sci. 2021;22:5471. doi: 10.3390/ijms22115471. PubMed DOI PMC

Karasova D., Faldynova M., Matiasovicova J., Sebkova A., Crhanova M., Kubasova T., Seidlerova Z., Prikrylova H., Volf J., Zeman M., et al. Host Species Adaptation of Obligate Gut Anaerobes Is Dependent on Their Environmental Survival. Microorganisms. 2022;10:1085. doi: 10.3390/microorganisms10061085. PubMed DOI PMC

Papouskova A., Rychlik I., Harustiakova D., Cizek A. Research Note: A mixture of Bacteroides spp. and other probiotic intestinal anaerobes reduces colonization by pathogenic E. coli strain O78:H4-ST117 in newly hatched chickens. Poult. Sci. 2023;102:102529. doi: 10.1016/j.psj.2023.102529. PubMed DOI PMC

Medvecky M., Cejkova D., Polansky O., Karasova D., Kubasova T., Cizek A., Rychlik I. Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures. BMC Genom. 2018;19:561. doi: 10.1186/s12864-018-4959-4. PubMed DOI PMC

Kubasova T., Kollarcikova M., Crhanova M., Karasova D., Cejkova D., Sebkova A., Matiasovicova J., Faldynova M., Sisak F., Babak V., et al. Gut anaerobes capable of chicken caecum colonisation. Microorganisms. 2019;7:597. doi: 10.3390/microorganisms7120597. PubMed DOI PMC

Bolyen E., Rideout J.R., Dillon M.R., Bokulich N.A., Abnet C.C., Al-Ghalith G.A., Alexander H., Alm E.J., Arumugam M., Asnicar F., et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 2019;37:852–857. doi: 10.1038/s41587-019-0209-9. PubMed DOI PMC

Girardot C., Scholtalbers J., Sauer S., Su S.Y., Furlong E.E. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinform. 2016;17:419. doi: 10.1186/s12859-016-1284-2. PubMed DOI PMC

Chen S., Zhou Y., Chen Y., Gu J. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–i890. doi: 10.1093/bioinformatics/bty560. PubMed DOI PMC

Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J., 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

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

Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J., Glockner F.O. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596. doi: 10.1093/nar/gks1219. PubMed DOI PMC

Rajova J., Zeman M., Seidlerova Z., Vlasatikova L., Matiasovicova J., Sebkova A., Faldynova M., Prikrylova H., Karasova D., Crhanova M., et al. In Vivo Expression of Chicken Gut Anaerobes Identifies Carbohydrate- or Amino Acid-Utilising, Motile or Type VI Secretion System-Expressing Bacteria. Int. J. Mol. Sci. 2024;25:6505. doi: 10.3390/ijms25126505. PubMed DOI PMC

Vlasatikova L., Zeman M., Crhanova M., Matiasovicova J., Karasova D., Faldynova M., Prikrylova H., Sebkova A., Rychlik I. Colonization of chickens with competitive exclusion products results in extensive differences in metabolite composition in cecal digesta. Poult. Sci. 2024;103:103217. doi: 10.1016/j.psj.2023.103217. PubMed DOI PMC

Hapfelmeier S., Lawson M.A., Slack E., Kirundi J.K., Stoel M., Heikenwalder M., Cahenzli J., Velykoredko Y., Balmer M.L., Endt K., et al. Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses. Science. 2010;328:1705–1709. doi: 10.1126/science.1188454. PubMed DOI PMC

Takeuchi T., Miyauchi E., Kanaya T., Kato T., Nakanishi Y., Watanabe T., Kitami T., Taida T., Sasaki T., Negishi H., et al. Acetate differentially regulates IgA reactivity to commensal bacteria. Nature. 2021;595:560–564. doi: 10.1038/s41586-021-03727-5. PubMed DOI

Ty M., Taha-Abdelaziz K., Demey V., Castex M., Sharif S., Parkinson J. Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry. Anim. Microbiome. 2022;4:2. doi: 10.1186/s42523-021-00157-6. PubMed DOI PMC

Polansky O., Sekelova Z., Faldynova M., Sebkova A., Sisak F., Rychlik I. Important Metabolic Pathways and Biological Processes Expressed by Chicken Cecal Microbiota. Appl. Environ. Microbiol. 2015;82:1569–1576. doi: 10.1128/AEM.03473-15. PubMed DOI PMC

Iqbal M., Philbin V.J., Withanage G.S., Wigley P., Beal R.K., Goodchild M.J., Barrow P., McConnell I., Maskell D.J., Young J., et al. Identification and functional characterization of chicken toll-like receptor 5 reveals a fundamental role in the biology of infection with Salmonella enterica serovar typhimurium. Infect. Immun. 2005;73:2344–2350. doi: 10.1128/IAI.73.4.2344-2350.2005. PubMed DOI PMC

Hayashi F., Smith K.D., Ozinsky A., Hawn T.R., Yi E.C., Goodlett D.R., Eng J.K., Akira S., Underhill D.M., Aderem A. The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature. 2001;410:1099–1103. doi: 10.1038/35074106. PubMed DOI

Jeong J.S., Kim I.H. Effect of Bacillus subtilis C-3102 spores as a probiotic feed supplement on growth performance, noxious gas emission, and intestinal microflora in broilers. Poult. Sci. 2014;93:3097–3103. doi: 10.3382/ps.2014-04086. PubMed DOI

Menconi A., Morgan M.J., Pumford N.R., Hargis B.M., Tellez G. Physiological Properties and Salmonella Growth Inhibition of Probiotic Bacillus Strains Isolated from Environmental and Poultry Sources. Int. J. Bacteriol. 2013;2013:958408. doi: 10.1155/2013/958408. PubMed DOI PMC

Coyne M.J., Roelofs K.G., Comstock L.E. Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. BMC Genom. 2016;17:58. doi: 10.1186/s12864-016-2377-z. PubMed DOI PMC

Verster A.J., Ross B.D., Radey M.C., Bao Y., Goodman A.L., Mougous J.D., Borenstein E. The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition. Cell Host Microbe. 2017;22:411–419.e4. doi: 10.1016/j.chom.2017.08.010. PubMed DOI PMC

The immune response modulated by inoculation of commensal bacteria at birth impacts the gut microbiota and prevents Salmonella colonization