The chicken caecum is colonised by hundreds of different bacterial species. Which of these are targeted by immunoglobulins and how immunoglobulin expression shapes chicken caecal microbiota has been addressed in this study. Using cell sorting followed by sequencing of V3/V4 variable region of 16S rRNA, bacterial species with increased or decreased immunoglobulin coating were determined. Next, we determined also caecal microbiota composition in immunoglobulin knockout chickens. We found that immunoglobulin coating was common and major taxa were coated with immunoglobulins. Similarly, more taxa required immunoglobulin production for caecum colonisation compared to those which became abundant in immunoglobulin-deficient chickens. Taxa with low immunoglobulin coating such as Lactobacillus, Blautia, [Eubacterium] hallii, Megamonas, Fusobacterium and Desulfovibrio all encode S-layer proteins which may reduce interactions with immunoglobulins. Although there were taxa which overgrew in Ig-deficient chickens (e.g. Akkermansia) indicating immunoglobulin production acted to exclude them from the chicken caecum, in most of the cases, immunoglobulin production more likely contributed to fixing the desired microbiota in the chicken caecum.

Center for Infection Prevention Technical University of Munich Freising Germany

Reproductive Biotechnology TUM School of Life Sciences Technical University of Munich Munich Germany

Veterinary Faculty Department for Veterinary Sciences Ludwig Maximilians University Munich Planegg Germany

Veterinary Research Institute Hudcova 70 621 00 Brno Czech Republic

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Cheng, H. Y., Ning, M. X., Chen, D. K. & Ma, W. T. Interactions between the gut microbiota and the host innate immune response against pathogens. Front Immunol10, 607 (2019). PubMed PMC

Cullender, T. C. et al. Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host Microbe14, 571–581 (2013). PubMed PMC

Peterson, D. A., McNulty, N. P., Guruge, J. L. & Gordon, J. I. IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe2, 328–339 (2007). PubMed

Nakajima, A. et al. IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria. J Exp Med215, 2019–2034 (2018). PubMed PMC

Benjdia, A., Martens, E. C., Gordon, J. I. & Berteau, O. Sulfatases and a radical S-adenosyl-L-methionine (AdoMet) enzyme are key for mucosal foraging and fitness of the prominent human gut symbiont. Bacteroides thetaiotaomicron. J Biol Chem286, 25973–25982 (2011). PubMed PMC

Medvecky, M. et al. Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures. BMC Genomics19, 561 (2018). PubMed PMC

Roediger, W. E. Utilization of nutrients by isolated epithelial cells of the rat colon. Gastroenterology83, 424–429 (1982). PubMed

Vermeulen, K. et al. Reduced particle size wheat bran is butyrogenic and lowers Salmonella colonization, when added to poultry feed. Vet Microbiol198, 64–71 (2017). PubMed

Polansky, O. et al. Important metabolic pathways and biological processes expressed by chicken cecal microbiota. Appl Environ Microbiol82, 1569–1576 (2015). PubMed PMC

Jaglin, M. et al. Indole, a signaling molecule produced by the gut microbiota, negatively impacts emotional behaviors in rats. Front Neurosci12, 216 (2018). PubMed PMC

De Palma, G. et al. Histamine production by the gut microbiota induces visceral hyperalgesia through histamine 4 receptor signaling in mice. Sci Transl Med14, eabj1895 (2022). PubMed

Vlasatikova, L. et al. Colonization of chickens with competitive exclusion products results in extensive differences in metabolite composition in cecal digesta. Poult Sci103, 103217 (2024). PubMed PMC

Rengarajan, S. et al. Dynamic immunoglobulin responses to gut bacteria during inflammatory bowel disease. Gut Microbes11, 405–420 (2020). PubMed PMC

Olm, M. R., Spencer, S. P., Silva, E. L. & Sonnenburg, J. L. Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes patterns of IgA antibody binding in the healthy human gut microbiome. bioRxiv (2023).

Palm, N. W. et al. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell158, 1000–1010 (2014). PubMed PMC

Volf, J. et al. Transient and prolonged response of chicken cecum mucosa to colonization with different gut microbiota. PLoS One11, e0163932 (2016). PubMed PMC

Macpherson, A. J., McCoy, K. D., Johansen, F. E. & Brandtzaeg, P. The immune geography of IgA induction and function. Mucosal Immunol1, 11–22 (2008). PubMed

Hapfelmeier, S. et al. Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses. Science328, 1705–1709 (2010). PubMed PMC

Takeuchi, T. et al. Acetate differentially regulates IgA reactivity to commensal bacteria. Nature595, 560–564 (2021). PubMed

Volf, J. et al. Gene expression in the chicken caecum is dependent on microbiota composition. Vet Res48, 85 (2017). PubMed PMC

Van Immerseel, F. et al. Dynamics of immune cell infiltration in the caecal lamina propria of chickens after neonatal infection with a Salmonella enteritidis strain. Dev Comp Immunol26, 355–364 (2002). PubMed

Matulova, M. et al. Characterization of chicken spleen transcriptome after infection with Salmonella enterica serovar Enteritidis. PLoS One7, e48101 (2012). PubMed PMC

Matulova, M. et al. Chicken innate immune response to oral infection with Salmonella enterica serovar Enteritidis. Vet Res44, 37 (2013). PubMed PMC

Suzuki, K. et al. Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proc Natl Acad Sci U S A101, 1981–1986 (2004). PubMed PMC

Donaldson, G. P. et al. Gut microbiota utilize immunoglobulin A for mucosal colonization. Science360, 795–800 (2018). PubMed PMC

Weis, A. M. & Round, J. L. Microbiota-antibody interactions that regulate gut homeostasis. Cell Host Microbe29, 334–346 (2021). PubMed PMC

Duke, G. E., Eccleston, E., Kirkwood, S., Louis, C. F. & Bedbury, H. P. Cellulose digestion by domestic turkeys fed low or high fiber diets. J Nutr114, 95–102 (1984). PubMed

Duke, G. E. Relationship of cecal and colonic motility to diet, habitat, and cecal anatomy in several avian species. J Exp Zool Suppl3, 38–47 (1989). PubMed

Kollarcikova, M. et al. Different Bacteroides species colonise human and chicken intestinal tract. Microorganisms8, 1483 (2020). PubMed PMC

Kollarcikova, M. et al. Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota. Poult Sci98, 2347–2353 (2019). PubMed

Schusser, B. et al. Immunoglobulin knockout chickens via efficient homologous recombination in primordial germ cells. Proc Natl Acad Sci U S A110, 20170–20175 (2013). PubMed PMC

Kubasova, T. et al. Contact with adult hen affects development of caecal microbiota in newly hatched chicks. PLoS One14, e0212446 (2019). PubMed PMC

Faldynova, M. et al. Contact with adult hens affects the composition of skin and respiratory tract microbiota in newly hatched chicks. Poult Sci103, 103302 (2024). PubMed PMC

Kubasova, T. et al. Gut anaerobes capable of chicken caecum colonisation. Microorganisms7, 597 (2019). PubMed PMC

Karasova, D. et al. Host species adaptation of obligate gut anaerobes is dependent on their environmental survival. Microorganisms10, 1085 (2022). PubMed 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 Sci22, 5471 (2021). PubMed PMC

Bunker, J. J. et al. Innate and adaptive humoral responses coat distinct commensal bacteria with immunoglobulin A. Immunity43, 541–553 (2015). PubMed PMC

Videnska, P. et al. Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life. PLoS One9, e115142 (2014). PubMed 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 One8, e84290 (2013). PubMed PMC

Mathias, A. & Corthesy, B. Recognition of gram-positive intestinal bacteria by hybridoma- and colostrum-derived secretory immunoglobulin A is mediated by carbohydrates. J Biol Chem286, 17239–17247 (2011). PubMed PMC

Zeng, M. Y. et al. Gut microbiota-induced immunoglobulin G controls systemic infection by symbiotic bacteria and pathogens. Immunity44, 647–658 (2016). PubMed PMC

Fransen, F. et al. BALB/c and C57BL/6 mice differ in polyreactive IgA abundance, which impacts the generation of antigen-specific IgA and microbiota diversity. Immunity43, 527–540 (2015). PubMed

Hynonen, U. & Palva, A. Lactobacillus surface layer proteins: structure, function and applications. Appl Microbiol Biotechnol97, 5225–5243 (2013). PubMed PMC

Collado, M. C., Derrien, M., Isolauri, E., de Vos, W. M. & Salminen, S. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol73, 7767–7770 (2007). PubMed PMC

Kothlow, S., Schenk-Weibhauser, K., Ratcliffe, M. J. & Kaspers, B. Prolonged effect of BAFF on chicken B cell development revealed by RCAS retroviral gene transfer in vivo. Mol Immunol47, 1619–1628 (2010). PubMed

Bolyen, E. et al. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol37, 1091 (2019). PubMed

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 Bioinformatics17, 419 (2016). PubMed PMC

Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics34, i884–i890 (2018). PubMed PMC

Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods13, 581–583 (2016). PubMed PMC

Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome6, 90 (2018). PubMed PMC

Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res41, D590-596 (2013). PubMed PMC

Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res (2024). PubMed PMC

Feed supplementation with a mixture of C1 to C12 monoacylglycerides increases chicken resistance to Salmonella Enteritidis infection