Composition of microbiota from chicken caecal mucosa considerably differs from microbiota in the caecal lumen

Despite the importance of microbiota at mucosal surfaces of the gut and their different composition in comparison to those colonising the gut lumen, only a few papers specifically addressed this topic. In this study, we therefore defined mucosa-associated and lumen-associated microbiota from the chicken caecum.

To identify mucosa-adapted microbiota members, caeca from adult hens instead of chicks should be analysed. Mucosa-adapted microbiota included Treponema-like species, Brachyspira innocens, Mucispirillum sp., Helicobacter pullorum, Desulfovibrio sp. and Anaerobiospirillum sp. On the other hand, representatives of Bacteroidota were enriched in the caecal lumen. Reduced colonization of the mucosal surface in one-week-old chicks was a consequence of the lack of appropriate microbiota source in chicks obtained from hatcheries since when the chicks were raised in the presence of adult hens, they were efficiently colonised by mucosa-adapted microbiota within the first week of life. The identified mucosa-associated bacteria were of helical shape, chemotactic and motile, and expressed type VI secretion system in vivo. Brachyspira innocens and Anaerobiospirillum fermented carbohydrates while Mucispirillum sp. and Helicobacter pullorum preferred amino-acid fermentation.

Here, we defined mucosal microbiota of chicken caecum, microbiota which are in closer contact with chicken host than the luminal microbiota and may therefore considerably affect the behaviour of chickens.