Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter

Abstract

Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barré syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of Campylobacter, how and when Campylobacter appears within chickens remains unclear. The lack of day to day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a comprehensive day to day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; final n = 379). We combined metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter can appear. Campylobacter was identified at day 16 which was 1 day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and help reduce the burden of Campylobacter within the food chain.

Salmonella Phage cocktail, its effects and benefits on the gut of chickens in a commercial farm.

“…2). This behaviour is in agreement with previous reports where the microbiome stabilizes at approximately day 12 [48]. Regarding the maturation process of the microbiota, the microbial communities have a similar diversity at day 17 between samples (3rd week), at the beginning of the experiment.…”

Galacto-oligosaccharides modulate the juvenile gut microbiome and innate immunity to improve broiler chicken performance

“…The provision of dietary GOS increased the density of goblet cells populating ileal villi in the developing chicken gut. Goblet cell increases were accompanied by significant differences in the villus height and crypt depth at 15 da, a period when transitions in the development of the chicken microbiota from a juvenile to a mature composition are observed (70)(71)(72). Using molecular methods, we have demonstrated a significant correlation between the market weight of chickens at 35 da and the cecal abundance of a specific L. johnsonii isolate identified as differentially abundant in the juvenile microbiota of GOS-fed birds.…”

Prebiotic Driven Increases in IL-17A Do Not Prevent Campylobacter jejuni Colonization of Chickens

“…These studies have noted differences in the relative abundance of Bifidobacterium, Lactobacillaceae, Clostridium cluster XIVa and Mollicutes, with transient age related shifts in specific members of the Lachnospiraceae and Ruminococcaceae (Thibodeau et al, 2015(Thibodeau et al, , 2017Connerton et al, 2018;Richards et al, 2019a). As an extension of the outputs from these studies it was recognized that transitions in the cecal microbiota were evident between 14 and 18 days that coincide with the reduced availability of maternal antibodies, and represent a window of opportunity for the entry for bacteria to bloom and new intestinal microbes to become established that can affect changes in gut health (Awad et al, 2016;Connerton et al, 2018;Ijaz et al, 2018). Early prebiotic diets offer the prospect of achieving a stable microbiota that can resist opportunist expansion or colonists.…”