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.
Highlights
Chickens (Gallus gallus domesticus) are an important food source for humans with over 50 billion reared annually for meat and eggs (Part et al, 2016)
Alpha diversity (Shannon) on microbial counts (Figure 1A) shows a rapid increase over the first ten days, it follows a plateauing effect where the microbiome normalizes at approximately day 12
When considering phylogenetic distances only (Unweighted Unifrac; Figure 1C), the decrease in beta diversity contributions is marginally slower than the abundance counts counterpart, there is a sudden increase around day 20
Summary
Chickens (Gallus gallus domesticus) are an important food source for humans with over 50 billion reared annually for meat and eggs (Part et al, 2016). The organ with the highest number and variety of bacteria is the cecum (1010-1011 cells/g) which plays an essential role in the digestion of non-starch polysaccharides (NSPs) found in chicken feed (Barnes et al, 1972; Józefiak et al, 2004; Bjerrum et al, 2006). The importance of this organ is demonstrated when up to 10% of energy needs can be recovered from a well-functioning cecum (Hegde et al, 1982; Józefiak et al, 2004). Natural colonization of chickens is reported to be at approximately day 14 of the chicken life cycle, we do not know how and why this occurs, and what the impact of Campylobacter is on the microbiome (Neill et al, 1984; Kalupahana et al, 2013; Thibodeau et al, 2015)
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