Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter

Abstract

21Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to 22 humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and 23 is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to 24 secondary sequelae such as Guillain-Barré syndrome and stunted growth in children from low-resource 25 areas. Despite the global health impact and economic burden of Campylobacter, how and when 26 Campylobacter appears within chickens remains unclear. As such, there has been a motivation to decrease 27 the number of Campylobacter within chickens and thus reduce the risk of infection to humans. The lack of 28 2 day-to-day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have 29 delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a 30 comprehensive day-to-day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each 31 day; n=396) combining metadata such as chicken weight and feed conversion rates to investigate what the 32 driving forces are for the microbial changes within the chicken gut over time, and how this relates to 33 Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity 34 up to day 12 with variation observed both in terms of genera and abundance, before a stabilisation of the 35 microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers 36 of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter 37 appears. Campylobacter was identified at day 16 which was one day after the most substantial changes in 38 metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet 39 of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often 40 corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither 41 sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed 42 in a natural setting. We believe that our findings can be useful for future intervention strategies and can help 43 elucidate the mechanism through which Campylobacter within chickens can be reduced.

Comparing gut resistome composition among patients with acute Campylobacter infections and healthy family members

“…Indeed, studies in mice with varying degrees of microbial imbalance prior to infection demonstrated that disturbed gut communities were more susceptible to infection by Salmonella enterica serovar Typhimurium 28 . Another study in chickens observed Campylobacter invasion of the cecal microbiome only after substantial changes to the metabolic profile were detected 29 . Direct interactions between the normal gut microbiota and invading pathogens via resource competition, metabolite production, and direct antagonism, coupled with the complexity of pathogen-induced inflammation, have also been shown to influence enteric infections 30 , 31 .…”

The role of feed enzymes in maintaining poultry intestinal health

“…Evidence to support this transition has recently been reported in a study investigating daily changes in the caecal microbiota from 3 to 35 days of age and suggests that there is indeed a rapid evolution and increase in diversity in the caecal microbiota up to 12 days of age, this being driven by available space and food. 30 After 20 days of age the authors noted a stabilization in the microbiota in both diversity and abundance of species which was driven by the environmental conditions presented by each host chicken. In other words, the substrate and space available in the caeca were more or less constant after 20 days of age and hence the microbiota stabilizes into a structure best suited to the conditions which exist.…”

“…It is clear from analysis of the caecal microbiota over time that there is a transition from species able to ferment starch, protein and many other sources of carbohydrate towards one which is almost exclusively targeting fibre fermentation. 25,[28][29][30] Readily fermentable carbohydrates such as starch and saccharides most often result in production of lactate in both the ileum and caecum, 31 whereas fibre tends to promote more of an acetate and butyrate fermentation in chickens. If this transition to fibre fermentation is too slow then it may increase the likelihood of an imbalance between fermentation of carbohydrate relative to protein and as a result a slide towards problems related to production of toxic products of putrefaction.…”

“…It was noted that opportunistic Campylobacter spp. appeared in 25% of the birds by day 16, 30 possibly as a result of the 'turmoil' created by the loss of or imbalance between substrates entering the caeca and as a result a disruption in the environment (concentrations of SCFA, metabolites, toxins, redox potential, for example) which reduces resilience against opportunistic invaders. Similar work which evaluated broiler faecal microbial DNA (as a proxy for ileal populations) showed a similar rapid increase in diversity to 10 days of age followed by a period of significant adaptation between 14 and 21 days of age where perturbations of the ileal microbiota were most likely, 32 and thus interventions most likely to succeed.…”

Advancements In Developing Anti-Campylobacter Vaccine For Poultry

“…kompleksowe, codzienne badania mikrobiomu kurcząt od 3 do 35 dnia życia ptaków wykazały, że Campylobacter pojawia się w 16 dniu życia, tuż po zaobserwowaniu najbardziej znaczących zmian w profilach metabolicznych. Nie można wykluczyć, że jest to wynik pojawienia się środowiskowych czynników stymulujących rozwój tych drobnoustrojów [41].…”