Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter
Date
2018-10-15
Journal Title
Journal ISSN
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Publisher
Frontiers Media
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.
Description
Publication history: Accepted - 25 September 2018; Published - 15 October 2018.
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Article
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Keywords
chicken, microbiome, Campylobacter, environmental filtering, phylogenetic signal, competitive exclusion, diversity
Citation
Ijaz, U. Z., Sivaloganathan, L., McKenna, A., Richmond, A., Kelly, C., Linton, M., Stratakos, A. Ch., Lavery, U., Elmi, A., Wren, B. W., Dorrell, N., Corcionivoschi, N. and Gundogdu, O. (2018) ‘Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter’, Frontiers in Microbiology, 9. doi: 10.3389/fmicb.2018.02452.