Abstract
To better understand the ecology of the poultry gastrointestinal (GI) microbiome and its interactions with the host, we compared GI bacterial communities by sample type (fecal or cecal), time (1, 3, and 6 weeks posthatch), and experimental pen (1, 2, 3, or 4), and measured cecal mRNA transcription of the cytokines IL18, IL1β, and IL6, IL10, and TGF-β4. The microbiome was characterized by sequencing of 16S rRNA gene amplicons, and cytokine gene expression was measured by a panel of quantitative-PCR assays targeting mRNAs. Significant differences were observed in the microbiome by GI location (fecal versus cecal) and bird age as determined by permutational MANOVA and UniFrac phylogenetic hypothesis tests. At 1-week posthatch, bacterial genera significantly over-represented in fecal versus cecal samples included Gallibacterium and Lactobacillus, while the genus Bacteroides was significantly more abundant in the cecum. By 6-week posthatch, Clostridium and Caloramator (also a Clostridiales) sequence types had increased significantly in the cecum and Lactobacillus remained over-represented in fecal samples. In the ceca, the relative abundance of sequences classified as Clostridium increased by ca. 10-fold each sampling period from 0.1% at 1 week to 1% at 3 week and 18% at 6 week. Increasing community complexity through time were observed in increased taxonomic richness and diversity. IL18 and IL1β significantly (p < 0.05, pairwise t-tests) increased to maximum mean expression levels 1.5 fold greater at week 3 than 1, while IL6 significantly decreased to 0.8- and 0.5-fold expression at 3- and 6-week posthatch, respectively relative to week 1. Transcription of pro-inflammatory cytokines was generally negatively correlated with the relative abundance of various members of the phylum Firmicutes and positively correlated with Proteobacteria. Correlations of the microbiome with specific cytokine mRNA transcription highlight the importance of the GI microbiome for bird health and productivity and may be a successful high-throughput strategy to identify bacterial taxa with specific immune-modulatory properties.
Highlights
Poultry are naturally adapted to hosting a complex gastrointestinal (GI) microbial community with hundreds of bacterial species and up to 1011 CFU per gram of gut contents [1]
Significant differences were observed in the microbiome depending on sampling location and bird age (1, 3, or 6 weeks of age) using a variety of metrics
We used a variety of taxonomic classifications or taxonomicindependent classifications to Degrees of Sums of and only one bird had marginally (p = 0.05) different communities in fecal versus cecal samples while all other comparisons were highly significant (p < 0.0001; Figure 1)
Summary
Poultry are naturally adapted to hosting a complex gastrointestinal (GI) microbial community with hundreds of bacterial species and up to 1011 CFU per gram of gut contents [1]. With the use of high-throughput sequencing, we have begun to open this black box with important insights into the taxonomic [10,11,12,13,14,15,16] and genomic [6, 17,18,19] composition of the poultry GI microbiome as summarized in several recent reviews [9, 20,21,22]. Proper understanding of temporal and spatial changes in the chicken GI microbiome is critically important for designing probiotic supplements, monitoring gut health, and choosing sample types to assess feed additive effects or pathogen shedding
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