Spatial and Temporal Changes in the Broiler Chicken Cecal and Fecal Microbiomes and Correlations of Bacterial Taxa with Cytokine Gene Expression

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.

Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession

“…As expected, community richness increased rapidly over time, stabilizing by day 14. This is in accordance with other studies monitoring the development of the cecal microbiomes of broilers over time (Ballou et al., ; Oakley, Buhr, et al., ; Oakley & Kogut, ); however, the patterns observed during the first half of our experiment further show that the increase in diversity is highest during the first 7 days and is best represented by a linear regression with the logarithm of time as the explanatory variable, highlighting the importance of the first week after hatching in the development of the GIT microbiome in broilers (Nurmi & Rantala, ).…”

“…We sampled the fecal microbiome because our daily sampling scheme called for a rapid sampling methodology, and because we were interested in temporal dynamics rather than in the emergence of specific pathogens. Whether the fecal microbiome is representative of the GIT microbiome is the subject of debate: the fecal microbiome is considered a proxy for the composition of the small intestine; it has been found that the fecal microbiome is more variable than the cecal microbiome and exhibits higher proportions of Enterobacteriales and Lactobacillales (Oakley & Kogut, ; Oakley, Lillehoj, et al., ; Sekelja et al., ). Nevertheless, our results show temporally consistent patterns with age, and detected taxa which are commonly present in different segments of the GIT.…”

“…Available studies show that during early development, the chicken GIT microbiome undergoes rapid changes, and represents a successional landscape which is gradually colonized by bacteria over time (Lu et al, 2003;Oakley, Buhr, et al, 2014;Oakley & Kogut, 2016). A weekly sampling of broilers showed large shifts in the cecal and fecal microbiomes each week as well as a gradual increase in community complexity (Oakley & Kogut, 2016).…”

Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken

“…Furthermore, it also found that these differences do not follow any discernible pattern 563 during the acquisition period (first three weeks) or later. While overlap in the cecal and fecal 564 communities was observed, and they are in broad agreement with the findings of Stanley et al 565 (2015), and Oakley & Kogut (2016), this data shows that fecal samples are not a reliable 566 indicator of divergence in gut microbiota colonization, membership, or structure. As the present 567 study focused on the first four weeks, it is not clear how the findings apply to later life 568 microbiota.…”

Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits

“…Additionally, most currently published studies only described the structure and function of the chicken gut microbiota, and the spatial and temporal changes upon specific stimulations1517181920. Our study compared and contrasted the gut metagenome chickens selectively bred based on fatness traits.…”