Dataset Information

Development of the Caecal Microbiota in Three Broiler Breeds.

ABSTRACT: The development of the caecal microbiota plays a role in the metabolism and immune competence of chickens. A detailed understanding of normal succession in the caecal microbiota can inform the use of probiotics and other interventions to optimize the caecal microbiota. The development of the microbiota in caecal mucus and lumen samples from three breeds of broiler chicken (Cobb 500, n = 36; Hubbard JA87, n = 38; and Ross 308, n = 36) was observed between 0 and 42 days post hatch. Chicks were housed in the same room of a climate-controlled, biosecure chicken housing unit. Between 0 and 14 days post hatch, chicks were kept in brooder pens ensuring a mixture of breeds in each brooder. From 22 days post hatch, chicks were removed from the brooders and kept in the same room. DNA was extracted from a pooled sample of caecal mucus and luminal contents from five birds of each breed at 0, 3, 7, 14, 21, 28, and 42 days post hatch. High-throughput Illumina sequencing was performed for the V4 hypervariable region of the 16S rRNA gene. The early caecal microbiota was characterized by poor diversity and dominance by one or two bacterial species. Early colonizers of the caecum included Bifidobacteriaceae, Lachnospiraceae, Bacteroidaceae and Burkholderiaceae with some amplicon sequence variants (ASVs) assigned to Ruminococcaceae. Later colonizers of the caecal microbiota were most apparent from 14 d.p.h and included Ruminococcaceae, Clostridiales vadin BB60 group, Christensenellaceae and Bacillaceae. The caecal microbiota continued to change until 42 d.p.h when the microbiota was characterized by a high abundance of Bacteroidaceae, Lachnospiraceae and Ruminococcaceae. The lumen microbiota was significantly different to the mucus with some ASVs assigned to Lachnospiraceae, Ruminococcaceae, Christensenellaceae and Bacillaceae showing increased abundance in the mucus. ASVs assigned to Bacteroidaceae, Lactobacillaceae and Burkholderiaceae showed a preference for the lumen. Analysis of five caecal mucus samples from each breed at 42 days post hatch showed differences in microbiota composition between Ross and Cobb as well as between Ross and Hubbard. Since performance data was not collected no functional inferences as to the significance of this finding can be made.

SUBMITTER: Richards P

PROVIDER: S-EPMC6603203 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Development of the Caecal Microbiota in Three Broiler Breeds.

Richards Peter P Fothergill Jo J Bernardeau Marion M Wigley Paul P

Frontiers in veterinary science 20190625

The development of the caecal microbiota plays a role in the metabolism and immune competence of chickens. A detailed understanding of normal succession in the caecal microbiota can inform the use of probiotics and other interventions to optimize the caecal microbiota. The development of the microbiota in caecal mucus and lumen samples from three breeds of broiler chicken (Cobb 500, n = 36; Hubbard JA87, n = 38; and Ross 308, n = 36) was observed between 0 and 42 days post h ...[more]

PMID: 31294039

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Project description:BackgroundThe Black Soldier Fly larvae (BSFL) are a source of nutrients and bioactive compounds in broiler diets. Some components of the BSFL may serve as a prebiotic or may impact the intestinal microbiota of the broilers by other modes of action, which in turn can affect the health and performance of broilers. Here, we investigate the impact of up to 20% BSFL in broiler diets on the diversity and composition of the broiler's microbiota.MethodsFour hundred broilers were fed five iso-nutritious experimental diets with increasing levels of BSFL meal reaching 0%, 5%, 10%, 15%, 20% in the finisher diets. Eight caecal content samples coming from each of the eight replicates per treatment were collected at two time points (day 21 and day 42) for DNA extraction and sequencing of the V3-V4 regions using Illumina MiSeq 2 × 300 bp pair-end sequencing with 341f and 805r primers. Analysis of variance and Spearman's correlation were performed, while QIIME2, DADA2, and Calypso were used for data analysis.ResultsWhen broilers were 21 days of age, the abundance of two groups of sequence variants representing Enterococcus and unclassified Christensenellaceae was significantly lower (p-value = 0.048 and p-value = 0.025, respectively) in the 20% BSFL group compared to the 0% BSFL group. There was no relevant alteration in the microbiota diversity at that stage. On day 42, the Spearman correlation analysis demonstrated that the sequence variants representing the genus Coprococcus showed a negative relationship with the BSFL inclusion levels (p-value = 0.043). The sequence variants representing the genus Roseburia and Dehalobacterium demonstrated a positive relationship with the BSFL dietary inclusion (p-value = 0.0069 and p-value = 0.0034, respectively). There was a reduction in the dissimilarity index (ANOSIM) caused by the 20% BSFL dietary inclusion.ConclusionThe addition of up to 20% BSFL in broiler diets did not affect the overall caeca microbiota diversity or composition at day 21. On day 42, there was a reduction in the beta diversity caused by the 20% BSFL dietary inclusion. The abundance of the bacterial group Roseburia was increased by the BSFL dietary inclusion, and it may be beneficial to broiler immunity and performance.

Project description:Murine models are valuable tools to study the role of gut microbiota in health or disease. However, murine and human microbiota differ in species composition, so further investigation of the murine gut microbiota is important to gain a better mechanistic understanding. Continuous in vitro fermentation models are powerful tools to investigate microbe-microbe interactions while circumventing animal testing and host confounding factors, but are lacking for murine gut microbiota. We therefore developed a novel continuous fermentation model based on the PolyFermS platform adapted to the murine caecum and inoculated with immobilized caecal microbiota. We followed a stepwise model development approach by adjusting parameters [pH, retention time (RT), growth medium] to reach fermentation metabolite profiles and marker bacterial levels similar to the inoculum. The final model had a stable and inoculum-alike fermentation profile during continuous operation. A lower pH during startup and continuous operation stimulated bacterial fermentation (115 mM short-chain fatty acids at pH 7 to 159 mM at pH 6.5). Adjustments to nutritive medium, a decreased pH and increased RT helped control the in vitro Enterobacteriaceae levels, which often bloom in fermentation models, to 6.6 log gene copies/mL in final model. In parallel, the Lactobacillus, Lachnospiraceae, and Ruminococcaceae levels were better maintained in vitro with concentrations of 8.5 log gene copies/mL, 8.8 log gene copies/mL and 7.5 log gene copies/mL, respectively, in the final model. An independent repetition with final model parameters showed reproducible results in maintaining the inoculum fermentation metabolite profile and its marker bacterial levels. Microbiota community analysis of the final model showed a decreased bacterial diversity and compositional differences compared to caecal inoculum microbiota. Most of the caecal bacterial families were represented in vitro, but taxa of the Muribaculaceae family were not maintained. Functional metagenomics prediction showed conserved metabolic and functional KEGG pathways between in vitro and caecal inoculum microbiota. To conclude, we showed that a rational and stepwise approach allowed us to model in vitro the murine caecal microbiota and functions. Our model is a first step to develop murine microbiota model systems and offers the potential to study microbiota functionality and structure ex vivo.

Dataset Information

Development of the Caecal Microbiota in Three Broiler Breeds.

Publications

Development of the Caecal Microbiota in Three Broiler Breeds.

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