This also resulted in only one duodenum sample from the day 1 timepoint remaining. Prior to analysis, samples were subsampled to 10,000 reads 35 samples were discarded as they had less than 10,000 reads, including all reagent only controls. The composition of the mock community control can be found in Additional file 3: Tables S1 and S2. The most abundant bacteria in our negative controls were Clostridium_sensu_stricto_1 (0.23 ± 0.20), Lactobacillus (0.17 ± 0.12), unclassified members of the Lachnospiraceae (0.14 ± 0.19) and Enterococcus (0.10 ± 0.09). Additional file 1 contains the complete OTU table and Additional file 2 contains the taxonomic assignment of OTUs. A total of 6015 operational taxonomic units (OTUs) were identified. For each sample the average number of reads after quality control was 27,184 ± 44,159 (mean ± standard deviation). 59.9% of sequences were removed during quality control. The V4 region of the 16S rRNA gene was amplified and sequenced, producing a total of 11,115,696 paired-end reads from 164 samples. Similar to the studies above, we found significant differences in the microbiota compositions of specific sample types with age and significant differences between sample types within timepoints. In this study we compared the bacterial microbiota of duodenal, jejunal, ileal and caecal samples of Ross 308 broilers at 5 timepoints: 1 day, 3 days, 7 days, 14 days and 5 weeks of age. Ileal and caecal samples were also characterised at various timepoints starting at 1 week of age by Johnson et al. A separate study examined ileal and caecal samples from Hy-Line W-36 commercial layers at 9 timepoints, starting at 1 week of age. compared ileal and caecal samples from commercial Ross-hybrids, taking samples at day 1, 3, 7 14, 21, 28, and 49 days of age.
Several studies have directly compared samples taken from the small intestine with those from the caeca at specific timepoints, and at various life stages. Several studies have also examined samples from the small intestine which are less rich and diverse than caecal samples and contain a high abundance of Lactobacilli. However, the results from some studies do not entirely follow this pattern and variability in microbiota composition between flocks can be high. In early life it is generally observed that the caeca contain high abundances of Enterobacteriales and over the first few weeks of life these decline and members of the Clostridiales come to predominate, with some studies also showing a large increase in Bacteroidetes. The caecal microbiota has been suggested to play an important role in nutrition via the production of short chain fatty acids, nitrogen recycling and amino acid production. The vast majority of these studies have focussed on the chicken caeca as this is where the largest concentration of microbes can be found. Many studies have used 16S rRNA gene data to characterise the microbial communities which colonise the gastrointestinal tracts of chickens and to characterise the development of these communities over time. However, to do so would require a good understanding of the types of microbes which naturally occur in these animals and the role they play in nutrition and health.
Improvements in sequencing technologies have led to a better understanding of the microbiota of many livestock species, leading some to suggest that we could optimise the composition of microbiota in these economically important animals to improve production and sustainability.
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