Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses

Abstract

BackgroundChicken gut microbiota has paramount roles in host performance, health and immunity. Understanding the topological difference in gut microbial community composition is crucial to provide knowledge on the functions of each members of microbiota to the physiological maintenance of the host. The gut microbiota profiling of the chicken was commonly performed previously using culture-dependent and early culture-independent methods which had limited coverage and accuracy. Advances in technology based on next-generation sequencing (NGS), offers unparalleled coverage and depth in determining microbial gut dynamics. Thus, the aim of this study was to investigate the ileal and caecal microbiota development as chicken aged, which is important for future effective gut modulation.Material and methodsIleal and caecal contents of broiler chicken were extracted from 7, 14, 21 and 42-day old chicken. Genomic DNA was then extracted and amplified based on V3 hyper-variable region of 16S rRNA. Bioinformatics, ecological and statistical analyses such as Principal Coordinate Analysis (PCoA) was performed in mothur software and plotted using PRIMER 6. Additional analyses for predicted metagenomes were performed through PICRUSt and STAMP software package based on Greengenes databases.ResultsA distinctive difference in bacterial communities was observed between ilea and caeca as the chicken aged (P < 0.001). The microbial communities in the caeca were more diverse in comparison to the ilea communities. The potentially pathogenic bacteria such as Clostridium were elevated as the chicken aged and the population of beneficial microbe such as Lactobacillus was low at all intervals. On the other hand, based on predicted metagenomes analysed, clear distinction in functions and roles of gut microbiota such as gene pathways related to nutrient absorption (e.g. sugar and amino acid metabolism), and bacterial proliferation and colonization (e.g. bacterial motility proteins, two-component system and bacterial secretion system) were observed between ilea and caeca, respectively (P < 0.05).ConclusionsThe caeca microbial communities were more diverse in comparison to ilea. The main functional differences between the two sites were found to be related to nutrient absorption and bacterial colonization. Based on the composition of the microbial community, future gut modulation with beneficial bacteria such as probiotics may benefit the host.Electronic supplementary materialThe online version of this article (doi:10.1186/s13099-015-0051-7) contains supplementary material, which is available to authorized users.

Bacterial Succession in the Broiler Gastrointestinal Tract

“…This is in agreement with the low cecal counts of C. perfringens (see Table S1 in the supplemental material). The genus Bacteroides was not detected in the ileum or cecum at any time point, in contrast to reports by other authors of abundances of 1 to 20% in the ileum (55,63) and 18 to 22% in the cecum (55,(63)(64)(65). In the present study, the genus Alistipes, belonging to the same phylum (Bacteroidetes), was found to have an abundance similar to the reported Bacteroides abundances (up to 36%) in the cecum.…”

The use of random forests modelling to detect yeast-mannan sensitive bacterial changes in the broiler cecum

“…Bacteroides spp., are common bacteria in the intestine, involved in many important metabolic activities, including polysaccharide degradation, carbohydrate fermentation, and prevention of pathogen colonization 54,55 . Bacteroides spp., along with Alistipes spp., of the family Rikenellaceae are some of the main short chain fatty acid producers in the intestine 56 . An increase in short chain fatty acid production could be beneficial for gut health 57,58 .…”

Metagenomic Analysis of Total Microbial Diversity and Antibiotic Resistance of Culturable Microorganisms in Raw Chicken Meat and Mung Sprouts (<i>Phaseolus aureus</i>) Sold in Retail Markets of Mumbai, India

“…There are very few reports on microbiological diversity of different food samples studied by HT-NGS. Moreover, the available reports on metagenomics have identified limited microbial diversity in alfalfa sprouts, chicken caeca, gut 30,43,44 without much emphasis on pathogenic nature. V3 region was targeted and the total microbial diversity characterized up to species level.…”

“…V3 region was targeted and the total microbial diversity characterized up to species level. Presence of Firmicutes in chicken could be due to cross-contamination with other parts of chicken during meat processing as high incidence of Firmicutes in chicken gut, ilea and caeca have been reported 31,44 . Phylum composition of mung is similar to other metagenomic studies of fresh fruits and vegetable 45 .…”