Comparative Metagenomics Reveals Host Specific Metavirulomes and Horizontal Gene Transfer Elements in the Chicken Cecum Microbiome

Abstract

BackgroundThe complex microbiome of the ceca of chickens plays an important role in nutrient utilization, growth and well-being of these animals. Since we have a very limited understanding of the capabilities of most species present in the cecum, we investigated the role of the microbiome by comparative analyses of both the microbial community structure and functional gene content using random sample pyrosequencing. The overall goal of this study was to characterize the chicken cecal microbiome using a pathogen-free chicken and one that had been challenged with Campylobacter jejuni.Methodology/Principal FindingsComparative metagenomic pyrosequencing was used to generate 55,364,266 bases of random sampled pyrosequence data from two chicken cecal samples. SSU rDNA gene tags and environmental gene tags (EGTs) were identified using SEED subsystems-based annotations. The distribution of phylotypes and EGTs detected within each cecal sample were primarily from the Firmicutes, Bacteroidetes and Proteobacteria, consistent with previous SSU rDNA libraries of the chicken cecum. Carbohydrate metabolism and virulence genes are major components of the EGT content of both of these microbiomes. A comparison of the twelve major pathways in the SEED Virulence Subsystem (metavirulome) represented in the chicken cecum, mouse cecum and human fecal microbiomes showed that the metavirulomes differed between these microbiomes and the metavirulomes clustered by host environment. The chicken cecum microbiomes had the broadest range of EGTs within the SEED Conjugative Transposon Subsystem, however the mouse cecum microbiomes showed a greater abundance of EGTs in this subsystem. Gene assemblies (32 contigs) from one microbiome sample were predominately from the Bacteroidetes, and seven of these showed sequence similarity to transposases, whereas the remaining sequences were most similar to those from catabolic gene families.Conclusion/SignificanceThis analysis has demonstrated that mobile DNA elements are a major functional component of cecal microbiomes, thus contributing to horizontal gene transfer and functional microbiome evolution. Moreover, the metavirulomes of these microbiomes appear to associate by host environment. These data have implications for defining core and variable microbiome content in a host species. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

“…Similar relationships were seen between rRNA gene sequence hits for bacterial SSU against the Ribosomal Database Project, and archaeal and eukaryotic SSU against European Ribosomal RNA databases ( Table 1). The number of 16S rRNA gene hits in the metagenomic libraries (Table 1) is similar (228 to 722) to that found for our analysis of the chicken cecum where 401-510 SSU rRNA gene sequences per sample were observed (29). Rarefaction analysis (supporting information (SI) Fig.…”

“…Nonetheless, this approach does allow one to begin to harvest the remarkable and vast diversity present in a given metagenome (21). In this regard, next generation sequencing technologies, primarily the massively parallel DNA sequencing capacity of the 454 Genome Sequencer (Roche) (22), are now being applied to complex environmental samples (23)(24)(25)(26)(27)(28)(29). A comparison of the metabolic potential and functional genes in 45 distinct microbiomes showed that the 454 technology could describe the metabolic profiles of the microbial communities across 9 discrete environments and these could be related to biogeochemical characteristics of the environment (24).…”

Taxons of Chicken Cecum Microbiom Are Abundant, and Influenced by the Combined Feed Composition and Decreased Metabolizable Energy

“…In cecum, the representatives of phylum Firmicutes and families Ruminococcaceae (19,81±0,97 %) and Clostridiaceae (23,06±1,19 %) having amyloid and cellulolytic enzymes and of phylum Bacteroidetes (29,60±1.49 %) with amylo-and proteolytic activity were predominant. Our results confirmed the data of several authors who have demonstrated by NGS sequencing predominance of phylum Firmicutes [19,21] and genera Clostridium and Bacteroides bacteria [23] in broiler cecum. At the same time, our results are contrary to other reports which indicated the dominance of the phylum Proteobacteria representatives [22].…”

“…Despite the widespread use of these methods to study of numbers and taxonomic diversity of microbes in the human intestine [17,18], there are only a few reports on poultry. In particular, they relate to the GIT microbiome state in poultry infected by pathogenic bacteria Campylobacter jejuni [19,20] due to the effects of coccidiostats [21] and in relation to the productivity [22,23].…”

Defining the nature of human γδ T cells: a biographical sketch of the highly empathetic

“…For example, omnivorous rodents and primates may have less of a need to maintain peace with a diverse population of microbiota in comparison to cows, sheep, rabbits and chickens for which microbes play a more significant role in digestion and metabolism. [21][22][23][24] Therefore, the immune cell repertoire that recognize more variable 'non-self' as dangerous (i.e., the features that we depend on from the adaptive immune system) may be less advantageous when balancing the need to protect beneficial or non-threatening microbes that are needed for sustenance and/or to prevent chronic inflammation.…”