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. 2008 Aug 13;3(8):e2945.
doi: 10.1371/journal.pone.0002945.

"V体育2025版" Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome

Ani Qu  1 , Jennifer M Brulc, Melissa K Wilson, Bibiana F Law, James R Theoret, Lynn A Joens, Michael E Konkel, Florent Angly, Elizabeth A Dinsdale, Robert A Edwards, Karen E Nelson, Bryan A White
Affiliations

Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome

Ani Qu et al. PLoS One. .

Abstract

Background: The 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 VSports手机版. .

Methodology/principal findings: Comparative 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 V体育安卓版. 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/significance: This 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 V体育ios版. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens. .

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Phylogenetic composition of bacterial phyla from pyrosequence 16S rDNA sequences, and environmental gene tags (EGTs) from two pyrosequenced chicken cecum samples.
The percent of sequences in each of the bacterial phyla from the chicken cecum A and B microbiomes is shown. E-value cutoff for SSU rDNA hits for all databases used is 1×10−5 with a minimum length of 50 bp. The BLASTX cutoff for EGTs is 1×10−5.
Figure 2
Figure 2. The taxanomic distribution of Bacterial Phylum in eight microbial samples from the cecum of chickens.
Figure 3
Figure 3. Phylogenetic composition of archaeal and eukaryotic environmental gene tags (EGTs) from two pyrosequenced chicken cecum samples.
The percent of EGTs in each of the archaeal class or eukaryotic division from the two pyrosequenced chicken cecum samples microbiomes is shown.
Figure 4
Figure 4. SEED subsystem composition of chicken cecum A and B microbiomes is shown.
The percent of environmental gene tags (EGTs) in each of the SEED subsystems from the chicken cecum A and B microbiomes is shown. The BLASTX cutoff for EGTs is 1×10−5.
Figure 5
Figure 5. Virulence subsystem composition of chicken cecum A and B microbiomes is shown.
The percent of environmental gene tags (EGTs) in each of the virulence subsystems from the chicken cecum A and B microbiomes is shown. The BLASTX cutoff for EGTs is 1×10−5.
Figure 6
Figure 6. Resistance to antibiotics and toxic compounds subsystem composition of chicken cecum A and B microbiomes is shown.
The percent of environmental gene tags (EGTs) in each of the Resistance to antibiotics and toxic compounds subsystems from the chicken cecum A and B microbiomes is shown. The BLASTX cutoff for EGTs is 1×10−5.
Figure 7
Figure 7. DNA Metabolism subsystem composition of chicken cecum A and B microbiomes is shown.
The percent of environmental gene tags (EGTs) in each of the DNA Metabolism subsystems from the chicken cecum A and B microbiomes is shown. The BLASTX cutoff for EGTs is 1×10−5.
Figure 8
Figure 8. Conjugative transposon, Bacteriodales subsystem composition of chicken cecum A and B microbiomes is shown.
The percent of environmental gene tags (EGTs) in each of the Conjugative transposon, Bacteriodales subsystems from the chicken cecum A and B microbiomes is shown. The BLASTX cutoff for EGTs is 1×10−5.
Figure 9
Figure 9. The mean (SE) percent of sequences identified within the SEED Virulence Subsystem in the microbiomes from chicken cecum, bovine rumen, mouce cecum and human fecal samples.
Figure 10
Figure 10. A multi-dimensional representation of the SEED Virulence Subsystem EGTs in the microbiomes from chicken cecum, bovine rumen, mouce cecum and human fecal samples.
The groups were divided to create similar group sizes which ensures better statistical outcomes. Each subsystem was tested for normality and log transformed where required. A General Linear Model was used with a post hoc Tukey's test being used to identify group membership. The differences between the subsystem abundance in each organism were then visualized using proxscal multidimensional scaling (MDS). The MDS was conducted on a single start and required 594 iterations, with Stress value of 0.102. The arrows indicate the direction in which the proportion of sequences was increasing and was driving the separation between metagenomes.
Figure 11
Figure 11. The distribution of sequences similar to each transposon gene from the chicken cecum, mouse cecum, human fecal and rumen microbiomes.
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"V体育2025版" References

    1. Handelsman J. Metagenomics: Application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews. 2004;68:669–685. - PMC - PubMed
    1. Hyman ED. A New Method of Sequencing DNA. Analytical Biochemistry. 1988;174:423–436. - PubMed
    1. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Science. 1998;281:363–365. - "V体育平台登录" PubMed
    1. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Analytical Biochemistry. 1996;242:84–89. - PubMed
    1. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376–380. - PMC - PubMed

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