Qu Ani, Brulc Jennifer M, Wilson Melissa K, Law Bibiana F, Theoret James R, Joens Lynn A, Konkel Michael E, Angly Florent, Dinsdale Elizabeth A, Edwards Robert A, Nelson Karen E, White Bryan A
Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America.
PLoS One. 2008 Aug 13;3(8):e2945. doi: 10.1371/journal.pone.0002945.
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.
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. 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. Furthermore, this suggests that the evolution of host specific metavirulomes is a contributing factor in disease resistance to zoonotic pathogens.
鸡盲肠复杂的微生物群落在这些动物的营养利用、生长和健康方面发挥着重要作用。由于我们对盲肠中大多数物种的能力了解非常有限，我们通过使用随机样本焦磷酸测序对微生物群落结构和功能基因含量进行比较分析，研究了微生物群的作用。本研究的总体目标是使用无病原体鸡和感染空肠弯曲菌的鸡来表征鸡盲肠微生物群。
方法/主要发现：使用比较宏基因组焦磷酸测序从两个鸡盲肠样本中生成了55364266个碱基的随机样本焦磷酸序列数据。使用基于SEED子系统的注释鉴定了小亚基核糖体DNA（SSU rDNA）基因标签和环境基因标签（EGT）。每个盲肠样本中检测到的系统发育型和EGT的分布主要来自厚壁菌门、拟杆菌门和变形菌门，这与先前鸡盲肠的SSU rDNA文库一致。碳水化合物代谢和毒力基因是这两种微生物群EGT含量的主要组成部分。对鸡盲肠、小鼠盲肠和人类粪便微生物群中SEED毒力子系统（元病毒组）中的十二条主要途径进行比较，结果表明这些微生物群的元病毒组不同，且元病毒组按宿主环境聚类。鸡盲肠微生物群在SEED接合转座子子系统中具有最广泛的EGT范围，然而小鼠盲肠微生物群在该子系统中显示出更高丰度的EGT。来自一个微生物群样本的基因组装体（32个重叠群）主要来自拟杆菌门，其中七个与转座酶具有序列相似性，而其余序列与分解代谢基因家族的序列最相似。
结论/意义：该分析表明，移动DNA元件是盲肠微生物群的主要功能成分，从而促进水平基因转移和功能性微生物群进化。此外，这些微生物群的元病毒组似乎与宿主环境相关。这些数据对于定义宿主物种中的核心和可变微生物群含量具有重要意义。此外，这表明宿主特异性元病毒组的进化是对人畜共患病原体抗病性的一个促成因素。
