Molecular analysis of the bacterial microbiome in the forestomach fluid from the dromedary camel (Camelus dromedarius)
Molecular analysis of the bacterial microbiome in the forestomach fluid from the dromedary camel (Camelus dromedarius)
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DOI：
10.1007/s11033-012-2411-4
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发表时间：
2013-04-01
影响因子：
2.8
通讯作者：
Joshi, Chaitanya G.
中科院分区：
文献类型：
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作者：
Bhatt, Vaibhav D.;Dande, Suchitra S.;Joshi, Chaitanya G.
瘤胃微生物在反刍动物消化和吸收营养物质中起着重要作用，在调节瘤胃、食品发酵和生物质利用等领域具有巨大的应用潜力。为了研究骆驼瘤胃微生物的组成，本研究采用不依赖培养的方法研究了瘤胃微生物的多样性。它包括将本研究中调查的瘤胃样本与其他目前可用的宏基因组进行比较，以揭示瘤胃微生物系统的潜在差异。基于焦磷酸测序的宏基因组学应用MG-RAST分析系统发育和代谢谱。骆驼瘤胃样品焦磷酸测序得到8,979,755个核苷酸，组装成41,905个序列，平均读取长度为214个核苷酸。宏基因组分类分析显示，拟杆菌门（55.5%）、厚壁菌门（22.7%）和变形菌门（9.2%）是骆驼瘤胃的优势类群。在更精细的系统发育分辨率上，拟杆菌属在骆驼瘤胃宏基因组中占主导地位。功能分析表明，基于聚类的子系统和碳水化合物代谢子系统是最丰富的SEED子系统，分别占骆驼宏基因组的17%和13%。骆驼瘤胃的分类和功能与牛的元基因组高度相似，这并不奇怪，因为两者都是哺乳食草动物，具有相似的消化道结构和功能。结合焦磷酸测序方法和SEED数据库中基于子系统的注释，使我们能够了解这些微生物组的代谢潜力。总之，这些数据表明，无论瘤胃类型如何，农业和畜牧业实践都可能对瘤胃微生物群施加显著的选择压力。本研究为了解骆驼瘤胃微生物生态的复杂性提供了基础，同时也突出了与其他动物胃肠道环境的惊人相似性和差异性。
Rumen microorganisms play an important role in ruminant digestion and absorption of nutrients and have great potential applications in the field of rumen adjusting, food fermentation and biomass utilization etc. In order to investigate the composition of microorganisms in the rumen of camel (Camelus dromedarius), this study delves in the microbial diversity by culture-independent approach. It includes comparison of rumen samples investigated in the present study to other currently available metagenomes to reveal potential differences in rumen microbial systems. Pyrosequencing based metagenomics was applied to analyze phylogenetic and metabolic profiles by MG-RAST, a web based tool. Pyrosequencing of camel rumen sample yielded 8,979,755 nucleotides assembled to 41,905 sequence reads with an average read length of 214 nucleotides. Taxonomic analysis of metagenomic reads indicated Bacteroidetes (55.5 %), Firmicutes (22.7 %) and Proteobacteria (9.2 %) phyla as predominant camel rumen taxa. At a finer phylogenetic resolution, Bacteroides species dominated the camel rumen metagenome. Functional analysis revealed that clustering-based subsystem and carbohydrate metabolism were the most abundant SEED subsystem representing 17 and 13 % of camel metagenome, respectively. A high taxonomic and functional similarity of camel rumen was found with the cow metagenome which is not surprising given the fact that both are mammalian herbivores with similar digestive tract structures and functions. Combined pyrosequencing approach and subsystems-based annotations available in the SEED database allowed us access to understand the metabolic potential of these microbiomes. Altogether, these data suggest that agricultural and animal husbandry practices can impose significant selective pressures on the rumen microbiota regardless of rumen type. The present study provides a baseline for understanding the complexity of camel rumen microbial ecology while also highlighting striking similarities and differences when compared to other animal gastrointestinal environments.