Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA.
Marine Biological Laboratory, The Josephine Bay Paul Center Woods Hole, MA, USA.
Front Microbiol. 2014 Apr 17;5:151. doi: 10.3389/fmicb.2014.00151. eCollection 2014.
There are trillions of microbes found throughout the human body and they exceed the number of eukaryotic cells by 10-fold. Metagenomic studies have revealed that the majority of these microbes are found within the gut, playing an important role in the host's digestion and nutrition. The complexity of the animal digestive tract, unculturable microbes, and the lack of genetic tools for most culturable microbes make it challenging to explore the nature of these microbial interactions within this niche. The medicinal leech, Hirudo verbana, has been shown to be a useful tool in overcoming these challenges, due to the simplicity of the microbiome and the availability of genetic tools for one of the two dominant gut symbionts, Aeromonas veronii. In this study, we utilize 16S rRNA gene pyrosequencing to further explore the microbial composition of the leech digestive tract, confirming the dominance of two taxa, the Rikenella-like bacterium and A. veronii. The deep sequencing approach revealed the presence of additional members of the microbial community that suggests the presence of a moderately complex microbial community with a richness of 36 taxa. The presence of a Proteus strain as a newly identified resident in the leech crop was confirmed using fluorescence in situ hybridization (FISH). The metagenome of this community was also pyrosequenced and the contigs were binned into the following taxonomic groups: Rikenella-like (3.1 MB), Aeromonas (4.5 MB), Proteus (2.9 MB), Clostridium (1.8 MB), Eryspelothrix (0.96 MB), Desulfovibrio (0.14 MB), and Fusobacterium (0.27 MB). Functional analyses on the leech gut symbionts were explored using the metagenomic data and MG-RAST. A comparison of the COG and KEGG categories of the leech gut metagenome to that of other animal digestive-tract microbiomes revealed that the leech digestive tract had a similar metabolic potential to the human digestive tract, supporting the usefulness of this system as a model for studying digestive-tract microbiomes. This study lays the foundation for more detailed metatranscriptomic studies and the investigation of symbiont population dynamics.
人体内存在着数以万亿计的微生物，其数量是真核细胞的 10 倍。宏基因组研究表明，这些微生物大多数存在于肠道中，在宿主的消化和营养中发挥着重要作用。动物消化道的复杂性、不可培养的微生物以及大多数可培养微生物缺乏遗传工具，使得在这个生态位中探索这些微生物相互作用的性质具有挑战性。医用水蛭 Hirudo verbana 已被证明是克服这些挑战的有用工具，因为其微生物组简单，并且其中一种占主导地位的肠道共生菌 Aeromonas veronii 具有遗传工具。在这项研究中，我们利用 16S rRNA 基因焦磷酸测序进一步探索了水蛭消化道的微生物组成，证实了两种分类群的主导地位，即类似 Rikenella 的细菌和 A. veronii。深度测序方法揭示了微生物群落中存在其他成员，这表明存在一个中等复杂的微生物群落，具有 36 个分类群的丰富度。利用荧光原位杂交（FISH）证实了 Proteus 菌株作为新鉴定的水蛭胃内居民的存在。还对该群落的宏基因组进行了焦磷酸测序，并将 contigs 分类为以下分类群：类似 Rikenella（3.1 MB）、Aeromonas（4.5 MB）、Proteus（2.9 MB）、Clostridium（1.8 MB）、Eryspelothrix（0.96 MB）、Desulfovibrio（0.14 MB）和 Fusobacterium（0.27 MB）。利用宏基因组数据和 MG-RAST 对水蛭肠道共生菌进行了功能分析。将水蛭肠道宏基因组的 COG 和 KEGG 类别与其他动物消化道微生物组进行比较，表明水蛭消化道具有与人类消化道相似的代谢潜力，支持该系统作为研究消化道微生物组的模型的有用性。这项研究为更详细的宏转录组研究和共生体种群动态的研究奠定了基础。
