Metagenomic analysis of the medicinal leech gut microbiota

Abstract

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.

Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech

“…16S rRNA V4 deep sequencing of the H. verbana ILF identified the same two dominant taxa as reported previously from 454 pyrosequncing of the 16S rRNA V6 region (21), 16S rRNA V3-V4 deep sequencing (17), and 16S rRNA clone library analysis (14) (Table 1). The ILF microbiota of H. verbana has been described as being dominated by Mucinivorans and Aeromonas with occasional Clostridial spp (14, 21).…”

“…16S rRNA V4 deep sequencing of the H. verbana ILF identified the same two dominant taxa as reported previously from 454 pyrosequncing of the 16S rRNA V6 region (21), 16S rRNA V3-V4 deep sequencing (17), and 16S rRNA clone library analysis (14) (Table 1). The ILF microbiota of H. verbana has been described as being dominated by Mucinivorans and Aeromonas with occasional Clostridial spp (14, 21). In the 36 animals tested, Mucinivorans and Aeromonas together accounted for 30.6 – 99.8% (median = 81.8%) of the sequences from the ILF (Table 1) with Proteiniclasticum making up an additional 0 – 63.4% (median when present = 10.8%, present in 69% of animals) and Fusobacterium making up an additional 0 – 28.3% (median when present = 11.5%, present in 47% of animals) (Table S2).…”

“…Subsequent studies revealed the presence of additional Aeromonas spp in H. verbana and other hirudinid leeches (18-20). Clostridial species have also been detected in culture-independent studies of the ILF of H. verbana (14, 21) and H. orientalis (20). Several functions for the dominant crop microbiota have been proposed including providing essential nutrients to the host (9, 22, 23), preventing other bacteria from colonizing, inhibiting putrefaction of the ILF (24), aiding the host’s immune responses (25, 26), or initiating the digestion of erythrocytes (27).…”

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

“…In particular, members of the Desulfovibrionaceae have recently been identified in the intestines of the Chinese roe deer Capreolus pygargus (Li, Zhang, Xu, et al, 2014) and Pekin/Muscovy ducks (Vasaï et al, 2014), the digestive tract of the medicinal leech Hirudo verbena (Maltz et al, 2014) and larvae of the beetle Holotrichia parallela (Huang & Zhang, 2013), faecal samples of Mexican black howler (Alouatta pigra) monkeys (Nakamura et al, 2011) and chickens from Czech poultry farms (Videnska et al, 2014), homogenates of the deep-sea sponge Geodia spp. (Brück et al, 2010) and Asbestopluma hypogea (Dupont, Corre, Li, Vacelet, & BourguetKondracki, 2013).…”

An overview of leech and its therapeutic applications

“…Metagenomic studies have been conducted to get comprehensive information pertaining to leech gut microflora [28,70]. However, none of the study investigated the origin of the gut microflora, whether it is found in its habitat or not.…”