Metagenomic analysis of the medicinal leech gut microbiota.

Michele A Maltz,Joerg Graf,Emily Ann Mcclure,Mitchell L Sogin,Pascal Lapierre,Lindsey Bomar,Hilary G Morrison

doi:10.3389/fmicb.2014.00151

Michele A Maltz, Joerg Graf + Show 5 more

Open Access

https://doi.org/10.3389/fmicb.2014.00151

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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.

Highlights

Microbes residing within and on the human body are estimated to exceed the number of host eukaryotic cells 10-fold
SAMPLING AND DNA EXTRACTION For the 16S rRNA gene sequencing DNA was isolated from the intraluminal fluid (ILF) and intestinum of four H. verbana specimen 96 h after first feeding heparinized sheep blood (Quad5)
Prior studies of the leech gut microbiome relied on culturing or Sanger sequencing of clone libraries (Graf, 1999; Worthen et al, 2006; Siddall et al, 2007, 2011; Laufer et al, 2008)

Summary

Introduction

Microbes residing within and on the human body are estimated to exceed the number of host eukaryotic cells 10-fold. As most microbes are not culturable under laboratory conditions, culture-independent approaches are necessary to gain further knowledge about the roles these symbionts perform inside their host. One such cultureindependent technique is metagenomics, in which genomes of a microbial community are sequenced, thereby revealing the metabolic potential of the community. The complexity of the human gut community can encompass hundreds of operational taxonomic units (OTUs) (Human Microbiome Project, 2012a,b). This complexity of the human gut microbiome, sampling depth constraints, and large amounts of sequence data pose challenges for studying digestive-tract microbiota. Available versatile invertebrate models with simpler microbial communities may overcome these challenges and provide important new insights into gut microbial symbioses (Ruby, 2008)

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