16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus

Inga Reich,Umer Zeeshan Ijaz,Cindy J Smith,Mike Gormally

doi:10.1038/s41598-018-28720-3

Abstract

The EU-protected slug Geomalacus maculosus Allman occurs only in the West of Ireland and in northern Spain and Portugal. We explored the microbial community found within the faeces of Irish specimens with a view to determining whether a core microbiome existed among geographically isolated slugs which could give insight into the adaptations of G. maculosus to the available food resources within its habitat. Faecal samples of 30 wild specimens were collected throughout its Irish range and the V3 region of the bacterial 16S rRNA gene was sequenced using Illumina MiSeq. To investigate the influence of diet on the microbial composition, faecal samples were taken and sequenced from six laboratory reared slugs which were raised on two different foods. We found a widely diverse microbiome dominated by Enterobacteriales with three core OTUs shared between all specimens. While the reared specimens appeared clearly separated by diet in NMDS plots, no significant difference between the slugs fed on the two different diets was found. Our results indicate that while the majority of the faecal microbiome of G. maculosus is probably dependent on the microhabitat of the individual slugs, parts of it are likely selected for by the host.

Highlights

While the study of gut microbial communities is becoming increasingly popular, there is still a dearth of research focusing on those of wild animal populations[1]
Cardoso et al.[15] show that a change in diet causes a shift in the gut microbial community of Achatina fulica, similar to that observed in humans and other animals, and the authors suggest that the snail gut microbiota might be able to influence the energy balance equation and affect how much energy is extracted from the diet[15]
We employed a two-pronged approach, utilising faecal samples from slugs that were collected from the wild as well as from laboratory hatched specimens to address our aims: 1. To determine whether the slug is a major selector of its microbiome or whether their gut microbes are more reflective of their environment, we collected faecal samples from slugs which were sampled from eleven different sites/seven different habitats

Summary

Introduction

While the study of gut microbial communities is becoming increasingly popular, there is still a dearth of research focusing on those of wild animal populations[1] This is despite the large influence that factors such as habitat and food availability are likely to have on the gut microbial composition. Apart from habitat and diet specific microbes the gut harbours a “core microbiome”, members of which have likely co-evolved with their hosts and fulfil important functions including nutrient extraction such as cellulose degradation in termites[11] or aid with the breakdown of toxins which have been ingested with the diet[12,13] These bacteria are often specialized gut symbionts and are transmitted vertically from the eggs, through coprophagy or social interactions and it was found that gut communities of social insects were usually more distinctive and consistent than those of non-social invertebrates[4]. This study contributes to the further understanding of general invertebrate host-microbe interactions

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