Dataset Information

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

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.

SUBMITTER: Reich I

PROVIDER: S-EPMC6039444 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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

Reich Inga I Ijaz Umer Zeeshan UZ Gormally Mike M Smith Cindy J CJ

Scientific reports 20180710 1

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 ...[more]

PMID: 29991804

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Project description:Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson's correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism's metabolic activity and the microbes present in the gastro intestinal tract (GIT).

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Dataset Information

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

Publications

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

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