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Metagenomic insights into the faecal microbiota of roe deer in Western Pomerania

ABSTRACT: Metagenomic insights into the faecal microbiota of roe deer in Western Pomerania

PROVIDER: PRJEB81356 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR13868126_1.fastq.gz	Fastqsanger.gz
	ERR13868126_2.fastq.gz	Fastqsanger.gz
	ERR13868127_1.fastq.gz	Fastqsanger.gz
	ERR13868127_2.fastq.gz	Fastqsanger.gz
	ERR13868128_1.fastq.gz	Fastqsanger.gz

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Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania.

Project description:As an integral part of the global wellbeing, the health of wild animals should be regarded just as important as that of humans and livestock. The investigation of wildlife health, however, is limited by the availability of samples. In an attempt to implement a method with little invasiveness and broad areas of application, shotgun metagenomics were utilised to investigate the faecal microbiome and its antimicrobial resistance genes (AMRG) in roe deer. These genes can facilitate antimicrobial resistances (AMR) in bacteria and are therefore of increasing importance in global health. Accordingly, the abundance in potential vectors like wildlife needs to be assessed. The samples were additionally investigated for ESBL-E. coli, an antibiotic resistant pathogen of global concern, via cultivation. Twenty-seven hunt-harvested animals in Western Pomerania were sampled. This study is the first to our knowledge to describe the faecal microbiome of the European roe deer (Capreolus capreolus), providing insights into the bacterial and archaeal composition. Among the animals, the microbiome was mostly similar and showed a comparable composition to what has been reported in related species, with a ratio of 1.76 between Bacillota and Bacteroidota. The normalised abundance of AMR genes was found to be 0.035 on average, which is similar to other investigations on wild ruminants. Selective cultivation found no ESBL-E. coli in the animals. The prevalence of AMRG in roe deer of Western Pomerania was found to be in line with previous results. The use of shotgun metagenomics allowed for the simultaneous investigation of composition and AMR genes in the faecal microbiome of roe deer, which suggests it as a promising method for the health monitoring of wildlife. This study is the first to describe the prokaryotic assemblage in the faeces of roe deer and its differences to the microbiomes published on other cervids were discussed.

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Roe Deer Reproduction in Western Poland: The Late Autumn Rut Phenomenon.

Project description:Roe deer (Capreolus capreolus L.) populations in Poland are characterized by low productivity, which is why their reproductive potential was investigated. The presence of corpora lutea (CL) on the ovaries of females hunted in autumn and winter in the years 2015 and 2016 was assessed. Most animals were post-rut and most often had multiple ovulations. However, in early autumn 2015, 60% of the females had no CL. Therefore, they did not participate in mating at the turn of July/August. Those that did ovulate were found to have one CL. In late autumn, 97% of the females were post-rut, mostly with twin ovulations. This confirmed the occurrence of a late autumn rut. This phenomenon had been suggested in studies but not confirmed. In contrast, almost 100% of roe deer ovulated in summer in 2016. It was hypothesized that the reason for the low mating activity of roe deer in the summer of 2015 was heat stress and limited food resources. The summer was exceptionally hot, with many days in July and August when temperatures exceeded 30 °C. The heat combined with low rainfall led to extreme drought. Meanwhile, July and August are the months of mating activity for roe deer. The late autumn rut allowed the roe deer-a monoestrous species-to limit the consequences of a decrease in mating activity or fertility during the hot summer. Global warming may affect roe deer reproduction, so climatic conditions should be considered in population studies, not only in terms of food availability.

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