Exploring the Gut Microbiome Alteration of the European Hare (Lepus europaeus) after Short-Term Diet Modifications

Abstract

This study aimed to characterise the gut microbiome composition of European hares (Lepus europaeus) and its potential changes after a short-term diet modification. The high sensitivity of European hare to habitat changes makes this species a good model to analyse possible alterations in gut microbiome after the introduction of additional nourishment into the diet. In total, 20 pairs were chosen for the experiments; 10 pairs formed the control group and were fed with standard fodder. The other 10 pairs represented the experimental group, whose diet was integrated with apples and carrots. The DNA from fresh faecal pellets collected after 4 days from the start of the experiment was extracted and the V3-V4 hypervariable regions were amplified and sequenced using the Illumina MiSeq^® platform. The obtained amplicon sequence variants were classified into 735 bacterial genera belonging to 285 families and 36 phyla. The control and the experimental groups appeared to have a homogenous dispersion for the two taxonomic levels analysed with the most abundant phyla represented by Bacteroidetes and Firmicutes. No difference between control and experimental samples was detected, suggesting that the short-term variation in food availability did not alter the hares' gut microbiome. Further research is needed to estimate significant time threshold.

Keywords: Lepus europaeus; diet modification; faecal samples; gut microbiota; hindgut fermenters.

Figure 1

Rarefaction curves based on the number of reads (sample size) and the number of ASVs in each sample. Each line represents one sample. No significant differences were recorded.

Figure 2

Shannon diversity calculated on raw data. Box plots show the indices based on samples bacterial communities in control and experimental samples. No significant differences were recorded.

Figure 3

Bar plots showing the relative abundances of bacterial phyla in the control and experimental samples. We reported the ASVs > 3% of the whole community. The two groups showed similar bacterial composition.

Figure 4

Bar plots showing the 10most abundant bacterial genera. We represented the ASVs > 1% among the 10most abundant bacterial genera. Each column represents a sample.

Figure 5

Results of nMDS at the genus level. Controls and experimental samples are represented by red and black dots, respectively.