Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats

Abstract

Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.

Keywords: Bacteria; Capreolus capreolus; Habitat; Microbiota; Roe deer; Rumen content.

Fig. 1

Average crude nutrient contents [%/DM] in roe deer rumen content from different habitats. Yellowish shades in the habitat legend represent agricultural habitats, greenish-brownish different forest communities and grey alpine habitats. (for further details, see Table 1). Nutrient levels were determined using Weender and VanSoest analysis. The crude protein content is composed of plant and microbial protein. NFC stands for non-fibre-carbohydrates, which mainly includes sugars and starches and pectins

Fig. 2

Average ammonia and lactate contents [mM] in roe deer rumen liquid from different habitats, determined by photometric measurement

Fig. 3

Average volatile fatty acid contents [mM] in roe deer rumen liquid from different habitats, determined by gas chromatography

Fig. 4

A Principal coordinate analysis (Bray Curtis distances) with the distribution of rumen microbiota samples per habitat (Permanova test: p = 0.001) B: Chao1 and Shannon diversity index per habitat (p < 0.001)

Fig. 5

Distribution of the top 20 microbiota representatives per habitat

Fig. 6

Heatmap of the significant associations (-log(qval)*sign(coeff)) between the five members of the core microbiota and the crude nutrients and fermentation products. Positive or negative signs indicate an enrichment or decrease in the corresponding genera in parallel with increasing nutrient contents and fermentation products. The analysis was performed with the MaAsLin2 R package