Epsilon Archive for Student Projects

Abstract

Microbiota tightly linked to their hosts significantly affect vertebrates' early growth, health, and survival. However, their effects on the fitness of wild and semi-domesticated species remain poorly understood. In Reindeers husbandry, calf mortality is one of the most significant challenges. Previous studies have shown that mortality is influenced by many interconnected factors, such as environmental conditions, maternal condition, sickness, and the quality of the pasture. Both the field of ecology and the management of reindeer herds require an understanding of the biological elements that contribute to the individuals' ability to survive. Using 16S rRNA gene metabarcoding, this study examined the oral and rectal microbiota of reindeer calves and how these microbial communities were influenced by factors such as sampling location, calf sex, and survival in the early stages of life.

Sequencing was performed using a paired-end Illumina approach, and DADA2 was used to identify amplicon sequence variants (ASVs). I used R packages such as phyloseq and vegan to perform analyses that let us look closely at the data. I used Observed ASVs and the Shannon diversity index to assess microbial diversity, and I used Bray–Curtis ’ dissimilarity, ordination plots, PERMANOVA, and GLM to assess community changes. I used logistic regression models based on ordination axes to assess whether microbial community composition may predict calf survival. I used several differential abundance (ALDEx2, MaAsLin2, and ANCOM-BC) to identify genera linked to early-life survival.

Alpha diversity did not differ among body-site samples. This indicates that diversity alone may not guarantee survival. Beta diversity differed between samples collected from the mouth and the rectum. PERMANOVA shows that the location of a sample has a big effect on the diversity of microbial communities. GLM models explored that microbes may predict survival. There were only weak connections, especially in the oral microbiome. Alysiella was one of the main mouth taxa discovered in survivors' microbiome analyses. The genera identified by differential abundance methods were Roseisolibacter, Capnocytophaga, Monoglobus, and Parafilimonas.

The findings indicate that the composition of the oral microbiome is marginally associated with the survival of reindeer calves during their early life stages.