Microbial diversity in Swedish breeds of sheep analysed by amplicon based sequencing

Abstract: The gastrointestinal tract (GIT) of ruminants have divergent type of microbiome provides favourable environment for their growth. In many species, these microbiome considered as important source of assessing animal health & welfare. A total of 18 different Swedish sheep breeds (n = 15) and Landrace Goats as an out group (n = 3) were selected to examine the faecal microbiome, i.e., Rye (n=6), Gestrike (n=4), Roslag (n=3), and Cross-breed (Suffolk + Texel) (n=2) & Goat (n=3). The replicates of 32 faecal samples were subjected to DNA extraction, the gel electrophoresis method, and amplification for PCR products and mixing. The positive replicates of all extracted DNA samples were subjected to16s amplicon metagenomics coupled with next generation sequencing (Illumina), quality control (QC), and generated processed reads of total (1799435) for all bacteria and archaea. The total of (10734) amplicon sequence variants (ASV) after the filtration were employed for the phylogeny and taxonomy analysis of bacteria at the phylum and genus level. Bioinformatics and statistical analysis was done by using DADA2 pipeline in the R software and PRISM software (Graphpad) for further visual graphical presentation of data and compare the taxonomic classification. The highest relative abundance was measured for Firmicute (66%) and Bacteriodota (29%), Fibrobacteriota (1%), Proteobacteria (1%), and Verrucomicrobiota (2%) among top 10 phyla. While, in the top 15 genera, the highest relative abundance as shown in UCG-005 (24%), Rikenellaceae RC9 gut group (13%), Christensenellaceae R-7 group (12%), Bacteroides (8%), Monoglobus (6%), Alistipes (6%), Prevotellaceae UCG-004 (6%), Ruminococcus (5%), Akkermansia (4%) and Lachnospiraceae AC2044 group (5%). Bray–Curtis distances by Breed (PCoA and NMDS) showed clear difference in the clustering of sheep from goat samples and PERMANOVA showed significance results (P<0.05) but no significance difference were seen within different Swedish sheep breeds according to ANOVA and Tukeys test. This research is the first non-culture-based study to analyse the similarities and dissimilarities of the faecal microbiome by using 16S amplicon based metagenomics coupled with NGS (next generation sequencing) in different Swedish breeds of sheep and goat (outgroup).