Paper Title
Characterisation of Raw Milk Microbiome from Harrismith, Free-State using 16S rRNA Gene Sequencing

Abstract
Milk microbiota play a vital role in determining the safety and quality of milk and products derived from milk. Merely, few studies have been conducted to investigate and understand the microbial community of raw milk in South Africa. Thus, we explored the microbial diversity of raw milk from bulk tanks of small-scale farms using single-molecule real time (SMRT) sequencing from Pacific Biosciences (PacBio). A total of three (3) samples were collected from the selected small-scale farms in Harrismith, Free State Province, South Africa. The results showed that, total of 21,792 high-quality 16S rRNA gene sequences that were obtained, belonged to 2 phyla, 5 families, 7 genera and 131 species. The results showed that the family of Clostridiaceae was mostly abundant, followed by Peptostreptococcaceae and Erysipelotrichaceae. Whilst, Romboutsia was the most abundant genus followed Turicibacter. The species level analysis revealed that sample G3 had Turicibacter sp. as the most cluster size with 87 (1.18%) followed by Clostridium disporicum and Clostridiaceae bacterium at 21 (0.28%) and 19 (0.26%) respectively. Whilst, sample G4 had Aerococcus sp. as the dominant species with cluster size of 249 (4.76%), followed by Turicibacter sp. at 102 (1.95%) and Clostridium sp. at 14 (0.27%). Lastly, sample G6 had Turicibacter sp. at 196 (2.13%) followed by Enterococcus faecalis and Clostridium disporicum at 24 (0.26%) and 22 (0.24%) respectively. It was therefore evident that samples showed high microbial diversity. Moreover, it may be argued that this study will assist farmers and their suppliers to understand the full spectrum of the microbes associated with milk. Keywords - Milk, Microbiota, Metagenomics, 16S Ribosomal DNA Sequencing