Exploration and comparison of bacterial communities present in bovine milk, faeces and blood using 16S rRNA metagenomic sequencing

Abstract

Livestock rearing plays a vital role in sustenance of the livelihoods of rural communities. In contrast, livestock serves as a potent reservoir of different pathogenic organisms that could have devastating health and economic implications, especially when proper husbandry and hygiene practices are not in place. Rural communities utilize cattle products and by-products to provide nourishment and income; to perform many cultural traditions and rituals; and to facilitate day-to-day household activities. Bovine faeces, milk and blood respectively derived from the gut, mammary glands and bloodstream niches are no exception and they are amongst the most commonly used by the Waaihoek community. Ecologically, these niches carry a diverse array of microbial communities of commensals, mutualists and pathogens. Although each of them harbours its own distinct and specialized microbial profile, there is an interplay of factors among these and various body niches which influence their colonization and assembly. Any imbalance in the structure of the microbes in this complex ecosystem of niches can lead to increased pathogenicity of constituent microbes and occurrence of diseases. This study aimed to simultaneously explore the microbiota of corresponding faecal, milk and blood samples from lactating cows using 16S rRNA metagenomic sequencing. A total of 24 sample pools were sequenced. Bacterial communities were inferred through the Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline coupled with SILVA database v138. All downstream analyses were performed in R v3.6.1. Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but did not vary significantly between blood and milk (Kruskal-Wallis, P < 0.05). Beta-diversity metrics on Principal Coordinate Analysis (PCoA) and Non-Metric Dimensional Scaling (NMDS) clustered samples by type suggesting that microbial communities of the studied niches are significantly different (PERMANOVA, P < 0.05). A number of taxa were significantly differentially abundant (DA) between groups based on the Wald test implemented in DESeq2 package (Padj < 0.01). Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces than in milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the most abundant taxon overall. The entire analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. A total of 58 genus-level taxa occurred concurrently between the niches, while bacterial signatures of at least 8 of these (i.e. Romboutsia, UCG-005, Prevotellaceae_UCG-004, Rikenellaceae_RC9_gut_group, Bacteroides, Christensenellaceae_R-7_group, Turicibacter and Fusobacterium) concurrently occurred in corresponding faeces, milk and

blood samples from the same group of animals constituting a pool. Firmicutes, Bacteroidota, and Proteobacteria were the most abundant phyla overall. The important taxa could be categorized into four pathogenic clusters: i) arthropod-borne; ii) food-borne and zoonotic; iii) mastitogenic and; iv) metritic and abortigenic. This study provides insight into the microbial composition of bovine faeces, milk, and blood and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the rural based communities pertaining to their unsanitary practices associated with the use of cattle by-products.