Metagenomic analysis of fecal and environmental microbiota in rural mixed livestock farming systems in South Africa

Information from the abstract

In South African rural areas, farmers often practice mixed extensive livestock farming, facilitating microbial exchange among and between animal species and their environment. The composition and transmission potential of microbiomes between animals and their environments in these smallholder livestock systems remain largely unexplored, creating a gap in understanding how mixed-livestock farming affects gut and environmental microbiomes. Shotgun metagenomics was used to uncover the fecal and environmental microbiota in smallholder mixed livestock systems, aiming to understand microbiome transfer within these systems. A total of 111 samples were collected in KwaZulu-Natal and Eastern Cape provinces of South Africa, including 76 fecal samples from cattle, goats, sheep, pigs, and chickens; 18 soil samples; and 17 water samples. Taxonomic analysis of the sequencing data identified Proteobacteria as the dominant phylum across most hosts, except that pigs were dominated by Firmicutes. Moraxellaceae and Pseudomonadaceae were the differentiating families between monogastrics and ruminants. Although microbial diversity differences were significantly attributed to the host, genera such as Acinetobacter , Chryseobacterium , Flavobacterium , Pedobacter , and Pseudomonas were consistently found across all animal and environmental hosts. Cattle shared more genera with the environment than other animal species. Opportunistic pathogens, including Enterococcus spp., Escherichia coli , and Clostridium spp., were found across all the livestock species, and were highest in chickens. Additionally, some pathogens were detected in water but none in soil, suggesting water as a potential medium for pathogen transmission. The microbial exchange between livestock and their surroundings highlights the permeability of host-environment boundaries in smallholder systems.

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Related topics: Gut microbiota and health · Fecal contamination and water quality · Infections and bacterial resistance