Metagenomic analysis of faecal and environmental microbiota in rural mixed livestock farming systems in South Africa.
Mthembu, T.P.*1,2, Pierneef, R.E.2, Muchadeyi, F.C.3, Salawu-Rotimi, A.4, Hadebe, K.1
1 Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, South Africa
2 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
3 Animal Production and Health Section, Joint FAO\IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
4 Inqaba Biotec, Pretoria, Gauteng, South Africa
Smallholder livestock farming is crucial for economically disadvantaged farmers. In rural areas, farmers often practice mixed livestock extensive farming, rearing animals in limited space and sharing resources and the environment. However, the impact of mixed livestock farming on microbial transmission has not been thoroughly examined. This study aimed to explore faecal and environmental microbiomes in smallholder mixed livestock systems using a metagenomics approach. Twenty-eight fresh faecal samples from cattle (8), goats (7), chickens (7), and pigs (6) were collected from households in the Amathole district of Eastern Cape, South Africa. Water (5) and soil (6) samples were also collected to investigate the environmental contribution to host microbiomes. At the Phylum level, Proteobacteria were most abundant at 53.5%, followed by Bacteroidetes at 17.3%, Firmicutes at 15.1%, and Actinobacteria at 9.7%. Shannon and Simpson diversity indices indicated that soil had the highest microbial diversity, followed by goats, pigs, cattle, chickens, and water. Non-metric multidimensional scaling (NMDS) with Bray-Curtis dissimilarity revealed that soil and water samples formed separate clusters from faecal samples. Cattle formed a distinct cluster separate from other livestock species. Overlaps were observed between chickens and goats, as well as chickens and pigs. Significant differences in beta diversity for faecal and environmental samples were shown by PERMANOVA (P=0.001). Comparative analyses revealed that goats, chickens, and pigs shared 7.3% of the total genera, while cattle had the highest percentage of unique genera (16.1%). Cattle also shared a higher percentage of genera with water compared to the other animals. The metagenomic approach used enables surveillance of microbiota among animals in mixed livestock farming systems, which can be beneficial in investigating pathogen spread in these systems.
Keywords: metagenomics, livestock, microbiota, smallholder, environmental
