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

Khethiwe Mtshali; Zamantungwa Thobeka Happiness Khumalo; Stanford Kwenda; Ismail Arshad; Oriel Matlahane Molifi Thekisoe

doi:10.1371/journal.pone.0273799

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

PLoS One. 2022 Aug 31;17(8):e0273799. doi: 10.1371/journal.pone.0273799. eCollection 2022.

Authors

Khethiwe Mtshali^{1

2}, Zamantungwa Thobeka Happiness Khumalo^{3

4}, Stanford Kwenda⁵, Ismail Arshad^{5

6}, Oriel Matlahane Molifi Thekisoe²

Affiliations

¹ Biomedical Sciences Department, Tshwane University of Technology, Pretoria, South Africa.
² Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa.
³ Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, South Africa.
⁴ Study Management, ClinVet International, Bainsvlei, Bloemfontein, South Africa.
⁵ Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
⁶ Faculty of Science, Department of Biochemistry and Microbiology, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa.

Abstract

Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. 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 in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bacteria / genetics
Bacteroidetes / genetics
Cattle
Feces / microbiology
Female
Microbiota* / genetics
Milk* / microbiology
RNA, Ribosomal, 16S / genetics
South Africa

Substances

RNA, Ribosomal, 16S

Grants and funding

K received funding from the National Research Foundation – Thuthuka PhD Track Funding Instrument in collaboration with the Tshwane University of Technology, unique grant No. 107416. The funders did not play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.