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

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.DATA AVAILABILITY STATEMENT : All FastQ sequence files generated from this work are available from the National Center for Biotechnology Information’s Short Reads Archive, under BioProject number PRJNA777568, Accession numbers SRI168760 -SRI168784. All relevant data are within the manuscript and its Supporting Information files.SUPPLEMENTARY MATERIAL : S1 Fig. A: Alpha diversity box-plots showing Chao1 richness estimates per sample group. *Significant at P < 0,05. B: Alpha diversity box-plots showing Shannon diversity estimates per sample group. *Significant at P < 0,05. C: Alpha diversity box-plots showing Simpson’s diversity estimates per sample group. *Significant at P < 0,05. https://doi.org/10.1371/journal.pone.0273799.s001S2 Fig. UpSetR intersection plot showing number of unique and shared taxa at family level between faeces, milk and blood groups. https://doi.org/10.1371/journal.pone.0273799.s002S1 Table. Read counts tracked through the DADA2 pipeline including ASV counts, richness and genus level-resolved ASVs per sample. https://doi.org/10.1371/journal.pone.0273799.s003S2 Table. Alpha diversity values calculated using Shannon, Simpson and Chao1 indices. https://doi.org/10.1371/journal.pone.0273799.s004S3 Table. Total number of taxa detected per taxonomic rank across bovine faeces, milk and blood. https://doi.org/10.1371/journal.pone.0273799.s005S4 Table. Top 15 abundant taxa with their respective overall rankings and distribution across the three sample groups. https://doi.org/10.1371/journal.pone.0273799.s006S5 Table. Prevalence of potentially pathogenic genera of veterinary significance per sample group. https://doi.org/10.1371/journal.pone.0273799.s007S6 Table. Bacterial taxa shared between bovine faeces, milk and blood and their overall raw and relative abundances. https://doi.org/10.1371/journal.pone.0273799.s008S7 Table. Genus-level taxa exclusively detected and shared between faeces, milk and blood samples. https://doi.org/10.1371/journal.pone.0273799.s009S8 Table. A-C Differentially abundant taxa between blood and faeces; blood and milk and; faeces and milk (Padj < 0,01). https://doi.org/10.1371/journal.pone.0273799.s010S1 Raw images. Gel electrophoresis image of Anaplasma PCR targeting the 16S rRNA gene from blood samples. Image taken under UV transillumination using Enduro™ GOS gel documentation system. Lane 1 = 1 kb DNA ladder; 2–10 = Anaplasma positive samples; 11 = nuclease free H20 (-ve); 12 = A. marginale (+ve). https://doi.org/10.1371/journal.pone.0273799.s011The National Research Foundation – Thuthuka PhD Track Funding Instrument in collaboration with the Tshwane University of Technology.http://www.plosone.orgdm2022Veterinary Tropical Disease

Bacterial pathogens identified from houseflies in different human and animal settings : a systematic review and meta‐analysis.

Housefly (Musca domestica) is an excellent candidate for the distribution of susceptible and resistant bacterial strains that potentially threaten public health. To date, there is a paucity of information on the global distribution of pathogenic bacteria of medical and veterinary importance from diverse environmental settings. Therefore, this study was undertaken to conduct a systemic review and meta-analysis to estimate occurrence of various bacterial species of medical and veterinary importance harboured by houseflies around the world. Published articles from 1980 to 2020 were retrieved from electronic databases and assessed for eligibility according to Preferred Reporting Items for Systemic Reviews and Meta-Analysis guidelines. Seventy-eight studies were included in the review with only 44 studies being eligible for meta-analysis. Results indicated that eligible studies used in this review were from four continents, i.e., Asia (47.4%) America (23.1%), Africa (20.5%) and Europe (8.9%). The majority of the studies (56.4%) used the culture method for the identification of bacterial pathogens, while 30.7% used both culture and PCR techniques. For meta-analysis, we focused on five pathogenic bacterial species including Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus. High heterogeneity was found among studies investigating different pathogens including E. coli (Q = 10,739.55; I2 = 99.60; Q-p 0.0001), E. faecium (Q = 317.61; I2 = 86.46; Q-p < 0.0001), K. pneumonia (Q = 1,576.61; I2 = 97.27; Q-p < 0.0001), S. aureus (Q = 2,439.12; I2 = 98.24; Q-p < 0.0001) and P. aeruginosa (Q = 1,283.0; I2 = 96.65; Q-p < 0.0001). Furthermore, it was observed that houseflies carried a considerable number of susceptible and antibiotic-resistant bacterial strains that pose considerable threats to public health. Findings from this study have provided more insight on the vectoral potential of houseflies in the transmission of significant bacterial pathogens from different regions across the world. Further investigation is required to quantify the bacterial contamination and dissemination by houseflies