Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination

Background The blanket usage of antimicrobials at the end of lactation (or “drying off”) in dairy cattle is under increasing scrutiny due to concerns about antimicrobial resistance. To lower antimicrobial usage in dairy farming, farmers are now encouraged to use “selective dry cow therapy” whereby only cows viewed as at high risk of mastitis are administered antimicrobial agents. It is important to gain a better understanding of how this practice affects the udder-associated microbiota and the potential knock-on effects on antimicrobial-resistant bacterial populations circulating on the farm. However, there are challenges associated with studying low biomass environments such as milk, due to known contamination effects on microbiome datasets. Here, we obtained milk samples from cattle at drying off and at calving to measure potential shifts in bacterial load and microbiota composition, with a critical assessment of contamination effects. Results Several samples had no detectable 16S rRNA gene copies and crucially, exogenous contamination was detected in the initial microbiome dataset. The affected samples were removed from the final microbiome analysis, which compromised the experimental design and statistical analysis. There was no significant difference in bacterial load between treatments (P > 0.05), but load was lower at calving than at drying off (P = 0.039). Escherichia coli counts by both sequence and culture data increased significantly in the presence of reduced bacterial load and a decreasing trend of microbiome richness and diversity. The milk samples revealed diverse microbiomes not reflecting a typical infection profile and were largely comprised of gut- and skin-associated taxa, with the former decreasing somewhat after prolonged sealing of the teats. Conclusions The drying off period had a key influence on microbiota composition and bacterial load, which appeared to be independent of antimicrobial usage. The interactions between drying off treatment protocol and milk microbiome dynamics are clearly complex, and our evaluations of these interactions were restricted by low biomass samples and contamination effects. Therefore, our analysis will inform the design of future studies to establish whether different selection protocols could be implemented to further minimise antimicrobial usage.

Ground Water Contamination: Effects and Remedies

Studies on “ground water contamination : effects and remedies” have been conducted, in the light of these, field work studies in Obudu and Obanliku local Government Areas of Cross River State, South Eastern Nigeria, was conducted. Fifteen (15) locations of water for drinking and other domestic uses were carefully studied in the area, with their surface to water depth values recorded. Five(5) of the locations were at surface saturated water depressions(SWD), seven(7) were Hand dug wells(well), while three(3) were bore holes(BH). The physiochemical composition data compared with world Health Organization (WHO) standard shows that, the bore water was safer for drinking than the hand dug wells and surface water in saturated water depressions. Coliform count unite per 100ml of water, were detected in most of the locations in the saturated water depressions and hand dug wells, showing evidence of biogenic interference with the water. Coliform count unite per 100ml of water was not detected in any of the three bore holes, probably due to their depth distance from Biogenic activities. Phosphate and Nitrate levels were significantly above WHO standard in saturated water depressions and Hand dug wells, probably due to erosional and leaching actions of inorganic fertilizers from farm lands and waste from near dump site. It is important to note that most water borne diseases are as a result of ground water communication with contaminant, such as heavy metals, leachate from dump sites, pollutants from inorganic fertilizers, pith toilets sea water intrusion etc., most boreholes are contaminated by these processes. This is one of the reasons for the increase in the rate of cancer in most developing countries. Hence, heavy metals are known to be carcinogenic to the human cells, and also can cause mutation. The remedies to these include: The process of exploiting and storing ground water should be done with all safety precautions, such as making sure biochemical parameters in water are in line with WHO standard Thorough biochemical analysis and test for the presence of heavy metal contamination and coliform count and other contaminants should be done on ground water, before use for domestic and industrial purposes. Surface depth measurement of recharge zones in boreholes should be carried out to ensure that borehole water is from confined aquifers that are safe for domestic and industrial uses. Proper waste disposing system such as engineered toilet pits, engineered dump sites and effective management of electronic waste should be monitored and implemented Where the purity of the water is not satisfactory, such water should be properly treated before used for drinking and other domestic purposes.