The bacterial and archaeal communities of flies, manure, lagoons, and troughs at a working dairy

Abstract

Background: Fundamental investigations into the location, load, and persistence of microbes, whether beneficial or detrimental, are scarce. Many questions about the retention and survival of microbes on various surfaces, as well as the load necessary for spread, exist. To answer these questions, we must know more about where to find various microbes and in what concentrations, the composition of the microbial communities, and the extent of dissemination between various elements. This study investigated the diversity, composition, and relative abundance of the communities associated with manure, lagoons, troughs, house flies, and stable flies present at a dairy, implementing two different free-stall management systems: flow-through and cross-vent. Shotgun metagenomics at the community level was used to compare the microbiomes within the dairy, allowing confident interpretation at the species level.

Results: The results showed that there were significant difference in microbial composition between not only each of the dairy elements but also management styles. The primary exceptions were the microbiomes of the house fly and the stable fly. Their compositions heavily overlapped with one another, but interestingly, not with the other components sampled. Additionally, both species of flies carried more pathogens than the other elements of the dairy, indicating that they may not share these organisms with the other components, or that the environments offered by the other components are unsatisfactory for the survival of some pathogens..

Conclusion: The lack of overlapping pathogen profiles suggests a lack of transfer from flies to other dairy elements. Dairy health data, showing a low incidence of disease, suggests minimal sharing of bacteria by the flies at a level required for infection, given the health program of this dairy. While flies did carry a multitude of pathogenic bacteria, the mere presence of the bacteria associated with the flies did not necessarily translate into high risk leading to morbidity and mortality at this dairy. Thus, using flies as the sole sentinel of dairy health may not be appropriate for all bacterial pathogens or dairies.

Keywords: Diptera; bovine; microbiome; pathogen; xenosurveillance.

Figure 1

Alpha diversity graphic: box and whiskers diagram of the CHAO1 diversity results of the microbiomes of the elements within the dairy components (manure, lagoons, troughs, stable fly, and house fly) separated into results from both dairy management systems of cross-vent (CV) and flow-through (FT) free-stall styles.

Figure 2

Principal coordinate analysis scatter plot using the Bray–Curtis dissimilarity values of relative abundances of lineages within the dairy communities. Samples were collected from the components listed within the cross-vent (CV) and flow-through (FT) management areas.

Figure 3

Diagrams presented in Table 4. The number of species in a five-way comparison unique to the components sampled within the management style areas of cross-vent (A), flow-through (B) areas, and CV + FT data combined (C). The number of pathogenic species in a five-way comparison unique to the components sampled within the management style areas of cross-vent (D), flow-through (E) areas, and CV + FT data combined (F).

Figure 4

Heatmap of the percent relative abundance of 79 pathogens identified at the species level within the components (manure, lagoon, trough, house fly, and stable fly) of the cross-vent (CV) and flow-through (FT) free-stall management styles. For natural log transformation, “0” was converted to “0.001.”