Geography, niches, and transportation influence bovine respiratory microbiome and health

Abstract

Bovine respiratory disease (BRD), one of the most common and infectious diseases in the beef industry, is associated with the respiratory microbiome and stressors of transportation. The impacts of the bovine respiratory microbiota on health and disease across different geographic locations and sampling niches are poorly understood, resulting in difficult identification of BRD causes. In this study, we explored the effects of geography and niches on the bovine respiratory microbiome and its function by re-analyzing published metagenomic datasets and estimated the main opportunistic pathogens that changed after transportation. The results showed that diversity, composition, structure, and function of the bovine nasopharyngeal microbiota were different across three worldwide geographic locations. The lung microbiota also showed distinct microbial composition and function compared with nasopharyngeal communities from different locations. Although different signature microbiota for each geographic location were identified, a module with co-occurrence of Mycoplasma species was observed in all bovine respiratory communities regardless of geography. Moreover, transportation, especially long-distance shipping, could increase the relative abundance of BRD-associated pathogens. Lung microbiota from BRD calves shaped clusters dominated with different pathogens. In summary, geography, sampling niches, and transportation are important factors impacting the bovine respiratory microbiome and disease, and clusters of lung microbiota by different bacterial species may explain BRD pathogenesis, suggesting the importance of a deeper understanding of bovine respiratory microbiota in health.

The spatial dissimilarities and connections of the microbiota in the upper and lower respiratory tract of beef cattle

“…Geography serving an important role in affecting the bovine respiratory microbiota has been confirmed in our previous study (Chai et al, 2022b). In this study, we also found that either the upper or lower airway microbiota in the beef cattle from China (Asia), Canada and the United States (North America), and Italy (Europe) had different diversities and composition.…”

“…However, since the physiological and biochemical environments of different niches along the bovine respiratory tract result in the dissimilarities of microbial compositions, these opportunistic pathogens do not have great agreement with BRD onset (Dickson et al, 2016;Cirone et al, 2019). Moreover, the variation of geographic climate causes changes in the respiratory microbiota even in healthy cattle (Chai et al, 2022b), resulting in challenges to understanding the microbial ecology, and identifying pathogens and probiotics. Therefore, a deep investigation into the spatial dissimilarity and connection of the respiratory microbiota in healthy cattle is necessary and provides insights into bovine respiratory disease.…”

Long-distance movement dynamics shape host microbiome richness and turnover

“…Despite their broad parameterization, our simulations produce results that are analogous to those observed in real plant and animal communities (e.g. Bierlich et al 2018 , Risely et al 2018 , Webster et al 2020 , Skeen et al 2021 , Chai et al 2022 ), suggesting that even simple models can help explain ecological processes. Our simulations demonstrated that long-distance movement influences the membership and relative abundance of host microbiota (Fig.…”

“…Thus far, we have focused on the microbiota in a broader sense, but whether such a community is internal or external to the host will also make a difference to the influence of long-distance movements. In an artificial movement setting (translocations), equine caecal microbiota declined in species richness during travel (Perry et al 2018 ), whereas the bovine nasopharyngeal microbiota increased in richness (Chai et al 2022 ). Such shifts in microbiota structure may result from differences in exposure levels during movement, prior exposure to movement environments, or differential effects of movement-stressors on the microbiota (e.g.…”

Nasopharyngeal Bacterial Prevalence and Microbial Diversity at First Treatment for Bovine Respiratory Disease (BRD) and Its Associations with Health and Mortality Outcomes in Feedyard Cattle

“…Economically, mortality is severe as it results in a total loss of all resources invested in that animal. Thus, understanding factors that could result in fatality following treatment for disease is important [ 9 ]. While common pathogens associated with BRD cases have been identified, little research has been done evaluating differences in case outcomes based on deep nasopharyngeal microbiota at the time of treatment [ 10 , 11 , 12 ].…”