The Effects of Storage Temperature on the Bovine Nasal Microbiome

Bovine respiratory disease (BRD) is one of the largest economic burdens facing United States beef producer’s modern day. The complexity in the onset and development of this multifactorial disease necessitates further insights into its functions to alleviate the tremendous consequences it generates for producers. The respiratory microbiome and their metabolomics play an important role to maintain health and predict BRD. However, due to low biomass, new technology is needed to increase the microbial concentration for omics (e.g. metatranscriptomics) research. In this study, a novel self-enrichment storage technique on the bovine nasal microbiome was performed and compared to a traditional nasal sample storage method to further develop microbial communities. To assess these methods, two nasal swab samples from 2 cohorts (10 calves each) at two different locations were collected at two different timepoints. Subsequently, one set of samples was subjected to the novel technique (room temperature culture for 7 days in Amies buffer then stored at -80C, RT), while the other set followed traditional storage protocol (stored into -80C directly, UL) as a control. The nasal microbiome was then characterized using 16S rRNA sequencing of the V4 region. The RT storage technique was characterized by a significant decrease in microbial diversity and richness when compared to UL storage samples for both locations and timepoints (p\u3c0.05). Furthermore, RT samples showed distinct clustering from UL samples for both locations and timepoints when measured by both Jaccard and Bray-Curtis distances. Community structure between the storage techniques was also assessed at the genus level, characterized by a reduction in common airway genera such as Moraxella and Pasteurellaceae and an increase in common genera such as Enterococcus and Pseudomonas when the RT storage technique was compared to traditional UL storage. Random forest was found as an accurate model used to biomark and rank the most influential species differentiating the storage techniques. OTUs associated with BRD pathogens were identified as UL biomarkers, such as OTU53-Mycoplasma, OTU9-Moraxella and OTU35-Pasteurellaceae, while OTU1-Enterococcus and Otu18-Streptococcus were consistently observed to increase in RT, consistent with the corresponding genus shift. Finally, Procrustes analysis using Jaccard distance was used to determine the consistency in RT storage influence on the nasal microbiome among samples compared to UL storage. Consistent trend among samples was observed when comparing the RT storage technique to UL storage across both locations and timepoints. In summary, the novel self-enrichment room temperature storage technique was found to enrich specific microbiota but ultimately shifted the microbial structure of the “normal” respiratory community. Thus, future improvement and investigation into the novel self-enrichment technique is necessary to expand its uses for further analysis of the microbiomes function in the onset and development of BRD

Longitudinal Investigation of the Gut Microbiota in Goat Kids from Birth to Postweaning

Early microbial colonization in the gut impacts animal performance and lifelong health. However, research on gut microbial colonization and development in young ruminants, especially after weaning, is currently limited. In this study, next-generation sequencing technology was performed to investigate the temporal dynamic changes of the microbial community in the jejunum and colon of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days (d) of age. As age increased, significant increases in microbial diversity, including the number of Observed OTUs and the Shannon Index, were observed in both the jejunum and colon. Regarding beta diversity, significant shifts in community membership and structure from d1 to d84 were observed based on both Bray–Curtis and Jaccard distances. With increasing age, dominant genera in the jejunum shifted from Lactobacillus to unclassified Ruminococcaceae, unclassified Lachnospiraceae and unclassified Clostridiales through starter supplementation, whereas colonic dominant genera changed from Lactobacillus and Butyricicoccus, within d1–d28, to unclassified Ruminococcaceae, unclassified Clostridiales and Campylobacter after solid diet supplementation. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that are stage-specific in the jejunum and colon, respectively. In the jejunum and colon, a significantly distinct structure and membership of the microbiota was observed across all ages. The growth stage-associated microbiota in each gut compartment was also identified as a marker for biogeography. Our data indicate the temporal and spatial differences of the gut microbiota in goats are important for their performance and health. Early microbial colonization can influence microbial composition in later life (e.g., post-weaning phase). This study provides insights that the temporal dynamics of gut microbiota development from newborn to post-weaning can aid in developing feeding strategies to improve goat health and production