DataSheet_1_Geography, niches, and transportation influence bovine respiratory microbiome and health.docx

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.</p

Data_Sheet_1_Screening and evaluation of skin potential probiotic from high-altitude Tibetans to repair ultraviolet radiation damage.docx

Human skin microbes play critical roles in skin health and diseases. Microbes colonizing on the skin of Tibetans living in the high-altitude area for generations may have a stronger ability to resist the harsh environment, such as high ultraviolet radiation (UV). Isolation of a potential probiotic from Tibetans skin is beneficial for resistance of skin disease for humans in the world. In this study, the signature microbiota for Tibetan skin were characterized compared to low-altitude humans. Next, using culture-omics, 118 species were isolated. The culturability of high-altitude of Tibetan skin microbiome reached approximate 66.8%. Next, we found that one strain, Pantoea eucrina, had the greatest ability to repair UV damage to the skin as the lowest pathological score was observed in this group. Interestingly, another animal trial found this bacterium resisted UV rather than its metabolites. Using whole genome sequencing, this strain P. eucrina KBFS172 was confirmed, and its functions were annotated. It might involve in the metabolic pathway of carotenoid biosynthesis with anti-oxidative stress properties, which plays critical roles in UV-damage repair. In conclusion, we characterized the signature microbes of skin in high-altitude Tibetans, isolated a skin bacterium of Pantoea eucrina KBFS172 which could repair UV damage via involving the metabolic pathway of carotenoid biosynthesis. Our results provide a new potential skin probiotic for skin disease prevention or sunburn.</p

DataSheet_1_The spatial dissimilarities and connections of the microbiota in the upper and lower respiratory tract of beef cattle.docx

Bovine respiratory disease (BRD) causes morbidity and mortality in cattle. The critical roles of the respiratory microbiota in BRD have been widely studied. The nasopharynx was the most popular sampling niche for BRD pathogen studies. The oral cavity and other niches within the respiratory tract, such as nostrils and lung, are less assessed. In this study, oropharyngeal swabs (OS), nasal swabs (NS), nasopharyngeal swabs (NP), and bronchoalveolar lavage (BAL) were collected from calves located in four countries and analyzed for investigation of the dissimilarities and connections of the respiratory microbiota. The results showed that the microbial diversity, structure, and composition in the upper and lower respiratory tract in beef cattle from China, the USA, Canada, and Italy were significantly different. The microbial taxa for each sampling niche were specific and associated with their local physiology and geography. The signature microbiota for OS, NS, NP, and BAL were identified using the LEfSe algorithm. Although the spatial dissimilarities among the respiratory niches existed, the microbial connections were observed in beef cattle regardless of geography. Notably, the nostril and nasopharynx had more similar microbiomes compared to lung communities. The major bacterial immigration patterns in the bovine respiratory tract were estimated and some of them were associated with geography. In addition, the contribution of oral microbiota to the nasal and lung ecosystems was confirmed. Lastly, microbial interactions were characterized to reveal the correlation between the commercial microbiota and BRD-associated pathogens. In conclusion, shared airway microbiota among niches and geography provides the possibility to investigate the common knowledge for bovine respiratory health and diseases. In spite of the dissimilarities of the respiratory microbiota in cattle, the spatial connections among these sampling niches not only allow us to deeply understand the airway ecosystem but also benefit the research and development of probiotics for BRD.</p

MOESM8 of The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

Additional file 8: Figure S8. Relative abundance of predictive bacterial features in fecal samples at pre-breeding and first trimester and between open and bred cattle. 1, 2, 3 and 4 On the X-axis represent the pregnancy stage of pre-breeding, first trimester, second trimester, and third trimester, respectively

MOESM9 of The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

Additional file 9: Table S1. Sequencing results of mock community

MOESM2 of The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

Additional file 2: Figure S2. Rarefaction curve. (A) Rarefaction plot of vaginal samples (one curve per group). (B) Rarefaction plot of fecal samples. 1, 2, 3 and 4 in figure legend represent the pregnancy stage of pre-breeding, first trimester, second trimester, and third trimester, respectively

MOESM5 of The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

Additional file 5: Figure S5. Relative abundance of vaginal microbiota at phylum level for each sample with different pregnancy status. Multi-colored stack bar graphs represent the relative abundance. Each chart represents a stage (A: Pre-breeding, B: first trimester, C: second trimester, D: third trimester)

MOESM10 of The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

Additional file 10: Table S2. Summary of sequencing and alpha diversity results for fecal and vaginal samples

MOESM3 of The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

Additional file 3: Figure S3. Alpha diversity (Shannon index) change of vaginal microbiota for each sample. The bottom and top of each box are the first and third quartiles, respectively, and the band inside the box is the median. The connected point represent alpha diversity of animal vaginal samples at different stage

MOESM1 of The vaginal and fecal microbiomes are related to pregnancy status in beef heifers

Additional file 1: Figure S1. Flow chart of the experimental design and sample collection