Better understanding the spatial variation in resident pulmonary bacteria can help to link the disease severity of pulmonary tuberculosis (TB) with lung bacteriomes. This study aimed to investigate bacterial compositions in subniches of a lung lobe from pulmonary TB patient with two separate visible lesions. There were no significant differences between the bacterial compositions in normal tissue and TB lesions, but the bacterial compositions of the two TB lesions differed significantly (P = 0.009). Interestingly, 52 OTUs (relative abundance >1%) that specifically inhabiting certain lung niches were observed and they were affiliated with five phyla. Specific OTUs affiliated with Firmicutes mainly inhabited normal tissues. The dominant phylum in the lung subniches was Proteobacteria, with a relative abundance between 67.03% and 99.99%. Ralstonia, Achromobacter, and Pseudomonas were the most abundant genera, collectively accounting for 34.02% of total bacterial species. A total of 667 of the 700 bacterial connections in a co-correlation network of 145 OTUs (Operational Taxonomic Unit) were positive, indicating a cooperative relationship between bacterial members. Using PICRUSt tool, we do predict bacterial MetaCyc functions responsible for lipid synthesis and heme biosynthesis across the lung lobe that are essential for generation of caseous necrosis and TB disease pathology. MetaCyc pathways responsible for the degradation of aromatic biogenic amines, sulfur oxidation, and denitrification were all related to M.tb growth status, and they were significantly enriched in the lesion with necrosis than that with inflammation. These results open a new insight for us to comprehend the spatial profile of bacteriomes in a pulmonary TB human lung lobe, and shed light on the design of future diagnosis and treatment for pulmonary TB disease.

Diarrhea a serious disease, reported to be related with changes in microbial diversity is widely epidemic in the yaks on the Qinghai Tibet plateau. Herein, we preformed high-throughput sequencing of the parasitic diversity in 3 groups of yaks i.e. healthy adult yaks (HA), diarrheic adult yaks (DA) and diarrheic yak calves (DC) in Gannan Tibetan Autonomous Prefecture. The results showed that 2 Phyla, 3 Classes, 5 Orders, 4 Families and 6 Genera were discovered in HA yaks; 2 Phyla, 3 Classes, 6 Orders, 6 Families and 8 Genera were found in DA yaks while 2 Phyla, 5 Classes, 5 Orders, 10 Families and 7 Genera were observed in DC yaks. At Phylum level, Nematoda and Apicomplexa were detected in all three yak groups; however, Apicomplexa was found to be conspicuously higher in the DC yaks as compared to DA yaks (p < 0.05). At Class level, Litostomatea, Chromadorea and Gregarinasina were found in all three yak groups, while Spirotrichea and Colpodea were only found in the DC yaks. At Order level, Vestibuliferida, Tritrichomonadida, Rhabditida and Eugregarinorida were observed in all three yak groups; and Neogregarinorida was noted HA and DC yaks while Trichomonadida and Hypotrichomonadida were only found in DA yaks. Tritrichomonadida was found to be relatively higher in the DA yaks when compared with HA yaks (p < 0.05) and DC yaks (p < 0.05). At Family level, Simplicimonadidae and Haemonchidae were found in all three yak groups. Trichostrongylidae was observed in both HA and DA yak groups. Syncystidae was established in both HA and DC yak groups except DA yaks. Trichomonadidae and Dictyocaulidae were only found in DA yaks. Plectidae, Strongylidae, Echinamoebidae, Lecudinidae, Pseudokeronopsidae and Panagrolaimidae were only discovered in DC yaks. Simplicimonadidae was found to be remarkably higher in DA yaks as compared to HA and DC yak groups (p < 0.05); and Haemonchidae was detected at higher levels in HA yaks as compared to DA and DC yaks (p < 0.05). At Genus level, Entamoeba, Buxtonella and Haemonchus were found in all three yak groups. Plectus and Echinamoeba were only found in DC yaks; while Trichostrongylus and Trepomonas were observed in HA and DA yak groups. The genus Gregarina was found in both diarrheic yak groups; while the genera of Tetratrichomonas and Dictyocaulus were observed in DA yaks only. The present study herein reported an insight of the change of parasitic diversity in diarrheic yaks at high altitude area, which shall make contribution towards the solid prevention of diarrhea in yaks.

Diarrhea, the most common disease of perinatal yaks greatly affects the growth of animals. Changes in the number and structure of intestinal flora can cause the disorder of the intestinal environment leading to diarrhea. A study was conducted to investigate the impact of diarrhea on the number and structure of intestinal flora in perinatal yaks. Fecal samples were collected from healthy and diarrhea-affected perinatal yaks; and changes in number and structure of intestinal flora were compared by 16S rDNA V3-V4 region high-throughput sequencing. A total of 272071 optimized sequences were acquired from bacteria, which were identified from 9 phyla, 13 classes, 17 orders, 36 families and 72 genera. The number of bacterial species among diarrheac intestinal flora was lower than the healthy group, with no significant difference between two groups (P > 0.05); however, significant differences were observed at phylum, class, order, family and genus level between two groups (P < 0.05). This study has provided for the first time an insight of the changes occurring in intestinal flora in perinatal yaks at high altitudes of the world.

Mounting evidence revealed the importance of gut microbiota in host metabolism, immunity and physiology, and health. Yimeng black goats (YBGs) mainly distributed in Shandong province of China, displayed a complicated intestinal microecosystem, but studies of its gut microbiota are still insufficient to report. Therefore, this study was performed with an objective to characterize the intestinal microbial community structure and diversity in the small intestine (duodenum, jejunum and ileum) and cecum of YBGs and investigated the variability of gut microbiota of different intestinal segments. A total of 12 intestinal samples were collected from YBGs for high-throughput sequencing analysis based on V3-V4 variable region of 16S rRNA genes. Our results revealed alterations in gut microbial composition with obvious differences in relative abundance between the different intestinal segments. Additionally, small intestine including duodenum, jejunum and ileum not only displayed higher species abundance and diversity than cecum but also showed a significant difference among the main components of gut microbiota based on the analytical results of alpha and beta diversities. At the phylum level, Firmicutes and Proteobacteria were the most preponderant phyla in all the samples regardless of intestinal sites. Moreover, the microbiota in small intestine was significantly different from cecum, which were characterized by the higher relative abundance of Butyrivibrio_2, Megasphaera, Halomonas, Delftia, Hydrogenophaga, Limnobacter, Pseudoxanthomonas, Novosphingobium, Janibacter and Erythrobacter, whereas the levels of Butyricicoccus, unidentified_Lachnospiraceae, Fusicatenibacter, Akkermansia, Ruminococcaceae_NK4A214_group and Lactobacillus were lower. Overall, this study first characterized the profile of gut microbiota composition in different intestinal sites and provide better insight into intestinal microbial community structure and diversity of YBGs.