Dataset Information

Bacterial diversity and community in Qula from the Qinghai-Tibetan Plateau in China.

ABSTRACT: Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3-V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.

SUBMITTER: Zhu Y

PROVIDER: S-EPMC6286660 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Bacterial diversity and community in Qula from the Qinghai-Tibetan Plateau in China.

Zhu Yan Y Cao Yingying Y Yang Min M Wen Pengchen P Cao Lei L Ma Jiang J Zhang Zhongmin Z Zhang Weibing W

PeerJ 20181205

Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3-V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicatin ...[more]

PMID: 30568858

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Project description:BACKGROUND:Methane emissions by methanogen from livestock ruminants have significantly contributed to the agricultural greenhouse gas effect. It is worthwhile to compare methanogen from "energy-saving" animal (yak) and normal animal (cattle) in order to investigate the link between methanogen structure and low methane production. RESULTS:Diversity of methanogens from the yak and cattle rumen was investigated by analysis of 16S rRNA gene sequences from rumen digesta samples from four yaks (209 clones) and four cattle (205 clones) from the Qinghai-Tibetan Plateau area (QTP). Overall, a total of 414 clones (i.e. sequences) were examined and assigned to 95 operational taxonomic units (OTUs) using MOTHUR, based upon a 98% species-level identity criterion. Forty-six OTUs were unique to the yak clone library and 34 OTUs were unique to the cattle clone library, while 15 OTUs were found in both libraries. Of the 95 OTUs, 93 putative new species were identified. Sequences belonging to the Thermoplasmatales-affiliated Linage C (TALC) were found to dominate in both libraries, accounting for 80.9% and 62.9% of the sequences from the yak and cattle clone libraries, respectively. Sequences belonging to the Methanobacteriales represented the second largest clade in both libraries. However, Methanobrevibacter wolinii (QTPC 110) was only found in the cattle library. The number of clones from the order Methanomicrobiales was greater in cattle than in the yak clone library. Although the Shannon index value indicated similar diversity between the two libraries, the Libshuff analysis indicated that the methanogen community structure of the yak was significantly different than those from cattle. CONCLUSION:This study revealed for the first time the molecular diversity of methanogen community in yaks and cattle in Qinghai-Tibetan Plateau area in China. From the analysis, we conclude that yaks have a unique rumen microbial ecosystem that is significantly different from that of cattle, this may also help to explain why yak produce less methane than cattle.

Project description:Blastocystis is one of the most common enteric parasites in humans and domestic animals. For Tibetan sheep and Tibetan goats, the traditional grazing methods still occupy a dominant position, and the close contact between humans and domestic animals increases the risk of infection by Blastocystis between herdsmen and livestock. However, less pertinent information is available for Tibetan sheep or Tibetan goats. In this study, 880 fecal specimens from Tibetan sheep and Tibetan goats were collected from 6 sampling sites in Tibet to test for Blastocystis using the polymerase chain reaction and sequencing analysis of the partial SSU rRNA gene. The infection rate of Blastocystis was 8.55% for Tibetan sheep (53/620) and 8.46% for Tibetan goats (22/260). The genetic analysis of 53 positive samples from Tibetan sheep identified 4 known subtypes (ST4, ST5, ST10, and ST14). Four known subtypes (ST1, ST5, ST6, and ST10) were identified in Tibetan goats. ST10 was the dominant subtype in Tibetan sheep and Tibetan goats, accounting for 65.33% (49/75) of total subtypes. ST1, ST4, ST5, and ST6 were recognized as belonging to zoonotic subtypes. This report provides a detailed data on the prevalence and subtype distribution of Blastocystis in Tibetan sheep and Tibetan goats in Tibet, which enriches the epidemiological data of Blastocystis infection in Tibetan sheep and Tibetan goats in China. Our results indicated that Tibetan sheep and Tibetan goats can be infected with multiple Blastocystis subtypes, including zoonotic subtypes. More research is needed among humans, livestock and wild animals in Tibet to better understand their role in the spread of Blastocystis. And, One Health measures need to be taken to control and prevent its zoonotic transmission. Highlights • Tibetan sheep and Tibetan goats were examined the Blastocystis for the first time.• Subtypes ST4, ST5, ST10, ST14 in Tibetan sheep and subtypes ST1, ST5, ST6, ST10 in Tibetan goats were identified separately.• Four potential zoonotic subtypes (ST1, ST4, ST5, ST6) were detected in this article.

Project description:In ruminants, the bacterial community in the gastrointestinal tract (GIT) has an essential role in healthy growth. Examining the bacterial composition in the GIT between growth-retarded and normal yaks could improve our understanding of the role of microorganisms in yaks with growth retardation. In this study, eight male yaks with growth retardation were used as the growth-retarded yak (GRY) group, and another eight male growth normal yaks (GNYs) with the same breed and age were used as the GNY group. We compared the bacterial community in the rumen, duodenum, jejunum, ileum, cecum, and colon between GRY and GNY groups based on the 16S ribosomal RNA gene sequencing. Alpha-diversity revealed that the Shannon index in the duodenum and ileum of the GNY group was higher (P < 0.05) than that of the GRY group. However, the opposite trend was found in the jejunum and cecum. The principal coordinates analysis (PCoA) showed that the bacterial structure in all segments of GIT differed from each other between two groups. In the rumen, the relative abundances of Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-014, and Treponema 2 were higher (P < 0.05) in the GNY group as compared with the GRY group. However, the Christensenellaceae R-7 group exhibited an opposite trend. In the jejunum, compared with the GNY group, the unclassified Chitinophagaceae was enriched significantly (P < 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P < 0.05) in the GNY group. In the ileum, the relative abundances of the Rikenellaceae RC9 gut group and Prevotellaceae UCG-004 were higher (P < 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P < 0.05) relative abundance of Prevotellaceae UCG-003 as compared with the GRY group. In the colon, the relative abundances of Treponema 2 and unclassified Lachnospiraceae were slightly higher (0.05 < P < 0.10) in the GNY group than those in the GRY group. Overall, these results improve our knowledge about the bacterial composition in the GIT of growth-retarded and normal yaks, and regulating the bacterial community may be an effective solution to promote the compensatory growth of GRYs.

Project description:BACKGROUND:The schizothoracine fishes, an excellent model for several studies, is a dominant fish group of the Qinghai-Tibet Plateau (QTP). However, species populations have rapidly declined due to various factors, and infection with Echinorhynchus gymnocyprii is cited as a possible factor. In the present study, the molecular characteristics of E. gymnocyprii in four species of schizothoracine fishes from the QTP were explored. METHODS:We investigated the infection status of E. gymnocyprii in 156 schizothoracine fishes from the upper Yangtze River, upper Yellow River, and Qinghai Lake in Qinghai Province, China. The complete internal transcribed spacer (ITS) of the ribosomal RNA (rRNA) gene and part of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of 35 E. gymnocyprii isolates from these fishes were sequenced and their characteristics analyzed. In addition, we inferred phylogenetic relationships of the E. gymnocyprii populations based on the rRNA-ITS and cox1 sequences. RESULTS:The total prevalence of E. gymnocyprii in schizothoracine fishes was 57.69% (90/156). However, the prevalence among different species as well as that across the geographical locations of the schizothoracine fishes was significantly different. The results of sequence analysis showed that the four E. gymnocyprii populations from different hosts and regions of Qinghai Province were conspecific, exhibiting rich genetic diversity. Phylogenetic analysis based on rRNA-ITS and cox1 sequences supported the coalescence of branches within E. gymnocyprii; the cox1 gene of E. gymnocyprii populations inferred some geographical associations with water systems. In addition, three species of schizothoracine fishes were recorded as new definitive hosts for E. gymnocyprii. CONCLUSIONS:To the best of our knowledge, this is the first molecular description of E. gymnocyprii populations in schizothoracine fishes from the Qinghai-Tibet Plateau that provides basic data for epidemiological surveillance and control of acanthocephaliasis to protect endemic fish stocks.

Dataset Information

Bacterial diversity and community in Qula from the Qinghai-Tibetan Plateau in China.

Publications

Bacterial diversity and community in Qula from the Qinghai-Tibetan Plateau in China.

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