Characterization of fungus microbial diversity in healthy and diarrheal yaks in Gannan region of Tibet Autonomous Prefecture

Li, Kun; Mehmood, Khalid; Zhang, Hui; Jiang, Xiong; Shahzad, Muhammad; Dong, Xiaoqian; Li, Jiakui

doi:10.1016/j.actatropica.2018.02.017

Cited by 44 publications

(35 citation statements)

References 37 publications

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“…Libraries were constructed by utilizing NEB Next Ultra DNA Library Prep Kit for Illumina (NEB, USA) following the explanatory memorandum, and index codes were added as described in previous study [6, 13]. All the library products were quantified utilizing Qubit 2.0 Fluorometer (Thermo Fisher Scientific, US).…”

Section: Methodsmentioning

confidence: 99%

“…Quantitative Insights Into Microbial Ecology (QIIME, v1.8.0) was used to remove error or question sequences in the current study [14]. Operational taxonomic units (OTUs) were obtained by using USEARCH (Version 7.1 http://drive5.com/uparse/) via 97% similarity and removing the divergence sequences clustering (<3%) [6, 15]. OTUs were taxonomically analyzed via BLASTn tool against a curated UNITE database [16].…”

Section: Methodsmentioning

confidence: 99%

“…OTUs were taxonomically analyzed via BLASTn tool against a curated UNITE database [16]. The analysis of Alpha and Beta diversity was done according to previously reported studies [4, 6]. The microflora of birds at phylum and genus levels were identified by employing QIIME [6].…”

Section: Methodsmentioning

confidence: 99%

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Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing

Zhao

Luo

et al. 2019

BioMed Research International

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Birds are an important source of fecal contamination in environment. Many of diseases are spread through water contamination caused by poultry droppings. A study was conducted to compare the intestinal microbial structure of Shaoxing ducks with and without water. Thirty 1-day-old Shaoxing ducks (Qingke No. 3) were randomly divided into two groups; one group had free access to water (CC), while the other one was restricted from water (CT). After 8 months of breeding, caecal samples of 10 birds from each group were obtained on ice for high-throughput sequencing. A total of 1507978 valid sequences were examined and clustered into 1815 operational taxonomic units (OTUs). At phylum level, Firmicutes (41.37%), Bacteroidetes (33.26%), Proteobacteria (13.67%), and Actinobacteria (8.26%) were found to dominate the microbial community in CC birds, while Firmicutes (53.62%), Bacteroidetes (33.06%), and Actinobacteria (11.13%) were uncovered to be the prime phyla in CT ducks. At genus level, Bacteroides (25.02%), Escherichia-Shigella (11.02%), Peptococcus (7.73%) and Parabacteroides (5.86%) were revealed to be the mainly genera in the CC group ducks, while Bacteroides (18.11%), Erysipelatoclostridium (10.94%), Ruminococcaceae_unclassified (10.43%), Lachnospiraceae_unclassified (5.26%), Coriobacteriales_unclassified (5.89%), and Faecalibacterium (4.2%) were detected to staple the microbial flora in the CT birds. One phylum and 13 genera were found to have the significant difference between the two bird groups (p<0.05). At phylum level, Proteobacteria in CT ducks were found to be obviously lower than ducks in CC birds (p<0.05). At genus level, Escherichia-Shigella (p<0.05) and Peptococcus (p<0.05) were found to be notably lower in CT birds, while Erysipelatoclostridium (p<0.05), Ruminococcaceae_unclassified (p<0.01), Coriobacteriales_unclassified (p<0.05), Faecalibacterium (p<0.01), Atopobiaceae_unclassified (p<0.01), Alistipes (p<0.05), Eggerthellaceae_unclassified (p<0.05), Prevotella_7 (<0.05), Rikenellaceae_RC9_gut_group (p<0.05), Prevotellaceae_uncultured (p<0.05), and Shuttleworthia (p<0.05) were observed to be prominently higher in CT ducks. In conclusion, the present study revealed the effects of keeping ducks away from swimming with obvious changes in the microbial community. Though higher microbial richness was found in the ducks without swimming, more pathogenic genera including Eggerthella, Erysipelatoclostridium, Alistipes, Prevotella_7, and Shuttleworthia; zoonotic genera including Eggerthella and Shuttleworthia; inflammatory genus Alistipes; anti-inflammatory Faecalibacterium genus; and tumor genus Rikenellaceae were examined in these ducks. The CT ducks also showed significant changes at genera level regarding the metabolism (Peptococcus, Ruminococcaceae, and Coriobacteriales).

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing

Zhao

Luo

et al. 2019

BioMed Research International

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“…Yak and Tibetan sheep are indigenous animals in the Qinghai-Tibetan Plateau that is characterized by cold weather conditions and mountainous terrain with altitudes ranging from 4000 to 5500 m, which provide milk, meat, fuel (yak dung), and wool for local herdsmen [17]. Small Tail Han sheep, which originated from low land [18], later adapted to the grazing lifestyle on the Qinghai-Tibetan Plateau and became an indispensable species to the local life and economy [19].…”

Section: Introductionmentioning

confidence: 99%

Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau

Guo

Wang

et al. 2020

Animals

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The anaerobic rumen fungal community play a critical role in fibrous material degradation. However, there is a lack of data describing the composition of anaerobic rumen fungal community of full grazing ruminants in the Qinghai-Tibetan Plateau. For this reason, we employed the next-generation sequencing technique to elucidate the rumen fungal structure composition and evaluate the effects of host species on fungal communities. Community comparisons (Bray–Curtis index) between yak and Tibetan sheep revealed that the rumen fungal community was affected by host species (p < 0.05). The alpha diversity indices in the yak were significantly higher than in the Tibetan sheep and Small Tail Han sheep. Neocallimastigomycota was predominant regardless of host species. Within this phylum, unidentified genus of Neocallimastigaceae was the most dominant in all samples, followed by Piromyces and Orpinomyces. Moreover, the shared and unique OTUs in the rumen were identified and most of them belonged to the Orpinomyces. Co-occurrence network analysis identified that each animal species had their own keystone species and most of them were non-dominant flora. Our data indicate that host breeds override living environment as the key factor that determines fungal community in the rumen of grazing ruminants in the Qinghai-Tibetan Plateau.

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“…Previously, we performed high-throughput sequencing of intestinal micro ora from diarrheal yaks, our study found 41 genera of bacteria in perinatal healthy yaks, while 145 genera of bacteria were only tested in healthy perinatal yaks [5]. Moreover, 212 genera of fungus were found in healthy yaks, 373 and 208 genera of fungus were found in calves and diarrheal yaks respectively [38]. However, 16 s RNA sequencing was limited to genus level.…”

Section: Discussionmentioning

confidence: 93%

Effects of Short Chain Fatty Acids (SCFAs) Modulation on Potentially Diarrhea Causing Pathogens in Yaks Through Metagenomics Sequencing

Li¹,

Zeng²,

Liu³

et al. 2020

Preprint

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Yaks are of great importance on the plateau; however, an emerging endemic diarrheal disease during the last few years is posing a great threat to the health of these animals. Yaks have special gut microbiotal community and short-chain fatty acids (SCFAs) which are not only the principle nutrient substrates of intestinal epithelial cells but can also regulate the epithelial barrier. Until now, metagenomics sequencing has not been reported in diarrheal yaks. A scarce information is available regarding the levels of fecal SCFAs and diarrhea in yaks. The purpose of our study was to identify the potential pathogens that cause the emerging diarrhea and also to explore the potential relationship of short-chain fatty acids in this issue. We estimated diarrhea rate in yaks after collecting the equal number of fecal samples from affected animals. Metagenomics sequencing and quantitative analysis of SCFAs were performed which revealed 15-25% and 5-10% prevalence in diarrheal yak’s calves and adults yaks respectively. Significant difference was observed in GC contents (44.69%~46.08% vs 46.12%~46.38%) under two reference groups (p<0.05). Violin box plot also showed the higher degree of dispersion in gene abundance distribution of diarrhea yaks, while genes of normal yaks were relatively gathered. We found 366163 significant differential abundance genes in diarrheal yaks, with 141305 up-regulated and 224858 down-regulated genes as compared with normal yaks via DESeq analysis. Metagenomic binning analysis indicated the higher significant of bin 33 (Bacteroidales) (p<0.05) in diarrheal animals, while bin 10 (p<0.0001), bin 30 (Clostridiales) (p<0.05), bin 51 (Lactobacillales) (p<0.05), bin 8 (Lachnospiraceae) (p<0.05) and bin 47 (Bacteria) (p<0.05) were obviously higher in normal animals. At different levels, an obviously difference in Phylum, Class, Oder, Family, Genus and Species was noticed as 4, 8, 8, 16, 17 and 30 respectively. Compared with healthy yaks, Acetic acid (p<0.01), Propionic acid (p<0.01), Butyric acid (p<0.01), Isobutyric acid, Isovaleric acid (p<0.05) and Caproic acid (p<0.01) were all observed obviously at lower rate in diarrheal yaks. In conclusion, besides the increased pathogens level of Staphylococcus aureus, Babesia ovata, Anaplasma phagocytophilum, Bacteroides fluxus, viruses, Klebsiella pneumonia, and inflammation-related bacteria; the decreased of SCFAs caused by the imbalance of intestinal microbiota may potentially leads to emergence of diarrhea in yaks.

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Characterization of fungus microbial diversity in healthy and diarrheal yaks in Gannan region of Tibet Autonomous Prefecture

Cited by 44 publications

References 37 publications

Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing

Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing

Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau

Effects of Short Chain Fatty Acids (SCFAs) Modulation on Potentially Diarrhea Causing Pathogens in Yaks Through Metagenomics Sequencing

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