Tibetan wild asses (Equus Kiang) were superior to domestic donkeys (Equus Asinus) in terms of the composition and function of gut microbial community

Abstract Tibetan wild asses (Equus Kiang) are the only wild species of perissodactyls on the Qinghai-Tibetan Plateau, and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefor, understanding the gut microbita composition and function can provide a theoretical for the situ conservation of wild animals in the future. This study analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA regions. No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla of Bacteroidetes and Firmcutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214, Phascolarctobacterium, Coprostanoligenes_group, Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences. Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly included amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. The overall results indicated that wild asses were superior to that of domestic in gut bacteria community composition and function, and wild asses should be more suitable to survive in wild than to be domesticated or captive.

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Tibetan wild asses (Equus Kiang) were superior to domestic donkeys (Equus Asinus) in terms of the composition and function of gut microbial community

10.21203/rs.2.14192/v1 ◽

2019 ◽

Author(s):

Hongjin Liu ◽

Xinquan Zhao ◽

Shixiao Xu ◽

Liang Zhao ◽

Linyong Hu ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Intestinal Microbiota ◽

Species Interactions ◽

High Throughput Sequencing ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Significant Difference ◽

And Function ◽

Gut Microbial Community

Abstract Background: Tibetan wild asses are the only wild species of perissodactyls on the Qinghai-Tibetan Plateau, and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. The gut microbiota has a great effect on the health and nutrition of the host, however, scant research is available on the characteristics of their intestinal microbiota. Therefor, understanding the gut microbita composition and function of TWAs can provide a theoretical for the situ conservation of wild animals in the future. Results: To characterize its composition and function, we analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA regions. No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla of Bacteroidetes and Firmcutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214 , Phascolarctobacterium , Coprostanoligenes_group , Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences . Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. Conclusions: Wild asses were superior to that of domestic in gut microbial community composition and function. For wild animal conservation, wild asses are more suitable to survive in wild than to be domesticated or captive. Key words: Tibetan wild asses, domestic donkeys, 16S ribosomal RNA gene, gut microbiota

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Microbiome Analysis of Gut Bacterial Communities of Healthy and Diseased Malaysian Mahseer (Tor tambroides)

10.1101/2021.12.08.471852 ◽

2021 ◽

Author(s):

Melinda Mei Lin Lau ◽

Cindy Jia Yung Kho ◽

LEONARD WHYE KIT LIM ◽

Siew Chuiang Sia ◽

Hung Hui Chung ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Communities ◽

Alpha Diversity ◽

Microbiota Composition ◽

Petechial Haemorrhage ◽

Rdna Sequencing ◽

Degrading Bacteria ◽

And Function ◽

Gut Microbial Community ◽

Gut Microbiota Composition

Aims: The gut microbiota is referred to an extra organ and is ciritical in assisting the host in terms of nutrition and immunity. Environmental stressors could alter gut microbial community and cause gut inflammation. This study aimed to investigate and compare the gut microbiota community between healthy and diseased Tor tambroides. Methodology and results: In this study, such gut microbial alterations were explored using NGS-based 16S rDNA sequencing on the Malaysian mahseer (T. tambroides). Three adult healthy and three diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio and Pseudomonas were found within gut microbiota of the diseased fishes. In addition, cellulose-degrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides. Conclusion, significance and impact of study: Thus, our findings emphasised on the association between the alteration in gut microbiota composition and infectious abdominal dropsy (IAD) in T. tambroides. This finding is important to provide basic information for further diagnosis, prevention and treatment of intestinal diseases in fish.

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High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River

PeerJ ◽

10.7717/peerj.12105 ◽

2021 ◽

Vol 9 ◽

pp. e12105

Author(s):

Fangnan Xiao ◽

Yuanyuan Li ◽

Guifang Li ◽

Yaling He ◽

Xinhua Lv ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Metabolic Pathways ◽

Soil Bacteria ◽

High Throughput Sequencing ◽

Soil Bacterial Community ◽

Tarim River ◽

Soil Bacterial Communities ◽

Soil Bacterial ◽

And Function

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

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Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau

PeerJ ◽

10.7717/peerj.9032 ◽

2020 ◽

Vol 8 ◽

pp. e9032 ◽

Cited By ~ 2

Author(s):

Hongjin Liu ◽

Xinquan Zhao ◽

Xueping Han ◽

Shixiao Xu ◽

Liang Zhao ◽

...

Keyword(s):

Gut Microbiota ◽

Species Interactions ◽

Dry Matter ◽

High Throughput Sequencing ◽

Microbial Community Composition ◽

Intestinal Flora ◽

Tibet Plateau ◽

Significant Difference ◽

And Function ◽

Qinghai Tibet Plateau

Tibetan wild asses (Equus Kiang) are the only wild species of perissodactyls on the Qinghai-Tibet Plateau and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefore, understanding the gut microbiota composition and function of wild asses can provide a theoretical for the situ conservation of wild animals in the future.In this study, we measured the dry matter digestion by the 4 molar hydrochloric acid (4N HCL) acid-insoluble ash method and analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA genes in V3–V4 regions. The results showed that the dry matter digestion in wild asses was significantly higher than in domestic donkeys (P < 0.05). No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla Bacteroidetes and Firmicutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214, Phascolarctobacterium, Coprostanoligenes_group, Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than in domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences. Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly included amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. The overall results indicated that wild asses have advantages over domestic donkeys in dry matter digestion, gut microbial community composition and function, and wild asses have their unique intestinal flora to adapt high altitudes on the Qinghai-Tibet plateau.

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Effects of aging on the skin and gill microbiota of farmed seabass and seabream

10.21203/rs.3.rs-47924/v2 ◽

2020 ◽

Author(s):

Daniela Rosado ◽

Marcos Pérez-Losada ◽

Ana Pereira ◽

Ricardo Severino ◽

Raquel Xavier

Keyword(s):

Sexual Maturation ◽

Metabolic Pathways ◽

High Throughput Sequencing ◽

Developmental Stages ◽

Age Groups ◽

Somatic Growth ◽

Alpha Diversity ◽

Mature Adults ◽

Effects Of Aging ◽

The Impact

Abstract Background: Important changes in microbioal composition related to sexual maturation have been already reported in the gut of several vertebrates including mammals, amphibians and fish. Such changes in fish are linked to reproduction and growth during developmental stages, diet transitions and critical life events. We used amplicon (16S rRNA) high-throughput sequencing to characterize the skin and gill bacterial microbiota of farmed seabass and seabream belonging to three different developmental age groups: early and late juveniles and mature adults. We also assessed the impact of the surrounding estuarine water microbiota in shaping the fish skin and gill microbiota. Results: Microbial diversity, composition and potential metabolic functions varied across fish maturity stages. Alpha-diversity in the seabass microbiota varied significantly between age groups and was higher in older fish. Conversely, in the seabream, no significant differences were found in alpha diversity between age groups. Microbial structure varied significantly across age groups; moreover, high structural variation was also observed within groups. Different bacterial metabolic pathways were predicted to be enriched in the microbiota of both species. Finally, we found that the water microbiota is significantly distinct from all the fish microbiota across the studied age groups, although a high percentage of ASVs is shared with the skin and gill microbiota. Conclusions: We report important microbial differences in composition and potential functionality across the different ages of farmed seabass and seabream. These differences may be related to somatic growth and the onset of sexual maturation. Importantly, some of the inferred metabolic pathways could enhance the host coping mechanisms during stressful conditions. Our results provide new evidence suggesting that growth and sexual maturation have an important role in shaping the external mucosa microbiota of fish and highlight the importance of considering different life stages in microbiota studies.

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Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam

PeerJ ◽

10.7717/peerj.9612 ◽

2020 ◽

Vol 8 ◽

pp. e9612

Author(s):

Tong Jia ◽

Tingyan Guo ◽

Baofeng Chai

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Chemical Properties ◽

Alpha Diversity ◽

Imperata Cylindrica ◽

Copper Tailings ◽

Α Diversity ◽

Degraded Ecosystems ◽

And Function

This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.

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Evaluation of Bacterial Diversity and Quality Features of Traditional Sichuan Bacon from Different Geographical Region

Applied Sciences ◽

10.3390/app11209738 ◽

2021 ◽

Vol 11 (20) ◽

pp. 9738

Author(s):

Song Wang ◽

Xingjie Wang ◽

Wanshu Pan ◽

Aiping Liu ◽

Shuliang Liu ◽

...

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Physicochemical Characteristics ◽

Geographical Regions ◽

Significant Difference ◽

Geographic Regions ◽

Shared Otus ◽

Nitrite Content

Sichuan bacon is one of the most popular types of Chinese bacon in the domestic market. High-throughput sequencing was used to characterize the bacterial diversity of 39 Sichuan bacon samples collected from 3 geographical regions. The results showed that the bacterial diversity of Sichuan bacon in different regions demonstrated certain specificity as well as similarity, and the shared OTUs were close to 81% of the total number in the basin group, mountain group, and plateau group. At the genus level, Staphylococcus is the most dominant genus among the three groups, covering 26.7%, 20.6%, and 22.7%, respectively. Beta diversity shows significant differences in bacterial compositions in different geographic regions, especially for Pseudomonas, Brochothrix, Lactobacillus, Lactococcus, and Enterococcus. Meanwhile, some physicochemical characteristics were analyzed, and a significant difference (p < 0.05) among the three regions was shown in the Aw, pH, and nitrite content, which were significantly correlated with undesired bacteria. This study provides insights into the understanding of the role of bacterial communities in the microbial safety and quality improvement of Sichuan bacon.

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Comparative analysis of biofilm community on different coloured substrata in relation to mussel settlement

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315415002222 ◽

2016 ◽

Vol 97 (1) ◽

pp. 81-89 ◽

Cited By ~ 7

Author(s):

Yi-Feng Li ◽

Xing-Pan Guo ◽

Yu-Ru Chen ◽

De-Wen Ding ◽

Jin-Long Yang

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Current Knowledge ◽

Illumina Miseq ◽

Miseq Sequencing ◽

Significant Difference ◽

The World ◽

Community Variability ◽

Biofilm Community

Mussels are typical macrofouling organisms in the world. In this study, the interaction between the settlement ofMytilus coruscusplantigrades and bacterial community on coloured substrata was determined. Bacterial communities in biofilms developed on seven coloured substrata were analysed by Illumina Miseq sequencing. The mussel settlement response to coloured substrata with no biofilms was also examined.Flavobacteria, AlphaproteobacteriaandGammaproteobacteriawere the first, second and third most dominant groups in seven biofilm samples. The results suggest that the inducing activities of these biofilms on plantigrade settlement varied with coloured substrata and the lowest percentage of settlement was observed on biofilms on the green substratum. High-throughput sequencing showed that bacterial community in biofilms also changed with the substratum colour. No significant difference in the inducing activity on plantigrade settlement was observed between the coloured substrata with no biofilms. Thus, difference in plantigrade settlement response may be correlated to the changes in bacterial community on coloured substrata. This finding extends current knowledge of interaction among mussel settlement and bacterial community variability.

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Influence of intramuscular depot-medroxyprogesterone acetate initiation on vaginal microbiota in the postpartum period

Clinical Infectious Diseases ◽

10.1093/cid/ciaa1876 ◽

2020 ◽

Author(s):

Bridget M Whitney ◽

Sujatha Srinivasan ◽

Kenneth Tapia ◽

Eric Munene Muriuki ◽

Bhavna H Chohan ◽

...

Keyword(s):

Bacterial Community ◽

Medroxyprogesterone Acetate ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Bacterial Load ◽

Alpha Diversity ◽

Rrna Gene ◽

Nugent Score ◽

Depot Medroxyprogesterone Acetate ◽

Significant Difference

Abstract Background The vaginal microbiome plays a key role in women’s reproductive health. Use of exogenous hormones, such as intramuscular depot-medroxyprogesterone acetate (DMPA-IM), may alter the composition of vaginal bacterial community. Methods Vaginal swabs were collected from postpartum Kenyan women initiating DMPA-IM or non-hormonal contraception (non-HC). Bacterial vaginosis was assessed by Nugent score (Nugent-BV) and bacterial community composition was evaluated using broad-range 16S rRNA gene PCR with high-throughput sequencing. Changes in Nugent score, alpha diversity (Shannon diversity index), and total bacterial load between contraceptive groups from enrollment to three-months post-initiation were estimated using multivariable linear mixed effects regression. Results Among 54 HIV-negative women, 33 choosing DMPA-IM and 21 choosing non-HC, Nugent-BV was more common among DMPA-IM users at enrollment. At follow-up, Nugent score had decreased significantly among DMPA-IM users (Δ=-1.89 (95%CI:-3.53, -0.25; p=0.02) while alpha diversity remained stable (Δ=0.03, 95%CI:-0.24, 0.30; p=0.83). Conversely, Nugent score remained relatively stable among non-HC users (Δ=-0.73, 95%CI:-2.18, 0.73; p=0.33) while alpha diversity decreased (Δ=-0.34, 95%CI:-0.67, -0.001; p=0.05). Total bacterial load decreased slightly in DMPA-IM users and increased slightly among non-HC users, resulting in a significant difference in change between the contraceptive groups (difference=-0.64 log10 gene copies/swab, 95%CI:-1.19, -0.08; p=0.02). While significant changes in Nugent score and alpha diversity were observed within contraceptive groups, changes between groups were not significantly different. Conclusions Postpartum vaginal bacterial diversity did not change in DMPA-IM users despite a reduction in Nugent-BV, but decreased significantly among women using non-HC. Choice of contraception may influence Lactobacillus recovery in postpartum women.

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Niche specificity and functional diversity of the bacterial communities associated with Ginkgo biloba and Panax quinquefolius

Scientific Reports ◽

10.1038/s41598-021-90309-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hanan R. Shehata ◽

Subramanyam Ragupathy ◽

Thomas A. Henry ◽

Steven G. Newmaster

Keyword(s):

Functional Diversity ◽

Ginkgo Biloba ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Panax Quinquefolius ◽

Tissue Type ◽

Rrna Gene ◽

Associated Bacteria ◽

Kegg Pathways

AbstractPlant-associated bacteria can establish mutualistic relationships with plants to support plant health. Plant tissues represent heterogeneous niches with distinct characteristics and may thus host distinct microbial populations. The objectives of this study are to investigate the bacterial communities associated with two medicinally and commercially important plant species; Ginkgo biloba and Panax quinquefolius using high Throughput Sequencing (HTS) of 16S rRNA gene, and to evaluate the extent of heterogeneity in bacterial communities associated with different plant niches. Alpha diversity showed that number of operational taxonomic units (OTUs) varied significantly by tissue type. Beta diversity revealed that the composition of bacterial communities varied between tissue types. In Ginkgo biloba and Panax quinquefolius, 13% and 49% of OTUs, respectively, were ubiquitous in leaf, stem and root. Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria were the most abundant phyla in Ginkgo biloba while Proteobacteria, Bacteroidetes, Actinobacteria, Plantomycetes and Acidobacteria were the most abundant phyla in Panax quinquefolius. Functional prediction of these bacterial communities using MicrobiomeAnalyst revealed 5843 and 6251 KEGG orthologs in Ginkgo biloba and Panax quinquefolius, respectively. A number of these KEGG pathways were predicted at significantly different levels between tissues. These findings demonstrate the heterogeneity, niche specificity and functional diversity of plant-associated bacteria.

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