scholarly journals Cupriavidus in the intestinal microbiota of Tibet endemic fish Glyptosternum maculatum can help it adapt to habitat of the Qinghai Tibet Plateau

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Yingzi Pan ◽  
Zhichao Li ◽  
Jianshe Zhou ◽  
Qielu Wang ◽  
Huifen Xu ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Intestinal Microbiome ◽  
Tibet Plateau ◽  
The Tibetan Plateau ◽  
Intestinal Microorganisms ◽  
Cu Content ◽  
Α Diversity ◽  
Cultured Fish

Abstract Background Gut microbes play an important role in the growth and development of fish. The Tibetan Plateau fish Glyptosternum maculatum is a unique species of sisorid catfish living in the river up to 4200 m altitude. Results To understand the mechanisms underlying the ability of G. maculatum to adapt to the high-altitude habitat, the intestinal microbiota of G. maculatum was studied. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms of wild and cultured G. maculatum to explore the characteristics of intestinal microorganisms and compared the gut microbial community of wild and cultured G. maculatum. The results showed that the α-diversity and richness of the intestinal microbiome were higher in wild G. maculatum than in cultured fish. The most abundant phylum in both G. maculatum were Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes; Cetobacterium and Cupriavidus are the most dominant genus. The membership and structure of intestinal bacterial communities in wild G. maculatum are similar to the cultured fish, suggesting that a core microbiota is present in both G. maculatum intestinal bacterial communities. Metastats analysis showed that six genera were differentially represented between the wild and cultured G. maculatum. Conclusions The most interesting characteristic of the intestinal microbial communities of G. maculatum is that there were large numbers of Cupriavidus, which may play an important role in the adaptation of G. maculatum to the water of the Yarlung Zangbo River with a high Cu content. This result, in turn, can guide us on breeding G. maculatum.

scholarly journals Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Bing Li ◽  
Wei-Min Wu ◽  
David B. Watson ◽  
Erick Cardenas ◽  
Yuanqing Chao ◽  
...  
Keyword(s):  
Network Analysis ◽  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Ecological Niches ◽  
Content Type ◽  
Oak Ridge ◽  
Α Diversity ◽  
Before And After

ABSTRACTA site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilizedin situthrough intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A pairedttest indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion.Castellaniellahad the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing generaGeothrix,Desulfovibrio,Ferribacterium, andGeobacterdecreased significantly, whereas the denitrifyingAcidovoraxabundance increased significantly after groundwater invasion. Additionally, seven genera, i.e.,Castellaniella,Ignavibacterium,Simplicispira,Rhizomicrobium,AcidobacteriaGp1,AcidobacteriaGp14, andAcidobacteriaGp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.IMPORTANCEHigh-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites.

scholarly journals Intestinal Microbiota and Liver Diseases: Insights into Therapeutic Use of Traditional Chinese Medicine

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Tingshuai Wang ◽  
Shaodong Huang ◽  
Cong Wu ◽  
Na Wang ◽  
Rongzhen Zhang ◽  
...  
Keyword(s):  
Risk Factors ◽  
Liver Disease ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Rapid Development ◽  
Alternative Therapy ◽  
Intestinal Microbiome ◽  
Bile Acid Metabolism

Liver disease is a leading cause of global morbidity and mortality, for which inflammation, alcohol use, lipid metabolic disorders, disturbance to bile acid metabolism, and endotoxins are common risk factors. Traditional Chinese Medicine (TCM) with its “holistic approach” is widely used throughout the world as a complementary, alternative therapy, due to its clinical efficacy and reduced side effects compared with conventional medicines. However, due to a lack of reliable scientific evidence, the role of TCM in the prevention and treatment of liver disease remains unclear. Over recent years, with the rapid development of high-throughput sequencing, 16S rRNA detection, and bioinformatics methodology, it has been gradually recognized that the regulation of intestinal microbiota by TCM can play a substantial role in the treatment of liver disease. To better understand how TCM regulates the intestinal microbiota and suppresses liver disease, we have reviewed and analyzed the results of existing studies and summarized the relationship and risk factors between intestinal microbiota and liver disease. The present review summarizes the related mechanisms by which TCM affects the composition and metabolites of the intestinal microbiome.

Analysis of the bacterial communities in the waterlogged wooden cultural relics of the Xiaobaijiao No. 1 shipwreck via high-throughput sequencing technology

Holzforschung ◽  
2018 ◽  
Vol 72 (7) ◽  
pp. 609-619 ◽  
Author(s):  
Qiuxia Li ◽  
Lixiang Cao ◽  
Wenfeng Wang ◽  
Hongming Tan ◽  
Tao Jin ◽  
...  
Keyword(s):  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Sequence Similarity ◽  
Species Number ◽  
Sequencing Technology ◽  
Α Diversity ◽  
Sea Area ◽  
Cultural Relics

AbstractThe microbial impact on waterlogged wooden cultural relics fromXiaobaijiao No. 1shipwreck was investigated by means of a high-throughput sequencing technology, while the focus was on the composition of prokaryotic microorganisms in 10 wood samples collected from different parts of the shipwreck. A total of 28 501 different operational taxonomic units (OTUs) were obtained based on 97% sequence similarity. The α-diversity index is for the bacterial diversity, which was the highest and the lowest in the samples SS8 and SS5, respectively. Proteobacteria was the largest category of bacterial abundance (47.3%) followed by Bacteroidetes (10%). α-Proteobacteria was the first largest bacteria class with the maximum abundance (21.0%) followed by γ-Proteobacteria (16.9%). Other groups rich in the following species were found: Bacteroidales (13.3%), Thiotrichales (5.0%), Rhodobacterales (4.2%), Rhizobiales (4.0%), Chromatiales (3.5%), Oceanospirillales (3.3%), Flavobacteriales (2.9%) and Sphingomonadales (2.8%). At the level of the bacterial genus,Marinomonaswas the most abundant one. Phylogenetic analysis revealed that there are some differences in the composition of bacterial communities from different wood samples. The species number of bacteria in the relics of this shipwreck was far more than that reported in those found in Europe, and in which species composition was similar to the benthic bacteria in the corresponding sea area. The coexistence of anaerobic and aerobic bacteria is remarkable.

scholarly journals Comparison of the Intestinal Microbiota During the Different Growth Stages of Red Swamp Crayfish (Procambarus clarkii)

2021 ◽  
Vol 12 ◽  
Author(s):  
Mengqi Xie ◽  
Shiyu Zhang ◽  
Lili Xu ◽  
Zhixin Wu ◽  
Junfa Yuan ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Growth Stage ◽  
High Throughput Sequencing ◽  
Procambarus Clarkii ◽  
Intestinal Flora ◽  
Principal Component ◽  
The Body ◽  
Intestinal Microbiome ◽  
Growth Stages ◽  
Different Growth Stages

This study aimed to determine the effect of the growth stage of Procambarus clarkii on their intestinal microbiota. Intestinal samples of five different growth stages of P. clarkii (first instar, second instar, third instar, juvenile, and adult) from laboratory culture were analyzed through the Illumina MiSeq high-throughput sequencing platform to determine the intestinal microbiome of crayfish. The alpha diversity decreased along with the growth of the crayfish, with the relative abundance of the microbiota changing among stages; crayfish at closer development stages had a more comparable intestinal microbiota composition. A comparative analysis by principal component analysis and principal coordinate analysis showed that there were significant differences in the intestinal microbiota of crayfish among the different growth stages, except for the first two stages of larval crayfish, and the intestinal microbiota showed a consistent progression pattern from the larval stage to the juvenile stage. Some microbiota showed stage specificity, which might be the characteristic microbiota of different stages of growth. According to FAPROTAX functional clustering analysis, the three stages of larvae were clustered together, while the juvenile and adult stages were clustered separately according to the growth stage, indicating that, in the early stages of larval development, the function of the intestinal flora was similar; as the body grew and developed, the composition and function of the intestinal microbiota also changed.

scholarly journals Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab

2021 ◽  
Vol 12 ◽  
Author(s):  
Wencong Shi ◽  
Gaoya Su ◽  
Mingcong Li ◽  
Bing Wang ◽  
Rongshan Lin ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Global Economy ◽  
High Throughput Sequencing ◽  
Common Scab ◽  
Bacterial Endophytes ◽  
Potato Tubers ◽  
Substantial Impact ◽  
Operational Taxonomic Units ◽  
Α Diversity ◽  
Potato Common Scab

The response of plant endophytes to disease within infected tissues has been well demonstrated, but the corresponding response of endophytes in non-lesion tissues remains unclear. Here, we studied the composition and distribution of bacterial endophytes in potato roots (RE), stems (SE), and tubers (TE), and explored the response of endophytes in non-lesion tissues to potato common scab (PCS), which is a soil-borne disease caused by pathogenic Streptomyces and results in serious losses to the global economy every year. Via high-throughput sequencing, it was seen that the composition of endophytes in roots, stems, and tubers had significant differences (P < 0.05) and the distribution of the bacterial communities illustrated a gradient from soil to root to tuber/stem. PCS significantly reduced bacterial endophytes α-diversity indexes, including ACE and the number of observed operational taxonomic units (OTUs), of RE without significantly reducing the indexes of SE and TE. No significant effect on the composition of endophytes were caused by PCS in roots, tubers, or stems between high PCS severity (H) and low PCS severity (L) infections at the community level, but PCS did have a substantial impact on the relative abundance of several specific endophytes. Rhizobium and Sphingopyxis were significantly enriched in root endophytes with low PCS severity (REL); Delftia and Ochrobactrum were significantly enriched in stem endophytes with low PCS severity (SEL); Pedobacter, Delftia, and Asticcacaulis were significantly enriched in tuber endophytes with high PCS severity (TEH). OTU62, a potential PCS pathogen in this study, was capable of colonizing potato tubers, roots, and stems with few or no symptoms present. Co-occurrence networks showed that the number of correlations to OTU62 was higher than average in these three tissue types, suggesting the importance of OTU62 in endophytic communities. This study clarified the distribution and composition of potato endophytes in tubers, roots, and stems, and demonstrated the response of endophytes in non-lesion tissues to PCS.

scholarly journals Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

2021 ◽  
Vol 44 (2) ◽  
Author(s):  
Jumria Sutra ◽  
Hamidu Saadu ◽  
Amalia Mohd. Hashim ◽  
Mohd Zamri Saad ◽  
Ina Salwany Md Yasin ◽  
...  
Keyword(s):  
Information Processing ◽  
Intestinal Microbiota ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Intestinal Microbiome ◽  
Functional Genes ◽  
Rrna Gene ◽  
Wet Season ◽  
Asian Seabass ◽  
Tiger Grouper

Grouper and Asian seabass are among the economically important cultured marine fish in Malaysia. However, fry productions in large scale tend to introduce stress that changes the fish microbiota and increases susceptibility to diseases. Currently, high-throughput sequencing is used to study fish microbiota and their respective gene functions. In this study, we investigate the diversity, abundance and functional genes of intestinal microbiota of tiger grouper and Asian seabass that were reared in a semi-closed hatchery during dry and wet seasons. Intestinal samples were collected from tiger grouper and Asian seabass of different sizes before proceeded to DNA extraction. The extracted DNA were then subjected to 16S rRNA gene amplicon sequencing using the Illumina Miseq platform targeting V3 and V4 regions for determination of the bacterial diversity, abundance and functional genes in both seasons. The results revealed that intestinal microbiota of Asian seabass were dominated by the phylum Proteobacteria and order Vibrionales in both seasons. Meanwhile, intestinal microbiome of tiger groupers were shifted from domination of phylum Firmicutes and order Clostridiales in dry season to Proteobacteria and order Lactobacillales in wet season. PICRUSt analysis revealed that the functional genes that were dominantly present were the genes encoded for metabolism, genetic information processing, environmental information processing, cellular process and human diseases. Remarkably, SIMPER analysis showed several potential metagenomics biomarker genes in dry and wet seasons. This study revealed the importance of utilizing amplicon metagenomics approaches in microbiome studies for better identification of the microbial profiling in aquaculture systems.

scholarly journals Alternative Feed Raw Materials Modulate Intestinal Microbiota and Its Relationship with Digestibility in Yellowtail Kingfish Seriola lalandi

Fishes ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. 14
Author(s):  
Chinh Thi My Dam ◽  
Mark Booth ◽  
Igor Pirozzi ◽  
Michael Salini ◽  
Richard Smullen ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Raw Materials ◽  
Nutrient Digestibility ◽  
Rrna Gene ◽  
Distal Intestine ◽  
Alternative Feed ◽  
Yellowtail Kingfish ◽  
Seriola Lalandi

Gut microbiota plays a crucial role in nutrient digestibility and fish health. This study aimed to investigate the effects of alternative feed raw materials on the bacterial communities in the distal intestine and its relationship with nutrient digestibility in yellowtail kingfish (YTK), Seriola lalandi. Two 4-week digestibility trials were conducted to evaluate fish meal (FM), two sources of poultry by-product meal (PBM-1 & PBM-2), blood meal (BLM), faba bean meal (FBM), corn gluten meal (CGM), soy protein concentrate (SPC) and wheat flour (WH). The nutrient digestibility value was determined using the stripping fecal collection method. Bacterial communities were characterized by high-throughput sequencing based on V3-V4 region of the 16S rRNA gene. The most abundant phylum identified in the present study was Proteobacteria. A significant change in the distal intestine was observed in fish fed diets containing CGM and BLM, characterized by a reduction of species richness and diversity. Additionally, significant correlation between nutrient digestibility and intestinal microbiota was observed. Allivibrio, Vibrio, Curvibacter, Ruminococcaceae, and Clostridium were positively correlated, whereas Ralstonia genus was negatively correlated with nutrient digestibility. This study demonstrated that intestinal microbiota could be a useful tool for evaluating the digestibility of feed raw materials; however, further culture-based study is needed to confirm this observation.

scholarly journals The Distribution and Turnover of Bacterial Communities in the Root Zone of Seven Stipa Species Across an Arid and Semi-arid Steppe

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaodan Ma ◽  
Lumeng Chao ◽  
Jingpeng Li ◽  
Zhiying Ding ◽  
Siyu Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Root Zone ◽  
Regional Scale ◽  
Vegetation Coverage ◽  
Biogeographical Distribution ◽  
Α Diversity ◽  
Arid Steppe ◽  
Semi Arid

The bacterial communities of the root-zone soil are capable of regulating vital biogeochemical cycles and the succession of plant growth. Stipa as grassland constructive species is restricted by the difference features of east–west humidity and north–south heat, which shows the population substituting distribution. The distribution, turnover, and potential driving factors and ecological significance of the root-zone bacterial community along broad spatial gradients of Stipa taxa transition remain unclear. This paper investigated seven Stipa species root-zone soils based on high-throughput sequencing combined with the measurements of multiple environmental parameters in arid and semi-arid steppe. The communities of soil bacteria in root zone had considerable turnover, and some regular variations in structure along the Stipa taxa transition are largely determined by climatic factors, vegetation coverage, and pH at a regional scale. Bacterial communities had a clear Stipa population specificity, but they were more strongly affected by the main annual precipitation, which resulted in a biogeographical distribution pattern along precipitation gradient, among which Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi were the phyla that were most abundant. During the transformation of Stipa taxa from east to west, the trend of diversity shown by bacterial community in the root zone decreased first, and then increased sharply at S. breviflora, which was followed by continuous decreasing toward northwest afterwards. However, the richness and evenness showed an opposite trend, and α diversity had close association with altitude and pH. There would be specific and different bacterial taxa interactions in different Stipa species, in which S. krylovii had the simplest and most stable interaction network with the strongest resistance to the environment and S. breviflora had most complex and erratic. Moreover, the bacterial community was mainly affected by dispersal limitation at a certain period. These results are conducive to the prediction of sustainable ecosystem services and protection of microbial resources in a semi-arid grassland ecosystem.

scholarly journals The Structure and Species Co-Occurrence Networks of Soil Denitrifying Bacterial Communities Differ Between A Coniferous and A Broadleaved Forests

2019 ◽  
Vol 7 (9) ◽  
pp. 361 ◽  
Author(s):  
Jie Chen ◽  
Jiajia Li ◽  
Weijun Shen ◽  
Han Xu ◽  
Yide Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Environmental Changes ◽  
Southern China ◽  
Soil Microbial Communities ◽  
Sequencing Data ◽  
Microbial Biomass Nitrogen ◽  
N Transformations ◽  
Α Diversity

Acacia mangium (AM) and Pinus massoniana (PM) are widely planted in tropical regions, whereas their effects on soil microbial communities remain unclear. We did a comprehensive investigation of soil denitrifying bacterial communities in AM and PM monoculture plantations in Southern China based on the high throughput sequencing data of their functional genes: nirK, nirS, and nosZ. The average abundance of nosZ (1.3 × 107) was significantly higher than nirS (5.6 × 106) and nirK (4.9 × 105). Shannon estimator revealed a markedly higher α-diversity of nirS and nosZ communities in PM than in AM plantations. The AM and PM plantations were dominated by different nirS and nosZ taxa belonging to proteobacteria, actinobacteria, thermoleophilia, chloroflexia, and acidobacteria, while the dominant nirK taxa were mainly categorized into proteobacteria in both types of plantations. The structure of nirS and nosZ communities shifted substantially from AM to PM plantations with changes in soil moisture, NH4+, and microbial biomass nitrogen content. The species co-occurrence network of nirK community was better organized in a more modular manner compared to nirS and nosZ communities, and the network keystone species mostly occurred in PM plantations. These results indicated a highly species corporation of nirK community in response to environmental changes, especially in PM plantations. AM and PM plantations can form different soil denitrifying microbial communities via altering soil physicochemical properties, which may further affect soil N transformations.

scholarly journals Abundant and rare bacterial taxa structuring differently in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau

2021 ◽  
Author(s):  
Ze Ren ◽  
Cheng Zhang ◽  
Xia Li ◽  
Kang Ma ◽  
Kexin Feng ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Yellow River ◽  
Source Area ◽  
Tibet Plateau ◽  
The Yellow River ◽  
Thermokarst Lakes ◽  
Β Diversity ◽  
Α Diversity ◽  
Yellow River Source ◽  
Qinghai Tibet Plateau

Thermokarst lakes are forming from permafrost thaw and severely affected by accelerating climate change. Sediment and water in these lakes are distinct habitats but closely connected. However, our understanding of the differences and linkages between sediment and water in thermokarst lakes remain largely unknow, especially from the perspective of bacterial community patterns and underlying mechanisms. In this study, we examined bacterial communities in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau. Bacterial taxa were divided to abundant and rare according to their relative abundance, and the Sorensen dissimilarity (βsor) was partitioned into turnover (βturn) and nestedness (βnest). The results showed that the whole bacterial communities as well as the abundant and rare subcommunities differed substantially between sediment and water, in terms of taxonomical composition, α-diversity, and β-diversity. Sediment had significantly lower α-diversity indexes but higher β-diversity than water. Abundant taxa had significantly higher relative abundances but lower α-diversity and β-diversity than rare taxa. Moreover, bacterial communities are predominantly governed by strong turnover processes (βturn/βsor ratio of 0.925). Abundant subcommunities were significantly lower in βturn/βsor ratio compared to rare subcommunities. Bacterial communities in sediment had a significantly higher βturn/βsor ratio than in water. The results suggest that the bacterial communities of thermokarst lakes, especially rare subcommunities or particularly in sediment, might be strongly structured by environmental filtering and geographical isolation, leading to compositional distinct. By revealing bacterial communities in sediment and water, this integral study increased our current knowledge of thermokarst lakes, enhancing our understanding of the community assembly rules and ecosystem structures and processes of these rapid changing and vulnerable ecosystems.

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