scholarly journals Characterization of fungal microbial diversity in healthy and diarrheal Tibetan piglets

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Qinghui Kong ◽  
Suozhu Liu ◽  
Aoyun Li ◽  
Yaping Wang ◽  
Lihong Zhang ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Dynamic Balance ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Republic Of China ◽  
Tibet Autonomous Region ◽  
The Tibet Autonomous Region

Abstract Background Diarrhea is an important ailment limiting the production of the Tibetan pig industry. Dynamic balance of the intestinal microbiota is important for the physiology of the animal. The objective of this work was to study fungal diversity in the feces of early weaning Tibetan piglets in different health conditions. Results In the present study, we performed high-throughput sequencing to characterize the fungal microbial diversity in healthy, diarrheal and treated Tibetan piglets at the Tibet Autonomous Region of the People’s Republic of China. The four alpha diversity indices (Chao1, ACE, Shannon and Simpson) revealed no significant differences in the richness across the different groups (P > 0.05). In all samples, the predominant fungal phyla were Ascomycota, Basidiomycota and Rozellomycota. Moreover, the healthy piglets showed a higher abundance of Ascomycota than the treated ones with a decreased level of Basidiomycota. One phylum (Rozellomycota) showed higher abundance in the diarrheal piglets than in the treated. At genus level, compared with that to the healthy group, the proportion of Derxomyces and Lecanicillium decreased, whereas that of Cortinarius and Kazachstania increased in the diarrheal group. The relative abundances of Derxomyces, Phyllozyma and Hydnum were higher in treated piglets than in the diarrheal ones. Conclusions A decreased relative abundance of beneficial fungi (e.g. Derxomyces and Lecanicillium) may cause diarrhea in the early-weaned Tibetan piglets. Addition of probiotics into the feed may prevent diarrhea at this stage. This study presented the fungal diversity in healthy, diarrheal and treated early-weaned Tibetan piglets.

scholarly journals Bacterial and fungal diversity in the lorandite (TlAsS2) mine ‘Allchar' in the Republic of North Macedonia

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Vaso Taleski ◽  
Ivica Dimkić ◽  
Blazo Boev ◽  
Ivan Boev ◽  
Sanja Živković ◽  
...  
Keyword(s):  
Inductively Coupled Plasma ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Optical Emission ◽  
Diversity Indices ◽  
Emission Spectrometry ◽  
High Concentration ◽  
Bacterial Phyla ◽  
The Republic

ABSTRACT The Allchar mineral mine is one of the oldest arsenic–antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp. and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.

Characterization of microbial community in cold-chain hairtail fish by high-throughput sequencing technology

2021 ◽  
Author(s):  
Jiali Xing ◽  
Xiaorong Xu ◽  
Xiaohu Luo ◽  
Ruihang Zheng ◽  
Lingyan Mao ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Flora ◽  
Diversity Indices ◽  
Cold Chain ◽  
Class Level ◽  
The Family ◽  
Dominant Bacteria

Abstract: High-throughput sequencing was used to analyze the microbial communities in the muscle samples of hairtail fish to study their diversity and dynamic changes during cold-chain circulation. The results showed that the richness and diversity of the microbial community in hairtail fish had a transient decline in 0–24 h and decreased after the first rise during 24–216 h. The diversity and richness of bacteria in cold-chain hairtail fish reached the maximum at 168 h. The Shannon and Simpson diversity indices of the bacteria were 2.96 and 0.16, respectively, and their ACE and Chao1 richness indices were 254.84 and 155.10, respectively. In addition, the dominant bacteria were Proteobacteria in the phylum level, Gammaproteobacteria in the class level, Pseudomonadales in the order level, Pseudomonadaceae in the family level, and Pseudomonas in the genus level, and their relative abundance were 80.52%, 72.11%, 76.68%, 23.25%, and 53.50%, respectively. In this study, the structure of bacterial flora and the dominant bacteria in cold-chain hairtail fish were analyzed by high-throughput sequencing to provide a basis for exploring how to maintain the freshness of hairtail fish and for predicting the shelf-life of hairtail fish.

scholarly journals DNA metabarcoding of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Luiz Henrique Rosa ◽  
Otávio Henrique Bezerra Pinto ◽  
Tina Šantl-Temkiv ◽  
Peter Convey ◽  
Micheline Carvalho-Silva ◽  
...  
Keyword(s):  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Rank Order ◽  
Mesh Size ◽  
Diversity Indices ◽  
South Shetland Islands ◽  
Livingston Island ◽  
Dna Metabarcoding ◽  
Air Sample ◽  
Total Dna

AbstractWe assessed fungal diversity present in air and freshly deposited snow samples obtained from Livingston Island, Antarctica, using DNA metabarcoding through high throughput sequencing (HTS). A total of 740 m3 of air were pumped through a 0.22 µm membrane. Snow obtained shortly after deposition was kept at room temperature and yielded 3.760 L of water, which was filtered using Sterivex membranes of 0.22 µm mesh size. The total DNA present was extracted and sequenced. We detected 171 fungal amplicon sequence variants (ASVs), 70 from the air and 142 from the snow. They were dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Mucoromycota. Pseudogymnoascus, Cladosporium, Mortierella and Penicillium sp. were the most dominant ASVs detected in the air in rank order. In snow, Cladosporium, Pseudogymnoascus, Penicillium, Meyerozyma, Lecidea, Malassezia, Hanseniaspora, Austroplaca, Mortierella, Rhodotorula, Penicillium, Thelebolus, Aspergillus, Poaceicola, Glarea and Lecanora were the dominant ASVs present. In general, the two fungal assemblages displayed high diversity, richness, and dominance indices, with the assemblage found in snow having the highest diversity indices. Of the total fungal ASVs detected, 29 were only present in the air sample and 101 in the snow sample, with only 41 present in both samples; however, when only the dominant taxa from both samples were compared none occurred only in the air and, among the rare portion, 26 taxa occurred in both air and snow. Application of HTS revealed the presence of a more diverse fungal community in the air and snow of Livingston Island in comparison with studies using traditional isolation methods. The assemblages were dominated by cold-adapted and cosmopolitan fungal taxa, including members of the genera Pseudogymnoascus, Malassezia and Rhodotorula, which include some taxa reported as opportunistic. Our results support the hypothesis that the presence of microbiota in the airspora indicates the possibility of dispersal around Antarctica in the air column. However, further aeromycology studies are required to understand the dynamics of fungal dispersal within and beyond Antarctica.

scholarly journals Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6658 ◽  
Author(s):  
Bing Zhang ◽  
Jing Ren ◽  
Daode Yang ◽  
Shuoran Liu ◽  
Xinguo Gong
Keyword(s):  
Gut Microbiota ◽  
Host Species ◽  
High Throughput Sequencing ◽  
Southern China ◽  
Alpha Diversity ◽  
Operational Taxonomic Units ◽  
Close Relationship ◽  
Elaphe Carinata ◽  
Deinagkistrodon Acutus

Background The gut microbiota plays an important role in host immunity and metabolic homeostasis. Although analyses of gut microbiotas have been used to assess host health and foster disease prevention and treatment, no comparative comprehensive study, assessing gut microbiotas among several species of farmed snake, is yet available. In this study, we characterized and compared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosa, Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the 16S rDNA gene in southern China and tested whether there was a relationship between gut microbiotal composition and host species. Results A total of 629 operational taxonomic units across 22 samples were detected. The five most abundant phyla were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria, while the five most abundant genera were Bacteroides, Cetobacterium, Clostridium, Plesiomonas, and Paeniclostridium. This was the first report of the dominance of Fusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered a relatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversity analysis indicated that species richness and diversity were highest in the gut microbiota of D. acutus and lowest in that of E. carinata. Significant differences in alpha diversity were detected among the four farmed snake species. The gut microbiotas of conspecifics were more similar to each other than to those of heterospecifics. Conclusion This study provides the first comparative study of gut microbiotas among several species of farmed snakes, and provides valuable data for the management of farmed snakes. In farmed snakes, host species affected the species composition and diversity of the gut microbiota.

scholarly journals Changes in the gut microbiota diversity of brown frogs (Rana dybowskii) after an antibiotic bath

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Qing Tong ◽  
Li-Yong Cui ◽  
Jia Bie ◽  
Xiao-Yun Han ◽  
Zong-Fu Hu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Positive Association ◽  
Diversity Indices ◽  
Control Group ◽  
Functional Composition ◽  
Significant Positive Association ◽  
Collateral Effect

Abstract Background Captive amphibians frequently receive antibiotic baths to control bacterial diseases. The potential collateral effect of these antibiotics on the microbiota of frogs is largely unknown. To date, studies have mainly relied on oral administration to examine the effects of antibiotics on the gut microbiota; in contrast, little is known regarding the effects of bath-applied antibiotics on the gut microbiota. The gut microbiota compositions of the gentamicin, recovery, and control groups were compared by Illumina high-throughput sequencing, and the functional profiles were analysed using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Furthermore, the relationship between the structure and predicted functional composition of the gut microbiota was determined. Results The alpha diversity indices were significantly reduced by the gentamicin bath, illustrating that this treatment significantly changed the composition of the gut microbiota. After 7 days, the gut microbiota of the recovery group was not significantly different from that of the gentamicin group. Forty-four indicator taxa were selected at the genus level, comprising 42 indicators representing the control group and 2 indicators representing the gentamicin and recovery groups. Potential pathogenic bacteria of the genera Aeromonas, Citrobacter, and Chryseobacterium were significantly depleted after the gentamicin bath. There was no significant positive association between the community composition and functional composition of the gut microbiota in the gentamicin or control frogs, indicating that the functional redundancy of the gut bacterial community was high. Conclusions Gentamicin significantly changed the structure of the gut microbiota of R. dybowskii, and the gut microbiota exhibited weak resilience. However, the gentamicin bath did not change the functional composition of the gut microbiota of R. dybowskii, and there was no significant correlation between the structural composition and the functional composition of the gut microbiota.

scholarly journals Gut Microbiota: A New Strategy to Study the Mechanism of Electroacupuncture and Moxibustion in Treating Ulcerative Colitis

2019 ◽  
Vol 2019 ◽  
pp. 1-16 ◽  
Author(s):  
Daneng Wei ◽  
Lushuang Xie ◽  
Zhiqi Zhuang ◽  
Na Zhao ◽  
Biao Huang ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
High Throughput Sequencing ◽  
Intestinal Flora ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Treg Cells ◽  
Detailed Mechanism ◽  
New Strategy ◽  
Flora Diversity ◽  
The Relationship

Previous studies have confirmed that acupuncture and moxibustion is an effective way for treating ulcerative colitis (UC). However, the exact mechanism is unclear yet. In this study, DSS-induced UC mice were treated by electroacupuncture and moxibustion, and the genome of intestinal flora was subsequently detected by high-throughput sequencing in order to explore the detailed mechanism in terms of intestinal flora. The results indicated that the alpha diversity indices and beta diversity of intestinal flora were improved by electroacupuncture and moxibustion treatments, especially by the moxibustion treatment. These treatments inhibited Streptococcus, Odoribacter, and Allobaculum whereas it facilitated Lactobacillus on genus level. Further correlation analysis showed that the alpha diversity indices were positively correlated with the percentage of Treg cells in CD4+ cells but negatively correlated with the percentage of Th17 in CD4+ cells. These data indicated that both electroacupuncture and moxibustion can promote the intestinal flora diversity, providing a new view to understand the relationship between host and microbiome when using some external therapies.

scholarly journals Microbial Community Structure Drives Predatory Myxobacteria Distribution Under Different Compost Manures

2021 ◽  
Author(s):  
Wei Dai ◽  
Ning Wang ◽  
Wenhui Wang ◽  
Xianfeng Ye ◽  
Zhongli Cui ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Alpha Diversity ◽  
Distribution Patterns ◽  
Diversity Indices ◽  
Community Diversity ◽  
Microbial World ◽  
Significant Difference ◽  
Compost Manure

Abstract Myxobacteria are unique predatory microorganisms with a distinct social lifestyle. The associated taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, under organic conditions, myxobacteria abundance increases in the soil, which could be related to the presence of abundant myxobacteria in the applied compost manure. In the present study, high-throughput sequencing technologies were used to investigate the distribution patterns and drivers of predatory myxobacteria community distribution patterns in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (P < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg2+ and Ca2+ concentrations were the major factors influencing myxobacteria distribution patterns under different compost manure treatments. In addition, pH, total nitrogen, and organic carbon influenced myxobacteria distribution in compost manure. The predator–prey relationship between prey bacteria and myxobacteria and the interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure could explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ distribution patterns of predatory myxobacteria and the key bacteria influencing their distribution are would advance our understanding of the ecological distribution patterns and functions of predatory microorganisms in the microbial world.

scholarly journals Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China

2018 ◽  
Author(s):  
Bing Zhang ◽  
Jing Ren ◽  
Daode Yang ◽  
Shuoran Liu ◽  
Xinguo Gong
Keyword(s):  
Gut Microbiota ◽  
Comparative Study ◽  
Host Species ◽  
High Throughput Sequencing ◽  
Southern China ◽  
Alpha Diversity ◽  
Close Relationship ◽  
Elaphe Carinata ◽  
Deinagkistrodon Acutus

Background. The gut microbiota plays an important role in host immunity and metabolichomeostasis. Although analyses of gut microbiotas have been used to assess host health,as well as for disease prevention and treatment, no comparative study of gut microbiotasamong several species of farmed snake is yet available. In this study we characterized andcompared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosus,Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the16S rDNA gene in southern China and tested whether there was a relationship betweengut microbiotal composition and host species. Results. A total of 629 operationaltaxonomic units (OTUs) across 22 samples were detected. The dominant bacterial phylawere Bacteroidetes, Proteobacteria, Firmicutes, and Fusobacteria; the dominant bacterialgenera were Bacteroides and Cetobacterium. This was the first report of the dominance ofFusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered arelatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversityanalysis indicated that species richness and diversity were highest in the gut microbiota ofD. acutus and lowest in that of E. carinata. Significant differences in alpha diversity weredetected among the four farmed snake species. The gut microbiotas of conspecifics weremore similar to each other than to those of heterospecifics. Conclusion. This studyprovides the first comparative study of gut microbiotas among several species of farmedsnakes, and provides valuable data for the management of farmed snakes. In farmedsnakes, host species affected the species composition and diversity of the gut microbiota.

scholarly journals Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China

2018 ◽  
Author(s):  
Bing Zhang ◽  
Jing Ren ◽  
Daode Yang ◽  
Shuoran Liu ◽  
Xinguo Gong
Keyword(s):  
Gut Microbiota ◽  
Comparative Study ◽  
Host Species ◽  
High Throughput Sequencing ◽  
Southern China ◽  
Alpha Diversity ◽  
Close Relationship ◽  
Elaphe Carinata ◽  
Deinagkistrodon Acutus

Background. The gut microbiota plays an important role in host immunity and metabolichomeostasis. Although analyses of gut microbiotas have been used to assess host health,as well as for disease prevention and treatment, no comparative study of gut microbiotasamong several species of farmed snake is yet available. In this study we characterized andcompared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosus,Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the16S rDNA gene in southern China and tested whether there was a relationship betweengut microbiotal composition and host species. Results. A total of 629 operationaltaxonomic units (OTUs) across 22 samples were detected. The dominant bacterial phylawere Bacteroidetes, Proteobacteria, Firmicutes, and Fusobacteria; the dominant bacterialgenera were Bacteroides and Cetobacterium. This was the first report of the dominance ofFusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered arelatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversityanalysis indicated that species richness and diversity were highest in the gut microbiota ofD. acutus and lowest in that of E. carinata. Significant differences in alpha diversity weredetected among the four farmed snake species. The gut microbiotas of conspecifics weremore similar to each other than to those of heterospecifics. Conclusion. This studyprovides the first comparative study of gut microbiotas among several species of farmedsnakes, and provides valuable data for the management of farmed snakes. In farmedsnakes, host species affected the species composition and diversity of the gut microbiota.

Sign in / Sign up

Export Citation Format

Share Document