scholarly journals High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hongling Wei ◽  
Huan Wang ◽  
Lei Tang ◽  
Changkao Mu ◽  
Chunyu Ye ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Southern China ◽  
Scylla Paramamosain ◽  
Mud Crab ◽  
Sequencing Data ◽  
Coastal Regions ◽  
Female Crab ◽  
The Core ◽  
Commercially Important

Abstract Background Scylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health. Results Proteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Spirochaetae and Fusobacteria were the dominant phyla of the 36 representative phyla. Eleven genera of the 820 representative genera were considered as core gut microbiota and were distributed in the five dominant phyla. The core genus of the Proteobacteria included Arcobacter, Photobacterium, Vibrio, Shewanella and Desulfovibrio. The other four phyla contained one or two genera. Male and female crab samples had two different core genera, (male samples: Psychrilyobacter & Lactococcus; female samples: Clostridium_sensu_stricto_11 and Candidatus_Bacilloplasma). Conclusions This is the first time core intestinal microbiota have been identified in crab from nine coastal regions of southern China. This study provides sequencing data related to the gut microbiota of S. paramamosain, and may contribute to probiotic development for S. paramamosain aquaculture industries.

The miRNAs profiling revealed by high-throughput sequencing upon WSSV infection in mud crab Scylla paramamosain

2020 ◽  
Vol 100 ◽  
pp. 427-435 ◽  
Author(s):  
Xin Ren ◽  
Shanmeng Lin ◽  
Tongtong Kong ◽  
Yi Gong ◽  
Hongyu Ma ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Scylla Paramamosain ◽  
Mud Crab

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 Temperature potentially induced distinctive flavor of mud crab Scylla paramamosain mediated by gut microbiota

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lei Tang ◽  
Huan Wang ◽  
Chunlin Wang ◽  
Changkao Mu ◽  
Hongling Wei ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Scylla Paramamosain ◽  
Mud Crab

scholarly journals Experimental infection with the hookworm, Necator americanus, promotes gut microbial diversity in human volunteers with relapsing multiple sclerosis

2020 ◽  
Author(s):  
Timothy Jenkins ◽  
David Pritchard ◽  
Radu Tanasescu ◽  
Gary Telford ◽  
Marina Paraiakovou ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Gut Microbiota ◽  
Experimental Infection ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Placebo Treatment ◽  
Sequencing Data ◽  
Microbial Composition ◽  
Necator Americanus ◽  
Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been recently linked to alterations of gut microbial communities. Results In the present study we investigated, for the first time, qualitative and quantitative changes in gut microbial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus ( N+ ), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment ( PBO ). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased microbial alpha diversity in the gut microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the gut microbiota of N + individuals for which no relapses were recorded at the end of the trial. Conclusions Overall, these data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immunomodulatory properties of hookworm parasites.

scholarly journals Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lei Tian ◽  
Enze Wang ◽  
Xiaolong Lin ◽  
Li Ji ◽  
Jingjing Chang ◽  
...  
Keyword(s):  
Endophytic Fungi ◽  
Wild Rice ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
Cultivated Rice ◽  
The Core ◽  
Bacterial Genus ◽  
Wild Rice Species ◽  
Root Endophytic Fungi ◽  
Bacteria And Fungi

Abstract Background Rice, which serves as a staple food for more than half of the world’s population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined. Results In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together. Conclusions This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

scholarly journals Comparative Analysis of Gut Microbiota in Two Populations of Argopecten purpuratus (Lamarck, 1819) Based on 16S rRNA Gene Amplicon Data

2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Wilbert Serrano ◽  
Raul M. Olaechea ◽  
Ulrike I. Tarazona
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Distal Intestine ◽  
High Throughput Sequencing Data ◽  
Argopecten Purpuratus ◽  
Cultivated Species

Despite the importance of the Peruvian scallop Argopecten purpuratus as a major cultivated species, information on its microbiota is limited. Here, we provide a high-throughput sequencing data analysis of 16S rRNA gene amplicons from the distal intestine of A. purpuratus. Geographical and seasonal variation of the indigenous gut microbiota is shown.

scholarly journals Connection between the Gut Microbiota of Largemouth Bass (Micropterus salmoides) and Microbiota of the Pond Culture Environment

2021 ◽  
Vol 9 (8) ◽  
pp. 1770 ◽  
Author(s):  
Qianfu Liu ◽  
Zini Lai ◽  
Yuan Gao ◽  
Chao Wang ◽  
Yanyi Zeng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Largemouth Bass ◽  
High Throughput Sequencing ◽  
Southern China ◽  
Micropterus Salmoides ◽  
Bacterial Species ◽  
Pond Water ◽  
Fish Growth ◽  
Rrna Gene ◽  
Pond Culture

The vital role of the gut microbiota in fish growth, development, immunity, and health has been largely confirmed. However, the interaction between environmental microbiota and the gut microbiota of aquaculture species remains unclear. Therefore, we analyzed the gut microbiota of largemouth bass (Micropterus salmoides) collected from subtropical ponds in southern China, as well as the pond water and aquatic sediment microbiota, using high-throughput sequencing of the 16S rRNA gene. Our results demonstrated significant differences in the compositions of pond water, sediment, and the gut microbiota of largemouth bass. Moreover, these compositions changed throughout the culture period. Only approximately 1% of the bacterial species in the pond sediment and gut microbiota were exchanged. However, the bacterial proportion of the gut microbiota from pond water microbiota was approximately 7% in samples collected in June and August, which increased markedly to 73% in October. Similarly, the proportion of bacteria in the pond water microbiota from the gut microbiota was approximately 12% in June and August, which increased to 45% in October. The study findings provide basic information for understanding the interactions between environmental microbiota and the gut microbiota of cultured fish, which may contribute to improved pond culture practices for largemouth bass.

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 Xingnaojing injection can regulate dysbacteriosis and increase the concentration of short chain fatty acids in the feces after stroke in mice

2020 ◽  
Author(s):  
Jingfeng Lin ◽  
Ganlu Liu ◽  
Zhenyun Han ◽  
Qiang Gao ◽  
Zhenyi Wang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Enrichment Analysis ◽  
Illumina Miseq ◽  
Short Chain Fatty Acids ◽  
Normal Group ◽  
Sequencing Data ◽  
Germ Free ◽  
Xingnaojing Injection

AbstractBackgroundXingnaojing injection (XNJ) is extracted from the Chinese ancient prescription “An-Gong-Niu-Huang Pill”, is widely used for stroke in China. We mainly observe the effect of XNJ (Xingnaojing) injection on the gut microbiota in stroke model mice.MethodsForty-two 7-to 8-week-old male C57 mice weighing 22-24 g were chosen for the experiment. There were 6 mice in each group; the 7 groups were the normal group (NG), the MCAO group (CG), the MCAO+XNJ group (EG), the sham surgery group (SG), the sham germ-free normal group (SGFNG), the sham germ-free+MCAO group (SGFCG), and the sham germ-free+MCAO+XNJ group (SGFEG). Two days before modeling, we abdominally administered Xingnaojing (6 mg/kg) the SGFEG and EG groups. The processing time of sustained XNJ was 5 days. Three days after modeling, 1 ~ 2 mouse feces were collected, and after a MiSeq PE library was constructed, an Illumina MiSeq PE 300 platform was used for high-throughput sequencing. After cleaning the sequencing data, the microbiome and microbiomeseq packages were used for analysis using R software (version 3.6.2).ResultsAlpha diversity analysis revealed that the diversity was not different between the CG and EG. The Simpson index was different between the SGFCG and SGFEG. XNJ increased the levels of Sutterellaceae and decreased the level of Deferribacteres and Morganella. LEfSe analysis showed that SGFCG mice were also enriched with Morganella. XNJ increased the concentrations of the SCFAs PA (propionate), VA (valerate), IBA (isobutyrate), and IVA (isovalerate) in the feces of the SGFEG group. BA (butyrate) had greater positive correlation with gut bacteria than other acids in the SGFCG, and XNJ changed this trend. KEGG analysis showed that peptidoglycan biosynthesis was most different between the CG and EG.ConclusionIschemic stroke (IS) causes dysbiosis of some specific bacteria in the gut microbiota in MCAO mice. Xingnaojing ameliorated this condition by increasing the levels of Sutterellaceae and decreasing the level of Deferribacteres and Morganella. These results are in accordance with other research on Chinese medicines for IS that affect the gut microbiota. Enrichment analysis of SCFAs revealed that XNJ improved the levels of SCFAs through an energy metabolism-related pathway.

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