Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1221673 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gut microbiota were assessed in 540 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples. Investigators compared gut microbiota diversity, overall composition, and normalized taxon abundance among these groups.
| 2255499 | ecrin-mdr-crc
Project description:Because antibiotics have been widely used to prevent severe losses due to infectious fishery diseases, the liberal application and overuse of antibiotics has led to the spread and evolution of bacterial resistance, food safety hazards, and environmental issues. The use of some antibiotics, including florfenicol and enrofloxacin, is allowed in aquaculture in China. Accordingly, to better address the concerns and questions associated with the impact of administered enrofloxacin and florfenicol to grass carp, here we investigated the immune response, bacterial diversity, and transcriptome of the intestine of C. idella treated with these oral antibiotics. The aim of this study was to provide an in-depth evaluation of the antibiotic-induced patterns and dynamics of the microbiota grass carp and the potential mechanism involved.
2022-08-08 | E-MTAB-12057 | biostudies-arrayexpress
Project description:Purpose:Salinity is an important environmental factor that affects the physiological activities of fish. The goals of this study are investigating the effect of different saline-alkali stress on grass carp (Ctenopharyngodon idella). Methods: Grass carp individuals, averaging 12 cm in body length, were obtained from Duofu fish farm (Wuhan, China) and cultured at recirculating aquaculture system for 2 weeks before the experiment began. For the challenge, all grass carp were randomly divided into three groups, and then cultured at saline-alkali water with the concentration of 0, 3‰ and 6‰. After 30 days, some grass crap cultured at 3‰ and 6‰ saline-alkali water were injured. At the same time, gill samples of grass carp were collected from 0, 3‰ (grass carp was not injured), 3‰ (grass carp was injured), 6‰ (grass carp was not injured) and 6‰ (grass carp was injured)saline-alkali groups. Total RNA of all samples was isolated using TRIzol® Reagent (Invitrogen) according to the manufacturer's introduction. RNA integrity was assessed using an Agilent 2100 bioanalyzer (Agilent, USA). Samples with RNA integrity numbers (RINs) ≥ 7.5 were subjected to cDNA library construction using TruseqTM RNA sample prep Kit (Illumina). Results:A total of 15 were processed for transcriptome sequencing, generating 94.99Gb Clean Data. At least 5.76Gb clean data were generated for each sample with minimum 91.87% of clean data achieved quality score of Q30. Clean reads of each sample were mapped to specified reference genome. Mapping ratio ranged from 88.59% to 92.84%. The expression of genes was quantified and differentially expressed genes were identified based on their expression.Criteria for differentially expressed genes was set as Fold Change(FC)≥1.5 and Pvalue<0.05. Fold change(FC) refers to the ratio of gene expression in two samples. These DEGs were further processed for functional annotation and enrichment analysis. Conclusions: Our study represents Effects and molecular regulation mechanisms of saline-alkali stress on the healthy grass carp by using RNA-seqtechnology. Our results show that saline-alkali stress will impair the immune system of grass carp.
2021-12-31 | GSE185170 | GEO
Project description:Primary outcome(s): Analysis of the diversity and composition of the gut microbiome by 16S rRNA sequencing
Study Design: Observational Study Model : Others, Time Perspective : Prospective, Enrollment : 60, Biospecimen Retention : Collect & Archive- Sample with DNA, Biospecimen Description : Blood, Stool
| 26030 | ecrin-mdr-crc
Project description:It is well established that histone derived antimicrobial peptides (AMPs) have anti-microbial properties in various invertebrate and vertebrate species.To reveal the possible immunoregulatory functions of the engineered S. cerevisiae expressing gcH2A-4(7t) and gcH2A-11(2t) on the grass carp, the intestines from the immunized grass carp were collected at the first immunization for 7 days and used for transcriptome sequencing. The results found that the activation of PRRs-related pathways including TLRs, NLRs and RLRs was revealed in the engineered S. cerevisiae expressing gcH2A-4(7t) and gcH2A-11(2t) on the grass carp intestines."
2022-07-07 | GSE201422 | GEO
Project description:To compare the similarities and differences in species diversity of the gut microbiota between the patients with melasma and healthy subjects. The feces were collected for 16S rRNA sequencing analysis of the gut microbiota.
2022-10-25 | GSE214430 | GEO
Project description:Effect of High Temperature on Immune Response of Grass Carp (Ctenopharyngodon idellus) by Transcriptome Analysis To understand the immune response mechanisms of this fish in high temperature circumstance, the transcriptomic profiles of the spleens from grass carp groups undergoing heat stress and normal temperature were investigated.
2016-03-16 | E-GEOD-79265 | biostudies-arrayexpress
Project description:Opioids such as morphine have many beneficial properties as analgesics, however, opioids may induce multiple adverse gastrointestinal symptoms. We have recently demonstrated that morphine treatment results in significant disruption in gut barrier function leading to increased translocation of gut commensal bacteria. However, it is unclear how opioids modulate the gut homeostasis. By using a mouse model of morphine treatment, we studied effects of morphine treatment on gut microbiome. We characterized phylogenetic profiles of gut microbes, and found a significant shift in the gut microbiome and increase of pathogenic bacteria following morphine treatment when compared to placebo. In the present study, wild type mice (C57BL/6J) were implanted with placebo, morphine pellets subcutaneously. Fecal matter were taken for bacterial 16s rDNA sequencing analysis at day 3 post treatment. A scatter plot based on an unweighted UniFrac distance matrics obtained from the sequences at OTU level with 97% similarity showed a distinct clustering of the community composition between the morphine and placebo treated groups. By using the chao1 index to evaluate alpha diversity (that is diversity within a group) and using unweighted UniFrac distance to evaluate beta diversity (that is diversity between groups, comparing microbial community based on compositional structures), we found that morphine treatment results in a significant decrease in alpha diversity and shift in fecal microbiome at day 3 post treatment compared to placebo treatment. Taxonomical analysis showed that morphine treatment results in a significant increase of potential pathogenic bacteria. Our study shed light on effects of morphine on the gut microbiome, and its role in the gut homeostasis.
2018-04-16 | E-MTAB-5546 | biostudies-arrayexpress
Project description:SERPINA1, a member of the serine protease inhibitor family, plays a role in viral infection and inflammation by regulating the activities of serine and cysteine proteases. To further investigate the antiviral role SERPINA1 played in GCRV (Grass carp Reovirus) infection, a polyclonal antibody of SERPINA1 was prepared, and the protein interacting with SERPINA1 was screened by CoIP/MS in grass carp hepatopancreas tissue. Samples of hepatopancreas tissues from grass carp (n=3) before (healthy) and 8 days after the infection (post-infection) were selected. Grass carp were infected by intraperitoneal injection. The total tissue proteins were extracted according to the manufacturer’s instructions for cell lysate (Beyotime, Shanghai, China). The types and abundance of proteins bound to SERPINA1 before and after the infection were detected and analyzed using CoIP-MS.
2022-08-31 | PXD036356 | Pride