Ontology highlight
ABSTRACT:
PROVIDER: PRJNA700376 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13679911_1.fastq.gz | Fastqsanger.gz | |||
| SRR13679911_2.fastq.gz | Fastqsanger.gz | |||
| SRR13679912_1.fastq.gz | Fastqsanger.gz | |||
| SRR13679912_2.fastq.gz | Fastqsanger.gz | |||
| SRR13679913_1.fastq.gz | Fastqsanger.gz |
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Project description:Vibrio vulnificus is a marine zoonotic pathogen associated with fish farms that is considered a biomarker of climate change. Zoonotic strains trigger a rapid death of their susceptible hosts (fish or humans) by septicemia that has been linked to a cytokine storm in mice. A toxin called RtxA1 produced by the bacteria might play an important role in bacterial invasion and subsequent death by septic shock since animals infected with a mutant deficient in rtxA1 suffer from septicemia but do not die. The aim of this study was to globally analyze the early eel immune response in blood against V. vulnificus, as well as the role of the RtxA1 toxin on this interaction.
2022-02-18 | GSE196944 | GEO
Project description:Streptococcus agalactiae is one of the most important pathogens associated with outbreaks of streptococcis in Nile tilapia farms around the world. High water temperature (above 27°C) have been described as factor predisposing for disease in fish. On the other hand, at low temperature (below 25°C) fish mortalities are no usually observed in farms. The temperature variation can modulate the expression of genes and proteins involved with metabolism, adaptation and bacterial pathogenicity, increasing or decreasing the host susceptibility to infection. The aim of this study was to evaluate the transcriptome and proteome of fish-pathogenic S. agalactiae strain (SA53) submitted to in vitro growth under different temperatures using microarray and label-free shotgun LC-HDMSE approach, and to compare the expression trends of proteins shared among GBS strains from different hosts (SA53 and NEM316). Biological triplicates of isolates were cultured in BHIT broth at 22°C or 32°C for RNA and protein isolation and submitted to transcriptomic and proteomic analysis. Total of 1730 transcripts were identified in SA53, being 107 genes differentially expressed among the temperature evaluated. A higher number of genes related with metabolism were detected as up-regulated proteins at 32°C, mainly PTS system and ABC transport system. In proteome analysis, 1046 proteins were identified in SA53 strain, being 81 proteins differentially regulated at 22 and 32ºC. Proteins involved in Defense mechanisms (V), Lipid transport and metabolism (I), and Nucleotide transport and metabolism (F) were up-regulated at 32ºC. A higher number of interactions was observed in the category F. The induction of genes/proteins involved in virulence were detected in both temperatures evaluated. A low correlation between transcriptome and proteome datasets was observed. And there is a distinct adaptation between fish and human GBS strains at the proteome level. Our study showed that the transcriptome and proteome of fish-adapted GBS strain are modulated by temperature, especially regulating the differential expression of genes/proteins involved with metabolism, adaptation and virulence, and revealing a host specificity at proteome regulation for human and fish hosts
2018-11-30 | GSE112416 | GEO
Project description:Background: While the luminal microbiome composition in the human cervicovaginal tract has been defined, the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that they may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a clinically well-characterized cohort of Kenyan women. Results: We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners dominated luminal samples had a corresponding Gardnerella dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbiome was associated with epithelial remodeling and pro-inflammatory pathways. Communities dominated by L. iners and Gardnerella were associated with low host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, and with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. Conclusion: We identified ectocervical tissue-adherent bacterial communities in all study participants. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. This difference could possibly explain that L. iners dominant luminal communities have a high probability of transitioning to high diverse bacterial communities including high abundance of Gardnerella. By performing integrative multi-omics analyses we further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community is similar to vaginal biofilms that significantly impact women’s reproductive and sexual health.
2023-02-10 | GSE194276 | GEO
Project description:Bacterial communities associated with houseflies (Musca domestica L.) at danish farms
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Project description:Disrupted interactions between host and intestinal bacteria are implicated in the development of colorectal cancer (CRC). However, the functional impacts of these inter-kingdom interactions remain poorly defined. To examine this interplay, we performed mouse and microbiota RNA-sequencing on colon tissue from germ-free (GF) and gnotobiotic ApcMin/+;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BT) and biofilm-negative healthy (BX) tissues. The bacteria in BT mice differentially expressed >2,900 genes related to bacterial secretion, virulence and biofilms, but only affected 62 host genes. Importantly, the bacterial communities from BT mice were transmissible and carcinogenic when administered to a new GF ApcMin/+;Il10-/- cohort, maintaining a set of 13 bacterial genera. Our findings suggest complex interactions within bacterial communities affecting bacterial composition and CRC development.
2019-12-30 | GSE108156 | GEO
Project description:Anthropogenic activities have dramatically increased the inputs of reactive nitrogen (N) into terrestrial ecosystems, with potentially important effects on the soil microbial community and consequently soil C and N dynamics. Our analysis of microbial communities in soils subjected to 14 years of 7 g N m-2 year-1 Ca(NO3)2 amendment in a Californian grassland showed that the taxonomic composition of bacterial communities, examined by 16S rRNA gene amplicon sequencing, was significantly altered by nitrate amendment, supporting the hypothesis that N amendment- induced increased nutrient availability, yielded more fast-growing bacterial taxa while reduced slow-growing bacterial taxa. Nitrate amendment significantly increased genes associated with labile C degradation (e.g. amyA and xylA) but had no effect or decreased the relative abundances of genes associated with degradation of more recalcitrant C (e.g. mannanase and chitinase), as shown by data from GeoChip targeting a wide variety of functional genes. The abundances of most N cycling genes remained unchanged or decreased except for increases in both the nifH gene (associated with N fixation), and the amoA gene (associated with nitrification) concurrent with increases of ammonia-oxidizing bacteria. Based on those observations, we propose a conceptual model to illustrate how changes of functional microbial communities may correspond to soil C and N accumulation.
2017-11-21 | GSE107168 | GEO
Project description:Bacterial communities from marine sediment of salmon farms
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Project description:Tenacibaculum maritimum in Norwegian fish farms
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