Ontology highlight
ABSTRACT:
PROVIDER: PRJNA947092 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23945139_1.fastq.gz | Fastqsanger.gz | |||
| SRR23945139_2.fastq.gz | Fastqsanger.gz | |||
| SRR23945140_1.fastq.gz | Fastqsanger.gz | |||
| SRR23945140_2.fastq.gz | Fastqsanger.gz | |||
| SRR23945141_1.fastq.gz | Fastqsanger.gz |
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Project description:Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, it is unclear whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria in the root microbiome. Here we show how flavonoids preferentially attracts Aeromonadaceae in Arabidopsis thaliana root microbiome and how flavonoid-dependent recruitment of an Aeromona spp. results in enhanced plant Na_H1 resistance.
2022-10-19 | GSE184873 | GEO
Project description:Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, it is unclear whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria in the root microbiome. Here we show how flavonoids preferentially attracts Aeromonadaceae in Arabidopsis thaliana root microbiome and how flavonoid-dependent recruitment of an Aeromona spp. results in enhanced plant drought resistance.
2022-10-19 | GSE184872 | GEO
Project description:Background and aims: Gene mutations or variants leading to insufficient reactive oxygen species (ROS) production have been associated with inflammatory bowel disease (IBD). In particular, 40-50% of patients with chronic granulomatous disease have IBD (CGD-IBD). CGD is caused by inherited defects in any one of the 5 subunits forming the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex 2 (NOX2), leading to severely reduced or absent phagocyte-derived ROS production. While conventional IBD therapies can treat CGD-IBD, their benefits must be weighed against the risk of infection in this immune compromised population. Understanding the impact of NOX2 defects on the composition and function of the intestinal microbiota may lead to the identification of treatments for CGD-IBD. Methods: We evaluated GI symptom and quality of life scores, and clinical biomarkers of local (i.e. fecal occult blood and calprotectin) and systemic (i.e. CBC, CRP, ESR, and albumin) inflammation in a cohort of 79 patients with CGD, 8 mutation carriers and 17 healthy controls followed at the National Institutes of Health (NIH). We profiled the intestinal microbiome by 16S rRNA (V4 region) sequencing and the stool metabolome by mass spectrometry in all fecal samples, and further validated our findings by profiling the stool microbiome in a second cohort of 36 patients with CGD recruited from 11 centers across North-America through the Primary Immune Deficiency Treatment Consortium (PIDTC). Predictive functional profiling of the microbial communities based on 16S rRNA sequencing was also performed. Results: After controlling for significant variables, we show decreased alpha diversity and identified distinct intestinal microbiome and metabolomic profiles in patients with CGD compared to healthy individuals. In particular, we observed enrichment for Erysipelatoclostridium spp., Sellimonas spp. and Lachnoclostridium spp. in stool samples from patients with CGD. Despite differences in alpha and beta diversity in samples from the NIH compared to the PIDTC cohort, there were several bacterial taxa that correlated significantly between both cohorts. We further demonstrate that patients with active IBD and/or a history of IBD have a distinct microbiome and metabolomic profile compared to patients without CGD-IBD and identified bacterial taxa to be evaluated as potential markers of disease severity, as well as targets for future therapeutic interventions. Conclusions: Intestinal microbiome and metabolomic signatures distinguished patients with CGD and CGD-IBD and identified microbial and metabolomic candidates to be further evaluated as potential targets to improve the management of patients with CGD-IBD.
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Project description:Leishmania braziliensis infection results in inflammation and skin injury, with highly variable and unpredictable clinical outcomes. Here, we investigated the potential impact of microbiota on infection-induced inflammatory responses and disease resolution by conducting an integrated analysis of the skin microbiome and host transcriptome on a cohort of 62 L. braziliensis-infected patients. We found that overall bacterial burden and microbiome configurations dominated with Staphylococcus spp. were associated with delayed healing and enhanced inflammatory responses, especially by IL-1 family members. Dual RNA-seq of human lesions revealed that high lesional S. aureus transcript abundance was associated with delayed healing and increased expression of IL-1β. This cytokine was critical for modulating disease outcome in L. braziliensis-infected mice colonized with S. aureus, as its neutralization reduced pathology and inflammation. These results implicate the microbiome in cutaneous leishmaniasis disease outcomes in humans and suggest host-directed therapies to mitigate the inflammatory consequences.
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Project description:The parasitic amoeba, Neoparamoeba perurans is the causative agent of Amoebic Gill Disease in salmonids. The parasite has previously been reported to lose virulence during prolonged in vitro maintenance. In this study, the impact of prolonged culture on N. perurans virulence and its proteome was investigated. Three isolates of N. perurans maintained in culture for varying durations were compared. Two isolates, attenuated and virulent, had their virulence assessed in an experimental trial using Atlantic salmon smolts and their bacterial community composition was evaluated by 16S rRNA Illumina MiSeq sequencing. Soluble proteins were isolated from a newly acquired, virulent and attenuated N. perurans culture and were analysed using two-dimensional electrophoresis (2D PAGE) coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS). An experimental challenge trial using Atlantic salmon smolts confirmed a loss in virulence in an N. perurans culture that was maintained in vitro for 3 years. A greater diversity of bacterial communities was found in the microbiome of the virulent isolate harbouring predominant genera belonging to Pseudoaltermonas spp, Vibrio spp and Fluviicola spp. Microbial community richness was reduced in the attenuated microbiome, with a singular species, Thalassopira xiamenensis, representing a large proportion of its microbiome. A collated proteome database of N. perurans, Amoebozoa and four bacterial genera resulted in 24 proteins differentially expressed between the three cultures. The present LC-MS/MS results indicate protein synthesis, oxidative stress and the plausible occurrence of immunomodulation are ultimately upregulated in a newly acquired N. perurans culture and future studies may exploit these protein identifications for therapeutic purposes in infected farmed fish.
2021-09-09 | PXD022328 | Pride
Project description:Association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonization patterns. This is due mainly to the current technical and analytical strategy limitations to characterise tumour-associated bacteria. Here, we propose an approach to detect bacterial signals in human RNA sequencing data and associate them with the clinical and molecular properties of the tumours. The method was tested on public datasets from The Cancer Genome Atlas and its accuracy was assessed on a new cohort of colorectal cancer patients. Our analysis shows that intratumoral microbiome composition is correlated with survival, anatomic location, microsatellite instability, consensus molecular subtype and immune cell infiltration in colon tumours. In particular, we find Faecalibacterium prausnitzii, Coprococcus comes, Bacteroides spp., Fusobacterium spp. and Clostridium spp. to be strongly associated with tumour properties. We implemented an approach to analyse concurrently clinical and molecular properties of the tumour and the composition of the associated microbiome. Our results may improve patient stratification and pave the path for mechanistic studies on microbiota-tumour crosstalk.
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