Bacteria
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ABSTRACT:
PROVIDER: PRJNA492917 | ENA |
REPOSITORIES: ENA
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Project description:Competition for limited iron resources is a key driver of microbial community structure in many regions of the surface ocean. The bacterial siderophores ferrioxamine and amphibactin have been identified in marine surface waters, suggesting that they may represent an important bacterial strategy for obtaining iron from a scarcely populated pool. We screened several strains of marine Vibrio for the presence of putative amphibactin biosynthesis gene homologues and amphibactin production. Whole cell proteomics, siderophore isolation, and isotopically labeled iron uptake experiments were performed. Here, we show that an amphibactin-producing marine bacterium, Vibrio cyclitrophicus str. 1F-53, harbors an independently regulated uptake pathway for ferrioxamines. Proteomic analyses identified upregulation of the amphibactin NRPS system and a putative amphibactin siderophore transporter in response to low iron concentrations. In addition, multiple other transporters were upregulated, however when desferrioxamine was present, amphibactin production decreased and the ferrioxamine receptor increased in abundance. Such cheating phenotypes, which appear widespread among marine amphibactin producers, highlight the strategies that contribute to the fitness of marine bacteria in the face of iron stress. These results demonstrate siderophore producer and cheater phenotypes and highlight the cellular restructuring which is involved due to competition for iron, that shapes the community structure of marine ecosystems.
2021-04-19 | PXD011427 | Pride
Project description:Humans and microorganisms, both symbiotic and pathogenic, have evolved means to communicate through the dissemination of biological signals. In addition to small molecules and proteins, mobile small RNAs (sRNAs) have recently emerged as signal molecules that mediate inter-species crosstalk by functional RNA interference (RNAi). However, the trafficking of sRNAs between humans and microorganisms, as well as the resulting biological consequences, remains unexplored. Here, we report that human cells secrete exosomes to deliver sRNAs into bacteria and induce bacterial gene silencing. The unprecedented RNAi in bacteria is accomplished primarily through translational repression without mRNA degradation, for which the participation of human AGO2 proteins co-transferred with sRNAs is essential. Exosome-mediated bacterial RNAi was further applied to fight superbug infection by targeting drug-resistance genes in a mouse model. Our discovery of this unique exosome-mediated sRNA delivery and gene silencing in bacteria paves the way to understanding and manipulating the cross-kingdom communication between human hosts and intestinal microbiota, as well as between humans and pathogenic bacteria.
2025-03-06 | GSE122212 | GEO
Project description:Protection against pathogens is a major function of the gut microbiota. Although bacterial natural products have emerged as crucial components of host-microbiota interactions, their exact role in microbiota-mediated protection is largely unexplored. We addressed this knowledge gap with the nematodeCaenorhabditis elegansand its microbiota isolatePseudomonas fluorescensMYb115 that is known to protect againstBacillus thuringiensis (Bt) infection. We find that MYb115-mediated protection depends on sphingolipids that are derived from an iterative type I polyketide synthase (PKS), thereby describing a noncanonical pathway of bacterial sphingolipid production. We provide evidence that MYb115-derived sphingolipids affectC. eleganstolerance to Bt infection by altering host sphingolipid metabolism. This work establishes sphingolipids as structural outputs of bacterial PKS and highlights the role of microbiota-derived sphingolipids in host protection against pathogens.
2023-10-14 | GSE245296 | GEO
Project description:A special immune system exists at distinct respiratory epithelium to combat invasion by Pseudomonas aeruginosa (PAO1). This study aimes to determine if interleukin-17C (IL-17C) is correlated with acute PAO1 infection in human nasal epithelium and to prove the role of IL-17C on iron sequestration during PAO1 infection. IL-17C has antipseudomonal effect by lowering iron sequestration and reducing siderophore activity. IL-17C could be efficient mediator to control PAO1 infection in human nasal epithelium.
2018-01-12 | GSE109118 | GEO
Project description:Microbiota-induced cytokine responses participate in gut homeostasis, but the cytokine balance at steady-state and the role of individual bacterial species in setting the balance remain elusive. Using gnotobiotic mouse models, we provide a systematic analysis of the role of microbiota in the induction of cytokine responses in the normal intestine. Colonization by a whole mouse microbiota orchestrated a broad spectrum of pro-inflammatory (Th1, Th17) and regulatory T cell responses. Unexpectedly, most tested complex microbiota and individual bacteria failed to efficiently stimulate intestinal cytokine responses. A potent cytokine-inducing function was however associated with non-culturable host-specific species, the prototype of which was the Clostridia-related Segmented Filamentous Bacterium, and this bacterial species recapitulated the coordinated maturation of T cell responses induced by the whole mouse microbiota. Our study demonstrates the non-redundant role of microbiota members in the regulation of gut immune homeostasis. Germfree (GF) female 8-9-week-old mice were gavaged twice at a 24-hr interval with 0.5 mL of fresh anaerobic cultures of fecal homogenate from SFB mono-associated mice, fresh feces from Cv mice (Cvd) or from a healthy human donor (Hum). All mice were sacrificed on d8, 20 and 60 post-colonization in parallel to age-matched Cv and GF controls. RNA was extracted from ileal tissue, and processed to biotin-labelled cRNA, and then hybridized to the NuGO array (mouse) NuGO_Mm1a520177. Microarray analysis compared gene expression in ileum tissue of all the treatment groups GF, Cv, Cvd, Hum and SFB (N=3 per treatment group per time-point). Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method.
2010-05-05 | E-GEOD-18056 | biostudies-arrayexpress
Project description:The human nasopharynx is colonized by a diverse community of commensal microbiota linked to many respiratory diseases, yet their interactions with the host remain unclear. In this study, we introduced a dual-transcriptomics analysis strategy, which can characterize the host transcriptome and microbiome from nasal samples simultaneously. RNA sequencing reads from human nasal swab samples were pre-processed and aligned to the human genome for host gene expression counting, while unmapped reads were further aligned to microbiota genome. After taxonomic classification, microbial abundance matrix was derived at each taxonomic level for differential and host-microbiota interaction analysis. We applied this workflow to a local SARS-CoV-2 cohort with 76 infected patients, among whom 55 (72.37%) were symptomatic at enrollment. Nasal swabs were collected from all 76 patients at enrollment and from 73 patients at one-week later follow-up. We detected a median of 4.81% reads unmapped from the human genome across all 149 samples, among which around half (median 48.63%) were successfully mapped to microbiome genome. Meta-transcriptomic analysis detected significantly higher SARS-related coronavirus loads in samples from the symptomatic group at enrollment, and both groups showed decreased loads one week later. Compared with benchmarking 16S rRNA sequencing on 53 samples, our computational strategy showed high correlation of relative abundance in all top 20 genus. A total of 685 bacteria species were identified to show a relative abundance >= 0.01% in at least 10% samples. Differential abundance analysis identified 66 species (DASs) from 6 phyla with significantly decreased abundance in samples from the symptomatic group compared to the asymptomatic group at enrollment. Integrating these symptom-associated DASs with host’s gene expression using an expression quantitative trait bacteria (eQTB) model, we found 58 symptom-associated DASs identified at enrollment were significantly associated with one to 16 genes. GSEA showed a series of symptom-associated DASs were significantly correlated with pathways related to the activation of olfactory, keratinocyte differentiation, and DNA methylation. In summary, our dual-transcriptomic analysis strategy effectively characterized host-microbiome interactions, offering insights into microbial contributions to respiratory diseases.
2025-12-06 | GSE309134 | GEO
Project description:The human nasopharynx is colonized by a diverse community of commensal microbiota linked to many respiratory diseases, yet their interactions with the host remain unclear. In this study, we introduced a dual-transcriptomics analysis strategy, which can characterize the host transcriptome and microbiome from nasal samples simultaneously. RNA sequencing reads from human nasal swab samples were pre-processed and aligned to the human genome for host gene expression counting, while unmapped reads were further aligned to microbiota genome. After taxonomic classification, microbial abundance matrix was derived at each taxonomic level for differential and host-microbiota interaction analysis. We applied this workflow to a local SARS-CoV-2 cohort with 76 infected patients, among whom 55 (72.37%) were symptomatic at enrollment. Nasal swabs were collected from all 76 patients at enrollment and from 73 patients at one-week later follow-up. We detected a median of 4.81% reads unmapped from the human genome across all 149 samples, among which around half (median 48.63%) were successfully mapped to microbiome genome. Meta-transcriptomic analysis detected significantly higher SARS-related coronavirus loads in samples from the symptomatic group at enrollment, and both groups showed decreased loads one week later. Compared with benchmarking 16S rRNA sequencing on 53 samples, our computational strategy showed high correlation of relative abundance in all top 20 genus. A total of 685 bacteria species were identified to show a relative abundance >= 0.01% in at least 10% samples. Differential abundance analysis identified 66 species (DASs) from 6 phyla with significantly decreased abundance in samples from the symptomatic group compared to the asymptomatic group at enrollment. Integrating these symptom-associated DASs with host’s gene expression using an expression quantitative trait bacteria (eQTB) model, we found 58 symptom-associated DASs identified at enrollment were significantly associated with one to 16 genes. GSEA showed a series of symptom-associated DASs were significantly correlated with pathways related to the activation of olfactory, keratinocyte differentiation, and DNA methylation. In summary, our dual-transcriptomic analysis strategy effectively characterized host-microbiome interactions, offering insights into microbial contributions to respiratory diseases.
2025-12-06 | GSE309130 | GEO
Project description:Microbiota-induced cytokine responses participate in gut homeostasis, but the cytokine balance at steady-state and the role of individual bacterial species in setting the balance remain elusive. Using gnotobiotic mouse models, we provide a systematic analysis of the role of microbiota in the induction of cytokine responses in the normal intestine. Colonization by a whole mouse microbiota orchestrated a broad spectrum of pro-inflammatory (Th1, Th17) and regulatory T cell responses. Unexpectedly, most tested complex microbiota and individual bacteria failed to efficiently stimulate intestinal cytokine responses. A potent cytokine-inducing function was however associated with non-culturable host-specific species, the prototype of which was the Clostridia-related Segmented Filamentous Bacterium, and this bacterial species recapitulated the coordinated maturation of T cell responses induced by the whole mouse microbiota. Our study demonstrates the non-redundant role of microbiota members in the regulation of gut immune homeostasis.
2009-09-11 | GSE18056 | GEO
Project description:This pilot research trial studies the effects of chemotherapy on intestinal bacteria/organisms (microbiota) in patients newly diagnosed with breast cancer. Change in intestinal microbiota may be associated with weight gain in patients treated with chemotherapy. Weight gain has been also associated with cancer recurrence. Examining the types and quantity of bacterial composition in the stool of breast cancer patients treated with chemotherapy may help determine whether body weight and composition are associated with changes in the intestinal microbiota and allow doctors to plan better treatment to prevent weight gain and possibly disease recurrence.
| 2184354 | ecrin-mdr-crc