Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30791122_1.fastq.gz | Fastqsanger.gz | |||
| SRR30791122_2.fastq.gz | Fastqsanger.gz |
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Project description:This study provides comparative RNA-seq datasets for four freshwater bacterial isolates, Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738, cultured under iron-replete (+100 uM FeCl3) and iron-limited (no FeCl3) conditions. Iron availability is a key factor influencing bacterial fitness, and iron limitation is known to activate siderophore biosynthesis, iron transport, and homeostasis pathways. A total of eight libraries generated in 2024 and 2025 were analyzed, comprising 349.9 million processed reads. Reference-guided mapping rates varied among strains, with higher mapping efficiency observed in Pseudomonas, Herbaspirillum, and Pantoea, while Micrococcus showed comparatively lower mapping rates under both conditions. Differential expression analysis revealed strain-specific responses to iron limitation. Genes related to pyoverdine and ferrichrome uptake were enriched in Pseudomonas and Herbaspirillum, enterobactin-associated pathways were prominent in Pantoea, and genes associated with siderophore production, heme utilization, and Fe-S cluster assembly were identified in Micrococcus. Raw sequencing data are available in the NCBI Sequence Read Archive under BioProject PRJNA1456794, and processed data are deposited in a public repository. These datasets provide a valuable resource for understanding bacterial adaptation to iron availability and for comparative transcriptomic analyses.
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Project description:Pantoea sp. YR343, isolated from the Populus deltoides rhizosphere, is a robust plant root colonizer that produces indole-3-acetic acid (IAA). Genomic and metabolomic analyses predicted that Pantoea sp. YR343 synthesizes IAA primarily using the indole-3-pyruvate pathway. Pantoea sp. YR343 proteomes showed upregulation of IpdC for growth in the presence of tryptophan or IAA versus controls.
2017-08-23 | MSV000081478 | MassIVE
Project description:The microbiota of the mouth disperses into the lungs and both compartments share similar phyla. Considering the importance of the microbiota in the maturation of the immunity and physiology during the first days of life, we hypothesized that primo-colonizing bacteria of the oral cavity may induce immune responses in bronchial epithelial cells. Herein, we have isolated and characterized 57 strains of the buccal cavity of two human new-borns. These strains belong to Streptococcus, Staphylococcus, Enterococcus, Rothia and Pantoea genera; Streptococcus being the most represented. The strains were co-incubated with a bronchial epithelial cell line (BEAS-2B) and we established their impact on a panel of cytokines/chemokines and global changes in gene expression. The Staphylococcus strains, which appeared soon after birth, induced a high production of IL-8, suggesting they can trigger inflammation, whereas the Streptococcus strains were less associated with inflammation pathways. The genera Streptococcus, Enterococcus and Pantoea induced differential profiles of cytokine/chemokine/growth factor and set of genes associated with maturation of morphology. Altogether, our results demonstrate that the micro-organisms, primo-colonizing the oral cavity, impact immunity and morphology of the lung epithelial cells, with specific effects depending on the phylogeny of the strains.
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Project description:Ticks are obligate hematophagous arthropods that transmit a wide range of pathogens to humans as well as wild and domestic animals. They also harbor a non-pathogenic microbiota, although our previous study has shown that the diverse bacterial microbiome in the midgut of Ixodes ricinus is quantitatively poor and lacks a core microbe. In artificial infections by capillary feeding of ticks with two model bacteria (Gram-positive Micrococcus luteus and Gram-negative Pantoea sp.), rapid clearance of these microbes from the midgut was observed, indicating the presence of active immune mechanisms in this organ. In the current study, RNA-seq analysis was performed on the midgut of I. ricinus females inoculated with either M. luteus or Pantoea sp. or with sterile water as a control. While no immune-related transcripts were upregulated by microbial inoculation compared to the sterile control, capillary feeding itself triggered dramatic transcriptional changes in the tick midgut. Manual curation of the transcriptome from the midgut of unfed I. ricinus females, complemented by proteomic analysis, revealed the presence of several constitutively expressed putative antimicrobial peptides (AMPs) that are independent of microbial stimulation and are referred to here as ‘guard’ AMPs. These included two types of midgut-specific defensins, two different domesticated amidase effector 2 (Dae2), microplusin/ricinusin-related molecules, two lysozymes and two gamma interferon-inducible lysosomal thiol reductases (GILTs). The in vitro antimicrobial activity assays of two synthetic mature defensins, defensin 1 and defensin 8, confirmed their specificity against Gram-positive bacteria showing exceptional potency to inhibit the growth of M. luteus at nanomolar concentrations. The antimicrobial activity of midgut defensins is likely part of a multicomponent system responsible for the rapid clearance of bacteria in the tick midgut. Further studies are needed to evaluate the role of other identified ‘guard‘ AMPs in controlling microorganisms entering the tick midgut.
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