Biofilm isolates
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PROVIDER: PRJEB21932 | ENA |
REPOSITORIES: ENA
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Project description:Background. Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continiouslly fed biofilm reactor, and compared to both batch and reactor planktonic populations. The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenases as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion.
2012-04-01 | GSE35883 | GEO
Project description:Background. Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continiouslly fed biofilm reactor, and compared to both batch and reactor planktonic populations. The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenases as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion. Biofilms grown in reactors were compared to reference samples of reactor, planktonic and batch, planktonic. Each sample had a biological triplicate.
2012-03-31 | E-GEOD-35883 | biostudies-arrayexpress
Project description:Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.
2019-10-30 | PXD015073 | Pride
Project description:Candida albicans is an opportunistic fungal pathogen and a natural component of the human microbial flora. One central C. albicans virulence trait is the ability to produce a biofilm, which is regulated by several transcription factors. Mutations of some biofilm transcriptional regulators cause the same severe biofilm-defective phenotype in multiple clinical isolates. Mutations of others, such as Wor3, Bcr1, Ndt80, and Ume6, have mild or variable phenotypes among clinical isolates. We hypothesized that Wor3 may have a shared function with one of the other variable-phenotype biofilm regulators. This hypothesis predicts that a double mutant lacking Wor3 and the shared-function regulator will have a severe biofilm defect in all clinical isolates. We observed that a wor3Δ/Δ bcr1Δ/Δ has a severe biofilm defect in vitro in 5 strain backgrounds tested. It also has a severe oral biofilm defect in a mouse oropharyngeal candidiasis model in the SC5314 reference strain background. RNA-seq data indicate that 5 genes encoding cell surface/secreted proteins are upregulated in wor3Δ/Δ, bcr1Δ/Δ, and wor3Δ/Δ bcr1Δ/Δ strains: CWH8, DAG7, JEN2, PGA6, and YWP1. Deletion mutations of CWH8, DAG7, PGA6, or YWP1 enables biofilm formation in vitro in an SC5314-derived wor3Δ/Δ bcr1Δ/Δ strain, and deletion of YWP1 enables biofilm formation in vitro in wor3Δ/Δ bcr1Δ/Δ strains from 4 other genetic backgrounds. YWP1 has been shown to have anti-biofilm activity previously, but CWH8, DAG7, and PGA6 are newly described anti-biofilm genes. Our study illustrates the value of strain variation considerations for gene function analysis and the importance of repression targets of biofilm regulators. In addition, our results expand the number of anti-biofilm genes.
2026-04-15 | GSE289081 | GEO
Project description:Candida albicans is an opportunistic fungal pathogen and a natural component of the human microbial flora. One central C. albicans virulence trait is the ability to produce a biofilm, which is regulated by several transcription factors. Mutations of some biofilm transcriptional regulators cause the same severe biofilm-defective phenotype in multiple clinical isolates. Mutations of others, such as Wor3, Bcr1, Ndt80, and Ume6, have mild or variable phenotypes among clinical isolates. We hypothesized that Wor3 may have a shared function with one of the other variable-phenotype biofilm regulators. This hypothesis predicts that a double mutant lacking Wor3 and the shared-function regulator will have a severe biofilm defect in all clinical isolates. We observed that a wor3Δ/Δ bcr1Δ/Δ has a severe biofilm defect in vitro in 5 strain backgrounds tested. It also has a severe oral biofilm defect in a mouse oropharyngeal candidiasis model in the SC5314 reference strain background. RNA-seq data indicate that 5 genes encoding cell surface/secreted proteins are upregulated in wor3Δ/Δ, bcr1Δ/Δ, and wor3Δ/Δ bcr1Δ/Δ strains: CWH8, DAG7, JEN2, PGA6, and YWP1. Deletion mutations of CWH8, DAG7, PGA6, or YWP1 enables biofilm formation in vitro in an SC5314-derived wor3Δ/Δ bcr1Δ/Δ strain, and deletion of YWP1 enables biofilm formation in vitro in wor3Δ/Δ bcr1Δ/Δ strains from 4 other genetic backgrounds. YWP1 has been shown to have anti-biofilm activity previously, but CWH8, DAG7, and PGA6 are newly described anti-biofilm genes. Our study illustrates the value of strain variation considerations for gene function analysis and the importance of repression targets of biofilm regulators. In addition, our results expand the number of anti-biofilm genes.
2026-04-15 | GSE319691 | GEO
Project description:Pseudomonas aeruginosa has a notorious ability to form biofilms, which often facilitate chronic infections. Despite we lack a consensus methodology for its biofilm quantifica-tion/classification for clinical use. Furthermore, the problem gets exacerbated due to het-erogeneity in its matrix composition due to nutritional and oxygen cues, resulting in phe-notypic variations. Here, we formulated the supplement mix for isolate classification based on biofilm forming capacity and tried to profile multiple clinical isolates of Pseu-domonas aeruginosa that revealed many common and some distinct metabolic and pro-teomic signatures among high, medium, low and non-biofilm producing isolates. We further noted the biofilm degrading and inhibiting effects of some in vogue antibiotics in sub-inhibitory doses. We validated our findings employing growth kinetics, confocal mi-croscopy, scanning electron microscopy, Liquid chromatography-Orbitrap-based high resolution mass spectrometry (LC-HRMS). We noted high level resistance against ceftazidime (43.88%), meropenem (43.17%), imipenem (33.09%), and piperacil-lin-tazobactam (30.94%). Also, we noted, that upon our supplementation, 38.84% isolates were found to be high slime producing, while only 1.14% isolates were non-slime pro-ducing. We noted active anoxic metabolism although P. aeruginosa is a strict aerobe. We noted abundant proteins for cellular adaptation to chemical gradients, including glucose catabolism, arginine and polyamine metabolism, and potential virulence and stress me-diation in high slime producer matrix. This work provides insight toward the potential for metabolic speciation in biofilm and supports the development of biofilm-specific diagnos-tics, and development of futuristic therapeutic modalities.
2026-05-18 | PXD057726 | Pride
Project description:We performed differential RNA-seq of two Staphylococcus epidermidis clinical isolates (PS2 and PS10) to compare their transcription profiles. The isolates were originally obtained from blood cultures during a systemic infection in an immunocompromised patient (Weisser et al. 2010. J Clin Microbiol 48: 2407-2412). They are of clonal origin, but differ phenotypically with respect to extracellular biofilm matrix production. Thus PS2, isolated in the early stage of the infection, forms a weak biofilm mediated by protein-protein interactions, while PS10, which was obtained at the end of the infection course, forms a strong biofilm through production of a polysaccharide intercellular adhesin (PIA) extracellular biofilm matrix. Transcription profiling by dRNA-seq was performed to elucidate differentially expressed metabolic pathways and regulators contributing to the switch in extracellular biofilm matrix producction between the two isolates.
2019-02-05 | GSE126097 | GEO
Project description:Persistence of Listeria monocytogenes in retail deli environments is a serious food safety issue, potentially leading to cross-contamination of ready-to-eat foods such as deli meats, salads, and cheeses. We previously discovered strong evidence of L. monocytogenes persistence in delis across multiple states. We hypothesized that this was correlated with isolates’ innate characteristics, such as biofilm-forming capacity or gene differences.We further chose four isolates for RNA-sequencing analysis and compared their global biofilm transcriptome to their global planktonic transcriptome. Analysis of biofilm vs planktonic gene expression did not show the expected differences in gene expression patterns. Overall, L. monocytogenes persistence in the deli environment is likely a matter of poor sanitation and/or facility design, rather than isolates’ biofilm-forming capacity, sanitizer tolerance, or genomic content
2021-06-11 | GSE176617 | GEO
Project description:Wastewater reactor biofilm Targeted Locus (Loci)
| PRJNA215989 | ENA