Transcriptomic analysis of bacterial vaginosis-associated bacteria living in single or multispecies biofilms
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1114702 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29127920.fastq.gz | Fastqsanger.gz | |||
| SRR29127921.fastq.gz | Fastqsanger.gz | |||
| SRR29127922.fastq.gz | Fastqsanger.gz | |||
| SRR29127923.fastq.gz | Fastqsanger.gz | |||
| SRR29127924.fastq.gz | Fastqsanger.gz |
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Project description:Bacterial vaginosis (BV) is the most common cause of vaginal discharge among women worldwide. BV is characterized by an imbalance in the vaginal microbiota with depletion of protective Lactobacillus species and overgrowth of facultative and strictly anaerobic bacteria. Although the development of a polymicrobial biofilm on the vaginal epithelium is a hallmark of BV, interactions between key BV-associated bacteria (BVAB) [i.e. Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia] present in the biofilm are still not completely understood. In this study, we aimed to analyse the transcriptome of single and triple-species biofilms growing in the rich medium, New York City III (NYCIII). A previous analysis of triple-species biofilms composition by qPCR showed that the biofilms were mainly composed of G. vaginalis, followed by F. vaginae and P. bivia. The transcriptomic analysis revealed a total of 431 (34 upregulated and 397 downregulated), 126 (36 upregulated and 90 downregulated), and 39 (31 upregulated and 8 downregulated) differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively. Gene ontology only detected enrichment for the downregulated genes of G. vaginalis and 47 GO terms were associated with molecular functions, cellular components and biological processes, mainly metabolism. Hence, this work showed the adaptation of 3 BVAB when growing in a triple-species biofilm, with several genes being differentially expressed in all the species growing in a polymicrobial biofilm.
2024-09-25 | GSE268115 | GEO
Project description:It is well known that bacteria often exist in naturally formed multispecies biofilms. Within these biofilms, interspecies interactions seem to play an important role in ecological processes. Little is known about the effects of interspecies interactions on gene expression in these multispecies biofilms. This study presents a comparative gene expression analysis of the Xanthomonas retroflexus transcriptome when grown in a single-species biofilm and in dual- and four-species consortia with Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus. The results revealed complex interdependent interaction patterns in the multispecies biofilms. Many of the regulated functions are related to interactions with the external environment and suggest a high phenotypic plasticity in response to coexistence with other species. Furthermore, the changed expression of genes involved in aromatic and branched chain amino acid biosynthesis suggests nutrient cross feeding as an contribution factor for the observed synergistic biofilm production when these four species coexists in a biofilm.
2016-07-22 | GSE80267 | GEO
Project description:Bacterial vaginosis (BV), the most common vaginal infection among women worldwide, is characterized by an imbalance in the vaginal microbiota with a reduction of protective Lactobacillus species and overgrowth of facultative and strictly anaerobic bacteria. Although the development of a polymicrobial biofilm on the vaginal epithelium is a hallmark of BV, interactions between key BV-associated bacteria (BVAB) [i.e. Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia] present in the biofilm remain largely unexplored. In this study, we aimed to analyze the transcriptome of triple-species biofilms growing in a medium simulating vaginal tract secretions (mGTS) compared to a rich medium, New York City III (NYCIII). As such, triple-species biofilms formed by G. vaginalis, F. vaginae, and P. bivia were grown in either NYCIII or mGTS in anaerobic conditions. After that, RNA was extracted and cDNA libraries were constructed and sequenced. We first characterized the biofilm composition in both media by qPCR and observed that G. vaginalis was the most prevalent species in both conditions. RNA-sequencing data analysis revealed a total of 964, 596, and 656 differentially expressed genes in G. vaginalis, F. vaginae, and P. bivia, respectively, when comparing the transcriptome of biofilms in mGTS versus NYCIII. We identified 927 upregulated and 37 downregulated genes for G. vaginalis, 492 upregulated and 104 downregulated for F. vaginae, and 166 upregulated and 490 downregulated for P. bivia. Gene ontology enrichment showed that metabolic and biosynthetic processes were common within upregulated genes for G. vaginalis, while downregulated genes were associated with transmembrane transporters. For F. vaginae, transmembrane transporters were identified among upregulated genes, while downregulated genes were related to metabolism and cellular process, in which several KEGG pathways linked to metabolism were recognized. For P. bivia, upregulated genes were associated with transmembrane processes while downregulated genes were associated with metabolic processes; KEGG pathways were also identified. This work highlighted the adaptation of 3 key BVAB growing on a medium that simulates in vivo conditions and will contribute to a better understanding of bacterial interactions that are important in the pathogenesis of incident BV.
2025-04-16 | GSE279623 | GEO
Project description:It is well known that bacteria often exist in naturally formed multispecies biofilms. Within these biofilms, interspecies interactions seem to play an important role in ecological processes. Little is known about the effects of interspecies interactions on gene expression in these multispecies biofilms. This study presents a comparative gene expression analysis of the Xanthomonas retroflexus transcriptome when grown in a single-species biofilm and in dual- and four-species consortia with Stenotrophomonas rhizophila, Microbacterium oxydans and Paenibacillus amylolyticus. The results revealed complex interdependent interaction patterns in the multispecies biofilms. Many of the regulated functions are related to interactions with the external environment and suggest a high phenotypic plasticity in response to coexistence with other species. Furthermore, the changed expression of genes involved in aromatic and branched chain amino acid biosynthesis suggests nutrient cross feeding as an contribution factor for the observed synergistic biofilm production when these four species coexists in a biofilm. X. retroflexus was cultivated in three replicates of single-species biofilm and combined with S. rhizophila, M. oxydans and P. amylolyticus in dual-species biofilms with three respective replicates. At last, we combined all four species in a multispecies biofilm with five replicates and conducted a RNA seq based comparative gene expression study utilizing the Illumina sequencing technology. Please note that the 'prodigal_all_new.txt' contains gene names (which are listed in the matrix_sum.txt) and their position in the genomes, which are included in the file 'all_contigs_500.fasta'.
2016-07-22 | E-GEOD-80267 | biostudies-arrayexpress
Project description:Multispecies biofilms are the predominant form of bacterial growth in natural and human-associated environments. Although the pathways involved in monospecies biofilm have been well characterized, less is known about the metabolic pathways and emergent traits of a multispecies biofilm community. Here, we performed a transcriptome survey of the developmental stages of a 3-species biofilm community and combined it with quantitative imaging and growth experiments. We report the remodelling of central metabolism of two of the three species in this community. Specifically, we observed an increase in the expression of genes associated with glycolysis and pentose phosphate pathways in K. pneumoniae. Similarly, a decrease in the expression of the same pathways in P. protegens was observed along with an increase in expression of glyoxalate cycle genes when grown as a mixed species biofilm, suggesting reorganisation of metabolic pathways and metabolite sharing for the community biofilms. To test the possibility of cross-feeding for the community, planktonic growth experiments revealed that both the Pseudomonads grew well in TCA cycle intermediates, while K. pneumoniae grew poorly when given those carbon sources. Despite this poor growth in mono-culture, K. pneumoniae was still the dominant species in mixed species biofilms cultivated in TCA intermediates as the sole source of carbon. The biofilm growth data, combined with the transcriptomics data, suggests there is reorganisation of metabolism for the community members and may allow for cross-feeding that allows K. pneumoniae to dominate the community. We also demonstrated that sdsA1 of P. aeruginosa was induced upon exposure to the surfactant SDS and that this gene was essential in protecting mono and mixed species biofilms from surfactant stress. This also suggests that the community members can share defence mechanisms. Overall, this study describes a comprehensive transcriptomics level investigation of shared resources, metabolites and stress defence that may underpin the emergent properties of mixed species biofilm communities.
2022-10-07 | GSE214543 | GEO
Project description:Bacterial vaginosis (BV) is a common state of the vaginal microbiota characterized by increased bacterial diversity and decreased Lactobacillus abundance. Using untargeted metaproteomics, we identified host and bacterial proteins in a set of 29 cervicovaginal lavage samples from people with and without BV which revealed functions and interactions that likely contribute to BV.
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Project description:The aim of the study was to investigate gene expression profiles of post-menopausal women receiving Premarin estrogen replacement therapy (ERT), compared to controls and to examine any correlations between the bacterial vaginosis (BV) status of the stubjects. This is the first study to use gene arrays to correlate changes in host expression to ERT and BV.
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Project description:Bacterial vaginosis (BV) treatment failures or recurrences are common. To identify features associated with treatment response, we compared vaginal microbiota and host ectocervical transcriptome before and after oral metronidazole therapy. Response to metronidazole is characterized by significant changes in chemokines and related transcripts suggesting that strategies to promote these pathways may prove beneficial.
2021-05-21 | GSE174799 | GEO