Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1130068 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29657332.fastq.gz | Fastqsanger.gz | |||
| SRR29657333.fastq.gz | Fastqsanger.gz | |||
| SRR29657334.fastq.gz | Fastqsanger.gz | |||
| SRR29657335.fastq.gz | Fastqsanger.gz | |||
| SRR29657336.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Microbial biofilms are omnipresent and implicated in a wide spectrum of areas ranging from bioremediation, food production and biomedical applications. To date little is understood about how biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we ap-ply a meta-proteomics approach to investigate the mechanism driving biofilm formation in a microbial model consortium of four bacterial soil isolates of Steno-trophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paeni-bacillus amylolyticus. The protein abundances between community and the single species biofilms were compared to describe how different metabolic pathways were influenced by inter-species interactions. Our results indicate that community development is dependent on interactions between community members facilitat-ing surface attachment and cross-feeding on specific amino acids. Opposite regu-lation patterns of fermentation and nitrogen pathways in Paenibacillus amylolyticus and Xanthomonas retroflexus may, however, also indicate that competition for lim-ited resources affects community development. Overall our results demonstrate the multitude of pathways characterizing biofilm formation in mixed communities. In order to obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for removing peptide sequences shared between community members from the ref-erence proteomes used for spectral database searches. This pipeline can readily be applied to other microbial communities.
2017-12-04 | PXD006281 | Pride
Project description:Bacteria growing as surface-adherent biofilms are better able to withstand chemical and physical stresses than their unattached, planktonic counterparts. Using transcriptional profiling and quantitative PCR, we observed a previously uncharacterized gene, yjfO, to be upregulated during Escherichia coli MG1655 biofilm growth in a chemostat on serine-limited defined medium. A yjfO mutant, developed through targeted insertion mutagenesis, and a yjfO-complemented strain, were obtained for further characterization. While bacterial surface colonization levels (CFU/cm2) were similar in all three strains, the mutant strain exhibited reduced microcolony formation when observed in flow cells, and greatly enhanced flagellar motility on soft (0.3%) agar. Complementation of yjfO restored microcolony formation and flagellar motility to wild type levels. Cell surface hydrophobicity and twitching motility were unaffected by the presence or absence of yjfO. In contrast to the parent strain, biofilms from the mutant strain were less able to resist acid and peroxide stresses. yjfO had no significant effect on E. coli biofilm susceptibility to alkali or heat stress. Planktonic cultures from all three strains showed similar responses to these stresses. Regardless of the presence of yjfO, planktonic E. coli withstood alkali stress better than biofilm populations. Complementation of yjfO restored viability following exposure to peroxide stress, but did not restore acid resistance. Based on its influence on biofilm formation, stress response, and effects on motility, we propose renaming the uncharacterized gene, yjfO, as bsmA (biofilm stress and motility). Transcriptional profiling of duplicate biofilm and planktonic cultures of E. coli MG1655 grown in serine-limited MOPS minimal media.
2010-06-21 | E-GEOD-18362 | biostudies-arrayexpress
Project description:Bacteria growing as surface-adherent biofilms are better able to withstand chemical and physical stresses than their unattached, planktonic counterparts. Using transcriptional profiling and quantitative PCR, we observed a previously uncharacterized gene, yjfO, to be upregulated during Escherichia coli MG1655 biofilm growth in a chemostat on serine-limited defined medium. A yjfO mutant, developed through targeted insertion mutagenesis, and a yjfO-complemented strain, were obtained for further characterization. While bacterial surface colonization levels (CFU/cm2) were similar in all three strains, the mutant strain exhibited reduced microcolony formation when observed in flow cells, and greatly enhanced flagellar motility on soft (0.3%) agar. Complementation of yjfO restored microcolony formation and flagellar motility to wild type levels. Cell surface hydrophobicity and twitching motility were unaffected by the presence or absence of yjfO. In contrast to the parent strain, biofilms from the mutant strain were less able to resist acid and peroxide stresses. yjfO had no significant effect on E. coli biofilm susceptibility to alkali or heat stress. Planktonic cultures from all three strains showed similar responses to these stresses. Regardless of the presence of yjfO, planktonic E. coli withstood alkali stress better than biofilm populations. Complementation of yjfO restored viability following exposure to peroxide stress, but did not restore acid resistance. Based on its influence on biofilm formation, stress response, and effects on motility, we propose renaming the uncharacterized gene, yjfO, as bsmA (biofilm stress and motility).
2009-10-17 | GSE18362 | GEO
Project description:Legionella pneumophila is a Gram-negative, environmental bacterium, which causes the life-threatening pneumonia Legionnaires’ disease. The facultative intracellular bacterium forms biofilms and employs the Icm/Dot type IV secretion system (T4SS) to replicate in amoebae and macrophages. The Legionella quorum sensing (Lqs) system and the transcription factor LvbR form a regulatory network controlling various traits, including bacterial motility, virulence and biofilm architecture. Here we show by comparative proteomics that in biofilms formed by L. pneumophila mutant strains lacking LvbR or the response regulator LqsR, proteins encoded by the 133 kb fitness island and components of the flagellum (FlaA) are downregulated. Confocal microscopy revealed that the ∆lqsR or ∆flaA mutant strains formed biofilms of the same patchy morphology as the parental strain JR32, while the ∆lvbR mutant forms a mat-like biofilm as previously shown. Acanthamoeba castellanii amoebae migrated more slowly through biofilms formed by the ∆lvbR, ∆lqsR or ∆flaA mutant strains, and amoebae migration was impaired in biofilms formed by L. pneumophila lacking a functional Icm/Dot T4SS (∆icmT) or the secreted effector proteins LegG1 and PpgA. Amoebae migrating through biofilms formed by JR32, ∆lvbR or ∆icmT were decorated by clusters of bacteria, while amoebae in ∆lqsR or ∆flaA biofilms were not. Taken together, the Lqs system, LvbR, FlaA and the Icm/Dot T4SS regulate migration of A. castellanii through L. pneumophila biofilms, and – with the exception of the T4SS – also regulate bacterial cluster formation on the amoeba. Hence, amoebae migration through L. pneumophila biofilms is regulated by bacterial quorum sensing, virulence and motility.
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