Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1311577 | ENA |
REPOSITORIES: ENA
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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: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:The aim of the present study to compare the transcriptomic profile of P.gingivalis when growing within an in vitro multispecies biofilm or in a planktonic state, using microarray technology.
2019-06-05 | GSE132157 | GEO
Project description:Arabidopsis Col-0 seeds were germinated and grown for two weeks on Arabidopsis thaliana salt media (ATS, control) or ATS media supplemented 50, 75, 100 or 125 mM NaCl that imposes both an ionic and osmotic stress; or ATS media supplemented with iso-osmolar concentrations of sorbitol (100, 150, 200 or 250 mM) that imposes only an osmotic stress. The aim of the study was to identify genes involved in plant growth and adaptation to ionic stress compared to genes involved in growth and adaptation to osmotic stress conditions. To do this we identified lists of genes that are differentially expressed in plants grown in NaCl (A) and lists of genes differentially expressed in plants grown in sorbitol (B). We then compared these lists to find ionic/salt-specific genes that are only expressed in plants grown in NaCl and not in plants grown in sorbitol; and osmotic genes that are expressed both in plants grown in NaCl and in plants grown in sorbitol. Associated publication: Cackett et al. (2022) Salt-specific gene expression reveals elevated auxin levels in Arabidopsis thaliana plants grown under saline conditions, DOI: 10.3389/fpls.2022.804716
2022-01-16 | GSE193762 | GEO
Project description:We sought to identify transcriptomic changes that arise when E. faecalis biofilms are cultivated in the presence of C. albicans. We used RNASeq analaysis to compare the transcriptome of 48 hr biofilm-grown cells of E. faecalis. We compared the transcriptome of E. faecalis cells grown as a mono-species biofilm to that of E. faecalis cells that were grown in a biofilm that was co-inoculated with the yeast C. albicans.
2025-03-03 | GSE290415 | GEO
Project description:Multispecies biofilms consist of complex communities where extracellular polymeric substances (EPS) are vital in their structure, adaptability, and function. However, characterizing the components of EPS, particularly glycans and proteins, remains a challenge due to the diverse species and their interactions within the matrix. This study examined how interactions between different species affect EPS components' production and spatial organization. We utilized a consortium of four bacterial soil isolates that have previously demonstrated various intrinsic properties in biofilm communities: Microbacterium oxydans, Paenibacillus amylolyticus, Stenotrophomonas rhizophila, and Xanthomonas retroflexus. We used fluorescence lectin-binding analysis (FLBA) to identify specific glycan components and meta-proteomics to characterize matrix proteins in mono- and multispecies biofilms. Our results revealed diverse glycan structures and compositions, including fucose and different amino sugar-containing polymers, with substantial differences between monospecies and multispecies biofilms. In isolation, M. oxydans produced galactose/N-Acetylgalactosamine network-like structures and influenced the matrix composition in multispecies biofilms. Proteomic analysis revealed flagellin proteins in Xanthomonas and Paenibacillus, particularly in multispecies biofilms. Additionally, surface-layer proteins and a unique peroxidase were found in P. amylolyticus multispecies biofilms, indicating enhanced oxidative stress resistance and structural stability under these conditions. This study highlights the crucial role of interspecies interactions in shaping biofilm matrices and the production of glycans and proteins. These findings deepen our understanding of biofilm complexity and may lead to new approaches for controlling biofilms in various environments.
2025-03-31 | PXD057669 | Pride
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:The Type VI Secretion System (T6SS) in bacteria is a versatile mechanism that facilitates protein transport into neighboring cells and can act as an antibacterial weapon by eliminating competing organisms in the vicinity. The objective of this study was to characterize the T6SS in Aggregatibacter aphrophilus and assess its antimicrobial capabilities through competition with Aggregatibacter actinomycetemcomitans in a multispecies biofilm. The proteomic analysis consisted of two parts, referred to as monospecies biofilm and multispecies biofilms, respectively. Initially, we examined the protein profiles of monospecies biofilms formed by two strains of Aggregatibacter aphrophilus, namely HK83 and CCUG 11575, along with their Hcp mutant derivatives (Hcp being a core protein for T6SS). Each strain was analyzed with six replicates (n=4 for HK83, HK83 hcp, CCUG 11575, and CCUG 11575 hcp). Subsequently, the HK83 and CCUG 11575 strains, as well as their Hcp mutant derivatives, were individually introduced into a multispecies biofilm. This multispecies biofilm consisted of seven species, namely A. actinomycetemcomitans JP2 strain (OMZ 295), Actinomyces oris (OMZ 745), Candida albicans (OMZ 110), Fusobacterium nucleatum subsp. nucleatum KP-F2 (OMZ 598), Streptococcus oralis SK248 (OMZ 607), Streptococcus mutans UA159 (OMZ 918), and Veillonella dispar ATCC 17748T (OMZ 493). These species were selected to mimic the natural co-habitat of A. aphrophilus and A. actinomycetemcomitans. Furthermore, control 7-species biofilms with A. aphrophilus strains HK83, HK83 hcp, CCUG 11575, and CCUG 11575 hcp (n=4 each) underwent proteomic analysis to gain insights into the protein expression and potential interactions within the biofilm community.
2024-05-24 | PXD042723 | Pride