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PROVIDER: PRJEB89783 | ENA |
REPOSITORIES: ENA
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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:Bacteriophage – host dynamics and interactions are important for microbial community composition and ecosystem function. Nonetheless, empirical evidence in engineered environment is scarce. Here, we examined phage and prokaryotic community composition of four anaerobic digestors in full-scale wastewater treatment plants (WWTPs) across China. Despite relatively stable process performance in biogas production, both phage and prokaryotic groups fluctuated monthly over a year of study period. Nonetheless, there were significant correlations in their α- and β-diversities between phage and prokaryotes. Phages explained 40.6% of total prokaryotic community composition, much higher than the explainable power by abiotic factors (14.5%). Consequently, phages were significantly (P<0.010) linked to parameters related to process performance including biogas production and volatile solid concentrations. Association network analyses showed that phage-prokaryote pairs were deeply rooted, and two network modules were exclusively comprised of phages, suggesting a possibility of co-infection. Those results collectively demonstrate phages as a major biotic factor in controlling bacterial composition. Therefore, phages may play a larger role in shaping prokaryotic dynamics and process performance of WWTPs than currently appreciated, enabling reliable prediction of microbial communities across time and space.
2016-12-29 | GSE92978 | GEO
Project description:The rate, timing, and mode of species dispersal is recognized as a key driver of the structure and function of communities of macroorganisms, and may be one ecological process that determines the diversity of microbiomes. Many previous studies have quantified the modes and mechanisms of bacterial motility using monocultures of a few model bacterial species. But most microbes live in multispecies microbial communities, where direct interactions between microbes may inhibit or facilitate dispersal through a number of physical (e.g., hydrodynamic) and biological (e.g., chemotaxis) mechanisms, which remain largely unexplored. Using cheese rinds as a model microbiome, we demonstrate that physical networks created by filamentous fungi can impact the extent of small-scale bacterial dispersal and can shape the composition of microbiomes. From the cheese rind of Saint Nectaire, we serendipitously observed the bacterium Serratia proteamaculans actively spreads on networks formed by the fungus Mucor. By experimentally recreating these pairwise interactions in the lab, we show that Serratia spreads on actively growing and previously established fungal networks. The extent of symbiotic dispersal is dependent on the fungal network: diffuse and fast-growing Mucor networks provide the greatest dispersal facilitation of the Serratia species, while dense and slow-growing Penicillium networks provide limited dispersal facilitation. Fungal-mediated dispersal occurs in closely related Serratia species isolated from other environments, suggesting that this bacterial-fungal interaction is widespread in nature. Both RNA-seq and transposon mutagenesis point to specific molecular mechanisms that play key roles in this bacterial-fungal interaction, including chitin utilization and flagellin biosynthesis. By manipulating the presence and type of fungal networks in multispecies communities, we provide the first evidence that fungal networks shape the composition of bacterial communities, with Mucor networks shifting experimental bacterial communities to complete dominance by motile Proteobacteria. Collectively, our work demonstrates that these strong biophysical interactions between bacterial and fungi can have community-level consequences and may be operating in many other microbiomes.
2017-08-02 | GSE85095 | GEO
Project description:Microglia renewal in old mice enhances the cellular fitness to cope with stroke
| PRJNA807138 | ENA
Project description:We are using a minimal model of interacting multispecies ecological communities that incorporates competition, immigration, and demographic noise. Importantly, the dynamics of the system are described by a birth-death process with interactions, whereby the abundance (the number of individuals) of any species is discrete, where the number of individuals from a given species increases or decreases by one following given birth or death rates (respectively).
We find rich behavior with many unexpected regimes. We apply the insights and implications of our model to the range of behaviors observed experimentally in different ecosystems—from bacteria to the immune system.
This repository stores the code used to study the population dynamics described in the PNAS publication: Phenomenology and Dynamics of Competitive Ecosystems Beyond the Niche-Neutral Regimes by Nava Leibovich, Jeremy Rothschild, Sidhartha Goyal and Anton Zilman. See more at (https://github.com/jbRothschild/project-abundance/tree/PNAS)
2023-03-17 | MODEL2212080001 | BioModels
Project description:Next Generation Sequencing to determine the fundamental mechanisms of Tribolium castaneum larvae to cope with hypoxia
| PRJNA464030 | ENA
Project description:We used high-throughput sequencing technology to determine the fundamental mechanisms of Tribolium castaneum to cope with hypoxia. Totals of 12,524,554 useful reads from the control group and 14,193,339 useful reads from the treatment group were generated after Q20 filtering. A total of 16,524 unigenes had been annotated. More than 300 transcripts showed differential expression between the control and hypoxia group, with a fold change ≥1.5 and p value <0.05. Of the 333 identified DEGs, 154 were downregulated and 179 were upregulated. Altered expression of 9 genes was confirmed with qRT–PCR, demonstrating the qRT-PCR data matched the RNA-seq results well. Finally, our results indicated that limiting the available oxygen to T. castaneum increased glycolysis and inhibited the Krebs cycle, and that accumulated pyruvic acid was preferentially converted to lactic acid via anaerobic metabolism. This study advances the field of pest control and makes it possible to develop more efficient strategies for hermetic storage.
2018-05-09 | GSE114049 | GEO
Project description:Phages are viruses that infect prokaryotes and can shape microbial communitiesby lysis, thus offering applications in various fields. However, challengesexist in sampling, isolation and accurate prediction of the host specificity ofphages as well as in the identification of newly replicated virions in response toenvironmental challenges. A new workflow using biorthogonal non-canonicalamino acid tagging (BONCAT) and click chemistry (CC) allowed combinedanalysis of phages and their hosts, the identification of newly replicated virions,and the specific tagging of phages with biotin for affinity chromatography.Replication of phage λ in Escherichia coli was selected as a model for workflowdevelopment. Specific labeling of phage λ proteins with the non-canonicalamino acid 4-azido-L-homoalanine (AHA) during phage development in E. coliwas confirmed by LC–MS/MS. Subsequent tagging of AHA with fluorescentdyes via CC allowed the visualization of phages adsorbed to the cell surfaceby fluorescence microscopy. Flow cytometry enabled the automated detectionof these fluorescent phage-host complexes. Alternatively, AHA-labeled phageswere tagged with biotin for purification by affinity chromatography. Despitebiotinylation the tagged phages could be purified and were infectious afterpurification. Applying this approach to environmental samples would enablehost screening without cultivation. A flexible and powerful workflow for thedetection and enrichment of phages and their hosts in pure cultures has beenestablished. The developed method lays the groundwork for future workflowsthat could enable the isolation of phage-host complexes from diverse complexmicrobial communities using fluorescence-activated cell sorting or biotinpurification. The ability to expand and customize the workflow through thegrowing range of compounds for CC offers the potential to develop a versatiletoolbox in phage research. This work provides a starting point for these furtherstudies by providing a comprehensive standard operating procedure.
2024-08-29 | PXD044316 | Pride
Project description:Retrons are bacterial genetic elements that encode a reverse transcriptase and, in combination with toxic effector proteins, can serve as antiphage defense systems. However, the mechanisms of action of most retron effectors, and how phages evade retrons, are not well understood. Here, we show that some phages can evade retrons and other defense systems by producing specific tRNAs. We find that expression of retron-Eco7 effector proteins (PtuA and PtuB) leads to degradation of tRNA-Tyr and abortive infection. The genomes of T5 phages that evade retron-Eco7 include a tRNA-rich region, including a highly expressed tRNA-Tyr gene, which confers protection against retron-Eco7. Furthermore, we show that other phages (T1, T7) can use a similar strategy, expressing a tRNA-Lys, to counteract a tRNA anticodon defense system (PrrC170).
2024-09-12 | GSE229290 | GEO