Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1284446 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The microbial community and enzymes in fermented rice using defined microbial starter, containing Rhizopus oryzae, Saccharomycopsis fibuligera, Saccharomyces cerevisiae and Pediococcus pentosaceus, play an important role in quality of the fermented rice product and its biological activities including melanogenesis inhibitory activity. The microbial metaproteome revealed large-scale proteins expressed by the microbial community to better understand the role of microbiota in the fermented rice.
2020-05-25 | PXD018081 | JPOST Repository
Project description:To understand microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and the effects of environmental factors on their structure, 12 activated sludge samples were collected from four WWTPs in Beijing. GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes. The results showed that, for each gene category, such as egl, amyA, nir, ppx, dsrA sox and benAB, there were a number of microorganisms shared by all 12 samples, suggestive of the presence of a core microbial community in the activated sludge of four WWTPs. Variance partitioning analyses (VPA) showed that a total of 53% of microbial community variation can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs. Four full-scale wastewater treatment systems located in Beijing were investigated. Triplicate samples were collected in each site.
2014-01-15 | E-GEOD-54055 | biostudies-arrayexpress
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:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.
2013-10-30 | GSE51592 | GEO
Project description:The response of soil microbial community to climate warming through both function shift and composition reorganization may profoundly influence global nutrient cycles, leading to potential significant carbon release from the terrain to the atmosphere. Despite the observed carbon flux change in northern permafrost, it remains unclear how soil microbial community contributes to this ecosystem alteration. Here, we applied microarray-based GeoChip 4.0 to investigate the functional and compositional response of subsurface (15~25cm) soil microbial community under about one year’s artificial heating (+2°C) in the Carbon in Permafrost Experimental Heating Research site on Alaska’s moist acidic tundra. Statistical analyses of GeoChip signal intensities showed significant microbial function shift in AK samples. Detrended correspondence analysis and dissimilarity tests (MRPP and ANOSIM) indicated significant functional structure difference between the warmed and the control communities. ANOVA revealed that 60% of the 70 detected individual genes in carbon, nitrogen, phosphorous and sulfur cyclings were substantially increased (p<0.05) by heating. 18 out of 33 detected carbon degradation genes were more abundant in warming samples in AK site, regardless of the discrepancy of labile or recalcitrant C, indicating a high temperature sensitivity of carbon degradation genes in rich carbon pool environment. These results demonstrated a rapid response of northern permafrost soil microbial community to warming. Considering the large carbon storage in northern permafrost region, microbial activity in this region may cause dramatic positive feedback to climate change, which is important and necessary to be integrated into climate change models.
2016-02-22 | GSE77866 | GEO
Project description:Genome scale metabolic model of Drosophila gut microbe Acetobacter fabarum
Abstract -
An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and their impact on host physiology. This research can be confounded by poorly understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multiway interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition, and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that, in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle, including 2-oxoglutarate and succinate, are produced at high flux and cross-fed between bacterial taxa, suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.IMPORTANCE Drosophila is an important model for microbiome research partly because of the low complexity of its mostly culturable gut microbiota. Our current understanding of how Drosophila interacts with its gut microbes and how these interactions influence host traits derives almost entirely from empirical studies that focus on individual microbial taxa or classes of metabolites. These studies have failed to capture fully the complexity of metabolic interactions that occur between host and microbe. To overcome this limitation, we reconstructed and analyzed 31 metabolic models for every combination of the five principal bacterial taxa in the gut microbiome of Drosophila This revealed that metabolic interactions between Drosophila gut bacterial taxa are highly dynamic and influenced by cooccurring bacteria and nutrient availability. Our results generate testable hypotheses about among-microbe ecological interactions in the Drosophila gut and the diversity of metabolites available to influence host traits.
2021-07-01 | MODEL2002040002 | BioModels