Results 201-220 of 254.
![]() Muller, Emilie ![]() ![]() Poster (2013) Natural microbial communities are heterogeneous and dynamic. Therefore, a major consideration for multiple omic data studies is the sample-to-sample heterogeneity, which can lead to inconsistent results ... [more ▼] Natural microbial communities are heterogeneous and dynamic. Therefore, a major consideration for multiple omic data studies is the sample-to-sample heterogeneity, which can lead to inconsistent results if the different biomolecular fractions are obtained from distinct sub-samples. Conversely, systematic omic measurements, i.e. the standardised, reproducible and simultaneous measurement of multiple features from a single undivided sample, result in fully integrable datasets. Objective In order to prove the feasibility and benefits of such systematic measurements in the study of the respective contributions of different populations to the community-wide phenotype, we purified and analysed all biomolecular fractions, i.e. DNA, RNA, proteins and metabolites, obtained from a unique undivided sample of lipid accumulating microbial community (LAMC) from wastewater treatment plant and integrate the resulting datasets. Methods One time point of particular interest was first selected out of 4 LAMC samples for its high diversity and strong lipid accumulation phenotype. Then, the systematic measurement strategy was applied to the selected undivided LAMC sample and the purified biomolecules were analysed by high-throughput techniques. DNA and RNA sequencing reads were assembled at the population-level using different binning strategies. A database, containing predicted proteins, was constructed to identify the detected peptides. Finally, all biomolecular information was mapped onto the assembled composite genomes to identify the precise roles of the different populations in the community-wide lipid accumulation phenotype. Results Metabolomics and 16S diversity analyses were used to select the sample of highest interest for detailed analysis. The systematic measurements of the selected sample followed by data integration have allowed us to probe the functional relevance of the population-level composite genomes, leading to the identification of the LAMC key players. Conclusion As community phenotype is not the sum of the different partner phenotypes, understanding a microbial community system requires more than the study of isolated organisms. Even if both approaches are complementary, top-down systematic approached only provides a holistic perspective of micro-ecological processes. [less ▲] Detailed reference viewed: 131 (5 UL)![]() Wilmes, Paul ![]() Presentation (2012, December) Detailed reference viewed: 31 (0 UL)![]() Wilmes, Paul ![]() Scientific Conference (2012, November) Detailed reference viewed: 30 (0 UL)![]() Wilmes, Paul ![]() Scientific Conference (2012, October) Detailed reference viewed: 31 (0 UL)![]() ![]() Shah, Pranjul ![]() ![]() Scientific Conference (2012, August 25) Detailed reference viewed: 162 (7 UL)![]() Wilmes, Paul ![]() Scientific Conference (2012, June) Detailed reference viewed: 33 (3 UL)![]() Wilmes, Paul ![]() Scientific Conference (2012, June) Detailed reference viewed: 40 (0 UL)![]() Wilmes, Paul ![]() Presentation (2012, May) Detailed reference viewed: 29 (0 UL)![]() Wilmes, Paul ![]() Presentation (2012, May) Detailed reference viewed: 25 (0 UL)![]() Wilmes, Paul ![]() in Ogilvie, L.A.; Hirsch, P.R (Eds.) Microbial Ecological Theory: Current Perspectives (2012) The recent application of high-throughput molecular biology methods to natural microbial communities is profoundly changing our view on the microbial world. In particular, our understanding of microbial ... [more ▼] The recent application of high-throughput molecular biology methods to natural microbial communities is profoundly changing our view on the microbial world. In particular, our understanding of microbial population-level differentiation for ecological adaptation that leads to microbial divergence and speciation has been profoundly altered. Numerous processes that underlie microbial differentiation have been identified but determining the relative significance of these processes remains challenging. For example, a major unresolved question is how much of observed genetic heterogeneity is due to neutral versus adaptive processes. Sequence-based and modelling analyses suggest that much of the observed variation is neutral but recent functional omic data suggest that at least some of it is functionally relevant and involved in adaption and divergence. From the limited amount of largely disjointed metagenomic and functional data obtained to date, extensive intra- and inter-system as well as extensive intra- and inter-population differences are apparent. Consequently, it is at present difficult to ascertain specific molecular patterns that define microbial groups that would be congruent with the definition of a microbial species. Concomitant analysis of community genomic complements, transcriptomes, proteomes and metabolomes over relevant spatial and temporal scales in the future will result in detailed molecular descriptions of distinct microbial entities. Such a system-level molecular organismal classification system will need to be solidly grounded in ecological theory, population genetic theory and evolutionary theory, and may be universally applicable to the three domains of life. [less ▲] Detailed reference viewed: 143 (8 UL)![]() Muller, Emilie ![]() ![]() Scientific Conference (2012) Detailed reference viewed: 71 (1 UL)![]() Roume, Hugo ![]() ![]() ![]() Poster (2012) The Molecular Systems Biology approach based on the integration of omic datasets is hampered by the complexity, dynamic and heterogeneity of mixed microbial communities. In order to facilitate meaningful ... [more ▼] The Molecular Systems Biology approach based on the integration of omic datasets is hampered by the complexity, dynamic and heterogeneity of mixed microbial communities. In order to facilitate meaningful data integration, individual biomolecular fractions need to be obtained from single unique samples. Our newly developed methodology allows for the isolation of high-quality genomic DNA, RNA, proteins and metabolites from single mixed microbial community samples (e.g. human faeces, freshwater filtrate), as well as from mammalian tissues. The framework lays the basis for standardized molecular (eco-)systematic studies on a range of different biological samples in the future. [less ▲] Detailed reference viewed: 116 (6 UL)![]() Muller, Emilie ![]() ![]() ![]() Poster (2012) With the advent of high-throughput omic technologies, powerful and sensitive methods are available for the analysis of nucleic acid, protein and small molecule complements obtained from biological samples ... [more ▼] With the advent of high-throughput omic technologies, powerful and sensitive methods are available for the analysis of nucleic acid, protein and small molecule complements obtained from biological samples. Molecular eco-systems biology studies based on the integration of genomic, transcriptomic, proteomic and metabolomic data are faced with major challenges arising from the complexity, dynamics and heterogeneity of mixed microbial consortia. In order to facilitate meaningful data integration, analysis and modeling, it is essential that biomolecular fractions obtained for high-throughput omic analyses are representative of single unique samples. We have developed a new methodological framework for the reproducible isolation of high-quality genomic DNA, large and small RNA, proteins, and polar and non-polar metabolites from single unique mixed microbial community samples. The methodology is based around reproducible cryogenic sample preservation and cell lysis. Metabolites are extracted first using organic solvents, followed by the sequential isolation of nucleic acids and proteins using chromatographic spin column technology. The methodology was validated by comparison to traditional dedicated and simultaneous biomolecular isolation methods. To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological, environmental and medical interest. Importantly, the developed methodology will allow exploitation of the inherent heterogeneity and dynamics within microbial consortia through spatial and temporal sampling of biological systems to allow later deconvolution of community-wide, population-wide and individual-level processes using the generated omic data. This approach has the potential to identify associations between distinct biomolecules and which may provide pointers towards unravelling previously unknown metabolic processes. Finally, by providing a standardized workflow, the methodology lays the foundation for comparative eco-systematic studies of different natural microbial consortia in the future. [less ▲] Detailed reference viewed: 113 (2 UL)![]() Roume, Hugo ![]() ![]() ![]() Poster (2012) Detailed reference viewed: 136 (2 UL)![]() ; Wilmes, Paul ![]() in Metabolomics : Official journal of the Metabolomic Society (2012), 8(4), 566-578 Natural microbial communities are extremely diverse and contain uncharacterized but functionally important small molecules. By coupling a deuterium (D) labeling technique to high mass accuracy untargeted ... [more ▼] Natural microbial communities are extremely diverse and contain uncharacterized but functionally important small molecules. By coupling a deuterium (D) labeling technique to high mass accuracy untargeted liquid chromatography-electrospray ionization-mass spec- trometry (LC–ESI–MS) metabolomic analysis, we found that natural acidophilic microbial biofilms dominated by bacteria of the genus Leptospirillum contained unusual lyso phosphatidylethanolamine (PE) lipids in high abundance (more than 10 nmol/mg of dry biomass). The unusual polar head group structure of these lipids is similar to lipids found in phylogenetically unrelated acidophilic chemo- autolithotrophs and may be related to the affinity of these lipids for iron and calcium ions. Correlations of lyso phospholipid and proteome abundance patterns suggest a link between the lyso phospholipids and the UBA-type substrain of Leptospirillum group II. By combining untar- geted metabolomics with D exchange we demonstrate the ability to identify cryptic but biologically functional small molecules in mixed microbial communities. [less ▲] Detailed reference viewed: 156 (6 UL)![]() ; ; et al in PLoS ONE (2012), 7(12), Human plasma has long been a rich source for biomarker discovery. It has recently become clear that plasma RNA molecules, such as microRNA, in addition to proteins are common and can serve as biomarkers ... [more ▼] Human plasma has long been a rich source for biomarker discovery. It has recently become clear that plasma RNA molecules, such as microRNA, in addition to proteins are common and can serve as biomarkers. Surveying human plasma for microRNA biomarkers using next generation sequencing technology, we observed that a significant fraction of the circulating RNA appear to originate from exogenous species. With careful analysis of sequence error statistics and other controls, we demonstrated that there is a wide range of RNA from many different organisms, including bacteria and fungi as well as from other species. These RNAs may be associated with protein, lipid or other molecules protecting them from RNase activity in plasma. Some of these RNAs are detected in intracellular complexes and may be able to influence cellular activities under in vitro conditions. These findings raise the possibility that plasma RNAs of exogenous origin may serve as signaling molecules mediating for example the human-microbiome interaction and may affect and/or indicate the state of human health [less ▲] Detailed reference viewed: 167 (7 UL)![]() Muller, Emilie ![]() in Journal of Bacteriology (2012), 194(23), 6670-6671 Candidatus Microthrix bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for ... [more ▼] Candidatus Microthrix bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: "Candidatus Microthrix parvicella" strain Bio17-1. [less ▲] Detailed reference viewed: 168 (7 UL)![]() Muller, Emilie ![]() ![]() Poster (2011, September 27) Biological wastewater treatment represents arguably the most widely used biotechnological process on Earth. Due to its high organic load, wastewater represents a potentially interesting energy commodity ... [more ▼] Biological wastewater treatment represents arguably the most widely used biotechnological process on Earth. Due to its high organic load, wastewater represents a potentially interesting energy commodity that is currently not exploited comprehensively. Molecules of particular interest for sustainable bioenergy production are lipids which represent up to 45 % of the organic fraction of wastewater. Within biological wastewater treatment plants, specific lipid accumulating organism (LAO) communities exhibit specialized phenotypes that might be harnessed for the concomitant treatment of wastewater and the production of biodiesel (long chain fatty acid (LCFA) methyl esters). Furthermore, due to the unusual high-density enrichments in the LAO communities, these represent ideal models for the development of relevant high-resolution ecosystems biology methodologies. The main aims are: determining the exact genetic inventories required for excess lipid uptake, storage and processing within lipid accumulating bacterial populations ; determining the metabolic fate of organic molecules (lipids) within LAO communities ; and determining the functional organisation in relation to genetic heterogeneity of lipid accumulating bacterial populations. [less ▲] Detailed reference viewed: 97 (10 UL)![]() Wilmes, Paul ![]() Scientific Conference (2011, August) Detailed reference viewed: 32 (0 UL)![]() Wilmes, Paul ![]() in de Bruijn, Frans (Ed.) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (2011) Detailed reference viewed: 134 (4 UL) |
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