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See detailGenome-based and functional differentiation: hallmarks of microbial adaptation, divergence and speciation?
Wilmes, Paul UL

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 ▲]

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See detailFrom gut to sludge: Molecular Eco-Systems Biology of Microbial Consortia
Muller, Emilie UL; Wilmes, Paul UL

Scientific Conference (2012)

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See detailA biomolecular isolation protocol for Eco-Systems Biology: How to isolate DNA, RNA, proteins and metabolites from a single unique sample
Roume, Hugo UL; Muller, Emilie UL; Shah, Pranjul UL et al

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 ▲]

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See detailA Biomolecular Isolation Framework for Molecular Eco-Systems Biology
Muller, Emilie UL; Roume, Hugo UL; Shah, Pranjul UL et al

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 ▲]

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See detailDeuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities
Fischer, C.R.; Wilmes, Paul UL; Bowen, B. P. et al

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 ▲]

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See detailThe complex exogenous RNA spectra in human plasma: an interface with human gut biota?
Wang, K.; Li, H.; Yuan, Y. 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 ▲]

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See detailGenome Sequence of "Candidatus Microthrix parvicella" Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant
Muller, Emilie UL; Pinel, Nicolás; Gillece, John D. et al

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 ▲]

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See detailEco-Systems Biology of Natural Lipid-Accumulating Microbial Communities
Muller, Emilie UL; Roume, Hugo; Lebrun, Laura UL et al

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 ▲]

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See detailMicrobial community proteomics
Wilmes, Paul UL

in de Bruijn, Frans (Ed.) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (2011)

Detailed reference viewed: 111 (4 UL)
See detailMicrobial Eco-Systems Biology: from molecules to ecosystems and back
Wilmes, Paul UL

Presentation (2011, April)

Detailed reference viewed: 19 (0 UL)
See detailCapturing the Structure and Dynamics of Complex Microbial Communities
Wilmes, Paul UL

Scientific Conference (2011, January)

Detailed reference viewed: 10 (0 UL)
See detailMicrobial Eco-Systems Biology: from molecules to ecosystems and back
Wilmes, Paul UL

Presentation (2011, January)

Detailed reference viewed: 24 (0 UL)
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See detailCorrelative microscopy for phylogenetic and ultrastructural characterization of microbial communities
Knierim, B.; Luef, B.; Wilmes, Paul UL et al

in Environmental Microbiology Reports (2011)

Transmission electron microscopy (TEM) can provide ultrastructural information for cells in microbial community samples and phylogenetic information can be recovered via molecular surveys. Here we report ... [more ▼]

Transmission electron microscopy (TEM) can provide ultrastructural information for cells in microbial community samples and phylogenetic information can be recovered via molecular surveys. Here we report an approach to link these data sets by coupling fluorescence in situ hybridization (FISH) with either conventional biological or cryogenic TEM. The method could fundamentally improve our understanding of the organization and functioning of microbial communities in natural systems. [less ▲]

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See detailA Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes
Yelton, Alexis P.; Thomas, Brian C.; Simmons, Sheri L. et al

in PLoS Computational Biology (2011), 7(10), 1002230

During microbial evolution, genome rearrangement increases with increasing sequence divergence. If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of ... [more ▼]

During microbial evolution, genome rearrangement increases with increasing sequence divergence. If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional conservation. We applied the phylogenetic pairwise comparison method to establish and model a strong correlation between synteny and sequence divergence in all 634 available Archaeal and Bacterial genomes from the NCBI database and four newly assembled genomes of uncultivated Archaea from an acid mine drainage (AMD) community. In parallel, we established and modeled the trend between synteny and functional relatedness in the 118 genomes available in the STRING database. By combining these models, we developed a gene functional annotation method that weights evolutionary distance to estimate the probability of functional associations of syntenous proteins between genome pairs. The method was applied to the hypothetical proteins and poorly annotated genes in newly assembled acid mine drainage Archaeal genomes to add or improve gene annotations. This is the first method to assign possible functions to poorly annotated genes through quantification of the probability of gene functional relationships based on synteny at a significant evolutionary distance, and has the potential for broad application. [less ▲]

Detailed reference viewed: 121 (3 UL)
See detailFrom molecules to ecosystems and back: bioinformatic approaches for Eco-Systems Biology
Wilmes, Paul UL

Scientific Conference (2010, November)

Detailed reference viewed: 16 (0 UL)