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See detailIntegrated omics of microbial communities
Wilmes, Paul UL

Presentation (2014, May)

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See detailIntegrated omics to eluciate structure-function relationships in microbial biofilms
Wilmes, Paul UL

Scientific Conference (2014, May)

Detailed reference viewed: 36 (0 UL)
See detailMetaproteomics for a functional insight to activated sludge
Wilmes, Paul UL

Scientific Conference (2014, April)

Detailed reference viewed: 31 (0 UL)
See detailDynamic change of host gastrointestinal microbiome and immune status in relation to mucosal barrier effects during chemotherapy and immune ablative intervention in humans
Kaysen, Anne UL; Heintz, Anna UL; Lebrun, Laura UL et al

Poster (2014, April)

The human gastrointestinal tract is colonized by communities of endogenous microbes, commonly referred to as the microbiome. Here, the microbiota are in close contact with the host intestinal mucosa and ... [more ▼]

The human gastrointestinal tract is colonized by communities of endogenous microbes, commonly referred to as the microbiome. Here, the microbiota are in close contact with the host intestinal mucosa and its innate and adaptive immune systems. The fact that certain stimuli induce an inflammatory response whereas others induce tolerance suggests, that the host immune system interacts with the microbiota and vice versa in different ways. However, the exact details of theses interactions remain largely unknown. It is known that cancer treatment can result in severe adverse effects like mucositis and in combination with allogeneic stem cell transplantation (Tx), in graft-versus host disease (GvHD). However, there is at present only sparse information available on the effects of chemotherapy on the intestinal microbiota and resulting changes in microbiome-immune system interactions. Almost no data exists on the effect of allogeneic stem cell Tx on the composition of the gastrointestinal microbiota. In this project, we are studying the complex interactions between the host and the intestinal microbiota after chemotherapy with or without allogeneic Tx and the occurrence of severe adverse side effects such as mucositis and GvHD. Using a systems biology approach including metagenomics and RNAseq, fecal samples and blood plasma samples from patients undergoing these treatments for malignancies will be analysed to identify the composition of the gastrointestinal microbiome and bacterial small RNAs. The main research hypothesis is that there are quantitative and qualitative changes in the gastrointestinal microbiome following chemotherapy and allogeneic Tx which are linked to the immune status of the patients and possible treatment side-effects, in particular mucositis and GvHD. We aim to provide knowledge on how the host's intestinal mucosa and immune system influence the gastrointestinal microbiome and on the role and involvement of the gastrointestinal microbiota in development in mucositis and GvHD. Importantly, this could help in the formulation of measures to prevent mucositis and GvHD development. [less ▲]

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See detailAlignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction
Laczny, Cedric Christian UL; Pinel, Nicolás; Vlassis, Nikos UL et al

in Scientific Reports (2014)

The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An ideal visualization ... [more ▼]

The visualization of metagenomic data, especially without prior taxonomic identification of reconstructed genomic fragments, is a challenging problem in computational biology. An ideal visualization method should, among others, enable clear distinction of congruent groups of sequences of closely related taxa, be applicable to fragments of lengths typically achievable following assembly, and allow the efficient analysis of the growing amounts of community genomic sequence data. Here, we report a scalable approach for the visualization of metagenomic data that is based on nonlinear dimension reduction via Barnes-Hut Stochastic Neighbor Embedding of centered log-ratio transformed oligonucleotide signatures extracted from assembled genomic sequence fragments. The approach allows for alignment-free assessment of the data-inherent taxonomic structure, and it can potentially facilitate the downstream binning of genomic fragments into uniform clusters reflecting organismal origin. We demonstrate the performance of our approach by visualizing community genomic sequence data from simulated as well as groundwater, human-derived and marine microbial communities. [less ▲]

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See detailMethod and kit for the isolation of genomic dna, rna, proteins and metabolites from a single biological sample
Wilmes, Paul UL

Patent (2014)

The invention provides method and kit for the separation and purification of cellular components including polar and non-polar metabolites, genomic DNA, RNA and proteins from a single biological sample ... [more ▼]

The invention provides method and kit for the separation and purification of cellular components including polar and non-polar metabolites, genomic DNA, RNA and proteins from a single biological sample where two steps of lysis of the cells are performed sequentially, before and after a metabolite isolation step. The first lysis step is mechanical and performed in order to be incomplete, whereas the second is chemical or both mechanical and chemical. A sequential isolation of genomic DNA, RNA and proteins is carried out after the second lysis step. [less ▲]

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See detailMEMBRANE ASSEMBLY
Shah, Pranjul UL; Wilmes, Paul UL

Patent (2014)

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See detailA hundred years of activated sludge: time for a rethink
Sheik, Abdul UL; Muller, Emilie UL; Wilmes, Paul UL

in Frontiers in Microbiology (2014), 5(47), 1-7

Biological wastewater treatment plants (BWWTPs) based on the activated sludge (AS) pro- cess have dramatically improved worldwide water sanitation despite increased urbanization and industrialization ... [more ▼]

Biological wastewater treatment plants (BWWTPs) based on the activated sludge (AS) pro- cess have dramatically improved worldwide water sanitation despite increased urbanization and industrialization. However, current AS-based operations are considered economically and environmentally unsustainable. In this Perspective, we discuss our current understanding of microbial populations and their metabolic transformations in AS-based BWWTPs in view of developing more sustainable processes in the future. In particular, much has been learned over the course of the past 25 years about specialized microorganisms, which could be more comprehensively leveraged to recover energy and/or nutrients from wastewater streams. To achieve this, we propose a bottom-up design approach, focused around the concept of a “wastewater biorefinery column”, which would rely on the engineering of distinct ecological niches into a BWWTP in order to guarantee the targeted enrichment of specific organismal groups which in turn will allow the harvest of high-value resources from wastewater. This concept could be seen as a possible grand challenge to microbial ecologists and engineers alike at the centenary of the discovery of the AS process. [less ▲]

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See detailTowards the Identification of Condition-Specific Microbial Populations from Human Metagenomic Data
Laczny, Cedric Christian UL; Wilmes, Paul UL

in Keller, Andreas; Meese, Eckart (Eds.) Nucleic Acids as Molecular Diagnostics (2014)

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See detailLipid-based biofuel production from wastewater
Muller, Emilie UL; Sheik, Abdul UL; Wilmes, Paul UL

in Current Opinion in Biotechnology (2014), 30

Increasing world population, urbanization and industrialization are driving global increases in wastewater production. Wastewater comprises significant amounts of chemical energy primarily in the form of ... [more ▼]

Increasing world population, urbanization and industrialization are driving global increases in wastewater production. Wastewater comprises significant amounts of chemical energy primarily in the form of organic molecules (in particular lipids), which are currently not being recovered comprehensively. Within biological wastewater treatment (BWWT) systems, specialized microorganisms assimilate and store lipids anaerobically. These intracellular stores represent interesting feedstocks for biofuel synthesis. Here, we review our current understanding of the genetic and functional basis for bacterial lipid accumulation and processing, and relate this to lipid accumulating bacterial populations which occur naturally in BWWT plants. A grand challenge for microbial ecologists and engineers now lies in translating this knowledge into the design of new BWWT processes for the comprehensive recovery of lipids from wastewater streams and their subsequent conversion into biofuel. [less ▲]

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See detailRNA in circulation: sources and functions of extracellular exogenous RNA in blood
Galas, David J. UL; Wilmes, Paul UL; Wang, Kai

in Nelson, Karen (Ed.) Encyclopedia of Metagenomics (2014)

Molecules of many kinds are abundant in circulating blood and play a wide range of important roles, both known and unknown. These include macromolecules like proteins and nucleic acids and a wide range of ... [more ▼]

Molecules of many kinds are abundant in circulating blood and play a wide range of important roles, both known and unknown. These include macromolecules like proteins and nucleic acids and a wide range of smaller molecules. A number of questions are raised by recent findings of stable RNA molecules in plasma that is circulating RNA outside of cells. Among the issues that need to be addressed are: what are the origins of these RNA molecules; what are the mechanisms by which they enter and are stabilized in the blood; what are their possible biological functions; and finally, what are the potential applications of these extracellular RNA molecules in diagnostic and therapeutic medicine? While the precise biological functions remain to be pinned down, extracellular RNA has been proposed as a vehicle for a previously unknown cell-cell communication system. Recent reports of the detection of foreign, exogenous sources of some of the extracellular RNA have thus intensified the need to investigate and understand these processes. This overview summarizes the findings, some recent developments, and the current state of research in the circulating RNA field, and some of the key open questions in the field are specifically addressed. [less ▲]

Detailed reference viewed: 316 (17 UL)
See detailThe sequential isolation of metabolites, RNA, DNA, and proteins from a single, undivided mixed microbial community sample
Muller, Emilie UL; Buschart, Anna UL; Roume, Hugo UL et al

in Protocol Exchange (2014)

Integrated omics of microbial consortia, comprising systematized metagenomic, metatranscriptomic, metaproteomic and meta-metabolomic analyses, allows in-depth characterization of organismal and functional ... [more ▼]

Integrated omics of microbial consortia, comprising systematized metagenomic, metatranscriptomic, metaproteomic and meta-metabolomic analyses, allows in-depth characterization of organismal and functional diversity in situ. To allow meaningful meta-omic data integration, truly systematic measurements of the typically heterogeneous sample biomass is required. Therefore, there is a need for analyzing biomolecular fractions obtained from single, undivided samples. Here, we share a methodological workflow for the reproducible isolation of concomitant polar and non-polar metabolites, RNA, DNA and proteins from samples obtained from a biological wastewater treatment plant. The methodological framework is applicable to other biological samples [1,2], is compatible with different kits for biomacromolecular isolation [1,2] with minimal tailoring, and represents an important first step in standardization for the emerging field of Molecular Eco-Systems Biology. [less ▲]

Detailed reference viewed: 352 (23 UL)
See detailA 16S rRNA gene Illumina–based barcoded assay design for high throughput characterisation of microbial communities from anaerobic digesters
Calusinska, Magdalena; Goux, Xavier; Muller, Emilie UL et al

Poster (2014)

High throughput sequencing of 16S/18S rRNA gene is becoming an indispensable tool to explore microbial community ecology. To date, most of the studies using next generation amplicon sequencing of ... [more ▼]

High throughput sequencing of 16S/18S rRNA gene is becoming an indispensable tool to explore microbial community ecology. To date, most of the studies using next generation amplicon sequencing of microorganisms involved in the anaerobic digestion process (AD) are based on the 454 pyrosequencing. However, the cost per read obtained with the Illumina technology is currently less than 1/100 of that for the 454 pyrosequencing, thus enabling throughout sequencing and larger number of samples to be analysed per study (e.g. given the current Miseq output, around 100 000 reads per sample can be expected for a pool of 96 libraries). Moreover, the Illumina technology is less biased by the GC content of the template and currently allows for a relatively long sequence read of 600 bp (2 x 300bp). This consideration is particularly important, since longer sequences permit for more accurate assignment to a taxonomic group. Here, we designed and optimized an Illumina–based 16S rRNA amplicon approach for a high throughput characterization of microbial communities from different AD. [less ▲]

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See detailSystematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
Hugerth, Luisa; Muller, Emilie UL; Hu, Yue et al

in PLoS ONE (2014)

High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by ... [more ▼]

High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems. [less ▲]

Detailed reference viewed: 239 (7 UL)
See detailCommunity integrated omics links the dominance of a microbial generalist to fine-tuned resource usage
Muller, Emilie UL; Pinel, Nicolás; Laczny, Cedric Christian UL et al

Poster (2014)

Microbial communities are complex and dynamic systems that are influenced by stochastic-neutral processes but are mainly structured by resource availability and usage. High-resolution “meta-omics” offer ... [more ▼]

Microbial communities are complex and dynamic systems that are influenced by stochastic-neutral processes but are mainly structured by resource availability and usage. High-resolution “meta-omics” offer exciting prospects to investigate microbial populations in their native environment. In particular, integrated meta-omics, by allowing simultaneous resolution of fundamental niches (genomics) and realised niches (transcriptomics, proteomics and metabolomics), can resolve microbial lifestyles strategies (generalist versus specialist) in situ. We have recently developed the necessary wet- and dry-lab methodologies to carry out systematic molecular measurements of microbial consortia over space and time, and to integrate and analyse the resulting data at the population-level. We applied these methods to oleaginous mixed microbial communities located on the surface of anoxic biological wastewater treatment tanks to investigate how niche breadth (generalist versus specialist strategies) relates to community-level phenotypes and ecological success (i.e. population size). Coupled metabolomics and 16S rRNA gene-based deep sequencing demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of Candidatus Microthrix parvicella. By integrating population-level genomic reconstructions with transcriptomic and proteomic data, we found that the dominance of this microbial generalist population results from finely tuned resource usage and optimal foraging behaviour. Moreover, the fluctuating environmental conditions constrain the accumulation of variations, leading to a genetically homogeneous population likely due to fitness trade-offs. By integrating metagenomic, metatranscriptomic, metaproteomic and metabolomic information, we demonstrate that natural microbial population sizes and structures are intricately linked to resource usage and that differing microbial lifestyle strategies may explain the varying degrees of within-population genetic heterogeneity observed in metagenomic datasets. Elucidating the exact mechanism driving fitness trade-offs, e.g., antagonistic pleiotropy or others, will require additional integrated omic datasets to be generated from samples taken over space and time. Based on our observations, niche breadth and lifestyle strategies (generalists versus specialists) have to be considered as important factors for understanding the evolutionary processes governing microbial population sizes and structures in situ. [less ▲]

Detailed reference viewed: 182 (12 UL)
See detailCommunity integrated omics links the dominance of a microbial generalist to fine-tuned resource usage
Muller, Emilie UL; Pinel, Nicolás; Laczny, Cedric Christian UL et al

Scientific Conference (2014)

Microbial communities are complex and dynamic systems that are influenced by stochastic-neutral processes but are mainly structured by resource availability and usage. High-resolution “meta-omics” offer ... [more ▼]

Microbial communities are complex and dynamic systems that are influenced by stochastic-neutral processes but are mainly structured by resource availability and usage. High-resolution “meta-omics” offer exciting prospects to investigate microbial populations in their native environment. In particular, integrated meta-omics, by allowing simultaneous resolution of fundamental niches (genomics) and realised niches (transcriptomics, proteomics and metabolomics), can resolve microbial lifestyles (generalist versus specialist lifestyle strategies) in situ. We have recently developed the necessary wet- and dry-lab methodologies to carry out systematic molecular measurements of microbial consortia over space and time, and to integrate and analyse the resulting data at the population-level. We applied these methods to oleaginous mixed microbial communities located on the surface of anoxic biological wastewater treatment tanks to investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to community-level phenotypes and ecological success (i.e. population size). Coupled metabolomics and 16S rRNA gene-based deep sequencing demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of Candidatus Microthrix parvicella. By integrating population-level genomic reconstructions with transcriptomic and proteomic data, we found that the dominance of this microbial generalist population results from finely tuned resource usage and optimal foraging behaviour. Moreover, the fluctuating environmental conditions constrain the accumulation of variations, leading to a genetically homogeneous population likely due to fitness trade-offs. By integrating metagenomic, metatranscriptomic, metaproteomic and metabolomic information, we demonstrate that natural microbial population sizes and structures are intricately linked to resource usage and that differing microbial lifestyle strategies may explain the varying degrees of within-population genetic heterogeneity observed in metagenomic datasets. Elucidating the exact mechanism driving fitness trade-offs, e.g., antagonistic pleiotropy or others, will require additional integrated omic datasets to be generated from samples taken over space and time. Based on our observations, niche breadth and lifestyle strategies (generalists versus specialists) have to be considered as important factors for understanding the evolutionary processes governing microbial population sizes and structures in situ. [less ▲]

Detailed reference viewed: 200 (9 UL)
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See detailMicrobiome and type 1 diabetes
Wampach, Linda UL; Wilmes, Paul UL; De Beaufort, Carine UL

E-print/Working paper (2013)

The human microbiome (the collective of microorganisms, which inhabit the human body) and changes therein (often referred to as microbial dysbiosis) is emerging as a potential player in the development of ... [more ▼]

The human microbiome (the collective of microorganisms, which inhabit the human body) and changes therein (often referred to as microbial dysbiosis) is emerging as a potential player in the development of type 1 diabetes mellitus. This section discusses the human microbiome and its potential involvement in type 1 diabetes through its central roles in energy metabolism and modulation of the immune system. [less ▲]

Detailed reference viewed: 320 (22 UL)
See detailEco-Systems Biology of activated sludge microbial communities
Wilmes, Paul UL

Presentation (2013, October)

Detailed reference viewed: 25 (0 UL)