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See detailSystems Biology of Acidophile Biofilms for Efficient Metal Extraction
Christel, Stephan; Dopson, Mark; Vera, Mario et al

in Advanced Materials Research (2015), 1130

This European Union ERASysApp funded study will investigate one of the major drawbacks of bioleaching of the copper containing mineral chalcopyrite, namely the long lag phase between construction and ... [more ▼]

This European Union ERASysApp funded study will investigate one of the major drawbacks of bioleaching of the copper containing mineral chalcopyrite, namely the long lag phase between construction and inoculation of bioleaching heaps and the release of dissolved metals. In practice, this lag phase can be up to three years and the long time period adds to the operating expenses of bioheaps for chalcopyrite dissolution. One of the major time determining factors in bioleaching heaps is suggested to be the speed of mineral colonization by the acidophilic microorganisms present. By applying confocal microscopy, metatranscriptomics, metaproteomics, bioinformatics, and computer modeling the authors aim to investigate the processes leading up to, and influencing the attachment of three moderately thermophilic sulfur-and/or iron-oxidizing model species: Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans. Stirred tank reactors containing chalcopyrite concentrate will be inoculated with these species in various orders and proportions and the effects on the lag phase and rates of metal release will be compared. Meanwhile, confocal microscopy studies of cell attachment to chalcopyrite mineral particles, as well as metatranscriptomics and metaproteomics of the formed biofilms will further increase understanding of the attachment process and help develop a model thereof. By fulfilling our goal to decrease the length of the lag phase of chalcopyrite bioleaching heaps we hope to increase their economic feasibility and therefore, industrial interest in bioleaching as a sustainable technology. [less ▲]

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See detailFrom integrated omics towards Eco-Systems Biology
Wilmes, Paul UL

Presentation (2014, November)

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See detailEcosystems Biology: from data to control of microbial communities
Wilmes, Paul UL

Presentation (2014, November)

Detailed reference viewed: 19 (0 UL)
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See detailCommunity-integrated omics links dominance of a microbial generalist to fine-tuned resource usage
Muller, Emilie UL; Pinel, Nicolas; Laczny, Cedric Christian UL et al

in Nature Communications (2014)

Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle ... [more ▼]

Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ. [less ▲]

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See detailHuMiX: A MICROFLUIDICS-BASED IN VITRO CO-CULTURE DEVICE FOR INVESTIGATING HOST-MICROBE INTERACTIONS
Wilmes, Paul UL; estes, matt; zenhausern, frederic et al

Scientific Conference (2014, October 30)

Detailed reference viewed: 332 (23 UL)
See detailIn situ single-cell investigations of substrate utilisation by Candidatus Microthrix parvicella
Sheik, Abdul UL; Muller, Emilie UL; Audinot, Jean-Nicolas et al

Poster (2014, October 16)

Detailed reference viewed: 142 (21 UL)
See detailEco-Systems Biology: from integrated omics to control strategies for mixed microbial communities
Wilmes, Paul UL

Scientific Conference (2014, October)

Detailed reference viewed: 16 (0 UL)
See detailBet-hedging strategy for substrate usage among single cells of Candidatus Microthrix parvicella?
Sheik, Abdul UL; Muller, Emilie UL; Audinot, Jean-Nicolas et al

Scientific Conference (2014, September 29)

Detailed reference viewed: 135 (14 UL)
See detailEco-Systems Biology of human-microbe molecular interactions along the gastrointestinal tract
Wilmes, Paul UL

Scientific Conference (2014, June)

Detailed reference viewed: 19 (0 UL)
See detailEco-Systems Biology of Natural Microbial Communities
Wilmes, Paul UL

Scientific Conference (2014, June)

Detailed reference viewed: 15 (0 UL)
See detailIntegrated omics of microbial communities
Wilmes, Paul UL

Presentation (2014, May)

Detailed reference viewed: 13 (2 UL)
See detailIntegrated omics to eluciate structure-function relationships in microbial biofilms
Wilmes, Paul UL

Scientific Conference (2014, May)

Detailed reference viewed: 20 (0 UL)
See detailMetaproteomics for a functional insight to activated sludge
Wilmes, Paul UL

Scientific Conference (2014, April)

Detailed reference viewed: 13 (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 ▲]

Detailed reference viewed: 239 (22 UL)
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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 ▲]

Detailed reference viewed: 257 (25 UL)
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See detailMEMBRANE ASSEMBLY
Shah, Pranjul UL; Wilmes, Paul UL

Patent (2014)

Detailed reference viewed: 166 (21 UL)