References of "Wilmes, Paul 50003335"
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See detailSystems ecology of the human microbiome
Wilmes, Paul UL

Scientific Conference (2018)

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See detailMechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.
Laloo, Andrew E.; Wei, Justin; Wang, Dongbo et al

in Environmental Science and Technology (2018), 52(9), 5386-5397

Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of ... [more ▼]

Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA. [less ▲]

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See detailMeasuring soil sustainability via soil resilience.
Ludwig, Marie; Wilmes, Paul UL; Schrader, Stefan

in The Science of the total environment (2018), 626

Soils are the nexus of water, energy and food, which illustrates the need for a holistic approach in sustainable soil management. The present study therefore aimed at identifying a bioindicator for the ... [more ▼]

Soils are the nexus of water, energy and food, which illustrates the need for a holistic approach in sustainable soil management. The present study therefore aimed at identifying a bioindicator for the evaluation of soil management sustainability in a cross-disciplinary approach between soil science and multi-omics research. For this purpose we first discuss the remaining problems and challenges of evaluating sustainability and consequently suggest one measurable bioindicator for soil management sustainability. In this concept, we define soil sustainability as the maintenance of soil functional integrity. The potential to recover functional and structural integrity after a disturbance is generally defined as resilience. This potential is a product of the past and the present soil management, and at the same time prospect of possible soil responses to future disturbances. Additionally, it is correlated with the multiple soil functions and hence reflecting the multifunctionality of the soil system. Consequently, resilience can serve as a bioindicator for soil sustainability. The measurable part of soil resilience is the response diversity, calculated from the systematic contrasting of multi-omic markers for genetic potential and functional activity, and referred to as potential Maximum Ecological Performance (MEPpot) in this study. Calculating MEPpot will allow to determine the thresholds of resistance and resilience and potential tipping points for a regime shift towards irreversible or permanent unfavorable soil states for each individual soil considered. The calculation of such ecosystem thresholds is to our opinion the current global cross-disciplinary challenge. [less ▲]

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See detailUsing metabolic networks to resolve ecological properties of microbiomes
Muller, Emilie UL; Faust, Karoline; Widder, Stefanie et al

in Current Opinion in Systems Biology (2018)

The systematic collection, integration and modelling of high-throughput molecular data (multi-omics) allows the detailed characterisation of microbiomes in situ. Through metabolic trait inference ... [more ▼]

The systematic collection, integration and modelling of high-throughput molecular data (multi-omics) allows the detailed characterisation of microbiomes in situ. Through metabolic trait inference, metabolic network reconstruction and modelling, we are now able to define ecological interactions based on metabolic exchanges, identify keystone genes, functions and species, and resolve ecological niches of constituent microbial populations. The resulting knowledge provides detailed information on ecosystem functioning. However, as microbial communities are dynamic in nature the field needs to move towards the integration of time- and space-resolved multi-omic data along with detailed environmental information to fully harness the power of community- and population-level metabolic network modelling. Such approaches will be fundamental for future targeted management strategies with wide-ranging applications in biotechnology and biomedicine. [less ▲]

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See detailDark Matter in host-microbiome metabolomics: Tackling the unknowns-A review
Peisl, Beatrice Yasmin Loulou UL; Schymanski, Emma UL; Wilmes, Paul UL

in Analytica Chimica Acta (2017)

The “dark matter” in metabolomics (unknowns) represents an exciting frontier with significant potential for discovery in relation to biochemistry, yet it also presents one of the largest challenges to ... [more ▼]

The “dark matter” in metabolomics (unknowns) represents an exciting frontier with significant potential for discovery in relation to biochemistry, yet it also presents one of the largest challenges to overcome. This focussed review takes a close look at the current state-of-the-art and future challenges in tackling the unknowns with specific focus on the human gut microbiome and host-microbe interactions. Metabolomics, like metabolism itself, is a very dynamic discipline, with many workflows and methods under development, both in terms of chemical analysis and post-analysis data processing. Here, we look at developments in the mutli-omic analyses and the use of mass spectrometry to investigate the exchange of metabolites between the host and the microbiome as well as the environment within the microbiome. A case study using HuMiX, a microfluidics-based human-microbial co-culture system that enables the co-culture of human and microbial cells under controlled conditions, is used to highlight opportunities and current limitations. Common definitions, approaches, databases and elucidation techniques from both the environmental and metabolomics fields are covered, with perspectives on how to merge these, as the boundaries blur between the fields. While reflecting on the number of unknowns remaining to be conquered in typical complexsamples measured with mass spectrometry (often ordersof magnitude above the “knowns”), we provide an outlook on future perspectives and challenges in elucidating the relevant “dark matter”. [less ▲]

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See detailIsolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants
Heintz-Buschart, Anna; Yusuf, Dilmurat; Kaysen, Anne UL et al

E-print/Working paper (2017)

Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. Due ... [more ▼]

Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. Due to its inherent instability, contamination with RNA is usually considered to be unlikely. Here we report the presence of small RNA (sRNA) contaminants in widely used microRNA extraction kits and means for their depletion. Sequencing of sRNAs extracted from human plasma samples was performed and significant levels of non-human (exogenous) sequences were detected. The source of the most abundant of these sequences could be traced to the microRNA extraction columns by qPCR-based analysis of laboratory reagents. The presence of artefactual sequences originating from the confirmed contaminants were furthermore replicated in a range of published datasets. To avoid artefacts in future experiments, several protocols for the removal of the contaminants were elaborated, minimal amounts of starting material for artefact-free analyses were defined, and the reduction of contaminant levels for identification of bona fide sequences using 'ultra-clean' extraction kits was confirmed. In conclusion, this is the first report of the presence of RNA molecules as contaminants in laboratory reagents. The described protocols should be applied in the future to avoid confounding sRNA studies. [less ▲]

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See detailMetaproteomics and integrated multi-omics: highlighting unknowns
Wilmes, Paul UL

Presentation (2017, November)

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See detailFunction First: Systems Ecology of the Human Gut Microbiome
Wilmes, Paul UL

Presentation (2017, November)

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See detailFirst draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ
Muller, Emilie UL; Narayanasamy, Shaman UL; Zeimes, Myriam et al

in Standards in Genomic Sciences (2017), 12(64),

The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome ... [more ▼]

The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome sequence and annotation together with a general physiological and genomic analysis, as the first sequenced representative of the Zoogloea genus. Moreover, Zoogloea sp. gene expression in its environment is described using metatranscriptomic data obtained from the same treatment plant. The presented genomic and transcriptomic information demonstrate a pronounced capacity of this genus to synthesize poly-β-hydroxyalkanoate within wastewater. [less ▲]

Detailed reference viewed: 198 (12 UL)
See detailIntegrated multi-omics for enhanced metaproteomics
Wilmes, Paul UL

Scientific Conference (2017, October)

Detailed reference viewed: 37 (0 UL)
See detailLe microbiome humain et son impact sur la santé
Wilmes, Paul UL

Scientific Conference (2017, October)

Detailed reference viewed: 37 (0 UL)
See detailForm follows function: systems ecology of the human gut microbiome
Wilmes, Paul UL

Presentation (2017, October)

Detailed reference viewed: 36 (2 UL)
See detailSystems ecology of microbial pioneers in the gut
Wilmes, Paul UL

Presentation (2017, October)

Detailed reference viewed: 39 (3 UL)
See detailForm follows function: integrated multi-omics of the human gut microbiome
Wilmes, Paul UL

Scientific Conference (2017, September)

Detailed reference viewed: 36 (0 UL)
See detailSystems ecology of microbiomes: a new frontier of discovery in microbiology
Wilmes, Paul UL

Scientific Conference (2017, September)

Detailed reference viewed: 43 (1 UL)
See detailFrom integrated multi-omics to microbial systems ecology: quo vadis?
Wilmes, Paul UL

Scientific Conference (2017, August)

Detailed reference viewed: 35 (1 UL)
See detailSystems ecology of microbiomes: a new frontier of discovery in microbiology
Wilmes, Paul UL

Presentation (2017, August)

Detailed reference viewed: 30 (0 UL)
See detailSystems ecology of microbiomes: a new frontier of discovery in microbiology
Wilmes, Paul UL

Presentation (2017, August)

Detailed reference viewed: 36 (0 UL)
See detailIntegrated multi-omics for identifying discriminant features in the human microbiome
Wilmes, Paul UL

Scientific Conference (2017, June)

Detailed reference viewed: 34 (3 UL)