Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes

To characterize the impact of gut microbiota on host metabolism, we investigated the multicompartmental metabolic profiles of a conventional mouse strain (C3H/HeJ) (n=5) and its germ-free (GF) equivalent (n=5). We confirm that the microbiome strongly impacts on the metabolism of bile acids through the enterohepatic cycle and gut metabolism (higher levels of phosphocholine and glycine in GF liver and marked higher levels of bile acids in three gut compartments). Furthermore we demonstrate that (1) well-defined metabolic differences exist in all examined compartments between the metabotypes of GF and conventional mice: bacterial co-metabolic products such as hippurate (urine) and 5-aminovalerate (colon epithelium) were found at reduced concentrations, whereas raffinose was only detected in GF colonic profiles. (2) The microbiome also influences kidney homeostasis with elevated levels of key cell volume regulators (betaine, choline, myo-inositol and so on) observed in GF kidneys. (3) Gut microbiota modulate metabotype expression at both local (gut) and global (biofluids, kidney, liver) system levels and hence influence the responses to a variety of dietary modulation and drug exposures relevant to personalized health-care investigations

A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model

Symbiotic gut microorganisms (microbiome) interact closely with the mammalian host's metabolism and are important determinants of human health. Here, we decipher the complex metabolic effects of microbial manipulation, by comparing germfree mice colonized by a human baby flora (HBF) or a normal flora to conventional mice. We perform parallel microbiological profiling, metabolic profiling by 1H nuclear magnetic resonance of liver, plasma, urine and ileal flushes, and targeted profiling of bile acids by ultra performance liquid chromatography–mass spectrometry and short-chain fatty acids in cecum by GC-FID. Top-down multivariate analysis of metabolic profiles reveals a significant association of specific metabotypes with the resident microbiome. We derive a transgenomic graph model showing that HBF flora has a remarkably simple microbiome/metabolome correlation network, impacting directly on the host's ability to metabolize lipids: HBF mice present higher ileal concentrations of tauro-conjugated bile acids, reduced plasma levels of lipoproteins but higher hepatic triglyceride content associated with depletion of glutathione. These data indicate that the microbiome modulates absorption, storage and the energy harvest from the diet at the systems level

Sediment source fingerprinting: benchmarking recent outputs, remaining challenges and emerging themes

Abstract: Purpose: This review of sediment source fingerprinting assesses the current state-of-the-art, remaining challenges and emerging themes. It combines inputs from international scientists either with track records in the approach or with expertise relevant to progressing the science. Methods: Web of Science and Google Scholar were used to review published papers spanning the period 2013–2019, inclusive, to confirm publication trends in quantities of papers by study area country and the types of tracers used. The most recent (2018–2019, inclusive) papers were also benchmarked using a methodological decision-tree published in 2017. Scope: Areas requiring further research and international consensus on methodological detail are reviewed, and these comprise spatial variability in tracers and corresponding sampling implications for end-members, temporal variability in tracers and sampling implications for end-members and target sediment, tracer conservation and knowledge-based pre-selection, the physico-chemical basis for source discrimination and dissemination of fingerprinting results to stakeholders. Emerging themes are also discussed: novel tracers, concentration-dependence for biomarkers, combining sediment fingerprinting and age-dating, applications to sediment-bound pollutants, incorporation of supportive spatial information to augment discrimination and modelling, aeolian sediment source fingerprinting, integration with process-based models and development of open-access software tools for data processing. Conclusions: The popularity of sediment source fingerprinting continues on an upward trend globally, but with this growth comes issues surrounding lack of standardisation and procedural diversity. Nonetheless, the last 2 years have also evidenced growing uptake of critical requirements for robust applications and this review is intended to signpost investigators, both old and new, towards these benchmarks and remaining research challenges for, and emerging options for different applications of, the fingerprinting approach

The challenges and opportunities of addressing particle size effects in sediment source fingerprinting: A review

publisher: Elsevier articletitle: The challenges and opportunities of addressing particle size effects in sediment source fingerprinting: A review journaltitle: Earth-Science Reviews articlelink: http://dx.doi.org/10.1016/j.earscirev.2017.04.009 content_type: article copyright: © 2017 Elsevier B.V. All rights reserved

Développement du couplage ELS/UV pour la détermination de composés spécifiques dans des matrices complexes

La politique réglementaire impose des contraintes de plus en plus importantes concernant les émissions de polluants dans l'environnement. La directive européenne du 22 décembre 2000 a établi une liste de composés spécifiques à considérer comme polluants prioritaires. Dans ce contexte , des outils simples et rapides doivent être développés afin de fournir des informations rapides aux décideurs chargés de la surveillance des milieux naturels. Cependant, les méthodes de laboratoire ne permettent que difficilement leur transposition sur le terrain. C'est pourquoi, dans le cadre de cette thèse, le développement de méthodes d'analyse basées sur le couplage de l'extraction liquide-solide (ELS) avec la spectrophotométrie UV/visible a été proposé. Dans un premier temps, cette thèse s'est attachée à définir le terme de matrice complexe afin d'aboutir à la méthodologie basée sur le couplage ELS/UV. Dans le cas de la démarche adoptée, la résolution de la complexité n'est plus réalisée exclusivement par l'étape physico-chimique. En effet, un traitement des données spectrales basé sur des méthodes d'étalonnage multidimensionnel permet d'obtenir les informations nécessaires à la quantification de composés spécifiques à partir d'un simple spectre UV/visible. Afin de démontrer les potentialités de la méthode, la démarche développée a été appliquée à l'analyse des HAP dans les sols contaminés et à la détermination des triazines dans les eaux de surface. Les résultats obtenus ont montré qu'avec un matériel simple, facilement transposable sur site, il est possible de déterminer les concentrations de composés spécifiques dans des matrices complexes.AIX-MARSEILLE1-BU Sci.St Charles (130552104) / SudocSudocFranceF

Kit de diagnostic rapide de la contamination des sols par les HAP: Principe, mise en œuvre et évaluation

Investigation of contaminated soils, assessment of treatment processes and environmental monitoring of remediated soils require screening many samples. Laboratory analyses (gaz or liquid chromatography) are expensive and time consuming. Moreover, the procedures are not suited to field conditions. In this context, a new field kit for PAH diagnosis has been developed. Based on the UV spectrophotometric analysis of a soil organic extract, the total PAH estimation, in reference to the 16 PAHs included in the US Environmental Protection Agency Priority Pollutants List, can be obtained on site within 20 minutes. Moreover, a “treatability index”, informing on the potential degradation of pollutants which may occur into the soil, is given. This last is connected with the proportion of PAH including two or three cycles in their structure (“light PAHs”) which are known to be more readily biodegradable. A validation on several contaminated soil samples, from different origins, has been carried out.This tool allows to give a rapid diagnosis of total PAHs concentration in a contaminated soil and to point out the most polluted areas on an industrial site. The proposed kit is well fitted for the monitoring of a treatment process and the survey of natural attenuation into a PAH contaminated soil.Le diagnostic des sols contaminés, le contrôle des procédés de traitement et le suivi environnemental des sols contaminés traités nécessitent le screening d’un grand nombre d’échantillons. Dans ce contexte, un kit de diagnostic rapide des HAP a été développé. La procédure inclut un pré-traitement de l’échantillon de sol suivi d’une extraction à l’acétonitrile. L’extrait organique est alors analysé par spectrophotométrie UV (analyseur portable). Ainsi, sur site et en une vingtaine de minutes, une estimation globale de la concentration en HAP, en référence aux 16 HAP de la liste EPA, est fournie. La limite de détection de la méthode est de 20 mg.kg-1. De plus, un indice de traitabilité biologique du sol est également donné. Il renseigne sur l’aptitude du sol contaminé à évoluer dans des conditions environnementales naturelles

How to deal with missing values in the high dimensional supervised context?

International audienc

Koh-Lanta, missing data imputation in supervised context

International audienc

Imputation for supervised learning problems in high dimension

International audienc