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[hal-05308646] Spatial distribution of gas–liquid mass transfer in a co-current upflow biological aerated filter
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Paola Ramirez Archila) 10 Oct 2025
https://hal.inrae.fr/hal-05308646v1
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[hal-05308873] Implicit Generalized Predictive Control of a Wastewater Treatment Plant: Application to the SimBio Model
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Yasmine Siahmed) 10 Oct 2025
https://hal.inrae.fr/hal-05308873v1
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[hal-05308832] Dynamiques du transfert gaz-liquide dans un pilote triphasique de biofiltration
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Paola Ramirez Archila) 10 Oct 2025
https://hal.science/hal-05308832v1
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[hal-05308870] Thermodynamic and Non-thermodynamic Effects on Anodic Electromicrobial Biofilm Growth under Controlled Hydrodynamics
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Elena Roques) 10 Oct 2025
https://hal.science/hal-05308870v1
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[hal-05162180] When bacteriophages enter the cheese ripening process: An overview of the PHAGOFROM project.
Cheese ripening is a crucial step in the production process during which microorganisms such as yeasts, molds, and bacteria transform the curd, developing its flavor, texture, and final characteristics. Like all bacteria, ripening bacteria can be infected by bacteriophages (or phages), viruses that specifically target bacteria. While phages infecting lactic acid bacteria used in milk acidification are well studied — along with the technological issues they cause — very little data exist on the phages of ripening bacteria or their potential involvement in ripening defects, such as altered aromas or textures, unwanted pigmentation, or irregular openings. In this context, the PHAGOFROM project aims to: (i) explore the diversity of phages infecting ripening bacteria, from farms and raw milk to the cheese surface, and identify potential phage reservoirs; (ii) develop innovative, practical, and industry-oriented tools for detecting relevant phages; and (iii) raise awareness and provide practical solutions to stakeholders in the dairy sector, especially those involved in quality-labeled cheese production. The project begins with an awareness phase regarding the issue of phage-related ripening defects, targeting dairy professionals through actions such as webinars and surveys of cheese producers. This step aims at identifying case studies where phages may be linked to ripening defects. Milk and cheese samples will be collected from these cases to study phage diversity and to build bank of characterized phages. In parallel, a metaviromic approach will be used to explore the broader diversity of phage communities. The impact of phages on ripening and on the development of potential defects will be assessed through pilot-scale cheese productions, and transferable detection tools will be developed for use by industry stakeholders. By improving our understanding of ripening defects potentially caused by phages, the PHAGOFROM project will contribute to better control cheese typicity, particularly in quality-labeled products.
ano.nymous@ccsd.cnrs.fr.invalid (Marion Dalmasso) 15 Jul 2025
https://normandie-univ.hal.science/hal-05162180v1
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[hal-05308868] Thermodynamic and Non-thermodynamic Effects on Anodic Electromicrobial Biofilm Growth under Controlled Hydrodynamics
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Elena Roques) 10 Oct 2025
https://hal.science/hal-05308868v1
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[pasteur-05212168] Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Archaeal Viruses Subcommittee, 2025
An erratum of this article has been published full details can be found at 10.1099/jgv.0.002145 The International Committee on Taxonomy of Viruses (ICTV) holds a ratification vote annually following the review of newly proposed taxa by ICTV Study Groups and members of the virology community. This article reports changes to the taxonomy of viruses infecting archaea that were approved and ratified by the ICTV in March 2025. Six new families of head-tailed viruses expanded the order Caudoviricetes (realm Duplodnaviria ); one new family of filamentous viruses was added to the order Ligamenvirales (realm Adnaviria ); one new family of viruses with pleomorphic virions was included within a new phylum, new order and new class in the kingdom Trapavirae (realm Monodnaviria ); finally, three new families were created for spindle-shaped viruses that remain unassigned to higher level taxa. The 25 new species represent viruses infecting a broad range of archaea, including members of the classes Archaeoglobi, Bathyarchaeia, Methanobacteria, Methanomicrobia, Nitrososphaeria and Poseidoniia. Most of these viruses have been discovered by metagenomics in samples derived from diverse environments, including ambient and extreme marine ecosystems, the gastrointestinal tract of humans and animals, anaerobic digesters and terrestrial hot springs. Following this taxonomic update, archaeal viruses are officially classified into a total of 163 virus species in 94 genera within 62 families.
ano.nymous@ccsd.cnrs.fr.invalid (Mart Krupovic) 17 Aug 2025
https://pasteur.hal.science/pasteur-05212168v1
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[hal-05308879] Émissions de N2O en traitement et valorisation des boues d’épuration
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 10 Oct 2025
https://hal.inrae.fr/hal-05308879v1
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[hal-05073170] Conception d'une ontologie pour la gestion des connaissances en bioraffinerie environnementale, EBO
L'organisation et la structuration des données sont devenues des enjeux majeurs dans le domaine des sciences du vivant et de l'environnement. Face à l'augmentation des volumes de données expérimentales hétérogènes, le besoin d'interopérabilité et de raisonnement automatisé devient crucial. Dans le cadre du développement du système d'information EnviBIS au sein du LBE (INRAE), l'ontologie EBO (Environmental Biorefinery Ontology) a été conçue afin de formaliser et structurer les connaissances relatives aux procédés de bioraffinerie environnementale. En s'appuyant sur la méthode Linked Open Terms (LOT), la construction de l'ontologie repose sur une analyse approfondie du domaine, enrichie par des techniques de traitement appliquées à un corpus scientifique. Implémentée en OWL et alignée avec des standards, EBO est exploitée via RDF4J et Apache Jena. Elle permet d'assurer l'interopérabilité avec d'autres SI. Ce travail s'inscrit dans une dynamique de structuration et de partage des connaissances à l'échelle interinstitutionnelle et nationale.
ano.nymous@ccsd.cnrs.fr.invalid (Emilie Fernandez) 19 May 2025
https://hal.inrae.fr/hal-05073170v1
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[hal-04964196] Pratiques intègres de publication scientifique à l’heure de la science ouverte. Note de recommandations
La science ouverte a pour but explicite de rendre accessible à l’ensemble de la communauté scientifique, et plus largement au grand public, les connaissances produites par la recherche scientifique. Les publications qui en résultent concernent les multiples facettes de la recherche telles que les résultats, mais aussi les hypothèses, les méthodes employées ou de larges collections de données. La transparence est une des valeurs fondamentales de l’intégrité scientifique à laquelle la science ouverte peut largement contribuer en la promouvant et l’organisant. La science ouverte encourage en effet les pratiques honnêtes et rigoureuses en mettant à disposition toutes les informations sur le processus de recherche, et permet entre autres d’améliorer la reproductibilité des résultats de recherche. Elle contribue également à instaurer, restaurer, consolider la confiance dans la recherche et la sérénité des débats scientifiques. Elle permet en outre de rendre perceptibles les débats internes essentiels à la recherche de consensus scientifique sur les questions traitées. La diffusion des connaissances par la publication scientifique est considérée comme le cœur de l’activité de tout personnel scientifique tant vis-à-vis de la communauté scientifique que de la société. Le mouvement de fond que constitue la science ouverte est venu fortement modifier les pratiques de publication : libre accès aux contenus (open access), pré-enregistrements des hypothèses et protocoles (pre-registrations, registered reports), libre accès aux rapports de reviewing par les pairs (open peer reviewing), libre accès aux données et aux codes en sont quelques exemples. La nature même du contenu des publications évolue également : certaines revues offrent désormais la possibilité de faire évaluer par les pairs et de publier des hypothèses, des données (data papers) mais aussi des codes de calcul, des « matériels et méthodes » exhaustifs et opérationnels, voire des résultats négatifs ou des réplications de résultats, ainsi que certaines étapes des processus éditoriaux. Ces (r)évolutions contribuent à renforcer les pratiques intègres de la science. INRAE, établissement engagé dans une politique de science ouverte comme il est énoncé dans son document d’orientation 2030, a formulé un ensemble de recommandations aux auteurs de publications scientifiques pour que ces dernières soient librement accessibles. L’ouverture de la science ne présente pas que des opportunités et certains risques pour l’intégrité scientifique peuvent émerger, tels que la diffusion de résultats insuffisamment validés ou la divulgation de données confidentielles (individuelles, administratives ou industrielles). Même s’il ne représente pas en soi un risque pour l’intégrité, le libre accès (open access) avec paiement par les auteurs a cependant favorisé l’émergence de maisons d’édition douteuses (souvent qualifiées de « prédatrices ») proposant en libre accès des articles qui peuvent faire l’objet de processus indigents de validation par les pairs et/ou s’appuyant sur des processus éditoriaux de qualité insuffisante. Très récemment, la mise en accès libre de systèmes d’intelligence artificielle générative présente un risque certain d’utilisation pour des pratiques frauduleuses comme la rédaction automatique, le plagiat ou la fabrication de données. Le présent document a pour objectif de fournir aux scientifiques d’INRAE impliqués dans le processus de publication scientifique quelques recommandations pour une pratique intègre de la publication dans un contexte de science ouverte, en complément du document précédemment cité . Ce texte est le fruit de la réflexion d’un groupe de travail réuni à l’initiative de la Délégation à la déontologie, l’intégrité scientifique et l’éthique des projets de recherche, conjointement à la Direction pour la Science Ouverte (DipSO) et constitué de scientifiques, d’édit.eur.rice.s de revues scientifiques et techniques portées par INRAE et de représentant.e.s de la Délégation ainsi que de membres de la Direction pour la Science Ouverte, de la Direction de l’Évaluation et de la Direction des Affaires Juridiques. Ce document traite spécifiquement des pratiques intègres de publication en lien direct avec la science ouverte et ne prétend pas couvrir l’intégralité des questions générales de science ouverte, ni de publication ou d’intégrité scientifique.
ano.nymous@ccsd.cnrs.fr.invalid (Sabine Arbeille) 25 Mar 2025
https://hal.inrae.fr/hal-04964196v1
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[hal-04915064] Chemistry-based vectors map the chemical space of natural biomes from untargeted mass spectrometry data
Untargeted metabolomics can comprehensively map the chemical space of a biome, but is limited by low annotation rates (<10%). We used chemistry-based vectors, consisting of molecular fingerprints or chemical compound classes, predicted from mass spectrometry data, to characterize compounds and samples. These chemical characteristics vectors (CCVs) estimate the fraction of compounds with specific chemical properties in a sample. Unlike the aligned MS1 data with intensity information, CCVs incorporate actual chemical properties of compounds, offering deeper insights into sample comparisons. Thus, we identified key compound classes differentiating biomes, such as ethers which are enriched in environmental biomes, while steroids enriched in animal host-related biomes. In biomes with greater variability, CCVs revealed key clustering compound classes, such as organonitrogen compounds in animal distal gut and lipids in animal secretions. CCVs thus enhance the interpretation of untargeted metabolomic data, providing a quantifiable and generalizable understanding of the chemical space of natural biomes.
ano.nymous@ccsd.cnrs.fr.invalid (Pilleriin Peets) 27 Jan 2025
https://hal.science/hal-04915064v1
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[hal-04872524] Healthy gut microbiomes are host-controllable microbiomes
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Théodore Bouchez) 08 Jan 2025
https://hal.science/hal-04872524v1
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[hal-04893611] An open source ultrasonic flowmeter for monitoring the input/output flow rates of wastewater treatment plants
Sensors play an important role in both the continuous monitoring and intermittent analyses, which are essential for the study of wastewater treatment plant management and conducting related research. Given the significant environmental impact of the issues involved, accurate measurement of the volume of water flowing into and out of treatment plants is a key parameter for plant management, ecotoxicological studies and academic research programs. Traditionally, flow measurements have been based on calibrated weirs or venturi flumes, using water level measurements for conversion into flow, according to established relationships. In this article, the authors propose an innovative approach to explore the feasibility of developing an open-source, reparable and cost-effective data logger for flow monitoring using ultrasonic technology. By leveraging Arduino modules and a complementary Grove shield, the proposed data logger offers seamless integration and affordability. In particular, it features an on-board web server to facilitate data collection and device testing, offering accessibility through Wi-Fi connectivity with smartphones or computers. The authors demonstrate the effectiveness of their flowmeter by comparing its performance with that of a commercial reference flowmeter, yielding a maximum permissible measurement error of 0.6 mm on the water level measurement. Furthermore, they demonstrate the durability and reliability of the developed data logger through extensive field-testing over a 9-month period.
ano.nymous@ccsd.cnrs.fr.invalid (Hélène Guyard) 17 Jan 2025
https://hal.science/hal-04893611v1
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[hal-04748797] Impact of cationic polyacrylamide degradation on flocculation in wastewater treatment
In wastewater treatment plants, flocculating agents, primarily polymers, are widely employed to cluster sludge particles into larger flocs or aggregates. The flocculation process not only accelerates sedimentation rates of particles but also aids in water release during thickening and dewatering operations This study explores the effects of cationic polyacrylamide (CPAM) degradation on the flocculation process in wastewater treatment. CPAM undergoes noticeable degradation upon contact with specific metal surfaces, resulting in a substantial alteration in its rheological behavior. These modifications have broad implications for sludge flocculation: 1) accelerating polymer/sludge mixing dynamics, and flocculation kinetics, 2) inducing alterations in the resulting floc morphology, ultimately leading to smaller and less filamentous flocs. Notably, degraded CPAM requires a substantially less polymer quantity to achieve complete sludge flocculation, leading to a reduction in the excessive use of flocculating agents in wastewater treatment.
ano.nymous@ccsd.cnrs.fr.invalid (N Loukili) 22 Oct 2024
https://hal.science/hal-04748797v1
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[hal-05308907] Déploiement du suivi en ligne des émissions de protoxyde d’azote et comparaison de modèles statistiques pour décrire les émissions de protoxyde d’azote. Rapport annuel du programme Mocopée 2024
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 10 Oct 2025
https://hal.inrae.fr/hal-05308907v1
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[hal-05308905] Evaluation de stratégies de réduction des émissions de N2O en pilote de biofiltration. Rapport annuel du programme Mocopée 2024
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Alejandro Cialzeta) 10 Oct 2025
https://hal.inrae.fr/hal-05308905v1
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[hal-04811996] Discovery of alternative stable states in a synthetic human gut microbial community
Several human-associated microbial communities exist in multiple configurations and can change their composition in response to perturbations, remaining in an altered state even after the perturbation ends. Multistability has been previously proposed to explain this behavior for gut microbiota in particular, but has not been clearly demonstrated experimentally. Here, we first investigated the life history strategies of three common human gut bacteria to identify mechanisms driving alternative states. We then used this data to build and parameterize a kinetic model, which predicted that alternative states emerge due to phenotype switching between subpopulations of the same species. Perturbation experiments supported these predictions, and confirmed the existence of alternative states. Finally, simulations showed that phenotype switching can also explain alternative states in larger communities. Thus, a transient perturbation combined with metabolic flexibility is sufficient for alternative communities to emerge, implying that they are not necessarily explained by differences between individuals.
ano.nymous@ccsd.cnrs.fr.invalid (Daniel Rios Garza) 29 Nov 2024
https://hal.science/hal-04811996v1
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[hal-05308909] Dynamiques du transfert gaz-liquide dans un pilote triphasique de biofiltration
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Paola Ramirez) 10 Oct 2025
https://hal.inrae.fr/hal-05308909v1
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[hal-04785149] Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 15 Nov 2024
https://hal.inrae.fr/hal-04785149v1
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[hal-04810527] Improving genome-scale metabolic models of incomplete genomes with deep learning
Deciphering microbial metabolism is essential for understanding ecosystem functions. Genome-scale metabolic models (GSMMs) predict metabolic traits from genomic data, but constructing GSMMs for uncultured bacteria is challenging due to incomplete metagenome-assembled genomes, resulting in many gaps. We introduce the deep neural network guided imputation of reactomes (DNNGIOR), which uses AI to improve gap-filling by learning from the presence and absence of metabolic reactions across diverse bacterial genomes. Key factors for prediction accuracy are: (1) reaction frequency across all bacteria and (2) phylogenetic distance of the query to the training genomes. DNNGIOR predictions achieve an average F1 score of 0.85 for reactions present in over 30% of training genomes. DNNGIOR guided gap-filling was 14 times more accurate for draft reconstructions and 2–9 times for curated models than unweighted gap-filling.
ano.nymous@ccsd.cnrs.fr.invalid (Meine D Boer) 29 Nov 2024
https://hal.science/hal-04810527v1
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[hal-05306554] Inhibition de la digestion anaérobie des boues d'épuration urbaines par le propionate de sodium : production de biogaz et évolution de la communauté microbienne dans des réacteurs semi-continus
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 09 Oct 2025
https://hal.science/hal-05306554v1
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[hal-05308913] Emissions de N2O des stations de traitement des eaux usées : Etat des lieux, verrous et opportunités
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 11 Oct 2025
https://hal.inrae.fr/hal-05308913v1
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[hal-04926148] Converting biowaste into biomolecules using saline and non-saline microbial electrolyzers
Microbial electrolysis cells (MECs) are promising technologies for the production of multi-carbon compounds by electrotrophic microorganisms at the cathode, using energy and carbon extracted from organic waste by electrogenic microorganisms at the anode. The nature of the products formed depends on the taxonomic composition of the microbial community. This study examines the impact of electrolyte salinity on the microbial assembly of electroactive consortia. Salinity is a key performance parameter in bioelectrochemical systems, as it helps reduce internal resistance and optimize energy efficiency. The study compares hypersaline reactors developed from inocula collected from salt marshes with a non-saline reference system using sludge from an industrial digester (Desmond-Le Quéméner et al., 2019). Both types of reactors are operated in triplicates, each combining a bioanode with a homoacetogenic biocathode obtained by heat treatment of the inocula to eliminate methanogenic archaea. An intermediate compartment, separated by ion-exchange membranes, is integrated to extract and concentrate carboxylates formed at the cathode via electrodialysis. Different electrode configurations are used: a flat anode to maximize electrocatalytic activity and a granular cathode to increase the exchange surface between electrons and the microbial community. These design elements allow for the selection and adaptation of specific communities in each compartment. Initial tests with different types of saline electrolytes revealed the impact of salt composition on the catalytic performance of microbial electrolysis reactors. Reactors operated with NaCl-based salt solutions showed promising results in terms of energy efficiency, with high current density measurements. The production of carboxylates at the cathode by both types of microbial communities was demonstrated, providing a technological proof of concept for the proper functioning of the electrolysis cells. Ribotag sequencing analyses of 16S rDNA and rRNA are used to describe the adaptation process of microbial consortia to specific electrode configurations and the structuring of taxonomic and functional assemblages from the same initial community under saline and non-saline conditions. Reference: Desmond-Le Quéméner, E., Bridier, A., Tian, J.-H., Madigou, C., Bureau, C., Qi, Y., & Bouchez, T. (2019). Biorefinery for heterogeneous organic waste using microbial electrochemical technology. Bioresource Technology, 292, 121943. https://doi.org/10.1016/j.biortech.2019.121943
ano.nymous@ccsd.cnrs.fr.invalid (Louise Rigaud) 03 Feb 2025
https://hal.inrae.fr/hal-04926148v1
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[hal-04712649] PLAN DE GESTION DE DONNEES Projet SETIER II
Plan de gestion de donnée du projet SETIER II
ano.nymous@ccsd.cnrs.fr.invalid (Rémi Clément) 27 Sep 2024
https://hal.inrae.fr/hal-04712649v1
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[hal-04715274] Harnessing Lignocellulolytic and Electrogenic Potential: Insights from Shewanella oneidensis MR-1 and Cellulomonas Strains on Lignocellulosic Biomass
The biodegradable and renewable nature of lignocellulosic biomass (LCB) has gained significant interest in recent years. This study explores the lignocellulolytic and electrogenic potential of Shewanella oneidensis MR-1, Cellulomonas fimi ATCC 484, and Cellulomonas biazotea NBRC 12680 on LCB. Two strategies were tested: assessing strains LCB degradation ability under non-electrochemical and electrochemical conditions. Strain selection was based on literature, and bioinformatical analyses were conducted to predict CAZymes and carbohydrate degradation pathways. Cellulomonas strains have a potential to degrade LCB due to high CAZyme count and specific metabolic pathways. Strains growth capacity on LCB was evaluated by culturing without electrodes on LCB for 12 days, showing superior growth on wheat bran compared to wheat straw. Enzymatic assays indicate laccase activity in all strains, highest in C. biazotea NBRC 12680 (11.66 IU). The strains ability to form electrogenic biofilms on carbon cloth anodes polarized at +0.2 V (vs Ag/AgCl) was evaluated. The results indicate that bioanodes can function with wheat bran (max current density: 14.92 mA m −2 ), with voltammograms showing redox activities. Attenuated total reflection Fourier transform infrared spectroscopy shows lignin and protein degradation in both electrochemical and non-electrochemical experiments. These findings suggest potential use of these strains in electro-microbial systems with LCB.
ano.nymous@ccsd.cnrs.fr.invalid (Animut Assefa Molla) 30 Sep 2024
https://hal.science/hal-04715274v1
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[hal-04304559] Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 14 Aug 2024
https://hal.science/hal-04304559v2
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[pasteur-04647500] Establishing Host–Virus Link Through Host Metabolism: Viral DNA SIP Validation Using T4 Bacteriophage and E. coli
Abstract DNA Stable Isotope Probing is emerging as a potent methodology for investigating host–virus interactions, based on the essential reliance of viruses on host organisms for the production of virions. Despite the anticipated link between host isotopic compositions and the generated virions, the application of stable isotope probing to viral DNA has never been evaluated on simple biological models. In this study, we assessed the efficacy of this method on the bacteriophage T4 and its host, Escherichia coli . Through the cultivation of E. coli cells on a 13 C-enriched substrate and subsequent propagation of T4 bacteriophage, we examine the degree of isotopic enrichment in viral DNA. Our investigation reveals a strong correlation between the proportion of 13 C 6 - d -glucose in the growth substrate and the buoyant density in CsCl gradient of T4 DNA, confirming the validity of DNA SIP in viral ecology. These findings underscore the potential of DNA SIP as a robust tool for characterizing the diversity of viruses infecting hosts with specific metabolic activities and provide then a foundation for further exploration in viral ecology research.
ano.nymous@ccsd.cnrs.fr.invalid (Vuong Quoc Hoang Ngo) 14 Jul 2024
https://pasteur.hal.science/pasteur-04647500v1
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[hal-05308910] Mesure et modélisation des émissions de N2O des biofiltres des stations Seine centre et Seine aval : Enseignements pour la mitigation
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 11 Oct 2025
https://hal.inrae.fr/hal-05308910v1
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[hal-04903224] Generic mitigating and promoting effect of zeolite on anaerobic digestion: Physicochemical and metataxonomic data
This article provides comprehensive data on degradation performance and microbial dynamics derived from a set of 24 lab-scale batch anaerobic digesters involving various types of inhibitors and the addition of zeolite as a support material. In the first series of 12 digesters, three inhibitors were investigated at the following concentrations: 20 g/L of sodium chloride, 400 mg/L of erythromycin, and 5 mg/L of S-metolachlor. Each inhibitor was tested in triplicate, along with a control condition without inhibition. A parallel series was set up identically, except that 15 g/L of zeolite was introduced into each digester to mitigate the inhibition and promote the degradation process. The provided data comprises information regarding the experimental setup, monitoring measurements that assess the degradation performance (production, composition, and apparent isotopic factor of biogas, pH, dissolved inorganic and organic carbon and volatile fatty acids concentrations), microbial samples information, and 16S rRNA gene sequencing data that decipher changes in microbial structure. This datapaper is associated with research article [1] and presents both the sequencing data and the associated physicochemical data in a structured table format. The sequencing data were generated using the Ion Torrent PGM sequencer and have been deposited in the European Nucleotide Archive (ENA) database at EMBL-EBI under accession number PRJEB65129 (https://www.ebi.ac.uk/ena/browser/view/PRJEB65129), with sample accession numbers ranging from ERS16257742 to ERS16257691 [2]. The data serves as a valuable resource for comparisons with data from other studies on lab-scale batch anaerobic digesters, particularly those utilizing zeolite as a support material or involving inhibition caused by similar types of inhibitors (salts, antibiotics, or pesticides).
ano.nymous@ccsd.cnrs.fr.invalid (Xiaoqing Wang) 21 Jan 2025
https://hal.inrae.fr/hal-04903224v1
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[hal-04664121] Combining the analysis of omics data and bioprocess data in environmental biorefineries
The scientific community needs tools to harness the potential of data in the field of environmental biotechnology, ensuring that these data complies with the principles of Findable, Accessible, Interoperable, and Reusable (FAIR) data management. Here we introduce two information systems developed at INRAE:On one hand, EnviBIS [1], Environmental Biorefinery Information System is an ontology-driven information system for managing bioprocess data in an environmental biorefinery context, using the OpenSILEX [2] open-source software suite. This system handles the acquisition of heterogeneous data from sensors, observations or analytical devices, as well as on-line data management and bioprocess monitoring. The core ontology of OpenSILEX is based on standards ontologies (e.g. Dublin Core, FOAF, SOSA, PROV-O). It has been extended to specialize the EnviBIS tool by domain ontologies such as the Environmental Biorefinery Ontology (EBO) which, coupled with the Process and Observation Ontology (PO2), enables the description of biological and physical transformation processes. On the other hand, DeepOmics [3] is an information system designed to store meta-omic data pertaining to environmental biotechnology processes. It enables storing and, in the future querying, cross-referenced amplicon sequencing data, to metadata associated with samples from lab-scale reactors, pilots, or industrial sites. The aim of DeepOmics is to create a comprehensive framework for leveraging meta-omic data and metadata.The interoperability between these two tools is currently under development. It will enable researchers to access and analyze data from heterogeneous sources, thus promoting interdisciplinary knowledge aggregation. A demonstration is planned, to illustrate in concrete terms the added value of our approach regarding ease of use and efficiency in data processing, in the field of environmental biorefinery.
ano.nymous@ccsd.cnrs.fr.invalid (Emilie Fernandez) 29 Jul 2024
https://hal.inrae.fr/hal-04664121v1
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[hal-04619395] DeepOmics, a Digital Environnemental Engineering Platform for Omics data
DeePomics, for Digital Environmental Engineering Platform for Omics Data, is an information system (IS) that meets the needs for 1) storing and querying data from environmental bioprocesses (such as anaerobic digestion, activated sludge etc... ) at the scale of laboratory reactors, pilots or industrial installations, 2) compare and cross-reference these operational data (or metadata) with data characterizing the microbial communities involved and their dynamics, to produce knowledge and 3) promote the production of FAIR data and interoperability with EnviBIS another IS (see poster ?).Since the presentation of its prototype poster [1] at JOBIM 2020, DeepOmics has been in production, available at deepomics.inrae.fr (an authentification is required). It has evolved considerably functionally, structurally and in terms of the quantity of data captured.These changes include A) continuous integration of developments, automation of IS deployment using Docker-containment, implementation of user interface testing and use of a directory federation for user authentication, B) functional innovations range from the opening of the API and the "semantization" of Symfony entities and services for ontology-based dialog with the EnviBIS IS, to the acceptance of paired fastq files, C) the entry of 25 projects corresponding to 47/7 experiments/measurement campaigns and 423 sample sequence files, and D) the creation of a DeepOmics logo and visual with the information and documentation site. site d’information et de documentation.The perspectives include the development of an intra- and inter-project data query module to enable users to answer biological questions, a connector for the automatic deposit of sequences and their metadata into ENA, the possibility of integrating shotgun sequencing or metabolomics data, and finally an improved description of additional process categories, such as bioelectrochemical processes.
ano.nymous@ccsd.cnrs.fr.invalid (Véronique Jamilloux) 20 Jun 2024
https://hal.inrae.fr/hal-04619395v1
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[hal-04843798] Plateforme bioinformatique MIGALE
Migale est une infrastructure scientifique collective INRAE ouverte à tous. Elle est membre de l’infrastructure de recherche INRAE BioinfOmics, de l’Institut Français de Bioinformatique et de France-Génomique. Ses activités sont certifiées ISO9001 depuis avril 2011.
ano.nymous@ccsd.cnrs.fr.invalid (Mouhamadou Ba) 17 Dec 2024
https://hal.inrae.fr/hal-04843798v1
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[hal-04611225] Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data
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ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 13 Jun 2024
https://hal.inrae.fr/hal-04611225v1
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[hal-04647882] Inhibition of anaerobic digestion of urban sewage sludge by sodium propionate: biogas production and microbial community shift in continuous reactors
Anaerobic digestion (AD) is a well-established technology for processing waste streams such as sewage sludge and agricultural waste to produce biogas. However, the accumulation of volatile fatty acids, particularly propionic acid (an intermediate product), can hinder biogas production. Studies have indicated that even low propionic acid concentrations can impede biogas generation from digestion. However, propionic acid is usually in its ionized form in the pH range in which AD processes work. Limited data exist regarding the precise propionate concentration that inhibits anaerobic digestion of various substrates. In this recent study using 5-L reactors for the AD of urban sewage sludge, no inhibition was observed at low NaPro concentrations (up to 1.95 g/L). At 7.78 g NaPro/L, slight biogas disruption occurred, and significant inhibition (− 40%) was noted at the highest concentration (13 g NaPro/L). While the inhibitory NaPro concentration in this study exceeded the literature values (typically <2 g/L), this aligns with our previous findings in smaller-scale batch experiments.
ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 15 Jul 2024
https://hal.science/hal-04647882v1
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[hal-04647849] Deciphering the effect of propionic acid on anaerobic digestion of sludge: gas production and microbial community structure
This study investigates the impact of propionic acid (HPro) on anaerobic digestion (AD). HPro is an intermediate compound naturally generated during AD but inhibitory at excessive concentrations. To decipher the inhibition mechanisms, propionate, pH changes, and sodium ions were tested in addition to HPro, in batch mesophilic AD microcosms fed with municipal sewage sludge. Methane production experienced greater inhibition as the initial concentration of HPro increased, and was totally inhibited at 6 g/L HPro. The primary cause of inhibition was the low pH, as shown by comparison with NaPro, NaCl and HCl. Consistent with the inhibition, the abundance of methanogenic archaea and of the bacterium Syntrophomonas decreased with the addition of HPro. Methanogens and their syntrophic partners could therefore be interesting targets to develop inhibition biomarkers. We thereby provide one of the most in-depth study regarding HPro inhibition mechanisms during AD.
ano.nymous@ccsd.cnrs.fr.invalid (Chloé Soulard) 15 Jul 2024
https://hal.science/hal-04647849v1
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[hal-04528996] Biological valorization of urban solid biowaste: A study among circular bioeconomy start-ups in France
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ano.nymous@ccsd.cnrs.fr.invalid (Sandrine Costa) 02 Apr 2024
https://hal.inrae.fr/hal-04528996v1
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[hal-04625314] A comprehensive dataset for assessing the impact of ammonium salts and zeolite on anaerobic digestion performance, microbial dynamics, and metabolomic profiles
This article presents comprehensive data derived from lab-scale batch anaerobic digesters that were subjected to inhibition by various sources of ammonia. To counter this inhibition, zeolite was introduced into selected digesters. The provided dataset offers a detailed depiction of degradation performance dynamics over time, as well as insights into both microbial and metabolic changes during the inhibition. In detail, 10 conditions were tested in triplicate. In a first series of 15 bioreactors ammonia was introduced to achieve a TAN concentration of 8 g/L, utilizing NH3 solution, NH4Cl salt, (NH4)(2)CO3 salt, or (NH4)(2)PO4 salt as inhibitors. A control condition without ammonia was also set up. A second series of 15 bioreactors was set up exactly as the first one, with the addition of zeolite at a concentration of 15 g/L. The data provided includes information on operational conditions, degradation performance measurements throughout the entire process (using biogas production and composition, dissolved organic and inorganic carbon, volatile fatty acids, pH, free and total ammonia nitrogen, apparent isotopic fractionation of biogas as indicators), microbial community analysis using 16S rRNA gene sequencing (50 samples analysed), and metabolomic analysis through liquid chromatography-mass spectrometry (LC-MS) (108 samples analysed). Sequencing data were generated by using IonTorrent PGM sequencer. The sequencing data have been deposited with links to project PRJEB52324, in ENA database from EBI (https://www.ebi.ac.uk/ena/browser/view/PRJEB52324). Sample accession numbers go from SAMEA14277573 to SAMEA14277621. The metabolomic data were generated using an LTQ Orbitrap XL mass spectrometer (Thermo Fisher Scientific, MA, US). The metabolomic data have been deposited to the EMBL-EBI MetaboLights database with the identifier MTBLS7859 (https://www.ebi.ac.uk/metabolights/MTBLS7859). This data can be used as a source for comparisons with other studies focusing on the inhibition of anaerobic digestion by ammonia, particularly in the context of exploring microbial or metabolomic dynamics during inhibition. Additionally it provides a multi-omic dataset (metataxonomic and metabolomic) with detailed associated metadata describing anaerobic digesters. The dataset is directly is associated to the research article titled "Inhibition of anaerobic digestion by various ammonia sources resulted in subtle differences in metabolite dynamics." [1]
ano.nymous@ccsd.cnrs.fr.invalid (Stephany Damaris Campuzano Zagal) 26 Jun 2024
https://hal.inrae.fr/hal-04625314v1
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[hal-04549290] Easy16S : a user-friendly Shiny web-service for exploration and visualization of microbiome data.
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ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 17 Apr 2024
https://hal.inrae.fr/hal-04549290v1
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[hal-04772409] The SETIER project: An open source flowmeter for monitoring flow rates of wastewater treatment plants
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ano.nymous@ccsd.cnrs.fr.invalid (Arnold-Fred Imig) 07 Nov 2024
https://hal.science/hal-04772409v1
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[hal-04533737] Exploiting gut microbial traits and trade-offs in microbiome-based therapeutics
The clinical translation of therapeutics on the basis of human gut microorganisms is hampered by our limited knowledge of how microbes survive and adapt to fluctuating conditions in the gut. The systematic exploration of gut microbiome survival strategies and trade-offs will thus enable the design of more efficient microbiome-based interventions.
ano.nymous@ccsd.cnrs.fr.invalid (Bin Liu) 22 Aug 2024
https://hal.science/hal-04533737v1
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[hal-04528643] Generic role of zeolite in enhancing anaerobic digestion and mitigating diverse inhibitions: Insights from degradation performance and microbial characteristics
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ano.nymous@ccsd.cnrs.fr.invalid (Xiaoqing Wang) 02 Apr 2024
https://hal.inrae.fr/hal-04528643v1
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[hal-04555541] Calibration of a sewage sludge anaerobic digestion model with multiple mineral precipitation for two case studies
Including multiple mineral precipitation in anaerobic digestion models is important to accurately assess the quantity of phosphates (PO4-P) in the liquid phase of digested sludge that can be recovered as a fertilizer in struvite precipitation reactors or by emerging processes such as ion exchange membranes. However, the performance of such processes is highly impacted by the presence of potassium (K+) or calcium (Ca2+) ions, which are most often neglected when validating precipitation models. The novelty of this work was to provide a calibration procedure of an anaerobic digestion model with multiple mineral precipitation that can be used for different case studies and do not focus only on PO4-P but also on K+, Ca2+ Mg2+. To draw this calibration procedure, data from two anaerobic digesters located near Lyon (France) and in the Navarra region (Spain), treating sludge with different biodegradability and concentration ranges of phosphorus (P), calcium (Ca), magnesium (Mg), potassium (K) and soluble inorganic carbon (SIC), have been used. This procedure includes the calibration of the inert COD fraction (fXI,COD) and kinetic precipitation constants (Kr) using Bayesian Monte Carlo techniques. However, a unique parameter set for both anaerobic digesters cannot be identified, leading to site- specific parameters for fXI,COD (0.30 and 0.43), Kr,MgCO3 (274 and 0.4), Kr,CaCO3 (21 and 0.12) and Kr,ACP (270 and 58). The calibrated model was able to estimate PO4-P, Ca2+, Mg2+ and K+ concentration in digested sludge with a relative error below 10 %.
ano.nymous@ccsd.cnrs.fr.invalid (Perrine Devos) 23 Apr 2024
https://hal.inrae.fr/hal-04555541v1
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[hal-05306597] Inhibition de la digestion anaérobie des boues d'épuration urbaines par le propionate de sodium : production de biogaz et évolution de la communauté microbienne dans des réacteurs semi-continus
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ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 13 Oct 2025
https://hal.science/hal-05306597v1
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[hal-04556153] Amélioration du modèle phénoménologique de biofiltration pour décrire les émissions de protoxyde d’azote
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ano.nymous@ccsd.cnrs.fr.invalid (Justine Fiat) 23 Apr 2024
https://hal.inrae.fr/hal-04556153v1
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[hal-05308911] Analyse des émissions de N2O par les biofiltres nitrifiants des usines Seine aval et Seine centre du SIAAP
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ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 11 Oct 2025
https://hal.inrae.fr/hal-05308911v1
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[hal-04556144] Analyse des émissions de N2O par les biofiltres nitrifiants des usines Seine aval et Seine centre du SIAAP
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ano.nymous@ccsd.cnrs.fr.invalid (Sylvain Pageot) 23 Apr 2024
https://hal.inrae.fr/hal-04556144v1
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[hal-04556375] Assessment of nitrous oxide emissions at Spernal - Redditch site (United Kingdom)
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ano.nymous@ccsd.cnrs.fr.invalid (Ahlem Filali) 23 Apr 2024
https://hal.inrae.fr/hal-04556375v1
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[hal-04528641] Inhibition of anaerobic digestion by various ammonia sources resulted in subtle differences in metabolite dynamics
The impact of ammonia on anaerobic digestion performance and microbial dynamics has been extensively studied, but the concurrent effect of anions brought by ammonium salt should not be neglected. This paper studied this effect using metabolomics and a time-course statistical framework. Metabolomics provides novel perspectives to study microbial processes and facilitates a more profound understanding at the metabolic level. The advanced statistical framework enables deciphering the complexity of large metabolomics data sets. More specifically, a series of lab-scale batch reactors were set up with different ammonia sources added. Samples of nine time points over the degradation were analyzed with liquid chromatography-mass spectrometry. A filtering procedure was applied to select the promising metabolomic peaks from 1262 peaks, followed by modeling their intensities across time. The metabolomic peaks with similar time profiles were clustered, evidencing the correlation of different biological processes. Differential analysis was performed to seek the differences in metabolite dynamics caused by different anions. Finally, tandem mass spectrometry and metabolite annotation provided further information on the molecular structure and possible metabolic pathways. For example, the consumption of 5-aminovaleric acid, a short-chain fatty acid obtained from l-lysine degradation, was slowed down by phosphates. Overall, by investigating the effect of anions on anaerobic digestion, our study demonstrated the effectiveness of metabolomics in providing detailed information in a set of samples from different experimental conditions. With the statistical framework, the approach enables capturing subtle differences in metabolite dynamics between samples while accounting for the differences caused by time variations.
ano.nymous@ccsd.cnrs.fr.invalid (Xiaoqing Wang) 02 Apr 2024
https://hal.inrae.fr/hal-04528641v1
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[hal-05309064] Rapport d'étude n°2 sur la mesure des émissions de protoxyde d’azote à la station d’épuration Petite Californie – Rezé (44)
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ano.nymous@ccsd.cnrs.fr.invalid (Sylvain Pageot) 11 Oct 2025
https://hal.inrae.fr/hal-05309064v1
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[tel-05056747] Improving the anaerobic digestion process through omics approaches : inhibition mechanisms and mitigation strategies
The escalating global volume of organic waste presents both an environmental challenge and an opportunity for renewable energy generation. Anaerobic digestion (AD) serves as an efficient waste management method that not only effectively reduces organic waste volume but also converts it into clean energy in the form of biogas. Nevertheless, AD encounters challenges in maintaining process stability due to the vulnerability of the involved anaerobic microbial communities, which are highly sensitive to changes in operational parameters and digestive conditions. Consequently, it is imperative to understand the factors contributing to instability and propose strategies to enhance process stability, with a primary focus on understanding the response of microbial communities in this context. The development of high-throughput omics techniques, particularly metabolomics, has greatly facilitated the investigation of microbial metabolic processes, offering new opportunities to comprehensively understand the AD microbiota. This thesis is centered on the stability of AD, delving into understanding the inhibitory effects of various inhibitors and the mitigating role of different support materials using omics approaches coupled with biostatistics. In the first study, the applicability of metabolomics in AD was demonstrated by exploring the impacts of different anions originating from ammonium salts. The analytical framework developed for metabolomics data analysis, which took time evolution into account, revealed subtle variations in metabolite dynamics influenced by anions. The second study proposed the generic and beneficial impact of zeolite on AD. Zeolite effectively alleviated inhibition caused by erythromycin and sodium chloride while also enhancing AD performance under non-inhibited conditions. Microbial analysis and common components analysis uncovered that zeolite promoted specific bacterial and archaeal populations, regardless of the presence or type of inhibitor. Microbial populations closely associated with the zeolite effect were identified. The final study explored the effects of various support materials, including activated carbon, magnetite, nickel foam, and zeolite, on mitigating sodium chloride inhibition, which is a common issue in industrial AD. The digesters added with support materials exhibited lower VFAs accumulation and higher methane production ratio, with nickel foam and magnetite demonstrating a superior effect. Common components analysis disclosed differences in microbial and metabolite dynamics between several support materials, identifying characteristic microbial groups and metabolites correlated to each specific material.
ano.nymous@ccsd.cnrs.fr.invalid (Xiaoqing Wang) 05 May 2025
https://pastel.hal.science/tel-05056747v1
