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[hal-05683287] Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion
Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.709 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions established by CRISPR-Cas spacer, tRNA and homology matches revealed 889 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 18 ARG transduction events. Further analysis showed that the relative abundance of vOTUs assigned to the reduction role (4.11% ± 3.19%) was substantially higher than that of reproduction (0.72% ± 0.64%) and transduction (0.19% ± 0.30%), demonstrating that, among viral processes, lysis outweighs transduction in contributing to ARG abundance reduction in AD systems. Furthermore, an antiviral defense system (ADS) catalogue (GADSC_LMAD), derived from 2,760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS, with ADS prevalence in ARB (7.8 ± 6.0 per MAG), indicating an intensified virus-host arms race in AD that may shield ARB from phage lysis. The resulting CRISPR-Cas immune network with expressed spacers targets foreign ARG-carrying sequences (primarily plasmids and ICEs), suggesting a mechanism that restricts horizontal gene transfer (HGT) via conjugation and transformation, despite shielding ARB from phage lysis. Collectively, these findings highlight that viral communities significantly contribute to ARG reduction through phage lysis relative to transduction, while the ADS-mediated arms race, despite protecting ARB, constructs a biological firewall that potentially limits HGT of ARGs. This study provides novel insights into virus-host dynamics as a key mechanism for controlling ARG dissemination in AD systems.
ano.nymous@ccsd.cnrs.fr.invalid (Qihe Tang) 07 Jul 2026
https://hal.science/hal-05683287v1
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[hal-05695906] Host-virus dynamics in anaerobic digesters facing abiotic inhibition
Viruses play a major role in controlling the structure and dynamics of microbial communities in anaerobic digesters, ecosystems sensitive to disturbances that inhibit methane production. Here, we studied the interplay between abiotic disturbances, microbiome and virome composition, and process performance, to assess whether provirus induction can be triggered by abiotic stresses known to inhibit anaerobic digestion (ammonium, phenol and sodium chloride). We monitored viral dynamics in batch mesophilic anaerobic digesters fed with biowaste through shotgun metavirome sequencing. The diversity of both prokaryotes and viruses was high, with Clostridiales dominating the prokaryotic community and Caudoviricetes dominating the viromes. We identified 132 viral contigs and 19 host genera that were differentially abundant under disturbed conditions. No significant impact of the tested abiotic stresses on provirus induction was observed under the current experimental and analytical framework. The results were consistent with viruses exerting steady, background-level predation through a putative combination of kill-the-winner dynamics at the sub-genus level and piggyback-the-winner dynamics, rather than stress-triggered, synchronous lytic bursts. A few auxiliary metabolic genes were detected, potentially targeting carbon, sulfur and cofactor metabolism in anaerobic digestion. Temperate viruses were dominant, representing up to 71% of the viral genomes confirmed as complete across all conditions. Electron microscopy analysis revealed diverse virus-like particles, including head-tailed particles typical of Caudoviricetes, but also spherical, rod-shaped and spindle-shaped particles typical of archaeal viruses. Notably, we present a new virus family, Eurekaviridae, of spindle-shaped viruses associated with methanogenic archaea.
ano.nymous@ccsd.cnrs.fr.invalid (Marion Coves) 17 Jul 2026
https://hal.science/hal-05695906v1
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[hal-05644280] {affiliationExplorer} a Shiny webapp to resolve taxonomy conflicts
Metabarcoding studies in microbial ecology generate taxonomic abundance profiles, with each taxon usually represented by an ASV (Amplicon Sequence Variant). Some taxa may be associated with several, sometimes conflicting, taxonomic affiliations. These ambiguities (or multi-affilia-tions) [1], may be frequent when analysing short sequences and/or when reference databases are incomplete. This complicates ecological interpretation and decreases the reproducibility of results. According to the origin of the samples (e.g. food, fecal, biowaste, etc.) or the conflict source (spelling typo in the reference databases) , manual curation can sometimes resolve these ambigui-ties. Likewise, some inconsistencies can be easily corrected programmatically if a manual curation was performed on a similar dataset and needs to be reapplied. The {affiliationExplorer} R-package provides a user interface dedicated to exploring and resolving these conflicts, and can easily be inserting in BIOM (Biological Observation Matrix) data analysis workflows. Developed in Shiny with the {golem} framework, this package offers a user-friendly interface for ① loading a BIOM file, a multi-affiliation file, and, optionally, one or more expert-verified sequence–taxonomy dictionaries (in FASTA format), ② visualising and ordering multi-affiliated taxa by abundance, ③ automatically resolving conflicts using the provided dictionaries for curated ASV references, ④ performing expert manual curation by selecting the most relevant affiliation among those proposed or specifying it manually, and ⑤ exporting a corrected BIOM file and a sequence–taxonomy dictionary to log the performed curations and for potential reuse in subse-quent curation sessions. The produced BIOM file follows the standards of biom-format.org and is fully compatible with standard metabarcoding workflows. The exported FASTA files can be reused as is in the interface.
ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 12 Jun 2026
https://hal.inrae.fr/hal-05644280v1
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[hal-05683273] Antiviral defense systems drive persistence of antimicrobial‐resistant bacteria but limit the transfer of antimicrobial resistance genes in anaerobic digestion
Phage–host interactions critically shape environmental antimicrobial resistance (AMR). Using swine manure anaerobic digestion and multi-omics (metagenomics, meta-transcriptomics, and Hi-C), we mapped the phage–bacteria arms race and its impact on AMR dynamics. We revealed that phage-mediated lysis overwhelmingly dominates transduction, while phages rarely carry antimicrobial resistance genes (ARGs), and phage-borne ARGs showed no expression, challenging the paradigm of phages as primary vectors of ARGs. Crucially, the intense on-going phage–host arms race drives the widespread presence and expression of antiviral defense systems (ADSs) in antimicrobial-resistant bacteria (ARB). These ADSs exhibit a vital ecological dual role: they protect ARBs from phage lysis promoting persistence while simultaneously suppressing horizontal gene transfer (HGT, e.g., conjugation), as validated by in vitro conjugation assays. Our findings elucidate this duality, offering a novel framework to harness phage lytic pressure and ADS-mediated HGT suppression for environmental AMR mitigation.
ano.nymous@ccsd.cnrs.fr.invalid (Junya Zhang) 07 Jul 2026
https://hal.science/hal-05683273v1
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[hal-05698089] Création d’un réseau SHINY::ESR
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Élise Maigné) 20 Jul 2026
https://hal.inrae.fr/hal-05698089v1
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[hal-05687855] Modelling Nitrification in Densified Activated Sludge Systems requires to consider a dynamic KO2 for granules
Densified activated sludge (DAS) systems enhance conventional activated sludge performance by combining flocculated sludge and granular biomass, improving settleability and treatment capacity. However, oxygen diffusion limitations within granules can impact nitrifier activity and affect system efficiency. This study addresses the challenge of modelling the partitioning of ammonia-oxidizing bacteria (AOB) between flocs and granules in continuous-flow DAS systems. The apparent oxygen half-saturation coefficient of nitrifiers (KO2,NIT) was experimentally determined via respirometry on DAS and granules from three full-scale treatment plants. A positive correlation between granule size and KO2,NIT was established and incorporated into a zero-dimensional plant-wide model with hydrocyclones. Model simulations demonstrated that using a dynamic oxygen diffusion resistance (DRO2,NIT) better predicted the balanced distribution of ammonia-oxidising bacteria (AOB) between flocs and granules compared to a fixed DRO2,NIT. While the later tends to overestimate granule nitrifier fractions and to hinder early AOB growth in granules, a dynamic DRO2,NIT better reflects AOB partitioning during granulation.
ano.nymous@ccsd.cnrs.fr.invalid (Mathilde Lepage) 09 Jul 2026
https://hal.science/hal-05687855v1
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[hal-05658485] Mesophilic Anaerobic Digestion of Municipal Sewage Sludge under High Sodium Propionate Concentrations in Semi-continuous Conditions
Anaerobic digestion (AD) treats sewage sludge and agricultural waste, but the accumulation of volatile fatty acids, particularly propionic acid (HPr) or sodium propionate (NaPr), can inhibit performance. This study examined NaPr inhibition in AD using four semi-continuous 5-L reactors operated at 37 °C for 81 days and loaded with increasing NaPr concentrations (0–135.3 mmol L⁻¹). No inhibition occurred at 20.3 mmol L⁻¹, while moderate reductions in methane and biogas production were seen at 81 mmol L⁻¹, and severe inhibition (40%) at 135.3 mmol L⁻¹.Microbial community structure was driven primarily by incubation time and secondarily by NaPr concentration. Higher NaPr levels suppressed methanogens such as Methanothrix and Methanobrevibacter while enriching syntrophic propionate oxidizers, including Pelotomaculum and Cryptanaerobacter, demonstrating the sensitivity and adaptive response of AD microbiomes to propionate stress.
ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 16 Jun 2026
https://hal.science/hal-05658485v1
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[hal-05674009] Electromethanogenesis from H2S containing biogas: H2S and cathode potential drive microbial selection and methane yields
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Ankit Rao) 30 Jun 2026
https://hal.inrae.fr/hal-05674009v1
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[hal-05674029] Propionic acid-related inhibition during anaerobic digestion: insights into methane production and microbial community responses
Propionic acid (HPr) accumulation is a major indicator of anaerobic digestion (AD) dysfunction, yet the respective contributions of acidity, undissociated HPr and the propionate ion (Pr⁻) to inhibition and microbial community composition remain unclear. Using mesophilic batch microcosms fed with municipal sewage sludge, we compared HPr, sodium propionate (NaPr), NaCl and HCl across two experimental series. Inhibition by HPr was governed by the pH drop rather than by Pr⁻: 20 mM HPr reduced the maximal methane rate by 22%, while 81 mM HPr (pH 5.1) abolished methane production, an effect reproduced by HCl at the same pH. At near-neutral pH, the propionate salt had only a secondary, concentration-dependent effect (81 mM NaPr, -40% on the rate), largely attributable to ionic strength (81 mM NaCl, -23%). 16S rRNA gene amplicon sequencing revealed compound-specific community restructuring: methanogenic archaea fell from 2–3% to <0.2% of relative abundance under 81 mM HPr, and the >100 differentially abundant ASVs were largely shared with HCl reactors, confirming the dominant role of acidity. The number of differentially abundant ASVs was negatively correlated with the methane rate (R² = 0.97). These results clarify the respective roles of pH, undissociated HPr and Pr⁻ in both methane inhibition and microbial community restructuring.
ano.nymous@ccsd.cnrs.fr.invalid (Xiaojun Liu) 30 Jun 2026
https://hal.inrae.fr/hal-05674029v1
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[hal-05676003] Teindre durable sans se tromper de ton. Représentations des professionnels et consommateurs sur l'adoption de colorants biosourcés dans l'industrie de la mode
La couleur, critère clé dans le choix des vêtements, engendre une forte pollution liée aux teintures textiles, rendant indispensable une transition vers une mode plus éthique et durable (Lara et al., 2022; Niinimäki et al., 2020). Alors que les colorants synthétiques pétrosourcés dominent encore le marché, des alternatives biosourcées issues de biotechnologies émergent et peuvent s’inscrire dans une démarche circulaire en valorisant des biodéchets (Fried et al., 2022; Mazotto et al., 2021). Ces solutions innovantes offrent un potentiel environnemental et social important pour la mode, mais les perceptions des professionnels et consommateurs restent peu étudiées, tant concernant la teinture que les biotechnologies « vertes » (Mabuza et al., 2023). Cette recherche vise à comprendre comment les colorants biosourcés issus de biotechnologie peuvent s’intégrer dans la chaîne de valeur tout en conciliant les intérêts divergents des acteurs, des intermédiaires aux consommateurs. Elle mobilise deux cadres théoriques complémentaires : le modèle TOE pour analyser les déterminants de l’adoption par les professionnels (Tornatzky et Fleischer, 1990) et la théorie de la résistance à l’innovation (TRI) pour étudier les freins à l’acceptation chez les consommateurs (Ram et Sheth, 1989). Une enquête qualitative par entretiens semi-directifs a été réalisée auprès de professionnels de la filière (n=11) et de consommateurs ou influenceurs de mode (n=18), à partir de guides adaptés à leurs pratiques mais incluant un tronc commun sur la mode durable et les colorants biosourcés. Les entretiens, enregistrés et analysés thématiquement avec MAXQDA, ont permis d’identifier les bénéfices et obstacles perçus selon les cadres du modèle TOE pour les professionnels et de la théorie de la résistance à l’innovation (TRI) pour les consommateurs. Les professionnels perçoivent les colorants biosourcés comme un levier potentiel de différenciation et de communication, mais doutent de leurs réels bénéfices environnementaux et soulignent plusieurs obstacles techniques, économiques et structurels. Leur adoption semble conditionnée à la compatibilité avec les procédés existants et à des gains mesurables en efficacité (eau, énergie, coûts). Enfin, les contraintes réglementaires et la pression contradictoire des consommateurs entre durabilité et prix limitent encore leur déploiement. Les consommateurs accordent une grande importance à la couleur mais peu au type de colorant utilisé, exprimant globalement une confiance dans les procédés industriels et la réglementation. Si l’aspect circulaire des colorants biosourcés est perçu positivement, certaines réticences subsistent face à l’usage de biodéchets et à une technologie jugée compatible avec la surconsommation. Enfin, la valorisation de procédés traditionnels perçus comme plus “propres” peut constituer une barrière culturelle à l’adoption. Ces résultats impliquent que le développement de ces biocolorants doit répondre aux attentes environnementales des consommateurs et aux contraintes techniques et économiques des professionnels, la seule circularité ne suffisant pas sans impacts environnementaux positifs clairement identifiés. L’adoption de vêtements bio-colorés passerait surtout par des stratégies de marque, compte tenu du faible intérêt direct des consommateurs pour les colorants.
ano.nymous@ccsd.cnrs.fr.invalid (Arnaud Lamy) 01 Jul 2026
https://hal.science/hal-05676003v1
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[hal-05569770] Digestion anaérobie mésophile des boues d'épuration municipales sous fortes concentrations de propionate de sodium en conditions semicontinues : inhibition et modifications de la communauté microbienne
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 27 Mar 2026
https://hal.science/hal-05569770v1
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[hal-05687840] Spatially-Resolved Characterization of Gas Hold-up and Gas-Liquid Mass Transfer in an Operating Large-Scale BAF
This study presents the first quantitative evaluation of gas distribution in a large-scale biological aerated filter (BAF) operated under realistic conditions. A 6.2 m pilot, installed at a WRRF, was continuously fed with real pre-treated wastewater. A key finding is that bed porosity, which evolves with fouling, governs the spatial and temporal dynamics of gas hold-up during biofiltration. Existing correlations based on clean-bed systems failed to capture in-bed gas behavior. New correlations accounting for superficial liquid/gas velocities and fouling significantly improved prediction accuracy, reducing errors from over 50% to around 10%. The results related to oxygen transfer are currently under analysis and will complement the findings presented here on gas hold-up.
ano.nymous@ccsd.cnrs.fr.invalid (Paola Ramirez-Archila) 09 Jul 2026
https://hal.science/hal-05687840v1
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[hal-05502139] Spatial structure: Shaping the ecology and evolution of microbial communities
Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.
ano.nymous@ccsd.cnrs.fr.invalid (Marcel Bäcker) 10 Feb 2026
https://hal.inrae.fr/hal-05502139v1
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[hal-05644678] MIFE and MIFD: Minimum information for fermentation experiments and devices
Abstract Background As the technological advancements of the early 21st century are pushing industrial biotechnology (IB) into the realm of Big Data–driven innovation, the requirement for trustworthy data management, annotation, and standardization is emerging as a necessity. Minimum information models (MIMs) have long been used across disciplines as the backbone of good data management practices by providing the scaffold upon which standardized recording of metadata can adequately and succinctly describe an understudied phenomenon. Findings Here we present a minimum set of metadata, named the minimum information for fermentation experiments (MIFE) and devices (MIFD), that has been specifically designed to accommodate the data management and annotation needs of IB-related fermentation experiments. Although the proposed schema is tailored to IB applications, MIFE and MIFD build upon well-established models and community standards to facilitate easier integration with existing infrastructure and easier adoption by the community, as well as aim to integrate Findable, Accessible, Interoperable, and Reproducible (FAIR) principles in the IB field. In addition, the integration with FAIR Data Station (FAIR DS), a tool that offers metadata validation and enables the automated uptake of (meta)data from data management repositories such as FAIRDOM-SEEK, is showcased. The proposed models are accompanied by a Python package that enables their programmatic use by creating a Linked Data Modeling Language (LinkML) schema that can fuel subsequent analyses. Conclusions Through the promotion and simplification of knowledge discovery, we believe that MIFE and MIFD can accelerate the application of state-of-the-art artificial intelligence (AI) methods and the adoption of explainable AI to better understand bioprocesses at scale.
ano.nymous@ccsd.cnrs.fr.invalid (Georgios Georgakilas) 04 Jun 2026
https://hal.science/hal-05644678v1
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[hal-05440960] Keystone concept revisited: insights into microbial community dynamics and control
Different definitions of keystone taxa and functions agree that they have an outsized role in maintaining community composition, and thus, the keystone concept continues to attract attention even 50 years after its introduction. In this Perspective, we base our definition of microbial keystones on the original one to explore its implications and limitations. We review different mechanisms behind keystoneness, cover the strengths and weaknesses of current keystone prediction methods and present findings on keystones discovered in recent experiments. In addition, we suggest a new prediction method for keystones based on metabolic modelling. Finally, we discuss the role of keystones in community control strategies. Overall, the development of new prediction methods and the insights from recent experiments illustrate the continued relevance of the keystone concept for microbial communities.
ano.nymous@ccsd.cnrs.fr.invalid (Daniel Rios Garza) 05 Jan 2026
https://hal.science/hal-05440960v1
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[hal-05653713] Mesophilic Anaerobic Digestion of Municipal Sewage Sludge Under High Sodium Propionate Concentrations in Semi-Continuous Conditions: Inhibition and Microbial Community Shifts
The accumulation of intermediate products, particularly volatile fatty acids (VFAs) like propionic acid (HPr) or its dissociated form, can inhibit biogas production during anaerobic digestion (AD) at low concentrations. Knowledge about the response of microorganisms to VFA inhibition can help control the digesters. In this study, we aimed to determine how sodium propionate (NaPr) inhibits the AD of municipal sewage sludge by identifying shifts in the microbial community. Four 5 L reactors were operated in semi-continuous mode using sewage sludge and then loaded with different levels of NaPr. The reactors operated at 37 °C with two hydraulic retention times. The results show that there was no apparent inhibition of biogas production at NaPr loading up to 20.3 mmol·L−1. However, moderate inhibition was observed at 81 mmol·L−1, corresponding to an approximate 10% decrease in methane production, while a ≈40% decrease in methane production was observed at 135.3 mmol·L−1. Sequencing analysis revealed that the community composition was dominated by Bacillota, Bacteroidota, Proteobacteria, Chloroflexi, and Cloacimonadota, with Halobacterota and Euryarchaeota as the main archaeal groups. PERMANOVA revealed incubation time as the primary driver of community structure, followed by NaPr concentration. Elevated NaPr levels resulted in a decline in Methanothrix and Methanobrevibacter and promoted distinct syntrophic propionate-oxidizing bacteria (SPOB).
ano.nymous@ccsd.cnrs.fr.invalid (Joel Awinzure Agumah) 11 Jun 2026
https://hal.science/hal-05653713v1
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[hal-05612073] From microbes to molecules: Gut microbiota as a prerequisite threshold determinant for cancer immunotherapy efficacy
Cancer immunotherapy, represented by immune checkpoint inhibitors, adoptive cell therapy, and cancer vaccines, has revolutionized the clinical management of multiple malignant tumors, yet profound interindividual heterogeneity in treatment response and widespread primary/acquired resistance remain the most critical bottlenecks restricting its long-term clinical benefits. Accumulating preclinical and clinical evidence has unequivocally established the gut microbiota as a pivotal regulator of host anti-tumor immune responses. However, the vast majority of existing studies and reviews frame the gut microbiota as a mere adjuvant enhancer of immunotherapy efficacy, focusing solely on its role in boosting the upper limit of treatment effects, while neglecting its more fundamental role as a prerequisite for establishing a responsive immune baseline. In this review, we propose a unifying, evidence-based original core hypothesis: the gut microbiota is not merely an enhancer of cancer immunotherapy efficacy, but an indispensable prerequisite condition that sets the minimal baseline threshold for therapeutic responsiveness-a central thesis that distinguishes this review from previous descriptive work. Guided by this hypothesis, we systematically dissect the taxonomic and functional characteristics of threshold-determining gut microbiota, and clarify that microbial metabolites (e.g., short-chain fatty acids, bile acids, tryptophan derivatives) act as core molecular mediators translating microbial signals into host immune activation, which is critical for establishing the baseline efficacy threshold required for effective immunotherapy. We further perform a critical synthesis of clinical data from prospective cohorts, randomized controlled trials, and microbiota intervention studies, validating that threshold-based microbial signatures serve as non-invasive predictive biomarkers for immunotherapy outcomes, and propose mechanism-driven translational strategies targeting the gut microbiota (e.g., fecal microbiota transplantation, probiotic supplementation, dietary modulation) to reset the impaired immunotherapy efficacy threshold. This review provides a novel theoretical framework for understanding the microbiota-immunotherapy axis, which not only deepens the mechanistic insight into microbial metabolite-mediated immune regulation, but also facilitates the development of microbiota-guided personalized cancer immunotherapy and the overcoming of primary treatment resistance.
ano.nymous@ccsd.cnrs.fr.invalid (Xin Su) 07 Jul 2026
https://hal.science/hal-05612073v1
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[hal-05693548] Lignocellulose-powered bioelectrochemical systems: microbial communities, controlling factors, and enhancement strategies
Lignocellulosic biomass (LCB) is the world’s most abundant renewable carbon source, yet its potential to drive a circular bioeconomy remains largely untapped. Microbial electrochemical technologies (METs) offer a promising route for converting this complex feedstock into electricity or valuable chemicals. However, LCB-MET advancement is hindered by a fundamental challenge: LCB recalcitrance necessitates depolymerization, a process mismatched with the metabolic capabilities of most electroactive microorganisms (EAMs). While EAMs excel at oxidizing simple substrates, most lack the hydrolytic machinery to break down LCB, creating a critical performance bottleneck. Addressing this requires a multi-disciplinary approach. At the heart of the biological challenge lie two core paradigms, each drawing on microorganisms sourced from nature or artificially engineered: (i) specialized strains capable of both hydrolytic and electrogenic functions, or (ii) synthetic consortia establishing division of labor between fermentative microbes and EAMs. These strategies do not operate in a vacuum; their performance is constrained by materials and environment. To evaluate the progress and potential of these interdependent biological, material, and engineering strategies, this review examines the landscape of LCB utilization in METs. It synthesizes recent advances in coupling depolymerization with extracellular electron transfer, critically evaluate microbial players from pure strains and mixed communities to genetically modified organisms and synthetic consortia, and assesses the key operational parameters, challenges, and potential solutions that define this field. Moving beyond, the review provides graphic representations and statistical analyses of recent publications to establish quantitative performance benchmarks.
ano.nymous@ccsd.cnrs.fr.invalid (Animut Assefa Molla) 15 Jul 2026
https://hal.inrae.fr/hal-05693548v1
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[hal-05442197] Plan de gestion des données de l’unité de recherche PROSE (UR1461 INRAE)
L’unité PROSE mène des recherches sur les biotechnologies environnementales, depuis l’échelle des communautés microbiennes jusqu’à celle des procédés (stations d’épuration, digesteurs anaérobies, procédés bioélectrochimiques pour la bioraffinerie, …), en articulation avec les grands enjeux sociétaux de développement durable, d’économie circulaire et de bioéconomie. Affiliée aux départements TRANSFORM et MICA d’INRAE, l’unité PROSE s’inscrit dans une démarche transdisciplinaire fondée sur l’écologie microbienne, la biogéochimie, le génie des procédés, les mesures physiques et la modélisation. L’unité PROSE est composée d’un pôle de chercheurs et chercheuses porteurs de projets, d’un pôle analytique regroupant un laboratoire de microbiologie moléculaire et un laboratoire de chimie dotés d’équipements de pointe, et d’un pôle expérimentation ayant une capacité à déployer ses compétences à la fois à l’échelle pilote et sur le terrain. Ce plan s’inscrit dans le cadre des activités de recherche de l’unité PROSE et des projets de recherche auxquels elle contribue.
ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 16 Jan 2026
https://hal.inrae.fr/hal-05442197v1
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[hal-05393313] Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Cédric Midoux) 02 Dec 2025
https://hal.inrae.fr/hal-05393313v1
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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-05397464] Analyse croisée de données métabarcoding et métagénomiques sur des microbiotes d'hôtes animaux
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Núria Mach) 04 Dec 2025
https://hal.science/hal-05397464v1
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[hal-05308873] Implicit Generalized Predictive Control of a Wastewater Treatment Plant: Application to the SimBio Model
This paper presents an implementation of an implicit Generalized Predictive Control (GPC) strategy applied to a wastewater treatment plant (WWTP) modeled via the SimBio simulator. Without identifying an explicit dynamic model, the control law is derived directly from system input-output behavior. The main goal is to regulate the effluent ammonium (NH<sub>4</sub><sup>+</sup>) concentration by manipulating the aeration rate, while coping with perturbations such as influent flow and ammonium concentration. Several configurations of the control parameters were tested and evaluated using process performance indicators. The obtained results show that the proposed controller allows a good tracking of the desired set-point while presenting a low energy consumption during the considered period of the experiment.
ano.nymous@ccsd.cnrs.fr.invalid (Yasmine Siahmed) 10 Oct 2025
https://hal.inrae.fr/hal-05308873v1
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[hal-05400292] COVID-19 and chronic liver disease: results from the 1219 patients French registry
The deleterious impact of Coronavirus SARS CoV-2 related Disease (COVID-19) in patients with chronic liver disease (CLD) has been previously described. We report here data from the largest French “real-life” cohort. Patients with CLD regardless of etiology and liver transplant recipients who developed COVID-19 confirmed by a positive PCR and/or an evocative chest CT scan were included. The primary outcome was 30-days mortality. Prognostic factors were analyzed using both uni- and multivariate models in subgroups of transplanted and non-transplanted patients. Between August, 2020, and December, 2021, 1219 patients were included, mostly men (n = 754), median age 61 years, 477 patients with advanced CLD (decompensated (Child–Pugh B or C) in 164 patients); 366 patients were immunocompromised, including 271 organ transplant recipients. Hospitalization in intensive care unit was required in 11% of cases. The median follow-up was 68 days. The overall 30-days mortality was 13% (159 deaths, 62% related to extra-hepatic causes). Among transplant recipients, age was the only independent prognostic factor. In the non-transplanted population, the independent prognostic factors were advanced liver fibrosis (F3 or F4, HR 2.5), obesity (HR 1.56) and age (HR 1.03), whereas immunosuppression was not. Within the subgroup of patients with advanced CLD, decompensation (Child–Pugh B or C) was an independent predictor of mortality (HR 3.8). In conclusion, our results highlight the increased vulnerability of patients with advanced CLD to COVID-19, particularly those with decompensated disease. Conversely, they confirm the absence of excess mortality related to immunosuppression, particularly in organ transplant recipients. Clinical trial registration: Clinical trial (NCT 04,375,670).
ano.nymous@ccsd.cnrs.fr.invalid (L. Blaise) 23 Apr 2026
https://normandie-univ.hal.science/hal-05400292v1
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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-05410146] Higher butanol titer and selectivity in electro-fermentation experiments with Clostridium acetobutylicum ATCC 824 are due mainly to methyl viologen rather than electrode polarization
Butanol selectivity is crucial for the development of an industrial process targeting butanol as the main product of acetone-butanol-ethanol (ABE) fermentation by solventogenic Clostridia. This study evaluated electro-fermentation (EF), with an electron carrier, methyl viologen (MV), as a strategy to modify solvent production in Clostridium acetobutylicum ATCC 824 under optimized batch fermentation conditions. Cathodic EF was performed with or without 0.5 mM MV in single-compartment reactors with two-chamber and a negative potential was applied to the cathode. The greatest differences in final products concentrations were observed with the addition of MV compared to the control and EF fermentations. The fermentation with MV only was slowed down and resulted in 11% more butanol (control: 14.2 g.L−1, MV: 15.8 g.L−1) and half as much acetone, increasing the butanol/acetone (B/A) ratio by 137% from 1.93 to 4.57 g C.g C−1. The pH profile was also modified with a final pH 0.5 unit higher. Conversely, EF did not appear to alter product formation significantly, even if slight differences were observed under our conditions. In addition, the reductase activity (RA) was measured by flow cytometry and showed that EF alone affected the intracellular redox state compared to the control fermentation, as did the addition of MV. However, electrode polarization had no effect on the extracellular oxidoreduction potential (ORP) profiles.
ano.nymous@ccsd.cnrs.fr.invalid (Edouard Beudy) 10 Dec 2025
https://ifp.hal.science/hal-05410146v1
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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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[hal-05408601] A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.
Abstract Cardiometabolic diseases (CMD) are on the rise globally with one billion people expected to suffer from obesity and 643 million from type 2 diabetes by 2030, of which one-third will likely develop chronic kidney disease and two-thirds will die from cardiovascular disease (CVD). However, the mechanistic and molecular drivers of the transition from health to disease remain elusive. Here, in 275 metabolically healthy individuals recruited to the MetaCardis study, we identify a gut microbiome-kidney-heart axis that is predictive of future cardiovascular events. This axis, as evidenced by the associations between gut microbial metabolism of phenylalanine and tyrosine with variations in both kidney functon(as measured by estimated glomerular filtration rate) and circulating pro-atrial natriuretic peptide concentration, shows a depletion pattern in metabolically unhealthy participants of the MetaCardis study (n = 1,602) indicating a loss of health-sustaining microbiome features with CMD progression. We then validate that microbial compounds from the phenylalanine and tyrosine pathways and their host co-metabolites act as mediators of the gut microbiome-kidney associations. Moreover, Mendelian Randomization analysis adds genetic evidence to suggest that the microbial mediator metabolites regulate host kidney function and vice versa. Finally, we demonstrate that plasma metabolites derived from the microbial metabolism of phenylalanine and tyrosine associate with incident CVD in the Canadian Longitudinal Study on Aging (n = 8,669). Collectively, our results depict the presence of a gut microbiome-kidney-heart axis in metabolically healthy individuals. Major aberrations of the gut microbiome as part of this axis throughout life may increase risk of CVD.
ano.nymous@ccsd.cnrs.fr.invalid (Kanta Chechi) 10 Dec 2025
https://hal.science/hal-05408601v1
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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-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 (&lt;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) 02 Dec 2025
https://hal.science/hal-04915064v2
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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-05445708] Harnessing Lignocellulolytic and Electrogenic Potential: Insights from Shewanella oneidensis MR-1 and Cellulomonas Strains on Lignocellulosic Biomass
In the context of depleting non-renewable resources and climate change, sustainable alternatives are crucial. Biomass is a promising platform for producing fuels, chemicals, and other valuable products. Lignocellulosic biomass (LCB) is the most abundant biomass on Earth, comprising cellulose, hemicellulose, and lignin. Annually, about 200 billion tons of LCB are generated globally, highlighting its potential for sustainable applications1. Microbial electrochemical technologies (METs) have gained attention for their diverse applications. Electroactive microorganisms (EAMs) are key to these technologies, enabling electron flow and microbial metabolism at electrochemical interfaces. LCB has been explored in METs for power generation, volatile fatty acids, hydrogen, and vanillin production, although its complex structure poses challenges2–5. One promising solution to overcoming the complexity of lignocellulosic biomass in METs is to identify microorganisms that exhibit both lignocellulose-degrading and electroactive capabilities. In this context, the research investigates the potential of three bacterial strains (S. oneidensis MR-1, C. biazotea NBRC 12680 and C. fimi ATCC 484) to grow on wheat bran and their electrogenic capabilities, which provides new insights into their applicability in LCB based bioelectrochemical systems. The research utilizes a combination of bioinformatic analysis, growth experiments, enzymatic assays, Attenuated Total Reflectance - Fourier Transform Infrared Spectroscopy (ATR-FTIR) analysis for lignocellulosic biomass degradation, and electrochemical characterization. This multi-faceted approach offers a thorough understanding of how these bacteria interact with lignocellulosic biomass and their electrochemical performance. The result showed that Cellulomonas strains show significant lignocellulose degradation potential, with high CAZyme counts and relevant carbohydrate degradation pathways and genes. Our findings reveal the varying growth of the strains on lignocellulosic substrates. Enzymatic assays demonstrated laccase activity, indicating lignin degradation. Electrochemical characterization shows bioanode of S. oneidensis MR-1 has the highest activity with the maximum current density of 14.92 mA.m-², followed by C. biazotea NBRC 12680 and C. fimi ATCC 484 on wheat bran. Cyclic voltammetry indicates redox activities at electrode surfaces, ATR-FTIR shows lignin, hemicellulose and protein degradation under the electrochemical conditions. These findings suggest potential applications of these strains in bioelectrochemical treatment and the development of METs for LCB conversion although current density is low. As a prospective, the utilization of mixed microbial communities to substantially improve the conversion efficiency of LCB in METs is highly recommended and will be a key focus of our future research.
ano.nymous@ccsd.cnrs.fr.invalid (Animut Assefa Molla) 07 Jan 2026
https://hal.science/hal-05445708v1
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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-04548488] Evaluating the electrode materials to improve electricity generation with the removal of multiple pollutants through microbial fuel cells
Microbial fuel cells (MFCs) are a new system that generates electricity and treats wastewater. The scientific community is interested in its applications; however, electron generation and transportation are key concerns. Thus, this research compares and studies common materials, which have never been widely investigated. The anode electrode is simple graphite (GE), mild steel (ME), and stainless steel (SE) to increase the transportation of electrons. Nypa fruticans Wurmb (Nira sap) is used as an easily available and highly beneficial organic substrate for bacterial populations. According to electrochemical tests, the GE offered 1.07 mW/m2 power density (PD), while the ME and SE delivered 2.75 mW/m2 and 5.85 mW/m2 within the first 35 days, respectively. The findings demonstrated that the SE anode had the highest specific capacitance values of 5.25 × 10−2 F/g, while the GE anode and ME anode had Cp values of 4.41 × 10−2 F/g, and 3.36 × 10−2 F/g, respectively. Bisphenol A (BPA) removal efficiency was maximum on the 65th day, with 96.25% for the SE anode, 94.55% for the ME, and 81.08% for the GE, while Pb2+ removal efficiency was 97.35% in the SE, 96.65% in the ME, and 96.60% in the GE. Bacillus sp. dominated all anodes during bacterial identification due to the same inoculation source. A comprehensive discussion of mechanisms is enclosed with future research directions.
ano.nymous@ccsd.cnrs.fr.invalid (Najwa Najihah Mohamad Daud) 16 Apr 2024
https://hal.inrae.fr/hal-04548488v1
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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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[tel-05351742] Les dynamiques hôte-virus dans les digesteurs anaérobies sous l'effet d'un stress abiotique
Les virus des microbes sont des acteurs majeurs dans divers écosystèmes, affectant la structuration et la dynamique des communautés microbiennes. Cependant, ils restent peu explorés dans le domaine de la digestion anaérobie (DA). Les écosystèmes de ces processus sont très sensibles aux perturbations, entraînant inhibition et diminution de la production de méthane. Cette thèse aborde l'interaction entre des perturbations abiotiques, la composition des communautés microbienne et virale et la performance du procédé.La dynamique des populations virales a été étudiée dans des digesteurs anaérobies, grâce au séquençage ‘shotgun' du métavirome. L'objectif était d'évaluer si la production de virus tempérés peut être déclenchée par des stress abiotiques connus pour inhiber la DA, via l'induction de provirus. Un second objectif était de déchiffrer de nouvelles paires virus-hôtes, grâce à des approches bioinformatiques. Nous avons constaté que les diversités des procaryotes et des virus étaient élevées, l'ordre Clostridiales dominant la communauté procaryote et la classe Caudoviricetes dominant la communauté virale. De nombreux virus et hôtes ont été identifiés comme étant différentiellement abondants dans des conditions perturbatrices, avec une bonne cohérence entre les dynamiques des hôtes et celles des virus. Nos résultats n'ont montré aucun impact significatif de ces stress abiotiques sur l'induction de prophage, ce qui indique que les virus pourraient avoir eu des effets modérés et sans rupture au fil du temps, plutôt que des effets massifs et soudains.Par ailleurs, cette étude étend les connaissances sur la DA et confirme l'importante diversité et la nouveauté des virus de la DA. Le génome d'un nouveau virus en forme de fuseau a été annoté manuellement avec d'autres génomes viraux. Cela pourrait conduire à l'établissement d'une nouvelle famille de virus d'archées méthanogènes.
ano.nymous@ccsd.cnrs.fr.invalid (Marion Coves) 06 Nov 2025
https://theses.hal.science/tel-05351742v1
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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-04820202] Assessing Flexibility in Biowaste Management Systems for Sustainable Solutions
Urban biorefineries play a pivotal role in the circular economy, promoting environmental sustainability by converting waste into valuable resources. Their importance has gained attention in France, especially with the introduction of the AGEC 2024 law, which mandates biowaste sorting at the source. This regulation calls for efficient recovery systems, making it essential to assess the flexibility of urban biorefineries to ensure they can adapt to future challenges. This study introduces a novel approach that combines mathematical flexibility assessment with field surveys conducted among stakeholders, specifically focusing on composting operations. The concept of flexibility, widely applied in chemical engineering, measures the capacity of a system to operate effectively under variable conditions. Introduced by Swaney and Grossmann in 1985, flexibility has since been refined by various researchers, including further refined by Patricia M. Hoch and Ana M. Eliceche (1996), Foudas and al (2001) and Di Pretoro et al. in (2019, 2020, 2024), who classified flexibility into deterministic and stochastic indices. The deterministic index evaluates system performance within predefined boundaries, while the stochastic index considers probabilistic variations in parameters. This research aims to develop a robust methodology for evaluating the flexibility of urban biorefineries, with a focus on composting processes. The study applies the deterministic flexibility index, coupled with field data from composting practitioners across France. Key parameters, including control variables and uncertain parameters, were identified through these surveys. These parameters helped define the range of operational variability, allowing for a more accurate flexibility index calculation. A key innovation of this study is the integration of real-world data through field surveys. An online questionnaire was distributed to composting stakeholders to collect detailed information on waste valorisation practices, raw materials used, and operational conditions. This data provided a broader understanding of the operational uncertainties and helped refine the flexibility assessment. The integration of established theoretical frameworks with field data strengthens the methodology, providing a comprehensive assessment of urban biorefineries' adaptability facing environmental challenges. This approach identifies key limiting factors within the composting process and supports system optimization, ensuring enhanced flexibility and operational feasibility across diverse scenarios.
ano.nymous@ccsd.cnrs.fr.invalid (Naouel Alileche) 01 Apr 2026
https://hal.science/hal-04820202v1
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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
