Biology subjects

Midoux, C.

Publications and source records attributed to Midoux, C..

6 recordsLinked to original sources

bioRxiv2025

A deeper study on propionic acid-related inhibition during anaerobic digestion: insights on methane production and identification of biomarker candidates for an early warning

Propionic acid (HPr) accumulation is a major indicator of anaerobic digestion (AD) dysfunction, yet the relative contributions of acidity, undissociated HPr, and propionate ions (Pr-) to process inhibition remain poorly understood. We investigated these effects in mesophilic batch AD microcosms fed with municipal sewage sludge, using a comparative design involving HPr, sodium propionate (NaPr), NaCl, and HCl treatments across two series of experiments. While 20 mM HPr caused a 22% reduction in the maximal methane production rate, 81 mM HPr led to complete inhibition, with the initial pH dropping to 5.1. By contrast, 81 mM NaPr reduced methane production rate by only 40%, and 81 mM NaCl caused no inhibition, demonstrating that acidity is the dominant inhibitory factor, with Pr- exerting a secondary concentration-dependent effect. 16S rRNA gene amplicon sequencing revealed strong, compound-specific shifts in microbial community composition, affecting key functional groups including syntrophs and methanogenic archaea. The proportion of methanogens dropped from 2-3% in control reactors to less than 0.2% under 81 mM HPr, consistent with the observed methane production inhibition. Under HPr81, over 100 ASVs were differentially abundant compared to controls, a pattern largely shared with HCl-treated reactors, further confirming the predominant role of acidity. The number of differentially abundant ASVs was negatively correlated with methane production rates (R{superscript 2} = 0.97), underscoring the link between community reshaping and process impairment. These results provide a unifying framework for propionate inhibition in AD and suggest that microbial community profiling could serve as an early warning tool for process imbalance detection.

bioengineering↗

bioRxiv2022

The first horse gut microbiome gene catalog reveals that rare microbiome ensures better cardiovascular fitness in endurance horses

Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance, but the extent of their functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built the first equine gut microbial gene catalog comprising more than 25 million non-redundant genes representing 4,696 genera spanning 95 phyla. The unprecedented resolution unrevealed functional pathways relevant for both the structure of the microbiome and the host health and recovered 369 novel metagenome-assembled bacterial genomes, providing useful reference for future studies. Integration of microbial and host omic datasets suggested that microbiomes harboring rare species were functionally dissimilar from those enriched in Lachnospiraceae taxa. Moreover, they offered expanded metabolic pathways to fine-tune the cardiovascular capacity through mitochondria-mediated mechanisms. The results identify an associative link between horse endurance capability and its microbiome gene function, laying the basis for nutritional interventions that could benefit endurance athletes.

microbiology↗

bioRxiv2020

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions

BackgroundTicks transmit pathogens of medical and veterinary importance, and represent an increasing threat for human and animal health. Important steps in assessing disease risk and developing possible new future control strategies involve identifying tick-borne microbes, their temporal dynamics and interactions. MethodsUsing high throughput sequencing, we studied the microbiota dynamics of Ixodes ricinus from 371 nymphs collected monthly over three consecutive years in a peri-urban forest. After adjusting a Poisson Log Normal model to our data set, the implementation of a principal component analysis as well as sparse network reconstruction and differential analysis allowed us to assess inter-annual, seasonal and monthly variability of I. ricinus microbial communities as well as their interactions. ResultsAround 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and potentially circulating in ticks: Candidatus Midichloria, Rickettsia, Spiroplasma, Arsenophonus and Wolbachia. The structure of the I. ricinus microbiota was temporally variable with interannual recurrence and seemed to be mainly driven by OTUs belonging to environmental genera. The total network analysis revealed a majority of positive (partial) correlations. We identified strong relationships between OTUs belonging to Wolbachia and Arsenophonus, betraying the presence of the parasitoid wasp Ixodiphagus hookeri in ticks, and the well known arthropod symbiont Spiroplasma, previously documented to be involved in the defense against parasitoid wasp in Drosophila melanogaster. Other associations were observed between the tick symbiont Candidatus Midichloria and pathogens belonging to Rickettsia, probably Rickettsia helvetica. More specific network analysis finally suggested that the presence of pathogens belonging to genera Borrelia, Anaplasma and Rickettsia might disrupt microbial interactions in I. ricinus. ConclusionsHere, we identified the I. ricinus microbiota and documented for the first time the existence and recurrence of marked temporal shifts in the tick microbial community dynamics. We statistically showed strong relationships between the presence of some pathogens and the structure of the I. ricinus non-pathogenic microbes. We interestingly detected close links between some tick symbionts and the potential presence of either pathogenic Rickettsia or a parasitoid in ticks. All these new findings might be very promising for the future development of new control strategies of ticks and tick-borne diseases.

microbiology↗

bioRxiv2020

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition

Anaerobic digestion (AD) is a microbial process that can efficiently degrade organic waste into renewable energies such as methane-rich biogas. However, the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds, leading to process failure and economic losses. High-throughput sequencing technologies enable the identification of microbial indicators of digesters inhibition and can provide new insights into the key phylotypes at stake during AD process. But yet, current studies have used different inocula, substrates, geographical sites and types of reactors, resulting in indicators that are not robust or reproducible across independent studies. In addition, such studies focus on the identification of a single microbial indicator that is not reflective of the complexity of AD. Our study proposes the first analysis of its kind that seeks for a robust signature of microbial indicators of phenol and ammonia inhibitions, whilst leveraging on 4 independent in-house and external AD microbial studies. We applied a recent multivariate integrative method on two-in-house studies to identify such signature, then predicted the inhibitory status of samples from two datasets with more than 90% accuracy. Our study demonstrates how we can efficiently analyze existing studies to extract robust microbial community patterns, predict AD inhibition, and deepen our understanding of AD towards better AD microbial management. HighlightsO_LIRobust biomarkers of AD inhibition were tagged by integrating independent 16S studies C_LIO_LIIncrease of the Clostridiales relative abundance is an early warning of AD inhibition C_LIO_LICloacimonetes is associated with good performance of biomethane production C_LIO_LIMultivariate model predicts ammonia inhibition with 90% accuracy in external data C_LI

microbiology↗

bioRxiv2019

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis

BackgroundThe development of high throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g. individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: crushing, DNA extraction, and DNA amplification.\n\nResultsControls yielded a significant number of sequences (1,126 to 13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e. the percentage of sequences belonging to OTUs identified as contaminants) varied with tick stage and gender: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in crushing and DNA extraction controls, highlighting the importance of carefully controlling these steps.\n\nConclusionHere, we showed that contaminant OTUs from extraction and amplification steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.

microbiology↗

bioRxiv2019

Upscaling of Microbial Electrolysis Cell Integrating Microbial Electrosynthesis: Insights, Challenges and Perspectives

Recent development of microbial electrochemical technologies has allowed microbial electrosynthesis (MES) of organic molecules with microbial electrolysis cell treating waste organic matter. An electrolytic cell with a MES cathode (ME-ME cell) can produce soluble organic molecules with higher market price than biomethane, and thus satisfy both economic and environmental interest. However, the sustainability of bioanode activity could become a major concern. In this work, a 15-liter ME-ME reactor was designed with specific electrode configurations. An electrochemical model was established to assess the feasibility and possible performance of the design, considering the \"aging\" effect of the bioanode. The reactor was then built and operated for performance evaluation as well as bioanode regeneration assay. Biowaste from an industrial deconditioning platform was used as substrate for bioanode. The COD removal rate in the anodic chamber reached 0.83 g day-1 L-1 of anolyte and the anodic coulombic efficiency reached 98.6%. Acetate was produced with a rate of 0.53 g day-1 L-1 of catholyte, reaching a maximum concentration of 8.3 g L-1. A potential difference was applied between the bioanode and biocathode independent of reference electrodes. The active biocathode was dominated by members of the Genus Pseudomonas, rarely reported so far for MES activity.

microbiology↗