Data analysis service
Presentation of the data analysis service offer
data analysis
migale
Presentation
The need for genomic data analysis continues to grow. To best help our collaborators in the analysis of their data, we have been offering since 2016 a range of services designed to meet their needs in term of training, support and collaboration for large-scale projects. Migale has a recognized expertise in data analysis and application/workflow development in bioinformatics, multi-omics analysis ((meta)genomics, (meta)transcriptomics) for microorganisms.
For now, 7 people of the Migale team dedicate time to this service:
- Olivier Rué is a bioinformatician engineer. He is in charge of the data analysis service on the Migale bioinformatics facility. He specializes in the analysis of metabarcoding and metagenomics data.
- Christelle Hennequet-Antier is a research engineer in statistics. She specializes in multi-omics data analysis using statistical approaches.
- Cédric Midoux is a bioinformatician engineer. He specializes in the analysis of metagenomics data, workflow development and development of visualization interfaces.
- Mahendra Mariadassou is a Ph.D. in statistics. He is involved in the development of new statistical methods and tools for metabarcoding analysis.
- Mouhamadou Ba is a Research Engineer. He is in charge of the text and data mining analysis on the Migale bioinformatics facility.
- Valentin Loux is the operational manager of the platform. He specializes in the assembly and comparison of bacterial genomes and metagenomics data analysis.
- Hélène Chiapello is a Ph.D. in bioinformatics. She specializes in the assembly and comparison of bacterial genomes.
Conditions
This service is open to each scientist who needs helps in analyzing his or her data in accordance with our themes/scope (INRAE, academic or private). You will have access to all the resources made available by the platform (https://documents.migale.inrae.fr/posts/tutorials/migale-infra/).
- The service is free of charge for academics. For members of the private sector, an offer will be made to you.
- Opening an account on the platform entitles you to 400 GB of space (save + work). If you need more disk space, a dedicated space on the server will be opened and invoiced (at the rate of 300€ / To / year)
Quality approach
The Data Analysis service is one of the process governed by the quality approach and under our quality certification. Consequently, some procedures have been set up to provide the best possible services. This procedure allows each party to know exactly what it has to do and what the other one has to do.
More details here.
FAIR principles and data management
We can accompany you in the implementation of the FAIR principles by:
Data management during the project
During the project, we are responsible for the data you provide us. Raw data are deposited on two distinct servers. During the analyses, you have access to intermediate results and to the companion analyses website.
At the end of the project, the expected deliverables are sent to you and we are no more responsible of your data. You can host them if you want in your own space. - helping to deposit your data on a dedicated infrastructure - reporting all commands (tools, versions) for reproducibility (in the companion website)
Scope of the data analysis service
Metabarcoding
We have extensive experience in metabarcoding data analysis (16S, ITS, RPB2, D1D2, gyrB…). According to your needs, we choose the most appropriate tool.
We develop and provide shiny interfaces to explore and manipulate metabarcoding data:
- easy16S is a user-friendly web application enabling you to easily explore, visualize and analyze amplicon sequencing metagenomics data.
- affiliationExplorer is a user-friendly graphical interface to choose between different conflicting affiliations that the FROGS pipeline produces.
Metagenomics / Metatranscriptomics
We have extensive experience in metagenomcis data analysis. From quality control to functional annotation, we have workflows to clean, assemble, predict and annotate genes from Illumina metagenomics data. Recently, we have implemented workflows for dealing with long-reads data.
Genome assembly, annotation and comparison
We have extensive experience in phage, archaeal and bacterial genome assembly, annotation and comparison of multiple assemblies.
Text-mining
We have experience in literature data analysis (textual data analysis). We have tools to cover the following analysis around microbiology from sources like PubMed:
- creation of thematic corpora (e.g., collecting a set of articles related to habitats of microorganisms from PubMed)
- classification of textual articles (e.g., selecting pertinent articles from a corpus)
- extraction of biological entities mentioned in articles (e.g., identifying mentions of genes in articles)
Procedures
We propose two different ways to collaborate: Collaboration and Counseling.
Collaboration
In Collaboration mode, we handle the analysis of the data.
Warning
If possible, we would like to be involved very early in the project design to give advice concerning the experimental design, the sequencing strategy, the number of samples/replicates, the randomization, etc.
We take care of storing sequencing data on our infrastructure and we provide a web report that tracks all performed analyses to facilitate reproducibility.
Support
This mode is quite different. Our role is to help you to analyze and interpret the results you obtain. We give assistance for debugging, choosing tools and parameters but don’t perform the analyses. With this service, you have access to an interlocutor available to answer your questions, supervise your treatments and help you in the analysis and interpretation of your results. It helps you to become progressively autonomous and confident in your bioinformatics skills.
Overview
Here is a breakdown of the projects according to their topic.
| Metabarcoding | Metagenomics | Metatranscriptomics | Genomics | Transcriptomics | Genome assembly | Text-mining |
|---|---|---|---|---|---|---|
| 72 | 15 | 7 | 10 | 8 | 6 | 2 |
Requests come from all over France (one from Germany is not shown here):
Users feedbacks
"The collaboration was great, all analyses and promises were performed on time" "The conversation was really great. All questions were answered very professional and the colleagues supported us very efficiently during the manuscript and Submission process. Thank you very much!!!" "Rien à redire, tout était parfait." "Very fast answers, make themselves available and clear explanations" "Grande réactivité" "Grâce aux discussions, XXX a réussi à écrire son pipeline pour downloader les données sur SRA" "C'est la première fois que nous faisions appel aux services de Migale et nous en sommes très satisfaits" "Olivier was very reactive, available and open for discussions" "J'ai toujours des réponses rapides et précises à toutes mes questions que ce soit sur Galaxy ou sur R" "Mes analyses seront plus fiables et complètes" "Perfect" "Great use of my Rmd with internal remarks! Like it a lot" "Excellent communication with fast solving problems and reactivity" "Yes, results were generated and gathered right on time, as expected" "Files corresponded to the discussed and expected deliverables. I especially appreciate the very detailed description of the followed methods and scripts" "very satisfied (and honored) to be able to discuss w/ INRAe experts. Discussions w/ Hélène Chiapello & Valentin Loux were constructive, stimulating and accessible for a non-expert. I also asked them to adjust the deliverable, which they did smoothly" "Delay were well-respected and milestones-meetings were setted up regularly" "The assembly went well for most of the 8 barcodes submitted" "Migale people were very interested in the development of a workflow for the analysis of viral and bacterial genomes from MinION sequencing" "Perfect! The quality of the report is outstanding and the scripts are reusable for other applications" "Constructive, reactive. We'll come back!" "More than happy of the exchanges with Valentin and Hélène did a great bioinformatic job with great attention of our competency leverage" "Impressive analysis obtained on a large collection of strains" "Migale has always been very professional in the delays and deliverables in our experience" "I've been extremely satisfied with the help provided by Cédric and Olivier and the positive results in terms of accuracy" "I've had no time yet to explore the data but I am sure we achieved the expected results" "They have provided a fast answering support!" "I am very satisfied." "Dans les temps comme toujours" "Une vraie collaboration ! c'est toujours très professionnel ! merci à Mahendra et Olivier pour leur travail" "The deadlines were met and the results were analysed very quickly (less than a week). We are very satisfied with this collaboration" "The aims of this analysis are was to assign operational taxonomic units (OTUs) to the reads, identify the species diversity present in each sample and analyze their abundance (read counts). All objectives were met" "The contacts and explanations provided by the team Migale (Olivier Rué) and the answers to all our questions about how the the analyses were conducted were more than satisfactory. It was an excellent experience that we will certainly repeat in the near future" "Délais impeccables" "Le rapport est très clair, avec des explications pas- à- pas. Tout y est très bien détaillé" "Beaucoup de réactivité et de rapidité" "Merci pour cet aide très précieuse !" "Parfaitement dans les temps malgré mes demandes de dernières minutes, encore merci à Olivier!" "Exactement ce dont nous avions besoin. Parfait" "Très bonne communication. Merci pour votre disponibilité" "Excellent" "Réponses rapides, discussions utiles, aide et conseils adaptés" "Toutes les analyses demandées ont été fournies" "Olivier a pu nous fournir des résultats rapidement bien que les délais soient courts" "Olivier a toujours été très disponible pour discuter des résultats et pour la compréhension de nos besoins en terme d'analyses" "Nous sommes très satisfaits de la collaboration et des échanges que nous avons eu avec l'équipe MIGALE" "The urgency of the deadline was well considered and respected" "The results were as expected" "Interactions were pleasant, efficient and constructive" "Olivier nous a rendu rapidement les résultats des analyses faites" "Olivier Rué a répondu aux différentes questions posées et a pris le temps de nous recevoir et de nous expliquer les résultats obtenus (ce n'était pas ceux que l'on attendait)." "Des travaux qui arrivent pil poil dans nos délais et nos attentes" "Très bons résultats" "Une bonne communication en amont et en aval de notre projet." "Nous avons défini avec Mouhamadou Ba des dates en fonction de chaque jalon et deliverable qui ont bien été determinés" "Nous avons effectué des Visio pour faire des points tous les 3 mois et affiner les deadlines et jalons" "Merci pour la réactivité des personnes impliquées" "Tout s'est déroulé selon le plan !" "La communication passe très bien" "Pas plus d'idées que ce qui est déjà proposé" "J'ai dû solliciter une extension d'un trimestre supplémentaire car j'avais sous-évalué le temps nécessaire pour constituer le jeu de données génomiques. Le délai supplémentaire est donc de mon fait" "j'ai beaucoup apprécié les échanges qui étaient très conviviaux, pleins de sollicitude et une source régulière de motivation. Très grande disponibilité, réactivité et efficacité pour accompagner mon projet et surtout orientation vers les outils adaptés que je testais ensuite seule (plus efficace pour une montée en compétence)." "Everything was OK, even with some delay due to the size of the dataset" "Very useful, and bringing expertise and advices essential for the project" "More projects with them !" "La demande d'analyse a été faite fin juillet , Olivier nous a envoyé les résultats début septembre" "Olivier a été très disponible pour répondre à toutes nos questions et nous expliquer les résultats" "The delay was very short (because we were about to submit the publication) but the deadline was perfectly respected" "We received the link to upload the results in less than 10 days" "I really appreciated the reactivity and professionalism of C. Hennequet to all the messages I sent but also the revisions and comments she made on the manuscript (that helped a lot to improve it before submission)" "Nothing, everything was perfect! As usal!" "Many thanks for your valuable contribution to this work" "Compétences, analyse des besoins et écoute +++" "Extrêmement satisfaite du service" "Le respect des échéances a été parfait. Les analyses ont toutes été faites dans les temps. Des discussions sur le temps du projet ont été prévues pour faire le point de l'avancée des travaux. L'organisation est vraiment excellente" "Là encore, tout a été parfait. Les delivrables ont été rendus, avec à chaque fois un point de discussion pour prendre connaissance des fichiers d'analyse. Les fichiers eux mêmes sont parfaitement détaillés et annotés pour les prendre en main" "Les interactions et discussions ont été excellentes, interactives et constructives. Olivier et Christelle ont été très réactifs, très à l'écoute, et force de proposition, et toujours disponibles pour chacune de nos questions" "Il est clair que nos analyses n'auraient pas été aussi pertinentes et abouties sans l'aide d'Olivier et Christelle. C'est une aide inestimable. Un grand merci !" "Very interesting exchange.Christelle is very available." "Great work !! Thank you Olivier" "-) !" "Mouhamadou Ba a été tres interactif avec notre équipe et à completer les bases de données ainsi qu'ajuster les nouvelles requetes (nouvelles tables pour integrer des recherche sur les especes, et les tissus) pour pouvoir utiliser les données dans le logiciel Gargantext rapidement" "Tous les livrables que nous avions défini ensemble en novembre ont été fournis dans les durées que nous avions estimées" "Nous avions eu plusieurs echanges réguliers pour affiner les livrables et qu'ils repondent a nos attentes. Mouhamadou Ba a été trés réactif et a notre ecoute pour comprendre nos questions et nous envoyer les analyses de datamining que nous avons commencé a analyser" "Nous aurions de notre coté a ameliorer la base de terme MESH pour limiter les faux positifs ou pouvoir obtenir des résultats plus precis : par exemple , nous n'avons pas toutes les especes car pour une meme espece plusieurs termes sont possibles ou sont notés au pluriel. Par ailleurs, Il serait interessant, par exemple dans un volet 3, de mettre les résultats de datamining sous forme graphique a l'aide d'un outils comme cytoscape afin de selectionner que quelques colonnes de resultats. Mouhamadou a pu adapter les données pour pouvoir les integrer dans le logiciel Gargantext developpé par l'Institut des Sciences Complexes et avoir une forme Graphique mais la representation est differente (et complementaire) de ce qui peut etre defini avec les données d'origine." "No particular deadline, the project started as the continuation of an internship in june 2021 and became a subpart of a PhD project in 2022-2023" "As a part of my PhD, I did most of the analyses and asked for help" "A lot of help for tools, methodologies, advices, debug." "Perfect" "Perfect" "Perfect" "Bravo ! Ton rapport est très très bien : précis, explicatif, synthétique, académique !" "Olivier a été très rapide pour l'envoi des résultats" "Olivier a été très disponible pour m'expliquer toute la technologie ainsi que les résultats" "Great work !!" "Excellent" "Excellent" "Extremely good" "lien très pratique pour suivre l'avancée des datas et comprendre le contexte, les délivrables de l'analyse rnaseq ont été discuté ensemble lors de la 1ere réunion puis préciser avec Christelle Hennequet-Antier, après analyse de ces délivrables, j'ai pu avec Christelle Hennequet-Antier reformuler un dernier délivrable cohérent avec les données pour aller plus loin dans l'analyse" "réunions constructives, informatives, toujours dans la bonne humeur, taches bien réparties (bioinfo vs biostat)" "Le projet a été enrichi par trois réunions organisées sur le site d'INRAE Nouzilly, qui ont abordé la sélection des outils bioinformatiques et biostatistiques appropriés. De plus, une réunion à distance a été tenue spécifiquement pour discuter de l'analyse fonctionnelle des gènes différentiellement exprimés en utilisant l'outil ViSEAGO" "Il serait judicieux de mettre en place des réunions régulières, par exemple mensuelles, afin de suivre de près l'avancement de la personne demandant le support dans sa démarche. Cela permettrait de résoudre les problèmes rencontrés, d'apporter des éclaircissements supplémentaires et de fournir un accompagnement adéquat. Une communication ouverte et fréquente favoriserait également une meilleure compréhension mutuelle des objectifs et des attentes, renforçant ainsi la qualité du support fourni"
Commonly used tools
FastQC [1], MultiQC [2], FROGS [3], dada2 [4], phyloseq [5], DESeq2 [6], Kraken [7], Kaiju [8], sortmerna [9], khmer [10], fastp [11], fastp [11], bwa [12], bowtie2 [13], megahit [14], MetaSpades [15], fraggenescan [16], Unicycler [17], minimap2 [18]
Publications
Collaborations have led to numerous publications, including the following list:
[1] M. Halgrain, N. Bernardet, C. Hennequet-Antier, et al. “RNA-seq analysis of the active chick embryo chorioallantoic membrane reveals genes that encode proteins assigned to ion transport and innate immunity”. In: Genomics 115.2 (2023), p. 110564. ISSN: 0888-7543. DOI: https://doi.org/10.1016/j.ygeno.2023.110564. URL: https://www.sciencedirect.com/science/article/pii/S0888754323000083.
[2] M. Mariadassou, L. X. Nouvel, F. Constant, et al. “Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd”. In: Animal Microbiome 5.1 (2023), pp. 1–17. DOI: 10.1186/s42523-023-00252-w.
[3] E. Michel, E. Masson, S. Bubbendorf, et al. “Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs”. In: Peer Community Journal 3 (2023). DOI: 10.24072/pcjournal.237. URL: https://peercommunityjournal.org/articles/10.24072/pcjournal.237/.
[4] O. Rué, M. Coton, E. Dugat-Bony, et al. “Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods”. In: bioRxiv (2023). DOI: 10.1101/2023.01.13.523754. eprint: https://www.biorxiv.org/content/early/2023/01/13/2023.01.13.523754.full.pdf. URL: https://www.biorxiv.org/content/early/2023/01/13/2023.01.13.523754.
[1] S. Auger, V. Mournetas, H. Chiapello, et al. “Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny”. In: Plos one 17.11 (2022), p. e0271847. DOI: 10.1371/journal.pone.0271847.
[2] M. Frétin, A. Gérard, A. Ferlay, et al. “Integration of Multiomic Data to Characterize the Influence of Milk Fat Composition on Cantal-Type Cheese Microbiota”. In: Microorganisms 10.2 (2022). ISSN: 2076-2607. DOI: 10.3390/microorganisms10020334. URL: https://www.mdpi.com/2076-2607/10/2/334.
[3] L. von Gastrow, E. Michel, J. Legrand, et al. “Microbial community dispersal from wheat grains to sourdoughs : a contribution of participatory research”. In: Molecular Ecology n/a.n/a (2022). DOI: https://doi.org/10.1111/mec.16630. eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16630. URL: https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16630.
[4] V. Guéneau, J. Piard, B. Frayssinet, et al. “Genome Sequence of Bacillus velezensis P1, a Strain Isolated from a Biofilm Captured on a Pig Farm Building”. In: Microbiology Resource Announcements 11.2 (2022), pp. e01219-21. DOI: 10.1128/MRA.01219-21. eprint: https://journals.asm.org/doi/pdf/10.1128/MRA.01219-21. URL: https://journals.asm.org/doi/abs/10.1128/MRA.01219-21.
[5] P. Ledormand, N. Desmasures, B. Bernay, et al. “Molecular approaches to uncover phage-lactic acid bacteria interactions in a model community simulating fermented beverages”. In: Food Microbiology 107 (2022), p. 104069. ISSN: 0740-0020. DOI: https://doi.org/10.1016/j.fm.2022.104069. URL: https://www.sciencedirect.com/science/article/pii/S0740002022000934.
[6] P. Ledormand, N. Desmasures, C. Midoux, et al. “Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage”. In: Microorganisms 10.6 (2022). ISSN: 2076-2607. DOI: 10.3390/microorganisms10061203. URL: https://www.mdpi.com/2076-2607/10/6/1203.
[7] L. P. Leonel, A. Bize, M. Mariadassou, et al. “Impacts of disinfected wastewater irrigation on soil characteristics, microbial community composition, and crop yield”. In: Blue-Green Systems (déc.. 2022). bgs2022126. ISSN: 2617-4782. DOI: 10.2166/bgs.2022.126. eprint: https://iwaponline.com/bgs/article-pdf/doi/10.2166/bgs.2022.126/1147726/bgs2022126.pdf. URL: https://doi.org/10.2166/bgs.2022.126.
[8] N. Mach, C. Midoux, S. Leclercq, et al. “Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes”. In: Communications biology 5.1 (2022), pp. 1–15. DOI: 10.1038/s42003-022-03977-7. URL: https://doi.org/10.1038/s42003-022-03977-7.
[9] V. Q. H. Ngo, F. Enault, C. Midoux, et al. “Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics”. In: Environmental Microbiology 24.10 (2022), pp. 4853–4868. DOI: 10.1111/1462-2920.16120. URL: https://doi.org/10.1111/1462-2920.16120.
[10] M. Olaisen, M. L. Richard, V. Beisvåg, et al. “The ileal fungal microbiota is altered in Crohn’s disease and is associated with the disease course”. In: Frontiers in Medicine 9 (2022). ISSN: 2296-858X. DOI: 10.3389/fmed.2022.868812. URL: https://www.frontiersin.org/articles/10.3389/fmed.2022.868812.
[11] T. Paillet, J. Lossouarn, C. Figueroa, et al. “Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory”. In: Viruses 14.8 (2022). ISSN: 1999-4915. DOI: 10.3390/v14081620. URL: https://www.mdpi.com/1999-4915/14/8/1620.
[12] F. Puig-Castellví, C. Midoux, A. Guenne, et al. “Metataxonomics, metagenomics and metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters”. In: Bioresource Technology 346 (2022), p. 126612. ISSN: 0960-8524. DOI: https://doi.org/10.1016/j.biortech.2021.126612. URL: https://www.sciencedirect.com/science/article/pii/S0960852421019544.
[13] H. Rakotoarivonina, V. Loux, C. Doliwa, et al. “Draft Genome Sequence of the Lignocellulolytic and Thermophilic Bacterium Thermobacillus xylanilyticus XE”. In: Microbiology Resource Announcements 11.4 (2022), pp. e00934-21. DOI: 10.1128/mra.00934-21. eprint: https://journals.asm.org/doi/pdf/10.1128/mra.00934-21. URL: https://journals.asm.org/doi/abs/10.1128/mra.00934-21.
[1] M. Aydin, C. Weisser, O. Rué, et al. “The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network”. In: Frontiers in Allergy 2 (2021), p. 11. ISSN: 2673-6101. DOI: 10.3389/falgy.2021.667562. URL: https://www.frontiersin.org/article/10.3389/falgy.2021.667562.
[2] M. Bernard, O. Rué, M. Mariadassou, et al. “FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers”. In: Briefings in Bioinformatics (août. 2021). bbab318. ISSN: 1477-4054. DOI: 10.1093/bib/bbab318. eprint: https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbab318/39805849/bbab318.pdf. URL: https://doi.org/10.1093/bib/bbab318.
[3] F. Combes, V. Loux, and Y. Vandenbrouck. “GO Enrichment Analysis for Differential Proteomics Using ProteoRE”. In: Proteomics Data Analysis. Ed. by D. Cecconi. New York, NY: Springer US, 2021, pp. 179–196. ISBN: 978-1-0716-1641-3. DOI: 10.1007/978-1-0716-1641-3_11. URL: https://doi.org/10.1007/978-1-0716-1641-3_11.
[4] M. Jollet, K. Nay, A. Chopard, et al. “Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model”. In: Nutrients 13.11 (2021). ISSN: 2072-6643. DOI: 10.3390/nu13113865. URL: https://www.mdpi.com/2072-6643/13/11/3865.
[5] M. Larroude, D. Onésime, O. Rué, et al. “A Yarrowia lipolytica Strain Engineered for Pyomelanin Production”. In: Microorganisms 9.4 (2021). ISSN: 2076-2607. DOI: 10.3390/microorganisms9040838. URL: https://www.mdpi.com/2076-2607/9/4/838.
[6] M. Leclerc, C. Bedu-Ferrari, L. Etienne-Mesmin, et al. “Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities”. In: mSystems 0.0 (2021), pp. e00558-21. DOI: 10.1128/mSystems.00558-21. eprint: https://journals.asm.org/doi/pdf/10.1128/mSystems.00558-21. URL: https://journals.asm.org/doi/abs/10.1128/mSystems.00558-21.
[7] E. Lejal, J. Chiquet, J. Aubert, et al. “Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions”. In: Microbiome 9.1 (2021), pp. 1–20. DOI: https://doi.org/10.1186/s40168-021-01051-8.
[8] B. Misery, P. Legendre, O. Rué, et al. “Diversity and dynamics of bacterial and fungal communities in cider for distillation”. In: International Journal of Food Microbiology 339 (2021), p. 108987. ISSN: 0168-1605. DOI: https://doi.org/10.1016/j.ijfoodmicro.2020.108987.
[9] N. Pascault, O. Rué, V. Loux, et al. “Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions?” In: Environmental Microbiology Reports 13.3 (2021), pp. 364-374. DOI: https://doi.org/10.1111/1758-2229.12944. eprint: https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1758-2229.12944. URL: https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1758-2229.12944.
[10] S. Zouiouich, M. Mariadassou, O. Rué, et al. “Comparison of fecal sample collection methods for microbial analysis embedded within colorectal cancer screening programs”. In: Cancer Epidemiology and Prevention Biomarkers (2021). ISSN: 1055-9965. DOI: 10.1158/1055-9965.EPI-21-0188. eprint: https://cebp.aacrjournals.org/content/early/2021/11/15/1055-9965.EPI-21-0188.full.pdf. URL: https://cebp.aacrjournals.org/content/early/2021/11/15/1055-9965.EPI-21-0188.
[1] V. Daugé, C. Philippe, M. Mariadassou, et al. “A probiotic mixture induces anxiolytic-and antidepressive-like effects in Fischer and maternally deprived Long Evans rats”. In: Frontiers in Behavioral Neuroscience 14 (2020). DOI:
[2] E. Lejal, A. Estrada-Pe~na, M. Marsot, et al. “Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiota analysis”. In: Frontiers in microbiology 11 (2020), p. 1093. DOI: https://doi.org/10.3389/fmicb.2020.01093.
[3] A. D. de Lira, C. I. Kothe, O. Rué, et al. “Assessing the quality of fresh Whitemouth croaker (Micropogonias furnieri) meat based on micro-organism and histamine analysis using NGS, qPCR and HPLC-DAD”. In: Journal of applied microbiology 128.5 (2020), pp. 1448–1459. DOI: https://doi.org/10.1111/jam.14566.
[4] L. Naudon, A. François, M. Mariadassou, et al. “First step of odorant detection in the olfactory epithelium and olfactory preferences differ according to the microbiota profile in mice”. In: Behavioural brain research 384 (2020), p. 112549. DOI: https://dx.doi.org/10.1016/j.bbr.2020.112549.
[5] S. Poirier, N. M. Luong, V. Anthoine, et al. “Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere”. In: Data in brief 30 (2020), p. 105453. DOI: https://doi.org/10.1016/j.dib.2020.105453.
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