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Article ; Online: CuReSim-LoRM: A Tool to Simulate Metabarcoding Long Reads.

Mesloub, Yasmina / Beury, Delphine / Vandermeeren, Félix / Caboche, Ségolène

International journal of molecular sciences

2023 Volume 24, Issue 18

Abstract: Metabarcoding DNA sequencing has revolutionized the study of microbial communities. Third-generation sequencing producing long reads had opened up new perspectives. Obtaining the full-length ribosomal RNA gene would permit one to reach a better taxonomic ...

Abstract	Metabarcoding DNA sequencing has revolutionized the study of microbial communities. Third-generation sequencing producing long reads had opened up new perspectives. Obtaining the full-length ribosomal RNA gene would permit one to reach a better taxonomic resolution at the species or the strain level. However, Oxford Nanopore Technologies (ONT) sequencing produces reads with high error rates, which introduces biases in analysis. Understanding the biases introduced during the analysis allows one to better interpret the biological results and take care of conclusions drawn from metabarcoding experiments. To benchmark an analysis process, the ground truth, i.e., the real composition of the microbial community, has to be known. In addition to artificial mock communities, simulated data are often used to evaluate the biases and performances of the bioinformatics analysis step. Currently, no specific tool has been developed to simulate metabarcoding long reads, mimic the error rate and the length distribution, and allow one to benchmark the analysis process. Here, we introduce CuReSim-LoRM, for the customized read simulator to generate long reads for metabarcoding. We showed that CuReSim-LoRM is able to produce reads with varying error rates and length distributions by mimicking the real data very well.
MeSH term(s)	Benchmarking ; Computational Biology ; Microbiota ; Nanopores ; Sequence Analysis, DNA
Language	English
Publishing date	2023-09-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241814005
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Article ; Online: Amoxicillin treatment of pneumococcal pneumonia impacts bone marrow neutrophil maturation and function.

Mondemé, Mélanie / Zeroual, Yasmine / Soulard, Daphnée / Hennart, Benjamin / Beury, Delphine / Saliou, Jean-Michel / Carnoy, Christophe / Sirard, Jean-Claude / Faveeuw, Christelle

Journal of leukocyte biology

2023 Volume 115, Issue 3, Page(s) 463–475

Abstract: Pneumonia caused by Streptococcus pneumoniae is a leading cause of death worldwide. A growing body of evidence indicates that the successful treatment of bacterial infections results from synergy between antibiotic-mediated direct antibacterial activity ... ...

Abstract	Pneumonia caused by Streptococcus pneumoniae is a leading cause of death worldwide. A growing body of evidence indicates that the successful treatment of bacterial infections results from synergy between antibiotic-mediated direct antibacterial activity and the host's immune defenses. However, the mechanisms underlying the protective immune responses induced by amoxicillin, a β-lactam antibiotic used as the first-line treatment of S. pneumoniae infections, have not been characterized. A better understanding of amoxicillin's effects on host-pathogen interactions might facilitate the development of other treatment options. Given the crucial role of neutrophils in the control of S. pneumoniae infections, we decided to investigate amoxicillin's impact on neutrophil development in a mouse model of pneumococcal superinfection. A single therapeutic dose of amoxicillin almost completely eradicated the bacteria and prevented local and systemic inflammatory responses. Interestingly, in this context, amoxicillin treatment did not impair the emergency granulopoiesis triggered in the bone marrow by S. pneumoniae. Importantly, treatment of pneumonia with amoxicillin was associated with a greater mature neutrophil count in the bone marrow; these neutrophils had specific transcriptomic and proteomic profiles. Furthermore, amoxicillin-conditioned, mature neutrophils in the bone marrow had a less activated phenotype and might be rapidly mobilized in peripheral tissues in response to systemic inflammation. Thus, by revealing a novel effect of amoxicillin on the development and functions of bone marrow neutrophils during S. pneumoniae pneumonia, our findings provide new insights into the impact of amoxicillin treatment on host immune responses.
MeSH term(s)	Mice ; Animals ; Pneumonia, Pneumococcal/drug therapy ; Neutrophils ; Amoxicillin/pharmacology ; Amoxicillin/therapeutic use ; Bone Marrow ; Lung ; Proteomics ; Streptococcus pneumoniae ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Pneumococcal Infections/drug therapy ; Pneumococcal Infections/microbiology
Chemical Substances	Amoxicillin (804826J2HU) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-10-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605722-6
ISSN	1938-3673 ; 0741-5400
ISSN (online)	1938-3673
ISSN	0741-5400
DOI	10.1093/jleuko/qiad125
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Zs.A 603: Show issues

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Article: A Novel Natural Siderophore Antibiotic Conjugate Reveals a Chemical Approach to Macromolecule Coupling.

Caradec, Thibault / Anoz-Carbonell, Ernesto / Petrov, Ravil / Billamboz, Muriel / Antraygues, Kevin / Cantrelle, Francois-Xavier / Boll, Emmanuelle / Beury, Delphine / Hot, David / Drobecq, Herve / Trivelli, Xavier / Hartkoorn, Ruben C

ACS central science

2023 Volume 9, Issue 11, Page(s) 2138–2149

Abstract: Inspired by natural sideromycins, the conjugation of antibiotics to siderophores is an attractive strategy to facilitate "Trojan horse" delivery of antibiotics into bacteria. Genome analysis of a soil bacterium, ...

Abstract	Inspired by natural sideromycins, the conjugation of antibiotics to siderophores is an attractive strategy to facilitate "Trojan horse" delivery of antibiotics into bacteria. Genome analysis of a soil bacterium,
Language	English
Publishing date	2023-11-10
Publishing country	United States
Document type	Journal Article
ISSN	2374-7943
ISSN	2374-7943
DOI	10.1021/acscentsci.3c00965
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Article ; Online: Low dose dietary contamination with deoxynivalenol mycotoxin exacerbates enteritis and colorectal cancer in mice.

Djouina, Madjid / Waxin, Christophe / Caboche, Ségolène / Lecointe, Karine / Steimle, Alexander / Beury, Delphine / Desai, Mahesh S / Hot, David / Dubuquoy, Laurent / Launay, David / Vignal, Cécile / Body-Malapel, Mathilde

The Science of the total environment

2023 Volume 900, Page(s) 165722

Abstract: Background: The mycotoxin deoxynivalenol (DON) is a frequent contaminant of grain and cereal products worldwide. Exposure to DON can cause gastrointestinal inflammation, disturb gut barrier function, and induce gut dysbiosis in vivo under basal ... ...

Abstract	Background: The mycotoxin deoxynivalenol (DON) is a frequent contaminant of grain and cereal products worldwide. Exposure to DON can cause gastrointestinal inflammation, disturb gut barrier function, and induce gut dysbiosis in vivo under basal conditions, but little is known about the effects of DON ingestion in individuals with pre-existing gastrointestinal disease. Objectives: Mice were orally exposed to 10 and 100 μg/kg bw/day of DON, corresponding to 10 to 100-fold human tolerable daily intake concentrations, and to the translation in mice of current human daily intake. The effects of DON exposure were explored under steady-state conditions, and in murine models of enteritis and colorectal cancer (CRC). Results: After 8 days of DON exposure, an increase of histomorphological and molecular parameters of epithelial proliferation were observed in normal mice, from the duodenum to the colon. The same exposure in a murine model of indomethacin-induced enteritis led to exacerbation of lesion development and induction of ileal cytokines. DON exposure also worsened the development of colitis-associated CRC in mice as shown by increases in endoscopic and histological colitis scores, tumor grades, and histological hyperplasia. In colon of DON-exposed mice, upstream and downstream ERK signaling genes were upregulated including Mapk1, Mapk3, Map 2k1, Map2k2 core ERK pathway effectors, and Bcl2 and Bcl2l1 antiapoptotic genes. The effects observed in the CRC model were associated with alterations in cecal microbiota taxonomic composition and metabolism of bacterial fucose and rhamnose. Strong Spearman's correlations were revealed between the relative abundance of the changed bacterial genera and CRC-related variables. Discussion: Ingestion of DON mycotoxin at concentrations representative of human real-world exposure worsened the development of indomethacin-induced enteritis and colitis-associated CRC in mice. Our results suggest that even at low doses, which are currently tolerated in the human diet, DON could promote the development of intestinal inflammatory diseases and CRC.
MeSH term(s)	Mice ; Humans ; Animals ; Mycotoxins ; Enteritis/chemically induced ; Enteritis/pathology ; Diet ; Colitis ; Indomethacin/toxicity ; Colorectal Neoplasms/chemically induced
Chemical Substances	Mycotoxins ; deoxynivalenol (JT37HYP23V) ; Indomethacin (XXE1CET956)
Language	English
Publishing date	2023-07-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.165722
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Zs.A 949: Show issues

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Article ; Online: Exposure to atmospheric Ag, TiO

Guilloteau, Eva / Djouina, Madjid / Caboche, Ségolène / Waxin, Christophe / Deboudt, Karine / Beury, Delphine / Hot, David / Pichavant, Muriel / Dubuquoy, Laurent / Launay, David / Vignal, Cécile / Choël, Marie / Body-Malapel, Mathilde

Ecotoxicology and environmental safety

2022 Volume 236, Page(s) 113442

Abstract: The development of nanotechnologies is leading to greater abundance of engineered nanoparticles (EN) in the environment, including in the atmospheric air. To date, it has been shown that the most prevalent EN found in the air are silver (Ag), titanium ... ...

Abstract	The development of nanotechnologies is leading to greater abundance of engineered nanoparticles (EN) in the environment, including in the atmospheric air. To date, it has been shown that the most prevalent EN found in the air are silver (Ag), titanium dioxide (TiO
MeSH term(s)	Animals ; Cytokines/genetics ; Female ; Gastrointestinal Microbiome ; Male ; Mice ; Microbiota ; Nanoparticles/metabolism ; Nanoparticles/toxicity ; Silicon Dioxide/toxicity ; Titanium/toxicity
Chemical Substances	Cytokines ; titanium dioxide (15FIX9V2JP) ; Silicon Dioxide (7631-86-9) ; Titanium (D1JT611TNE)
Language	English
Publishing date	2022-03-31
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	436536-7
ISSN	1090-2414 ; 0147-6513
ISSN (online)	1090-2414
ISSN	0147-6513
DOI	10.1016/j.ecoenv.2022.113442
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Article ; Online: Erratum: Rémy et al. Modelling the Impact of Chronic Cigarette Smoke Exposure in Obese Mice: Metabolic, Pulmonary, Intestinal, and Cardiac Issues.

Rémy, Gaëlle / Dubois-Deruy, Emilie / Alard, Jeanne / Kervoaze, Gwenola / Chwastyniak, Maggy / Baron, Morgane / Beury, Delphine / Siegwald, Léa / Caboche, Ségolène / Hot, David / Gosset, Philippe / Grangette, Corinne / Pinet, Florence / Wolowczuk, Isabelle / Pichavant, Muriel

Nutrients

2021 Volume 13, Issue 9

Abstract: The authors have requested that the following changes be made to their paper [ ... ]. ...

Abstract	The authors have requested that the following changes be made to their paper [...].
Language	English
Publishing date	2021-09-02
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2518386-2
ISSN	2072-6643 ; 2072-6643
ISSN (online)	2072-6643
ISSN	2072-6643
DOI	10.3390/nu13093084
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Article ; Online: Oral exposure to polyethylene microplastics alters gut morphology, immune response, and microbiota composition in mice.

Djouina, Madjid / Vignal, Cécile / Dehaut, Alexandre / Caboche, Ségolène / Hirt, Nell / Waxin, Christophe / Himber, Charlotte / Beury, Delphine / Hot, David / Dubuquoy, Laurent / Launay, David / Duflos, Guillaume / Body-Malapel, Mathilde

Environmental research

2022 Volume 212, Issue Pt B, Page(s) 113230

Abstract: The ubiquitous and growing presence of microplastics (MPs) in all compartments of the environment raises concerns about their possible harmful effects on human health. Human exposure to MPs occurs largely through ingestion. Polyethylene (PE) is widely ... ...

Abstract	The ubiquitous and growing presence of microplastics (MPs) in all compartments of the environment raises concerns about their possible harmful effects on human health. Human exposure to MPs occurs largely through ingestion. Polyethylene (PE) is widely employed for reusable bags and food packaging and found to be present in drinking water and food. It is also one of the major polymers detected in human stool. The aim of this study was to characterize the effects of intestinal exposure to PE MPs on gut homeostasis. Mice were orally exposed for 6 weeks to PE microbeads of 2 different sizes, 36 and 116 μm, that correspond to those found in human stool. They were administrated either individually or as a mixture at a dose of 100 μg/g of food. Both PE microbead sizes were detected in mouse stool. Different parameters related to major intestinal functions were compared between control mice, mice exposed to each type of microbead, or co-exposed to the 2 types of microbeads. Intestinal disturbances were observed after individual exposure to each size of PE microbead, and the most marked deleterious effects were found in co-exposed mice. At the histomorphological level, crypt depth was increased throughout the intestinal tissues. Significant variations of gene expression related to epithelial, permeability, and inflammatory biomarkers were quantified. Defective recruitment of some intestinal immune cells was observed from the proximal portion of the small intestine to the colon. Several bacterial taxa at the order level were found to be affected by exposure to the MPs by metagenomic analysis of cecal microbiota. These results show that ingestion of PE microbeads induces significant alterations of crucial intestinal markers in mice and underscores the need to further study the health impact of MP exposure in humans.
MeSH term(s)	Animals ; Biomarkers ; Immunity ; Mice ; Microbiota ; Microplastics/toxicity ; Plastics ; Polyethylene/toxicity ; Water Pollutants, Chemical/analysis
Chemical Substances	Biomarkers ; Microplastics ; Plastics ; Water Pollutants, Chemical ; Polyethylene (9002-88-4)
Language	English
Publishing date	2022-04-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205699-9
ISSN	1096-0953 ; 0013-9351
ISSN (online)	1096-0953
ISSN	0013-9351
DOI	10.1016/j.envres.2022.113230
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Zs.A 726: Show issues

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Article ; Online: Exposure to atmospheric Ag, TiO2, Ti and SiO2 engineered nanoparticles modulates gut inflammatory response and microbiota in mice

Eva Guilloteau / Madjid Djouina / Ségolène Caboche / Christophe Waxin / Karine Deboudt / Delphine Beury / David Hot / Muriel Pichavant / Laurent Dubuquoy / David Launay / Cécile Vignal / Marie Choël / Mathilde Body-Malapel

Ecotoxicology and Environmental Safety, Vol 236, Iss , Pp 113442- (2022)

2022

Abstract	The development of nanotechnologies is leading to greater abundance of engineered nanoparticles (EN) in the environment, including in the atmospheric air. To date, it has been shown that the most prevalent EN found in the air are silver (Ag), titanium dioxide (TiO2), titanium (Ti), and silicon dioxide (SiO2). As the intestinal tract is increasingly recognized as a target for adverse effects induced by inhalation of air particles, the aim of this study was to assess the impact of these 4 atmospheric EN on intestinal inflammation and microbiota. We assessed the combined toxicity effects of Ag, Ti, TiO2, and SiO2 following a 28-day inhalation protocol in male and female mice. In distal and proximal colon, and in jejunum, EN mixture inhalation did not induce overt histological damage, but led to a significant modulation of inflammatory cytokine transcript abundance, including downregulation of Tnfα, Ifnγ, Il1β, Il17a, Il22, IL10, and Cxcl1 mRNA levels in male jejunum. A dysbiosis was observed in cecal microbiota of male and female mice exposed to the EN mixture, characterized by sex-dependent modulations of specific bacterial taxa, as well as sex-independent decreased abundance of the Eggerthellaceae family. Under dextran sodium sulfate-induced inflammatory conditions, exposure to the EN mixture increased the development of colitis in both male and female mice. Moreover, the direct dose-response effects of individual and mixed EN on gut organoids was studied and Ag, TiO2, Ti, SiO2, and EN mixture were found to generate specific inflammatory responses in the intestinal epithelium. These results indicate that the 4 most prevalent atmospheric EN could have the ability to disturb intestinal homeostasis through direct modulation of cytokine expression in gut epithelium, and by altering the inflammatory response and microbiota composition following inhalation.
Keywords	Engineered nanoparticles ; Inhalation ; Inflammation ; Colitis ; Organoid ; Mixture ; Environmental pollution ; TD172-193.5 ; Environmental sciences ; GE1-350
Subject code	590
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rubrolone production by Dactylosporangium vinaceum: biosynthesis, modulation and possible biological function.

Moureu, Sophie / Caradec, Thibault / Trivelli, Xavier / Drobecq, Hervé / Beury, Delphine / Bouquet, Peggy / Caboche, Segolene / Desmecht, Eva / Maurier, Florence / Muharram, Ghaffar / Villemagne, Baptiste / Herledan, Adrien / Hot, David / Willand, Nicolas / Hartkoorn, Ruben Christiaan

Applied microbiology and biotechnology

2021 Volume 105, Issue 13, Page(s) 5541–5551

Abstract: Rare actinomycetes are likely treasure troves for bioactive natural products, and it is therefore important that we enrich our understanding of biosynthetic potential of these relatively understudied bacteria. Dactylosporangium are a genus of such rare ... ...

Abstract	Rare actinomycetes are likely treasure troves for bioactive natural products, and it is therefore important that we enrich our understanding of biosynthetic potential of these relatively understudied bacteria. Dactylosporangium are a genus of such rare Actinobacteria that are known to produce a number of important antibacterial compounds, but for which there are still no fully assembled reference genomes, and where the extent of encoded biosynthetic capacity is not defined. Dactylosporangium vinaceum (NRRL B-16297) is known to readily produce a deep wine red-coloured diffusible pigment of unknown origin, and it was decided to define the chemical identity of this natural product pigment, and in parallel use whole genome sequencing and transcriptional analysis to lay a foundation for understanding the biosynthetic capacity of these bacteria. Results show that the produced pigment is made of various rubrolone conjugates, the spontaneous product of the reactive pre-rubrolone, produced by the bacterium. Genome and transcriptome analysis identified the highly expressed biosynthetic gene cluster (BGC) for pre-rubrolone. Further analysis of the fully assembled genome found it to carry 24 additional BGCs, of which the majority were poorly transcribed, confirming the encoded capacity of this bacterium to produce natural products but also illustrating the main bottleneck to exploiting this capacity. Finally, analysis of the potential environmental role of pre-rubrolone found it to react with a number of amine containing antibiotics, antimicrobial peptides and siderophores pointing to its potential role as a "minesweeper" of xenobiotic molecules in the bacterial environment. KEY POINTS: • D. vinaceum encodes many BGC, but the majority are transcriptionally silent. • Chemical screening identifies molecules that modulate rubrolone production. • Pre-rubrolone is efficient at binding and inactivating many natural antibiotics.
MeSH term(s)	Actinobacteria/genetics ; Biological Products ; Micromonosporaceae ; Multigene Family ; Pyridines
Chemical Substances	Biological Products ; Pyridines ; rubrolone (65445-21-8)
Language	English
Publishing date	2021-06-30
Publishing country	Germany
Document type	Journal Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-021-11404-w
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Zs.A 2229: Show issues

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Article ; Online: A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43.

Maurier, Florence / Beury, Delphine / Fléchon, Léa / Varré, Jean-Stéphane / Touzet, Hélène / Goffard, Anne / Hot, David / Caboche, Ségolène

Virology

2019 Volume 531, Page(s) 141–148

Abstract: Genome sequencing of virus has become a useful tool for better understanding of virus pathogenicity and epidemiological surveillance. Obtaining virus genome sequence directly from clinical samples is still a challenging task due to the low load of virus ... ...

Abstract	Genome sequencing of virus has become a useful tool for better understanding of virus pathogenicity and epidemiological surveillance. Obtaining virus genome sequence directly from clinical samples is still a challenging task due to the low load of virus genetic material compared to the host DNA, and to the difficulty to get an accurate genome assembly. Here we introduce a complete sequencing and analyzing protocol called V-ASAP for Virus Amplicon Sequencing Assembly Pipeline. Our protocol is able to generate the viral dominant genome sequence starting from clinical samples. It is based on a multiplex PCR amplicon sequencing coupled with a reference-free analytical pipeline. This protocol was applied to 11 clinical samples infected with coronavirus OC43 (HcoV-OC43), and led to seven complete and two nearly complete genome assemblies. The protocol introduced here is shown to be robust, to produce a reliable sequence, and could be applied to other virus.
MeSH term(s)	Coronavirus Infections/virology ; Coronavirus OC43, Human/classification ; Coronavirus OC43, Human/genetics ; Coronavirus OC43, Human/isolation & purification ; Genome, Viral ; Humans ; Multiplex Polymerase Chain Reaction ; Whole Genome Sequencing/methods
Keywords	covid19
Language	English
Publishing date	2019-03-09
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2019.03.006
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