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Article ; Online: MICRA

Ségolène Caboche / Gaël Even / Alexandre Loywick / Christophe Audebert / David Hot

Genome Biology, Vol 18, Iss 1, Pp 1-

an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data

2017 Volume 14

Abstract: Abstract The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for ... ...

Abstract	Abstract The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data.
Keywords	Bioinformatics pipeline ; Comparative genomics ; Microbial genome characterization ; High-throughput sequencing ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
Language	English
Publishing date	2017-12-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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 ... ...

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: High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases

Ségolène Caboche / Christophe Audebert / David Hot

Pathogens, Vol 3, Iss 2, Pp 258-

Applications to Clinical Bacteriology

2014 Volume 279

Abstract: The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing ... ...

Abstract	The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose.
Keywords	high-throughput sequencing ; whole genome sequencing ; pathogenomics ; bioinformatics ; analysis pipeline ; P4-medicine ; genome-based diagnosis ; Medicine ; R
Subject code	004
Language	English
Publishing date	2014-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics.

Léa Siegwald / Hélène Touzet / Yves Lemoine / David Hot / Christophe Audebert / Ségolène Caboche

PLoS ONE, Vol 12, Iss 1, p e

2017 Volume 0169563

Abstract: Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing ...

Abstract	Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. No standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses. This article proposes an evaluation protocol containing real and simulated targeted metagenomics datasets, and adequate metrics allowing us to study the impact of different variables on the biological interpretation of results. This protocol was used to compare six different bioinformatics pipelines in the basic user context: Three common ones (mothur, QIIME and BMP) based on a clustering-first approach and three emerging ones (Kraken, CLARK and One Codex) using an assignment-first approach. This study surprisingly reveals that the effect of sequencing errors has a bigger impact on the results that choosing different amplified regions. Moreover, increasing sequencing throughput increases richness overestimation, even more so for microbiota of high complexity. Finally, the choice of the reference database has a bigger impact on richness estimation for clustering-first pipelines, and on correct taxa identification for assignment-first pipelines. Using emerging assignment-first pipelines is a valid approach for targeted metagenomics analyses, with a quality of results comparable to popular clustering-first pipelines, even with an error-prone sequencing technology like Ion Torrent. However, those pipelines are highly sensitive to the quality of databases and their annotations, which makes clustering-first pipelines still the only reliable approach for studying microbiomes that are not well described.
Keywords	Medicine ; R ; Science ; Q
Subject code	004
Language	English
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics.

Léa Siegwald / Hélène Touzet / Yves Lemoine / David Hot / Christophe Audebert / Ségolène Caboche

PLoS ONE, Vol 12, Iss 1, p e

2017 Volume 0169563

Abstract	Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. No standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses. This article proposes an evaluation protocol containing real and simulated targeted metagenomics datasets, and adequate metrics allowing us to study the impact of different variables on the biological interpretation of results. This protocol was used to compare six different bioinformatics pipelines in the basic user context: Three common ones (mothur, QIIME and BMP) based on a clustering-first approach and three emerging ones (Kraken, CLARK and One Codex) using an assignment-first approach. This study surprisingly reveals that the effect of sequencing errors has a bigger impact on the results that choosing different amplified regions. Moreover, increasing sequencing throughput increases richness overestimation, even more so for microbiota of high complexity. Finally, the choice of the reference database has a bigger impact on richness estimation for clustering-first pipelines, and on correct taxa identification for assignment-first pipelines. Using emerging assignment-first pipelines is a valid approach for targeted metagenomics analyses, with a quality of results comparable to popular clustering-first pipelines, even with an error-prone sequencing technology like Ion Torrent. However, those pipelines are highly sensitive to the quality of databases and their annotations, which makes clustering-first pipelines still the only reliable approach for studying microbiomes that are not well described.
Keywords	Medicine ; R ; Science ; Q
Subject code	004
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Let-7f

Rafaelle Spear / Ludovic Boytard / Renaud Blervaque / Maggy Chwastyniak / David Hot / Jonathan Vanhoutte / Nicolas Lamblin / Philippe Amouyel / Florence Pinet

International Journal of Molecular Sciences, Vol 20, Iss 21, p

A New Potential Circulating Biomarker Identified by miRNA Profiling of Cells Isolated from Human Abdominal Aortic Aneurysm

2019 Volume 5499

Abstract: Abdominal aortic aneurysm (AAA) is a progressive vascular disease responsible for 1−4% of the deaths in elderly men. This study aimed to characterize specific microRNA (miRNA) expression in aneurysmal smooth muscle cells (SMCs) and macrophages in order ... ...

Abstract	Abdominal aortic aneurysm (AAA) is a progressive vascular disease responsible for 1−4% of the deaths in elderly men. This study aimed to characterize specific microRNA (miRNA) expression in aneurysmal smooth muscle cells (SMCs) and macrophages in order to identify circulating miRNAs associated with AAA. We screened 850 miRNAs in aneurysmal SMCs, M1 and M2 macrophages, and in control SMCs isolated by micro-dissection from aortic biopsies using microarray analysis. In all, 92 miRNAs were detected and 10 miRNAs were selected for validation by qRT-PCR in isolated cells ( n = 5), whole control and aneurysmal aorta biopsies ( n = 13), and plasma from patients ( n = 24) undergoing AAA (over 50 mm) repair matched to patients ( n = 18) with peripheral arterial disease (PAD) with atherosclerosis but not AAA. Seven miRNAs were modulated similarly in all aneurysmal cells. The Let-7f was downregulated in aneurysmal cells compared to control SMCs with a significant lower expression in M1 compared to M2 macrophages (0.1 fold, p = 0.03), correlated with a significant downregulation in whole aneurysmal aorta compared to control aorta (0.2 fold, p = 0.03). Significant levels of circulating let-7f ( p = 0.048) were found in AAA patients compared to PAD patients with no significant correlation with aortic diameter ( R 2 = 0.03). Our study underlines the utility of profiling isolated aneurysmal cells to identify other miRNAs for which the modulation of expression might be masked when the whole aorta is used. The results highlight let-7f as a new potential biomarker for AAA.
Keywords	abdominal aortic aneurysm ; microrna ; macrophages ; smooth muscle cells ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	610
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Streamlined copper defenses make Bordetella pertussis reliant on custom-made operon

Alex Rivera-Millot / Stéphanie Slupek / Jonathan Chatagnon / Gauthier Roy / Jean-Michel Saliou / Gabriel Billon / Véronique Alaimo / David Hot / Sophie Salomé-Desnoulez / Camille Locht / Rudy Antoine / Françoise Jacob-Dubuisson

Communications Biology, Vol 4, Iss 1, Pp 1-

2021 Volume 12

Abstract: Alex Rivera-Millot et al. investigate copper homeostasis in the whooping cough agent Bordetella pertussis, which has a single copper defense mechanism via a metallochaperone diverted for copper passivation and two peroxide detoxification enzymes. This ... ...

Abstract	Alex Rivera-Millot et al. investigate copper homeostasis in the whooping cough agent Bordetella pertussis, which has a single copper defense mechanism via a metallochaperone diverted for copper passivation and two peroxide detoxification enzymes. This study demonstrates that copper up-regulates the copZ-prxgrx-gorB operon in macrophages, and this system appears to contribute to persistent infection in the nasal cavity of B. pertussis-infected mice. This study brings insight into strategies aimed to optimize survival of a host-restricted pathogen.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Distinct virulence ranges for infection of mice by Bordetella pertussis revealed by engineering of the sensor-kinase BvgS.

Elodie Lesne / Loic Coutte / Luis Solans / Stephanie Slupek / Anne-Sophie Debrie / Véronique Dhennin / Philippe Froguel / David Hot / Camille Locht / Rudy Antoine / Françoise Jacob-Dubuisson

PLoS ONE, Vol 13, Iss 10, p e

2018 Volume 0204861

Abstract: The whooping cough agent Bordetella pertussis coordinately regulates the expression of its virulence factors with the two-component system BvgAS. In laboratory conditions, specific chemical modulators are used to trigger phenotypic modulation of B. ... ...

Abstract	The whooping cough agent Bordetella pertussis coordinately regulates the expression of its virulence factors with the two-component system BvgAS. In laboratory conditions, specific chemical modulators are used to trigger phenotypic modulation of B. pertussis from its default virulent Bvg+ phase to avirulent Bvg- or intermediate Bvgi phases, in which no virulence factors or only a subset of them are produced, respectively. Whether phenotypic modulation occurs in the host remains unknown. In this work, recombinant B. pertussis strains harboring BvgS variants were tested in a mouse model of infection and analyzed using transcriptomic approaches. Recombinant BP-BvgΔ65, which is in the Bvgi phase by default and can be up-modulated to the Bvg+ phase in vitro, could colonize the mouse nose but was rapidly cleared from the lungs, while Bvg+-phase strains colonized both organs for up to four weeks. These results indicated that phenotypic modulation, which might have restored the full virulence capability of BP-BvgΔ65, does not occur in mice or is temporally or spatially restricted and has no effect in those conditions. Transcriptomic analyses of this and other recombinant Bvgi and Bvg+-phase strains revealed that two distinct ranges of virulence gene expression allow colonization of the mouse nose and lungs, respectively. We also showed that a recombinant strain expressing moderately lower levels of the virulence genes than its wild type parent was as efficient at colonizing both organs. Altogether, genetic modifications of BvgS generate a range of phenotypic phases, which are useful tools to decipher host-pathogen interactions.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Toxoplasma gondii chromodomain protein 1 binds to heterochromatin and colocalises with centromeres and telomeres at the nuclear periphery.

Mathieu Gissot / Robert Walker / Stephane Delhaye / Ludovic Huot / David Hot / Stanislas Tomavo

PLoS ONE, Vol 7, Iss 3, p e

2012 Volume 32671

Abstract: BACKGROUND: Apicomplexan parasites are responsible for some of the most deadly parasitic diseases afflicting humans, including malaria and toxoplasmosis. These obligate intracellular parasites exhibit a complex life cycle and a coordinated cell cycle- ... ...

Abstract	BACKGROUND: Apicomplexan parasites are responsible for some of the most deadly parasitic diseases afflicting humans, including malaria and toxoplasmosis. These obligate intracellular parasites exhibit a complex life cycle and a coordinated cell cycle-dependant expression program. Their cell division is a coordinated multistep process. How this complex mechanism is organised remains poorly understood. METHODS AND FINDINGS: In this study, we provide evidence for a link between heterochromatin, cell division and the compartmentalisation of the nucleus in Toxoplasma gondii. We characterised a T. gondii chromodomain containing protein (named TgChromo1) that specifically binds to heterochromatin. Using ChIP-on-chip on a genome-wide scale, we report TgChromo1 enrichment at the peri-centromeric chromatin. In addition, we demonstrate that TgChromo1 is cell-cycle regulated and co-localised with markers of the centrocone. Through the loci-specific FISH technique for T. gondii, we confirmed that TgChromo1 occupies the same nuclear localisation as the peri-centromeric sequences. CONCLUSION: We propose that TgChromo1 may play a role in the sequestration of chromosomes at the nuclear periphery and in the process of T. gondii cell division.
Keywords	Medicine ; R ; Science ; Q
Subject code	571
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Influenza infection rewires energy metabolism and induces browning features in adipose cells and tissues

Asma Ayari / Manuel Rosa-Calatrava / Steve Lancel / Johanna Barthelemy / Andrés Pizzorno / Alicia Mayeuf-Louchart / Morgane Baron / David Hot / Lucie Deruyter / Daphnée Soulard / Thomas Julien / Christelle Faveeuw / Olivier Molendi-Coste / David Dombrowicz / Laura Sedano / Valentin Sencio / Ronan Le Goffic / François Trottein / Isabelle Wolowczuk

Communications Biology, Vol 3, Iss 1, Pp 1-

2020 Volume 15

Abstract: Asma Ayari et al. report that mice infected with influenza A virus show persistent altered glucose metabolism. They find that infection is associated with the browning of the subcutaneous white adipose tissue (WAT), and this change is linked to viral ... ...

Abstract	Asma Ayari et al. report that mice infected with influenza A virus show persistent altered glucose metabolism. They find that infection is associated with the browning of the subcutaneous white adipose tissue (WAT), and this change is linked to viral infection in the fat tissues.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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