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Dr. Amine Boukerb
LMSM lab; Rouen Normandie University

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0 PSEUDOMONAS AERUGINOSA
0 campylobacter
0 Genome evolution
0 Bacteria adaptation
0 NGS(next generation sequencing)

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Journal article
Published: 31 July 2021 in International Journal of Molecular Sciences
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Biofilms are complex structures formed by a community of microbes adhering to a surface and/or to each other through the secretion of an adhesive and protective matrix. The establishment of these structures requires a coordination of action between microorganisms through powerful communication systems such as quorum-sensing. Therefore, auxiliary bacteria capable of interfering with these means of communication could be used to prevent biofilm formation and development. The phytopathogen Rhizobium rhizogenes, which causes hairy root disease and forms large biofilms in hydroponic crops, and the biocontrol agent Rhodococcus erythropolis R138 were used for this study. Changes in biofilm biovolume and structure, as well as interactions between rhizobia and rhodococci, were monitored by confocal laser scanning microscopy with appropriate fluorescent biosensors. We obtained direct visual evidence of an exchange of signals between rhizobia and the jamming of this communication by Rhodococcus within the biofilm. Signaling molecules were characterized as long chain (C14) N-acyl-homoserine lactones. The role of the Qsd quorum-quenching pathway in biofilm alteration was confirmed with an R. erythropolis mutant unable to produce the QsdA lactonase, and by expression of the qsdA gene in a heterologous host, Escherichia coli. Finally, Rhizobium biofilm formation was similarly inhibited by a purified extract of QsdA enzyme.

ACS Style

Yvann Bourigault; Sophie Rodrigues; Alexandre Crépin; Andrea Chane; Laure Taupin; Mathilde Bouteiller; Charly Dupont; Annabelle Merieau; Yoan Konto-Ghiorghi; Amine Boukerb; Marie Turner; Céline Hamon; Alain Dufour; Corinne Barbey; Xavier Latour. Biocontrol of Biofilm Formation: Jamming of Sessile-Associated Rhizobial Communication by Rhodococcal Quorum-Quenching. International Journal of Molecular Sciences 2021, 22, 8241 .

AMA Style

Yvann Bourigault, Sophie Rodrigues, Alexandre Crépin, Andrea Chane, Laure Taupin, Mathilde Bouteiller, Charly Dupont, Annabelle Merieau, Yoan Konto-Ghiorghi, Amine Boukerb, Marie Turner, Céline Hamon, Alain Dufour, Corinne Barbey, Xavier Latour. Biocontrol of Biofilm Formation: Jamming of Sessile-Associated Rhizobial Communication by Rhodococcal Quorum-Quenching. International Journal of Molecular Sciences. 2021; 22 (15):8241.

Chicago/Turabian Style

Yvann Bourigault; Sophie Rodrigues; Alexandre Crépin; Andrea Chane; Laure Taupin; Mathilde Bouteiller; Charly Dupont; Annabelle Merieau; Yoan Konto-Ghiorghi; Amine Boukerb; Marie Turner; Céline Hamon; Alain Dufour; Corinne Barbey; Xavier Latour. 2021. "Biocontrol of Biofilm Formation: Jamming of Sessile-Associated Rhizobial Communication by Rhodococcal Quorum-Quenching." International Journal of Molecular Sciences 22, no. 15: 8241.

Original research article
Published: 14 July 2021 in Frontiers in Microbiology
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Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their comparison to other sources and develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers to detect such pollution. Thus, by using 16S rRNA amplicon high-throughput sequencing, the aims of this study were (i) to explore and compare fecal bacterial communities from wild waterbirds (i.e., six families and 15 species, n = 275 samples) to that of poultry, cattle, pigs, and influent/effluent of wastewater treatment plants (n = 150 samples) and (ii) to develop new MST markers for waterbirds. Significant differences were observed between wild waterbirds and the four other groups. We identified 7,349 Amplicon Sequence Variants (ASVs) from the hypervariable V3–V4 region. Firmicutes and Proteobacteria and, in a lesser extent, Actinobacteria and Bacteroidetes were ubiquitous while Fusobacteria and Epsilonbacteraeota were mainly present in wild waterbirds. The clustering of samples in non-metric multidimensional scaling (NMDS) ordination indicated a by-group clustering shape, with a high diversity within wild waterbirds. In addition, the structure of the bacterial communities was distinct according to bird and/or animal species and families (Adonis R 2 = 0.13, p = 10–4, Adonis R 2 = 0.11, p = 10–4, respectively). The Analysis of Composition of Microbiomes (ANCOM) showed that the wild waterbird group differed from the others by the significant presence of sequences from Fusobacteriaceae (W = 566) and Enterococcaceae (W = 565) families, corresponding to the Cetobacterium (W = 1427) and Catellicoccus (W = 1427) genera, respectively. Altogether, our results suggest that some waterbird members present distinct fecal microbiomes allowing the design of qPCR MST markers. For instance, a swan- and an oystercatcher-associated markers (named Swan_2 and Oyscab, respectively) have been developed. Moreover, bacterial genera harboring potential human pathogens associated to bird droppings were detected in our dataset, including enteric pathogens, i.e., Arcobacter, Clostridium, Helicobacter, and Campylobacter, and environmental pathogens, i.e., Burkholderia and Pseudomonas. Future studies involving other wildlife hosts may improve gut microbiome studies and MST marker development, helping mitigation of yet unknown fecal pollution sources.

ACS Style

Amine M. Boukerb; Cyril Noël; Emmanuelle Quenot; Bernard Cadiou; Julien Chevé; Laure Quintric; Alexandre Cormier; Luc Dantan; Michèle Gourmelon. Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach. Frontiers in Microbiology 2021, 12, 1 .

AMA Style

Amine M. Boukerb, Cyril Noël, Emmanuelle Quenot, Bernard Cadiou, Julien Chevé, Laure Quintric, Alexandre Cormier, Luc Dantan, Michèle Gourmelon. Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach. Frontiers in Microbiology. 2021; 12 ():1.

Chicago/Turabian Style

Amine M. Boukerb; Cyril Noël; Emmanuelle Quenot; Bernard Cadiou; Julien Chevé; Laure Quintric; Alexandre Cormier; Luc Dantan; Michèle Gourmelon. 2021. "Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach." Frontiers in Microbiology 12, no. : 1.

Journal article
Published: 30 June 2021 in Agronomy
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Bacterial burn is one of the major diseases affecting pear trees worldwide, with serious impacts on producers and economy. In Morocco, several pear trees (Pyrus communis) have shown leaf burns since 2015. To characterize the causal agent of this disease, we isolated fourteen bacterial strains from different parts of symptomatic pear trees (leaves, shoots, fruits and flowers) that were tested in planta for their pathogenicity on Louise bonne and Williams cultivars. The results showed necrotic lesions with a significant severity range from 47.63 to 57.77% on leaves of the Louise bonne cultivar inoculated with isolate B10, while the other bacterial isolates did not induce any disease symptom. 16S rRNA gene sequencing did not allow robust taxonomic discrimination of the incriminated isolate. Thus, we conducted whole-genome sequencing (WGS) and phylogenetic analyzes based on gyrA, gyrB and cdaA gene sequences, indicating that this isolate belongs to the Bacillus altitudinis species. This taxonomic classification was further confirmed by the Average Nucleotide Identity (ANI) and the in silico DNA-DNA hybridization (isDDH) analyzes compared to sixty-five Bacillus spp. type strains. The genome was mined for genes encoding carbohydrate-active enzymes (CAZymes) known to play a role in the vegetal tissue degradation. 177 candidates with functions that may support the in planta phytopathogenicity results were identified. To the best of our knowledge, this is the first data reporting B. altitudinis as agent of leaf burn in P. communis in Morocco. Our dataset will improve our knowledge on spread and pathogenicity of B. altitudinis genotypes that appears as emergent phytopathogenic agent, unveiling virulence factors and their genomic location (i.e., within genomic islands or the accessory genome) to induce trees disease.

ACS Style

Naima Lemjiber; Khalid Naamani; Annabelle Merieau; Abdelhi Dihazi; Nawal Zhar; Hicham Jediyi; Amine Boukerb. Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco. Agronomy 2021, 11, 1344 .

AMA Style

Naima Lemjiber, Khalid Naamani, Annabelle Merieau, Abdelhi Dihazi, Nawal Zhar, Hicham Jediyi, Amine Boukerb. Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco. Agronomy. 2021; 11 (7):1344.

Chicago/Turabian Style

Naima Lemjiber; Khalid Naamani; Annabelle Merieau; Abdelhi Dihazi; Nawal Zhar; Hicham Jediyi; Amine Boukerb. 2021. "Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco." Agronomy 11, no. 7: 1344.

Brief report
Published: 07 January 2021 in Microbiology Resource Announcements
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Staphylococcus spp. and Pseudomonas spp. are widely distributed bacteria in the environment and are found in association with animals and humans. Here, we present the draft genome sequence data of the healthy human skin commensal strains Staphylococcus aureus MFP03, Staphylococcus epidermidis MFP04, Staphylococcus capitis MFP08, and Pseudomonas fluorescens MFP05.

ACS Style

Xavier Janvier; Amine M. Boukerb; Marc G. J. Feuilloley; Anne Groboillot. Draft Genome Sequences of Four Commensal Strains of Staphylococcus and Pseudomonas Isolated from Healthy Human Skin. Microbiology Resource Announcements 2021, 10, 1 .

AMA Style

Xavier Janvier, Amine M. Boukerb, Marc G. J. Feuilloley, Anne Groboillot. Draft Genome Sequences of Four Commensal Strains of Staphylococcus and Pseudomonas Isolated from Healthy Human Skin. Microbiology Resource Announcements. 2021; 10 (1):1.

Chicago/Turabian Style

Xavier Janvier; Amine M. Boukerb; Marc G. J. Feuilloley; Anne Groboillot. 2021. "Draft Genome Sequences of Four Commensal Strains of Staphylococcus and Pseudomonas Isolated from Healthy Human Skin." Microbiology Resource Announcements 10, no. 1: 1.

Journal article
Published: 30 October 2020 in Microorganisms
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Pseudomonas aeruginosa PAO1 has an integrated Pf4 prophage in its genome, encoding a relatively well-characterized filamentous phage, which contributes to the bacterial biofilm organization and maturation. Pf4 variants are considered as superinfectives when they can re-infect and kill the prophage-carrying host. Herein, the response of P. aeruginosa H103 to Pf4 variant infection was investigated. This phage variant caused partial lysis of the bacterial population and modulated H103 physiology. We show by confocal laser scanning microscopy that a Pf4 variant-infection altered P. aeruginosa H103 biofilm architecture either in static or dynamic conditions. Interestingly, in the latter condition, numerous cells displayed a filamentous morphology, suggesting a link between this phenotype and flow-related forces. In addition, Pf4 variant-infection resulted in cell envelope stress response, mostly mediated by the AlgU and SigX extracytoplasmic function sigma factors (ECFσ). AlgU and SigX involvement may account, at least partly, for the enhanced expression level of genes involved in the biosynthesis pathways of two matrix exopolysaccharides (Pel and alginates) and bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP) metabolism.

ACS Style

Damien Tortuel; Ali Tahrioui; Sophie Rodrigues; Mélyssa Cambronel; Amine M. Boukerb; Olivier Maillot; Julien Verdon; Emile Bere; Michael Nusser; Gerald Brenner-Weiss; Audrey David; Onyedikachi Cecil Azuama; Marc G. J. Feuilloley; Nicole Orange; Olivier Lesouhaitier; Pierre Cornelis; Sylvie Chevalier; Emeline Bouffartigues. Activation of the Cell Wall Stress Response in Pseudomonas aeruginosa Infected by a Pf4 Phage Variant. Microorganisms 2020, 8, 1700 .

AMA Style

Damien Tortuel, Ali Tahrioui, Sophie Rodrigues, Mélyssa Cambronel, Amine M. Boukerb, Olivier Maillot, Julien Verdon, Emile Bere, Michael Nusser, Gerald Brenner-Weiss, Audrey David, Onyedikachi Cecil Azuama, Marc G. J. Feuilloley, Nicole Orange, Olivier Lesouhaitier, Pierre Cornelis, Sylvie Chevalier, Emeline Bouffartigues. Activation of the Cell Wall Stress Response in Pseudomonas aeruginosa Infected by a Pf4 Phage Variant. Microorganisms. 2020; 8 (11):1700.

Chicago/Turabian Style

Damien Tortuel; Ali Tahrioui; Sophie Rodrigues; Mélyssa Cambronel; Amine M. Boukerb; Olivier Maillot; Julien Verdon; Emile Bere; Michael Nusser; Gerald Brenner-Weiss; Audrey David; Onyedikachi Cecil Azuama; Marc G. J. Feuilloley; Nicole Orange; Olivier Lesouhaitier; Pierre Cornelis; Sylvie Chevalier; Emeline Bouffartigues. 2020. "Activation of the Cell Wall Stress Response in Pseudomonas aeruginosa Infected by a Pf4 Phage Variant." Microorganisms 8, no. 11: 1700.

Journal article
Published: 18 June 2020 in Microbiology Resource Announcements
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We report the draft genome sequences of two Micrococcus luteus strains, MFP06 and MFP07, isolated from human skin. The genome assemblies consist of 2,480 and 2,417 kbp with 2,337 and 2,240 coding sequences, respectively. The genomes contain genes potentially involved in osmotic stress tolerance, DNA repair, monoacylglycerol hydrolysis, and beta-lactone synthesis.

ACS Style

Djouhar Souak; Amine M. Boukerb; Magalie Barreau; Cecile Duclairoir-Poc; Marc G. J. Feuilloley. Draft Genome Sequences of Micrococcus luteus MFP06 and MFP07, Isolated from the Skin of Healthy Volunteers. Microbiology Resource Announcements 2020, 9, 1 .

AMA Style

Djouhar Souak, Amine M. Boukerb, Magalie Barreau, Cecile Duclairoir-Poc, Marc G. J. Feuilloley. Draft Genome Sequences of Micrococcus luteus MFP06 and MFP07, Isolated from the Skin of Healthy Volunteers. Microbiology Resource Announcements. 2020; 9 (25):1.

Chicago/Turabian Style

Djouhar Souak; Amine M. Boukerb; Magalie Barreau; Cecile Duclairoir-Poc; Marc G. J. Feuilloley. 2020. "Draft Genome Sequences of Micrococcus luteus MFP06 and MFP07, Isolated from the Skin of Healthy Volunteers." Microbiology Resource Announcements 9, no. 25: 1.

Journal article
Published: 09 April 2020 in Microbiology Resource Announcements
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Enterococcus faecalis OB15 is a probiotic strain that was isolated from rigouta, a popular traditional Tunisian fermented cheese. We report here the draft genome sequence of this strain, consisting of 2,912,159 bp, with an average G+C content of 37.49%.

ACS Style

Olfa Baccouri; Amine M. Boukerb; Flore Nilly; Mélyssa Cambronel; Issam Smaali; Marc G. J. Feuilloley; Ferid Abidi; Nathalie Connil. Draft Genome Sequence of Enterococcus faecalis Strain OB15, a Probiotic Strain Recently Isolated from Tunisian Rigouta Cheese. Microbiology Resource Announcements 2020, 9, 1 .

AMA Style

Olfa Baccouri, Amine M. Boukerb, Flore Nilly, Mélyssa Cambronel, Issam Smaali, Marc G. J. Feuilloley, Ferid Abidi, Nathalie Connil. Draft Genome Sequence of Enterococcus faecalis Strain OB15, a Probiotic Strain Recently Isolated from Tunisian Rigouta Cheese. Microbiology Resource Announcements. 2020; 9 (15):1.

Chicago/Turabian Style

Olfa Baccouri; Amine M. Boukerb; Flore Nilly; Mélyssa Cambronel; Issam Smaali; Marc G. J. Feuilloley; Ferid Abidi; Nathalie Connil. 2020. "Draft Genome Sequence of Enterococcus faecalis Strain OB15, a Probiotic Strain Recently Isolated from Tunisian Rigouta Cheese." Microbiology Resource Announcements 9, no. 15: 1.

Published erratum
Published: 13 February 2020 in Microbiology Resource Announcements
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ACS Style

Amine M. Boukerb; Julien Schaeffer; Joëlle Serghine; Gregory Carrier; Françoise S. Le Guyader; Michèle Gourmelon. Correction for Boukerb et al., “Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies”. Microbiology Resource Announcements 2020, 9, 1 .

AMA Style

Amine M. Boukerb, Julien Schaeffer, Joëlle Serghine, Gregory Carrier, Françoise S. Le Guyader, Michèle Gourmelon. Correction for Boukerb et al., “Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies”. Microbiology Resource Announcements. 2020; 9 (7):1.

Chicago/Turabian Style

Amine M. Boukerb; Julien Schaeffer; Joëlle Serghine; Gregory Carrier; Françoise S. Le Guyader; Michèle Gourmelon. 2020. "Correction for Boukerb et al., “Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies”." Microbiology Resource Announcements 9, no. 7: 1.

Journal article
Published: 16 January 2020 in Microbiology Resource Announcements
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Here, we report the first draft genome sequences of five bacteriocinogenic and potentially probiotic Enterococcus faecium strains (MZF1 to MZF5), which were isolated from homemade Tunisian meat (dried ossban). The estimated median genome sizes were about 2,582,641 ± 109,039 bp, with a median G+C content of 40% ± 0.4%.

ACS Style

Mohamed Zommiti; Mounir Ferchichi; Khaled Sebei; Marc G. J. Feuilloley; Nathalie Connil; Amine M. Boukerb. Draft Genome Sequences of Five Potentially Probiotic Enterococcus faecium Strains Isolated from an Artisanal Tunisian Meat (Dried Ossban). Microbiology Resource Announcements 2020, 9, 1 .

AMA Style

Mohamed Zommiti, Mounir Ferchichi, Khaled Sebei, Marc G. J. Feuilloley, Nathalie Connil, Amine M. Boukerb. Draft Genome Sequences of Five Potentially Probiotic Enterococcus faecium Strains Isolated from an Artisanal Tunisian Meat (Dried Ossban). Microbiology Resource Announcements. 2020; 9 (3):1.

Chicago/Turabian Style

Mohamed Zommiti; Mounir Ferchichi; Khaled Sebei; Marc G. J. Feuilloley; Nathalie Connil; Amine M. Boukerb. 2020. "Draft Genome Sequences of Five Potentially Probiotic Enterococcus faecium Strains Isolated from an Artisanal Tunisian Meat (Dried Ossban)." Microbiology Resource Announcements 9, no. 3: 1.

Journal article
Published: 09 January 2020 in Microbiology Resource Announcements
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We report the draft genome sequence of Lactobacillus crispatus CIP 104459, isolated from a human vaginal swab. This draft genome consists of 1,993,673 bp, with 36.8% G+C content and 2,024 predicted protein-encoding sequences.

ACS Style

Maximilien Clabaut; Amine M. Boukerb; Pierre-Jean Racine; Chantal Pichon; Coralie Kremser; Jean-Pierre Picot; Madina Karsybayeva; Gérard Redziniak; Sylvie Chevalier; Marc G. J. Feuilloley. Draft Genome Sequence of Lactobacillus crispatus CIP 104459, Isolated from a Vaginal Swab. Microbiology Resource Announcements 2020, 9, 1 .

AMA Style

Maximilien Clabaut, Amine M. Boukerb, Pierre-Jean Racine, Chantal Pichon, Coralie Kremser, Jean-Pierre Picot, Madina Karsybayeva, Gérard Redziniak, Sylvie Chevalier, Marc G. J. Feuilloley. Draft Genome Sequence of Lactobacillus crispatus CIP 104459, Isolated from a Vaginal Swab. Microbiology Resource Announcements. 2020; 9 (2):1.

Chicago/Turabian Style

Maximilien Clabaut; Amine M. Boukerb; Pierre-Jean Racine; Chantal Pichon; Coralie Kremser; Jean-Pierre Picot; Madina Karsybayeva; Gérard Redziniak; Sylvie Chevalier; Marc G. J. Feuilloley. 2020. "Draft Genome Sequence of Lactobacillus crispatus CIP 104459, Isolated from a Vaginal Swab." Microbiology Resource Announcements 9, no. 2: 1.

Journal article
Published: 02 January 2020 in Microbiology Resource Announcements
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Biofilms produced by Pseudomonas aeruginosa present a serious threat to cystic fibrosis patients. Here, we report the draft genome sequences of four cystic fibrosis isolates displaying various mucoid and biofilm phenotypes. The estimated average genome size was about 6,255,986 ± 50,202 bp with a mean G+C content of 66.52 ± 0.06%.

ACS Style

Amine M. Boukerb; Marjolaine Simon; Erwan Pernet; Albane Jouault; Emilie Portier; Elise Persyn; Emeline Bouffartigues; Alexis Bazire; Sylvie Chevalier; Marc G. J. Feuilloley; Olivier Lesouhaitier; Jocelyne Caillon; Alain Dufour. Draft Genome Sequences of Four Pseudomonas aeruginosa Clinical Strains with Various Biofilm Phenotypes. Microbiology Resource Announcements 2020, 9, 1 .

AMA Style

Amine M. Boukerb, Marjolaine Simon, Erwan Pernet, Albane Jouault, Emilie Portier, Elise Persyn, Emeline Bouffartigues, Alexis Bazire, Sylvie Chevalier, Marc G. J. Feuilloley, Olivier Lesouhaitier, Jocelyne Caillon, Alain Dufour. Draft Genome Sequences of Four Pseudomonas aeruginosa Clinical Strains with Various Biofilm Phenotypes. Microbiology Resource Announcements. 2020; 9 (1):1.

Chicago/Turabian Style

Amine M. Boukerb; Marjolaine Simon; Erwan Pernet; Albane Jouault; Emilie Portier; Elise Persyn; Emeline Bouffartigues; Alexis Bazire; Sylvie Chevalier; Marc G. J. Feuilloley; Olivier Lesouhaitier; Jocelyne Caillon; Alain Dufour. 2020. "Draft Genome Sequences of Four Pseudomonas aeruginosa Clinical Strains with Various Biofilm Phenotypes." Microbiology Resource Announcements 9, no. 1: 1.

Journal article
Published: 02 January 2020 in Microbiology Resource Announcements
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As determined by a hybrid approach combining Oxford Nanopore MinION and Illumina MiniSeq sequence data, Campylobacter armoricus strain CA639 harbored a circular chromosome of 1,688,169 bp with a G+C content of 28.47% and two plasmids named pCA639-1 and pCA639-2, with lengths of 51,123 and 28,139 bp, and G+C contents of 26.5% and 28.45%, respectively.

ACS Style

Amine M. Boukerb; Julien Schaeffer; Joëlle Serghine; Gregory Carrier; Françoise S. Le Guyader; Michèle Gourmelon. Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies. Microbiology Resource Announcements 2020, 9, 1 .

AMA Style

Amine M. Boukerb, Julien Schaeffer, Joëlle Serghine, Gregory Carrier, Françoise S. Le Guyader, Michèle Gourmelon. Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies. Microbiology Resource Announcements. 2020; 9 (1):1.

Chicago/Turabian Style

Amine M. Boukerb; Julien Schaeffer; Joëlle Serghine; Gregory Carrier; Françoise S. Le Guyader; Michèle Gourmelon. 2020. "Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies." Microbiology Resource Announcements 9, no. 1: 1.

Journal article
Published: 01 December 2019 in International Journal of Systematic and Evolutionary Microbiology
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During a study on the prevalence and diversity of members of the genus Campylobacter in a shellfish-harvesting area and its catchment in Brittany, France, six urease-positive isolates of members of the genus Campylobacter were recovered from surface water samples, as well as three isolates from stools of humans displaying enteric infection in the same period. These strains were initially identified as members of the Campylobacter lari group by MALDI-TOF mass spectrometry and placed into a distinct group in the genus Campylobacter, following atpA gene sequence analysis based on whole-genome sequencing data. This taxonomic position was confirmed by phylogenetic analysis of the 16S rRNA, rpoB and hsp60 (groEL) loci, and an analysis of the core genome that provided an improved phylogenetic resolution. The average nucleotide identity between the representative strain CA656T (CCUG 73571T=CIP 111675T) and the type strain of the most closely related species Campylobacter ornithocola WBE38T was 88.5 %. The strains were found to be microaerobic and anaerobic, motile, non-spore-forming, Gram-stain-negative, spiral-shaped bacteria that exhibit catalase, oxidase and urease activities but not nitrate reduction. This study demonstrates clearly that the nine isolates represent a novel species within the C. lari group, for which the name Campylobacter armoricus is proposed. Here, we present phenotypic and morphological features of the nine strains and the description of their genome sequences. The proposed type strain CA656T has a 1.589 Mbp chromosome with a DNA G+C content of 28.5 mol% and encodes 1588 predicted coding sequences, 38 tRNAs, and 3 rRNA operons.

ACS Style

Amine M. Boukerb; Christian Penny; Joëlle Serghine; Cécile Walczak; Henry-Michel Cauchie; William G. Miller; Serge Losch; Catherine Ragimbeau; Joël Mossong; Francis Mégraud; Philippe Lehours; Lucie Bénéjat; Michèle Gourmelon. Campylobacter armoricus sp. nov., a novel member of the Campylobacter lari group isolated from surface water and stools from humans with enteric infection. International Journal of Systematic and Evolutionary Microbiology 2019, 69, 3969 -3979.

AMA Style

Amine M. Boukerb, Christian Penny, Joëlle Serghine, Cécile Walczak, Henry-Michel Cauchie, William G. Miller, Serge Losch, Catherine Ragimbeau, Joël Mossong, Francis Mégraud, Philippe Lehours, Lucie Bénéjat, Michèle Gourmelon. Campylobacter armoricus sp. nov., a novel member of the Campylobacter lari group isolated from surface water and stools from humans with enteric infection. International Journal of Systematic and Evolutionary Microbiology. 2019; 69 (12):3969-3979.

Chicago/Turabian Style

Amine M. Boukerb; Christian Penny; Joëlle Serghine; Cécile Walczak; Henry-Michel Cauchie; William G. Miller; Serge Losch; Catherine Ragimbeau; Joël Mossong; Francis Mégraud; Philippe Lehours; Lucie Bénéjat; Michèle Gourmelon. 2019. "Campylobacter armoricus sp. nov., a novel member of the Campylobacter lari group isolated from surface water and stools from humans with enteric infection." International Journal of Systematic and Evolutionary Microbiology 69, no. 12: 3969-3979.

Journal article
Published: 03 October 2019 in Microbiology Resource Announcements
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Kytococcus schroeteri strain H01 was isolated from the skin of a healthy volunteer who underwent erythromycin treatment for a skin disorder 1 year prior. The draft genome consists of 2.38 Mb, a G+C content of 73.06%, and 2,221 protein coding sequences. This is the first genome characterization of a K. schroeteri strain isolated from human skin.

ACS Style

Amine M. Boukerb; Magalie Robert; Nataliya A. Teteneva; Natalia D. Danilova; Marina V. Zhurina; Sergey V. Mart’Yanov; Vladimir K. Plakunov; Marc G. J. Feuilloley; Andrei V. Gannesen. Draft Genome Sequence of Kytococcus schroeteri Strain H01, Isolated from Human Skin. Microbiology Resource Announcements 2019, 8, 1 .

AMA Style

Amine M. Boukerb, Magalie Robert, Nataliya A. Teteneva, Natalia D. Danilova, Marina V. Zhurina, Sergey V. Mart’Yanov, Vladimir K. Plakunov, Marc G. J. Feuilloley, Andrei V. Gannesen. Draft Genome Sequence of Kytococcus schroeteri Strain H01, Isolated from Human Skin. Microbiology Resource Announcements. 2019; 8 (40):1.

Chicago/Turabian Style

Amine M. Boukerb; Magalie Robert; Nataliya A. Teteneva; Natalia D. Danilova; Marina V. Zhurina; Sergey V. Mart’Yanov; Vladimir K. Plakunov; Marc G. J. Feuilloley; Andrei V. Gannesen. 2019. "Draft Genome Sequence of Kytococcus schroeteri Strain H01, Isolated from Human Skin." Microbiology Resource Announcements 8, no. 40: 1.

Brief report
Published: 19 September 2019 in Microbiology Resource Announcements
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Lactobacillus crispatus strain V4 was isolated from a vaginal swab from a healthy nonmenopausal 35-year-old French woman. We report here its draft genome sequence of 2,091,889 bp, with an average G+C content of 37.02%.

ACS Style

Maximilien Clabaut; Amine Mohamed Boukerb; Pierre-Jean Racine; Chantal Pichon; Coralie Kremser; Aïna Queiroz; Madina Karsybayeva; Gérard Redziniak; Sylvie Chevalier; Marc G. J. Feuilloley. Draft Genome Sequence of Lactobacillus crispatus Strain V4, Isolated from a Vaginal Swab from a Young Healthy Nonmenopausal Woman. Microbiology Resource Announcements 2019, 8, e00856-19 .

AMA Style

Maximilien Clabaut, Amine Mohamed Boukerb, Pierre-Jean Racine, Chantal Pichon, Coralie Kremser, Aïna Queiroz, Madina Karsybayeva, Gérard Redziniak, Sylvie Chevalier, Marc G. J. Feuilloley. Draft Genome Sequence of Lactobacillus crispatus Strain V4, Isolated from a Vaginal Swab from a Young Healthy Nonmenopausal Woman. Microbiology Resource Announcements. 2019; 8 (38):e00856-19.

Chicago/Turabian Style

Maximilien Clabaut; Amine Mohamed Boukerb; Pierre-Jean Racine; Chantal Pichon; Coralie Kremser; Aïna Queiroz; Madina Karsybayeva; Gérard Redziniak; Sylvie Chevalier; Marc G. J. Feuilloley. 2019. "Draft Genome Sequence of Lactobacillus crispatus Strain V4, Isolated from a Vaginal Swab from a Young Healthy Nonmenopausal Woman." Microbiology Resource Announcements 8, no. 38: e00856-19.

Brief report
Published: 25 April 2019 in Microbiology Resource Announcements
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Pediococcus pentosaceus strain MZF16 was isolated from dried ossban, a Tunisian dry fermented meat. The MZF16 chromosome consisted of 28 contigs with a total draft genome size of 1,928,373 bp and a G+C content of 37.2%.

ACS Style

Mohamed Zommiti; Amine M. Boukerb; Marc G. J. Feuilloley; Mounir Ferchichi; Nathalie Connil. Draft Genome Sequence of Pediococcus pentosaceus MZF16, a Bacteriocinogenic Probiotic Strain Isolated from Dried Ossban in Tunisia. Microbiology Resource Announcements 2019, 8, e00285-19 .

AMA Style

Mohamed Zommiti, Amine M. Boukerb, Marc G. J. Feuilloley, Mounir Ferchichi, Nathalie Connil. Draft Genome Sequence of Pediococcus pentosaceus MZF16, a Bacteriocinogenic Probiotic Strain Isolated from Dried Ossban in Tunisia. Microbiology Resource Announcements. 2019; 8 (17):e00285-19.

Chicago/Turabian Style

Mohamed Zommiti; Amine M. Boukerb; Marc G. J. Feuilloley; Mounir Ferchichi; Nathalie Connil. 2019. "Draft Genome Sequence of Pediococcus pentosaceus MZF16, a Bacteriocinogenic Probiotic Strain Isolated from Dried Ossban in Tunisia." Microbiology Resource Announcements 8, no. 17: e00285-19.

Original research article
Published: 24 April 2019 in Frontiers in Microbiology
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Lactic acid bacteria (LAB) strains OB14 and OB15 were isolated from traditional Tunisian fermented dairy products, Testouri cheese and Rigouta, respectively. They were identified as Enterococcus faecalis by the MALDI TOF-MS (matrix assisted laser desorption-ionization time of flight mass spectrometry) biotyper system and molecular assays (species-specific PCR). These new isolates were evaluated for probiotic properties, compared to E. faecalis Symbioflor 1 clone DSM 16431, as reference. The bacteria were found to be tolerant to the harsh conditions of the gastrointestinal tract (acidity and bile salt). They were low to moderate biofilm producers, can adhere to Caco-2/TC7 intestinal cells and strengthen the intestinal barrier through the increase of the transepithelial electrical resistance (TER). Susceptibility to ampicillin, vancomycin, gentamicin and erythromycin has been tested using the broth microdilutions method. The results demonstrated that E. faecalis OB14 and OB15 were sensitive to the clinically important ampicillin (MIC = 1 μg/mL) and vancomycin (MIC = 2 μg/mL) antibiotics. However, Whole Genome Sequencing (WGS) showed the presence of tetracycline resistance and cytolysin genes in E. faecalis OB14, and this led to high mortality of Galleria Mellonella larvae in the virulence test. Hierarchical cluster analysis by MALDI TOF-MS biotyper showed that E. faecalis OB15 was closely related to the E. faecalis Symbioflor 1 probiotic strain than to OB14, and this has been confirmed by WGS using the average nucleotide identity (ANI) and Genome-to-Genome Hybridization similarity methods. According to these results, E. faecalis OB15 seems to be reliable for future development as probiotic, in food or feed industry.

ACS Style

Olfa Baccouri; Amine Mohamed Boukerb; Leila Ben Farhat; Arthur Zébré; Kurt Zimmermann; Eugen Domann; Mélyssa Cambronel; Magalie Barreau; Olivier Maillot; Isabelle Rincé; Cecile Muller; M. Nejib Marzouki; Marc Feuilloley; Ferid Abidi; Nathalie Connil. Probiotic Potential and Safety Evaluation of Enterococcus faecalis OB14 and OB15, Isolated From Traditional Tunisian Testouri Cheese and Rigouta, Using Physiological and Genomic Analysis. Frontiers in Microbiology 2019, 10, 881 .

AMA Style

Olfa Baccouri, Amine Mohamed Boukerb, Leila Ben Farhat, Arthur Zébré, Kurt Zimmermann, Eugen Domann, Mélyssa Cambronel, Magalie Barreau, Olivier Maillot, Isabelle Rincé, Cecile Muller, M. Nejib Marzouki, Marc Feuilloley, Ferid Abidi, Nathalie Connil. Probiotic Potential and Safety Evaluation of Enterococcus faecalis OB14 and OB15, Isolated From Traditional Tunisian Testouri Cheese and Rigouta, Using Physiological and Genomic Analysis. Frontiers in Microbiology. 2019; 10 ():881.

Chicago/Turabian Style

Olfa Baccouri; Amine Mohamed Boukerb; Leila Ben Farhat; Arthur Zébré; Kurt Zimmermann; Eugen Domann; Mélyssa Cambronel; Magalie Barreau; Olivier Maillot; Isabelle Rincé; Cecile Muller; M. Nejib Marzouki; Marc Feuilloley; Ferid Abidi; Nathalie Connil. 2019. "Probiotic Potential and Safety Evaluation of Enterococcus faecalis OB14 and OB15, Isolated From Traditional Tunisian Testouri Cheese and Rigouta, Using Physiological and Genomic Analysis." Frontiers in Microbiology 10, no. : 881.

Original research article
Published: 31 May 2016 in Frontiers in Microbiology
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LecA and LecB tetrameric lectins take part in oligosaccharide-mediated adhesion-processes of Pseudomonas aeruginosa. Glycomimetics have been designed to block these interactions. The great versatility of P. aeruginosa suggests that the range of application of these glycomimetics could be restricted to genotypes with particular lectin types. The likelihood of having genomic and genetic changes impacting LecA and LecB interactions with glycomimetics such as galactosylated and fucosylated calix[4]arene was investigated over a collection of strains from the main clades of P. aeruginosa. Lectin types were defined, and their ligand specificities were inferred. These analyses showed a loss of lecA among the PA7 clade. Genomic changes impacting lec loci were thus assessed using strains of this clade, and by making comparisons with the PAO1 genome. The lecA regions were found challenged by phage attacks and PAGI-2 (genomic island) integrations. A prophage was linked to the loss of lecA. The lecB regions were found less impacted by such rearrangements but greater lecB than lecA genetic divergences were recorded. Sixteen combinations of LecA and LecB types were observed. Amino acid variations were mapped on PAO1 crystal structures. Most significant changes were observed on LecBPA7, and found close to the fucose binding site. Glycan array analyses were performed with purified LecBPA7. LecBPA7 was found less specific for fucosylated oligosaccharides than LecBPAO1, with a preference for H type 2 rather than type 1, and Lewisa rather than Lewisx. Comparison of the crystal structures of LecBPA7 and LecBPAO1 in complex with Lewisa showed these changes in specificity to have resulted from a modification of the water network between the lectin, galactose and GlcNAc residues. Incidence of these modifications on the interactions with calix[4]arene glycomimetics at the cell level was investigated. An aggregation test was used to establish the efficacy of these ligands. Great variations in the responses were observed. Glycomimetics directed against LecB yielded the highest numbers of aggregates for strains from all clades. The use of a PAO1lecB strain confirmed a role of LecB in this aggregation phenotype. Fucosylated calix[4]arene showed the greatest potential for a use in the prevention of P. aeruginosa infections.

ACS Style

Amine Mohamed Boukerb; Aude Decor; Sébastien Ribun; Rachel Tabaroni; Audric Rousset; Loris Commin; Samuel Buff; Anne Doléans-Jordheim; Sébastien Vidal; Annabelle Varrot; Anne Imberty; Benoit Cournoyer. Genomic Rearrangements and Functional Diversification of lecA and lecB Lectin-Coding Regions Impacting the Efficacy of Glycomimetics Directed against Pseudomonas aeruginosa. Frontiers in Microbiology 2016, 7, 811 .

AMA Style

Amine Mohamed Boukerb, Aude Decor, Sébastien Ribun, Rachel Tabaroni, Audric Rousset, Loris Commin, Samuel Buff, Anne Doléans-Jordheim, Sébastien Vidal, Annabelle Varrot, Anne Imberty, Benoit Cournoyer. Genomic Rearrangements and Functional Diversification of lecA and lecB Lectin-Coding Regions Impacting the Efficacy of Glycomimetics Directed against Pseudomonas aeruginosa. Frontiers in Microbiology. 2016; 7 ():811.

Chicago/Turabian Style

Amine Mohamed Boukerb; Aude Decor; Sébastien Ribun; Rachel Tabaroni; Audric Rousset; Loris Commin; Samuel Buff; Anne Doléans-Jordheim; Sébastien Vidal; Annabelle Varrot; Anne Imberty; Benoit Cournoyer. 2016. "Genomic Rearrangements and Functional Diversification of lecA and lecB Lectin-Coding Regions Impacting the Efficacy of Glycomimetics Directed against Pseudomonas aeruginosa." Frontiers in Microbiology 7, no. : 811.

Journal article
Published: 31 December 2015 in Genome Announcements
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Draft genome sequences of three P. aeruginosa strains from the PA7 clade are presented here. Their lengths are 6.36 (EML528), 6.44 (EML545), and 6.33 Mb (EML548). Comparisons with the PA7 genome showed 5,113 conserved coding sequences (CDSs), and significant numbers of strain-specific CDSs. Their analysis will improve our understanding of this highly divergent clade.

ACS Style

Amine M. Boukerb; Romain Marti; Benoit Cournoyer. Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade. Genome Announcements 2015, 3, e01366-15 .

AMA Style

Amine M. Boukerb, Romain Marti, Benoit Cournoyer. Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade. Genome Announcements. 2015; 3 (6):e01366-15.

Chicago/Turabian Style

Amine M. Boukerb; Romain Marti; Benoit Cournoyer. 2015. "Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade." Genome Announcements 3, no. 6: e01366-15.

Research article
Published: 08 December 2014 in Journal of Medicinal Chemistry
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Pseudomonas aeruginosa lung infections are a major cause of death in cystic fibrosis and hospitalized patients. Treating these infections is becoming difficult due to the emergence of conventional antimicrobial multiresistance. While monosaccharides have proved beneficial against such bacterial lung infection, the design of several multivalent glycosylated macromolecules has been shown to be also beneficial on biofilm dispersion. In this study, calix[4]arene-based glycoclusters functionalized with galactosides or fucosides have been synthesized. The characterization of their inhibitory properties on Pseudomonas aeruginosa aggregation, biofilm formation, adhesion on epithelial cells, and destruction of alveolar tissues were performed. The antiadhesive properties of the designed glycoclusters were demonstrated through several in vitro bioassays. An in vivo mouse model of lung infection provided an almost complete protection against Pseudomonas aeruginosa with the designed glycoclusters.

ACS Style

Amine M. Boukerb; Audric Rousset; Nicolas Galanos; Jean-Baptiste Méar; Marion Thépaut; Teddy Grandjean; Emilie Gillon; Samy Cecioni; Claire Abderrahmen; Karine Faure; David Redelberger; Eric Kipnis; Rodrigue Dessein; Stéphane Havet; Benoit Darblade; Susan E. Matthews; Sophie de Bentzmann; Benoit Guéry; Benoit Cournoyer; Anne Imberty; Sébastien Vidal. Antiadhesive Properties of Glycoclusters against Pseudomonas aeruginosa Lung Infection. Journal of Medicinal Chemistry 2014, 57, 10275 -10289.

AMA Style

Amine M. Boukerb, Audric Rousset, Nicolas Galanos, Jean-Baptiste Méar, Marion Thépaut, Teddy Grandjean, Emilie Gillon, Samy Cecioni, Claire Abderrahmen, Karine Faure, David Redelberger, Eric Kipnis, Rodrigue Dessein, Stéphane Havet, Benoit Darblade, Susan E. Matthews, Sophie de Bentzmann, Benoit Guéry, Benoit Cournoyer, Anne Imberty, Sébastien Vidal. Antiadhesive Properties of Glycoclusters against Pseudomonas aeruginosa Lung Infection. Journal of Medicinal Chemistry. 2014; 57 (24):10275-10289.

Chicago/Turabian Style

Amine M. Boukerb; Audric Rousset; Nicolas Galanos; Jean-Baptiste Méar; Marion Thépaut; Teddy Grandjean; Emilie Gillon; Samy Cecioni; Claire Abderrahmen; Karine Faure; David Redelberger; Eric Kipnis; Rodrigue Dessein; Stéphane Havet; Benoit Darblade; Susan E. Matthews; Sophie de Bentzmann; Benoit Guéry; Benoit Cournoyer; Anne Imberty; Sébastien Vidal. 2014. "Antiadhesive Properties of Glycoclusters against Pseudomonas aeruginosa Lung Infection." Journal of Medicinal Chemistry 57, no. 24: 10275-10289.