Publications by authors named "Stéphanie Ferreira"

29 Publications

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SARS-CoV-2 infection in nonhuman primates alters the composition and functional activity of the gut microbiota.

Gut Microbes 2021 Jan-Dec;13(1):1-19

Univ. Lille, US 41 - UMS 2014 - PLBS, U1019 - UMR 9017 - CIIL - Centre d'Infection Et d'Immunité De Lille, Lille, France.

The current pandemic of coronavirus disease (COVID) 2019 constitutes a global public health issue. Regarding the emerging importance of the gut-lung axis in viral respiratory infections, analysis of the gut microbiota's composition and functional activity during a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection might be instrumental in understanding and controling COVID 19. We used a nonhuman primate model (the macaque), that recapitulates mild COVID-19 symptoms, to analyze the effects of a SARS-CoV-2 infection on dynamic changes of the gut microbiota. 16S rRNA gene profiling and analysis of β diversity indicated significant changes in the composition of the gut microbiota with a peak at 10-13 days post-infection (dpi). Analysis of bacterial abundance correlation networks confirmed disruption of the bacterial community at 10-13 dpi. Some alterations in microbiota persisted after the resolution of the infection until day 26. Some changes in the relative bacterial taxon abundance associated with infectious parameters. Interestingly, the relative abundance of (Proteobacteria) and some genera of the Ruminococcaceae family (Firmicutes) was positively correlated with the presence of SARS-CoV-2 in the upper respiratory tract. Targeted quantitative metabolomics indicated a drop in short-chain fatty acids (SCFAs) and changes in several bile acids and tryptophan metabolites in infected animals. The relative abundance of several taxa known to be SCFA producers (mostly from the Ruminococcaceae family) was negatively correlated with systemic inflammatory markers while the opposite correlation was seen with several members of the genus . Collectively, SARS-CoV-2 infection in a nonhuman primate is associated with changes in the gut microbiota's composition and functional activity.
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http://dx.doi.org/10.1080/19490976.2021.1893113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7951961PMC
March 2021

Reply.

J Allergy Clin Immunol 2021 Feb 1;147(2):779-780. Epub 2020 Dec 1.

Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, Département de Pharmacologie, Bordeaux, France; INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Bordeaux, France; CHU de Bordeaux, Laboratoire de Parasitologie, Mycologie, Service d'exploration fonctionnelle respiratoire, Service de pharmacologie, Pessac, France. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2020.10.021DOI Listing
February 2021

Chlorinated ethene biodegradation and associated bacterial taxa in multi-polluted groundwater: Insights from biomolecular markers and stable isotope analysis.

Sci Total Environ 2021 Apr 15;763:142950. Epub 2020 Oct 15.

Université de Strasbourg, CNRS/EOST, LHyGeS UMR 7517, Laboratory of Hydrology and Geochemistry of Strasbourg, Strasbourg, France.

Chlorinated ethenes (CEs) are most problematic pollutants in groundwater. Dehalogenating bacteria, and in particular organohalide-respiring bacteria (OHRB), can transform PCE to ethene under anaerobic conditions, and thus contribute to bioremediation of contaminated sites. Current approaches to characterize in situ biodegradation of CEs include hydrochemical analyses, quantification of the abundance of key species (e.g. Dehalococcoides mccartyi) and dehalogenase genes (pceA, vcrA, bvcA and tceA) involved in different steps of organohalide respiration (OHR) by qPCR, and compound-specific isotope analysis (CSIA) of CEs. Here we combined these approaches with sequencing of 16S rRNA gene amplicons to consider both OHRB and bacterial taxa involved in CE transformation at a multi-contaminated site. Integrated analysis of hydrogeochemical characteristics, gene abundances and bacterial diversity shows that bacterial diversity and OHRB mainly correlated with hydrogeochemical conditions, suggesting that pollutant exposure acts as a central driver of bacterial diversity. CSIA, abundances of four reductive dehalogenase encoding genes and the prevalence of Dehalococcoides highlighted sustained PCE, DCE and VC degradation in several wells of the polluted plume. These results suggest that bacterial taxa associated with OHR play an essential role in natural attenuation of CEs, and that representatives of taxa including Dehalobacterium and Desulfosporosinus co-occur with Dehalococcoides. Overall, our study emphasizes the benefits of combining several approaches to evaluate the interplay between the dynamics of bacterial diversity in CE-polluted plumes and in situ degradation of CEs, and to contribute to a more robust assessment of natural attenuation at multi-polluted sites.
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http://dx.doi.org/10.1016/j.scitotenv.2020.142950DOI Listing
April 2021

Type 2-high asthma is associated with a specific indoor mycobiome and microbiome.

J Allergy Clin Immunol 2021 Apr 12;147(4):1296-1305.e6. Epub 2020 Sep 12.

Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France. Electronic address:

Background: The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters.

Objective: The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA).

Methods: A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during "stable" or pulmonary "exacerbation" periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes.

Results: Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation.

Conclusion: These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.
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http://dx.doi.org/10.1016/j.jaci.2020.08.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486598PMC
April 2021

High-dose dietary supplementation with zinc prevents gut inflammation: Investigation of the role of metallothioneins and beyond by transcriptomic and metagenomic studies.

FASEB J 2020 09 30;34(9):12615-12633. Epub 2020 Jul 30.

Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France.

Although it is known that zinc has several beneficial roles in the context of gut inflammation, the underlying mechanisms have not been extensively characterized. Zinc (Zn) is known to be the primary physiological inducer of the expression of the metallothionein (MT) superfamily of small stress-responsive proteins. The expression of MTs in various tissues is induced or enhanced (including the gastrointestinal tract (GIT)) by a variety of stimuli, including infection and inflammation. However, the MTs' exact role in inflammation is still subject to debate. In order to establish whether or not MTs are the sole vectors in the Zn-based modulation of intestinal inflammation, we used transcriptomic and metagenomic approaches to assess the potential effect of dietary Zn, the mechanisms underlying the MTs' beneficial effects, and the induction of previously unidentified mediators. We found that the expression of endogenous MTs in the mouse GIT was stimulated by an optimized dietary supplementation with Zn. The protective effects of dietary supplementation with Zn were then evaluated in mouse models of chemically induced colitis. The potential contribution of MTs and other pathways was explored via transcriptomic analyses of the ileum and colon in Zn-treated mice. The microbiota's role was also assessed via fecal 16S rRNA sequencing. We found that high-dose dietary supplementation with Zn induced the expression of MT-encoding genes in the colon of healthy mice. We next demonstrated that the Zn diet significantly protected mice in the two models of induced colitis. When comparing Zn-treated and control mice, various genes were found to be differentially expressed in the colon and the ileum. Finally, we found that Zn supplementation did not modify the overall structure of the fecal microbiota, with the exception of (i) a significant increase in endogenous Clostridiaceae, and (ii) some subtle but specific changes at the family and genus levels. Our results emphasize the beneficial effects of excess dietary Zn on the prevention of colitis and inflammatory events in mouse models. The main underlying mechanisms were driven by the multifaceted roles of MTs and the other potential molecular mediators highlighted by our transcriptomic analyses although we cannot rule out contributions by other factors from the host and/or the microbiota.
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http://dx.doi.org/10.1096/fj.202000562RRDOI Listing
September 2020

Gut Dysbiosis during Influenza Contributes to Pulmonary Pneumococcal Superinfection through Altered Short-Chain Fatty Acid Production.

Cell Rep 2020 03;30(9):2934-2947.e6

Université de Lille, U1019 UMR 9017, Centre d'Infection et d'Immunité de Lille (CIIL), 59000 Lille, France; Centre National de la Recherche Scientifique, UMR 9017, 59000 Lille, France; Institut National de la Santé et de la Recherche Médicale, U1019, 59000 Lille, France; Centre Hospitalier Universitaire de Lille, 59000 Lille, France; Institut Pasteur de Lille, 59000 Lille, France. Electronic address:

Secondary bacterial infections often complicate viral respiratory infections. We hypothesize that perturbation of the gut microbiota during influenza A virus (IAV) infection might favor respiratory bacterial superinfection. Sublethal infection with influenza transiently alters the composition and fermentative activity of the gut microbiota in mice. These changes are attributed in part to reduced food consumption. Fecal transfer experiments demonstrate that the IAV-conditioned microbiota compromises lung defenses against pneumococcal infection. In mechanistic terms, reduced production of the predominant short-chain fatty acid (SCFA) acetate affects the bactericidal activity of alveolar macrophages. Following treatment with acetate, mice colonized with the IAV-conditioned microbiota display reduced bacterial loads. In the context of influenza infection, acetate supplementation reduces, in a free fatty acid receptor 2 (FFAR2)-dependent manner, local and systemic bacterial loads. This translates into reduced lung pathology and improved survival rates of double-infected mice. Lastly, pharmacological activation of the SCFA receptor FFAR2 during influenza reduces bacterial superinfection.
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http://dx.doi.org/10.1016/j.celrep.2020.02.013DOI Listing
March 2020

DAV131A Protects Hamsters from Lethal Infection Induced by Fluoroquinolones.

Antimicrob Agents Chemother 2019 12 20;64(1). Epub 2019 Dec 20.

Da Volterra, Paris, France

Fluoroquinolone treatments induce dysbiosis of the intestinal microbiota, resulting in loss of resistance to colonization by exogenous bacteria such as that may cause severe diarrhea in humans and lethal infection in hamsters. We show here that DAV131A, a charcoal-based adsorbent, decreases the intestinal levels of the fluoroquinolone antibiotics levofloxacin and ciprofloxacin in hamsters, protects their intestinal microbiota, and prevents lethal infection by .
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http://dx.doi.org/10.1128/AAC.01196-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187614PMC
December 2019

Impact of Antibiotic Gut Exposure on the Temporal Changes in Microbiome Diversity.

Antimicrob Agents Chemother 2019 10 23;63(10). Epub 2019 Sep 23.

IAME, INSERM, Université de Paris, Paris, France.

Although the global deleterious impact of antibiotics on the intestinal microbiota is well known, temporal changes in microbial diversity during and after an antibiotic treatment are still poorly characterized. We used plasma and fecal samples collected frequently during treatment and up to one month after from 22 healthy volunteers assigned to a 5-day treatment by moxifloxacin ( = 14) or no intervention ( = 8). Moxifloxacin concentrations were measured in both plasma and feces, and bacterial diversity was determined in feces by 16S rRNA gene profiling and quantified using the Shannon index and number of operational taxonomic units (OTUs). Nonlinear mixed effect models were used to relate drug pharmacokinetics and bacterial diversity over time. Moxifloxacin reduced bacterial diversity in a concentration-dependent manner, with a median maximal loss of 27.5% of the Shannon index (minimum [min], 17.5; maximum [max], 27.7) and 47.4% of the number of OTUs (min, 30.4; max, 48.3). As a consequence of both the long fecal half-life of moxifloxacin and the susceptibility of the gut microbiota to moxifloxacin, bacterial diversity indices did not return to their pretreatment levels until days 16 and 21, respectively. Finally, the model characterized the effect of moxifloxacin on bacterial diversity biomarkers and provides a novel framework for analyzing antibiotic effects on the intestinal microbiome.
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http://dx.doi.org/10.1128/AAC.00820-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761552PMC
October 2019

Functional Genes and Bacterial Communities During Organohalide Respiration of Chloroethenes in Microcosms of Multi-Contaminated Groundwater.

Front Microbiol 2019 12;10:89. Epub 2019 Feb 12.

Geomicrobiology and Environmental Monitoring Unit, Bureau de Recherches Géologiques et Minières (BRGM), Orléans, France.

Microcosm experiments with CE-contaminated groundwater from a former industrial site were set-up to evaluate the relationships between biological CE dissipation, dehalogenase genes abundance and bacterial genera diversity. Impact of high concentrations of PCE on organohalide respiration was also evaluated. Complete or partial dechlorination of PCE, TCE, -DCE and VC was observed independently of the addition of a reducing agent (NaS) or an electron donor (acetate). The addition of either 10 or 100 μM PCE had no effect on organohalide respiration. qPCR analysis of reductive dehalogenases genes (, and ) indicated that the version of gene found in the genus [hereafter named (Dhc)] and gene increased in abundance by one order of magnitude during the first 10 days of incubation. The version of the gene found, among others, in the genus , and [hereafter named (Dhb)] and gene showed very low abundance. The gene was not detected throughout the experiment. The proportion of (Dhc) or genes relative to the universal 16S ribosomal RNA (16S rRNA) gene increased by up to 6-fold upon completion of DCE dissipation. Sequencing of 16S rRNA amplicons indicated that the abundance of Operational Taxonomic Units (OTUs) affiliated to dehalogenating genera , and represented more than 20% sequence abundance in the microcosms. Among organohalide respiration associated genera, only abundance of spp. increased up to fourfold upon complete dissipation of PCE and -DCE, suggesting a major implication of in CEs organohalide respiration. The relative abundance of and genes correlated with the occurrence of and with dissipation extent of PCE, -DCE and CV. A new type of dehalogenating sp. phylotype affiliated to the Pinellas group, and suggested to contain both (Dhc) and genes, may be involved in organohalide respiration of CEs in groundwater of the study site. Overall, the results demonstrate dechlorination potential of CE in the plume, and suggest that taxonomic and functional biomarkers in laboratory microcosms of contaminated groundwater following pollutant exposure can help predict bioremediation potential at contaminated industrial sites.
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http://dx.doi.org/10.3389/fmicb.2019.00089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379275PMC
February 2019

Extract Induces Cell Death of Mammalian Cells.

Antiinfect Agents 2018 ;16(2):144-146

I3S, Instituto de Investigação e Inovação da Universidade do Porto, Portugal.

Background: Fascioliasis is a neglected tropical disease that affects poor people from poor and developing countries. In the world, it has been estimated that at least 2.6 million people are affected with this disease. The International agency for Research on Cancer, states that and , also liver flukes, are considered as definitive causes of cholangiocarcinoma. However, fascioliasis caused by has not been associated with cancer to date. There are not any known causative associations between this parasite and liver cancer (cholangiocarcinoma).

Methods: Chine Hamster Ovary (CHO) cells were treated with extracts and cell proliferation was assessed by using the indirect method for estimating cell number based on the mitochondrial activity with MTS cell proliferation reagent. We observed unexpected death of these cells when treated with extracts.

Results: We now hypothesize that this parasite could be used as a medically-important trematode pathogen in cancer therapy.
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http://dx.doi.org/10.2174/1570180815666180531102555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6075840PMC
January 2018

Antibiotic-Induced Dysbiosis Predicts Mortality in an Animal Model of Clostridium difficile Infection.

Antimicrob Agents Chemother 2018 10 24;62(10). Epub 2018 Sep 24.

Da Volterra, Paris, France

Antibiotic disruption of the intestinal microbiota favors colonization by Using a charcoal-based adsorbent to decrease intestinal antibiotic concentrations, we studied the relationship between antibiotic concentrations in feces and the intensity of dysbiosis and quantified the link between this intensity and mortality. We administered either moxifloxacin ( = 70) or clindamycin ( = 60) to hamsters by subcutaneous injection from day 1 (D) to D and challenged them with a toxigenic strain at D Hamsters received various doses of a charcoal-based adsorbent, DAV131A, to modulate intestinal antibiotic concentrations. Gut dysbiosis was evaluated at D and D using diversity indices determined from 16S rRNA gene profiling. Survival was monitored until D We analyzed the relationship between fecal antibiotic concentrations and dysbiosis at the time of challenge and studied their capacity to predict subsequent death of the animals. Increasing doses of DAV131A reduced fecal concentrations of both antibiotics, lowered dysbiosis, and increased survival from 0% to 100%. Mortality was related to the level of dysbiosis ( < 10 for the change of Shannon index in moxifloxacin-treated animals and < 10 in clindamycin-treated animals). The Shannon diversity index and unweighted UniFrac distance best predicted death, with areas under the receiver operating curve (ROC) of 0.89 (95% confidence interval [CI], 0.82, 0.95) and 0.95 (0.90, 0.98), respectively. Altogether, moxifloxacin and clindamycin disrupted the diversity of the intestinal microbiota with a dependency on the DAV131A dose; mortality after challenge was related to the intensity of dysbiosis in similar manners with the two antibiotics.
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http://dx.doi.org/10.1128/AAC.00925-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6153837PMC
October 2018

Commentary: Parasites Secrete a Prolyl Isomerase to Maintain Host Leukocyte Transformation.

Front Med (Lausanne) 2018 27;5:120. Epub 2018 Apr 27.

I3S, Instituto de Investigação e Inovação da Universidade do Porto, Porto, Portugal.

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http://dx.doi.org/10.3389/fmed.2018.00120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5934426PMC
April 2018

Highlighting the microbial diversity of 12 French cheese varieties.

Int J Food Microbiol 2016 Dec 28;238:265-273. Epub 2016 Sep 28.

UMR Génie et Microbiologie des Procédés Alimentaires, GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France.

Surface-ripened cheeses host complex microbial communities responsible for the transformation of milk into cheese as well as the development of important properties in terms of texture, color and sensory perception. In this study, we used high-throughput amplicon sequencing to decipher the bacterial and fungal diversity of 60 cheeses belonging to 12 popular French cheese varieties. Using this approach, 76 bacterial and 44 fungal phylotypes were identified. Major differences were observed between rind and core samples and also according to cheese varieties and manufacturing processes. Occurrence analysis revealed the presence of widespread taxa as well as operational taxonomic units (OTUs) specific to one or several cheese varieties. Finally, we observed patterns specific to the cheese production facility, supporting the importance of indigenous microorganisms for the microbial assemblage of cheese microbiota.
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http://dx.doi.org/10.1016/j.ijfoodmicro.2016.09.026DOI Listing
December 2016

Corrigendum to "Snapshot on a Pilot Metagenomic Study for the Appraisal of Gut Microbial Diversity in Mice, Cat, and Man".

Gastroenterol Res Pract 2016 28;2016:3053727. Epub 2016 Jul 28.

Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, Centre d'Infection et d'Immunité de Lille, 59000 Lille, France.

[This corrects the article DOI: 10.1155/2016/6587825.].
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http://dx.doi.org/10.1155/2016/3053727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980530PMC
August 2016

Snapshot on a Pilot Metagenomic Study for the Appraisal of Gut Microbial Diversity in Mice, Cat, and Man.

Gastroenterol Res Pract 2016 24;2016:6587825. Epub 2016 Apr 24.

Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019, UMR 8204, Centre d'Infection et d'Immunité de Lille, 59000 Lille, France.

Gut microbiota plays a key role in the maintenance of homeostasis and host physiology, comprising development, metabolism, and immunity. Profiling the composition and the gastrointestinal microbiome with a reliable methodology is of substantial interest to yield new insights into the pathogenesis of many diseases as well as defining new prophylactic and therapeutic interventions. Here, we briefly present our methodology applied to fecal samples from mice and then further extended to the samples from a cat and a single human subject at 4 different time points as examples to illustrate the methodological strengths. Both interindividual and time-related variations are demonstrated and discussed.
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http://dx.doi.org/10.1155/2016/6587825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860491PMC
May 2016

Draft genome sequence of the intestinal parasite Blastocystis subtype 4-isolate WR1.

Genom Data 2015 Jun 2;4:22-3. Epub 2015 Feb 2.

Clermont Université, Université Blaise Pascal-Université d'Auvergne-CNRS, UMR 6023 Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France.

The intestinal protistan parasite Blastocystis is characterized by an extensive genetic variability with 17 subtypes (ST1-ST17) described to date. Only the whole genome of a human ST7 isolate was previously sequenced. Here we report the draft genome sequence of Blastocystis ST4-WR1 isolated from a laboratory rodent at Singapore.
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http://dx.doi.org/10.1016/j.gdata.2015.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535960PMC
June 2015

Seasonal variations of marine protist community structure based on taxon-specific traits using the eastern English Channel as a model coastal system.

FEMS Microbiol Ecol 2015 May 30;91(5). Epub 2015 Mar 30.

Laboratoire d'Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d'Opale (ULCO), 32 av. Foch, 62930 Wimereux, France

Previous microscopy-based studies in the eastern English Channel have revealed it to be a productive meso-eutrophic coastal ecosystem, characterized by strong repeating patterns in microplankton succession. The present study examines the seasonal structure of the entire protistan community from March 2011 to July 2013, using tag pyrosequencing of the V2-V3 hypervariable region of the 18S rRNA gene. A total of 1242 OTUs and 28 high-level taxonomic groups, which included previously undetected taxa in the area, were identified. The detected OTUs were considered according to taxon-specific traits, which included their trophic role, abundance and specialization level. Taxa differentiation based on specialization level rather than abundance was more informative in describing community organization. While generalists were always abundant, numerous specialists that were either rare or absent in most samples, increased in abundance for short periods, appearing to be overall abundant. Statistical and network analyses showed that the protistan seasonal organization was influenced by environmental parameters. It also highlighted that in addition to grazers, fungi and parasites played potentially significant roles during phytoplankton blooms. Overall, while the protistan succession was mainly shaped by environmental variations, biotic interactions among co-occurring taxa were the main structural drivers of the temporal assemblages.
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http://dx.doi.org/10.1093/femsec/fiv034DOI Listing
May 2015

Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species.

PLoS One 2015 13;10(1):e0116337. Epub 2015 Jan 13.

Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece.

Background: Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex.

Methodology/principal Findings: We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198's acquisition is not a recent event.

Conclusions/significance: Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116337PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4293149PMC
December 2015

Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition.

Microb Biotechnol 2015 Jan 4;8(1):131-42. Epub 2014 Sep 4.

INRA, UMR1347 Agroécologie, Plateforme GenoSol, Dijon, France.

This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO-11063, GnS-GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. A meta-barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS-GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO-11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO-11063 standard.
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http://dx.doi.org/10.1111/1751-7915.12162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321379PMC
January 2015

'Core species' in three sources of indoor air belonging to the human micro-environment to the exclusion of outdoor air.

Sci Total Environ 2014 Jul 16;485-486:508-517. Epub 2014 Apr 16.

Université Paris-Est, Centre Scientifique et Technique du Bâtiment (CSTB), Laboratoire de Recherche et d'Innovation pour l'Hygiène des Bâtiments, 84, avenue Jean Jaurès, Champs-sur-Marne, 77447 Marne-la-Vallée Cedex 2, France.

Although we spend the majority of our lives indoors, the airborne microbial content of enclosed spaces still remains inadequately described. The objective of this study was to characterize the bacterial diversity of indoor air in three different enclosed spaces with three levels of occupancy, and, in particular, to highlight the 'core' species, the opportunistic pathogens and their origins. Our findings provide an overall description of bacterial diversity in these indoor environments. Data gathered from the three enclosed spaces revealed the presence of a common indoor signature (60% of total sequences in common). This work will provide a clearer understanding of the dominant groups of bacteria encountered in enclosed spaces: Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. Thus, certain evidence revealed a connection between 'core' species and the human micro-environment (20% of phylotypes and 12% of sequences of human origin). Overall PCA analysis showed that the indoor environment is influenced mainly by the microbial diversity from nose and skin. Among the 'core species' found during this study, a large number (72% of all pathogen-related sequences were concentrated in 'core species') of genera and species are known to be responsible for opportunistic or nosocomial diseases or to include human commensal bacteria such as Mycobacterium sp., Acinetobacter baumanii, Aerococcus viridians, Thermoactinomyces vulgaris or Clostridium perfringens.
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http://dx.doi.org/10.1016/j.scitotenv.2014.03.117DOI Listing
July 2014

Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex.

BMC Genomics 2014 Apr 8;15:272. Epub 2014 Apr 8.

Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece.

Background: Within the genus Streptococcus, only Streptococcus thermophilus is used as a starter culture in food fermentations. Streptococcus macedonicus though, which belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC), is also frequently isolated from fermented foods mainly of dairy origin. Members of the SBSEC have been implicated in human endocarditis and colon cancer. Here we compare the genome sequence of the dairy isolate S. macedonicus ACA-DC 198 to the other SBSEC genomes in order to assess in silico its potential adaptation to milk and its pathogenicity status.

Results: Despite the fact that the SBSEC species were found tightly related based on whole genome phylogeny of streptococci, two distinct patterns of evolution were identified among them. Streptococcus macedonicus, Streptococcus infantarius CJ18 and Streptococcus pasteurianus ATCC 43144 seem to have undergone reductive evolution resulting in significantly diminished genome sizes and increased percentages of potential pseudogenes when compared to Streptococcus gallolyticus subsp. gallolyticus. In addition, the three species seem to have lost genes for catabolizing complex plant carbohydrates and for detoxifying toxic substances previously linked to the ability of S. gallolyticus to survive in the rumen. Analysis of the S. macedonicus genome revealed features that could support adaptation to milk, including an extra gene cluster for lactose and galactose metabolism, a proteolytic system for casein hydrolysis, auxotrophy for several vitamins, an increased ability to resist bacteriophages and horizontal gene transfer events with the dairy Lactococcus lactis and S. thermophilus as potential donors. In addition, S. macedonicus lacks several pathogenicity-related genes found in S. gallolyticus. For example, S. macedonicus has retained only one (i.e. the pil3) of the three pilus gene clusters which may mediate the binding of S. gallolyticus to the extracellular matrix. Unexpectedly, similar findings were obtained not only for the dairy S. infantarius CJ18, but also for the blood isolate S. pasteurianus ATCC 43144.

Conclusions: Our whole genome analyses suggest traits of adaptation of S. macedonicus to the nutrient-rich dairy environment. During this process the bacterium gained genes presumably important for this new ecological niche. Finally, S. macedonicus carries a reduced number of putative SBSEC virulence factors, which suggests a diminished pathogenic potential.
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http://dx.doi.org/10.1186/1471-2164-15-272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051162PMC
April 2014

Role of the phosphoinositide phosphatase FIG4 gene in familial epilepsy with polymicrogyria.

Neurology 2014 Mar 5;82(12):1068-75. Epub 2014 Mar 5.

From INSERM (S.B., B.D., B.O.A.B., P.C., J.R., E.N., K.H.E.H., E.L.), U1127; Sorbonne Universités, UPMC Univ Paris 06 (S.B., B.D., B.O.A.B., P.C., J.R., E.N., K.H.E.H., E.L.), UM 75; CNRS (S.B., B.D., B.O.A.B., P.C., J.R., E.N., K.H.E.H., E.L.), UMR 7225, ICM, Paris, ICM, (S.B., B.D., B.O.A.B., P.C., J.R., E.N., K.H.E.H., E.L.) Paris, F-75013 Paris, France; Department of Human Genetics (G.M.L., P.A.L., C.J.F., M.H.M.), University of Michigan, Ann Arbor; Service de Neurophysiologie Clinique (B.O.A.B.), Hôpital des Spécialités, Centre Hospitalier Ibn Sina Rabat, Morocco; Genetics and Pathophysiology of Neurodevelopmental and Neuromuscular Diseases (K.P.), Cochin Institute, Paris; GenoScreen (C.H., S.F.), Lille, France; Neuroscience Department (R.G.), Children's Hospital A. Meyer, University of Florence and IRCCS Stella Maris, Pisa, Italy; Laboratoire de Neurogénétique (K.H.E.H.), Ecole Pratique des Hautes Etudes, Paris; and Département de Génétique et de Cytogénétique (E.L.), AP-HP Groupe hospitalier Pitié-Salpêtrière, Paris, France.

Objective: The aim of this study was to identify the causal gene in a consanguineous Moroccan family with temporo-occipital polymicrogyria, psychiatric manifestations, and epilepsy, previously mapped to the 6q16-q22 region.

Methods: We used exome sequencing and analyzed candidate variants in the 6q16-q22 locus, as well as a rescue assay in Fig4-null mouse fibroblasts and immunohistochemistry of Fig4-null mouse brains.

Results: A homozygous missense mutation (p.Asp783Val) in the phosphoinositide phosphatase gene FIG4 was identified. Pathogenicity of the variant was supported by impaired rescue of the enlarged vacuoles in transfected fibroblasts from Fig4-deficient mice. Histologic examination of Fig4-null mouse brain revealed neurodevelopmental impairment in the hippocampus, cortex, and cerebellum as well as impaired cerebellar gyration/foliation reminiscent of human cortical malformations.

Conclusions: This study extends the spectrum of phenotypes associated with FIG4 mutations to include cortical malformation associated with seizures and psychiatric manifestations, in addition to the previously described Charcot-Marie-Tooth disease type 4J and Yunis-Varón syndrome.
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http://dx.doi.org/10.1212/WNL.0000000000000241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962989PMC
March 2014

Complete genome sequence of the dairy isolate Streptococcus macedonicus ACA-DC 198.

J Bacteriol 2012 Apr;194(7):1838-9

Laboratory of Dairy Research, Department of Food Science and Technology, Agricultural University of Athens, Athens, Greece.

The species Streptococcus macedonicus is associated with the food environment, especially with fermented dairy products. Here we present the complete 2.1-Mb genome sequence of strain ACA-DC 198, which was isolated from naturally fermented Greek kasseri cheese.
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http://dx.doi.org/10.1128/JB.06804-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302469PMC
April 2012

High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries.

Mol Ecol Resour 2011 Jul 21;11(4):638-44. Epub 2011 Feb 21.

INRA, UMR 1301 IBSV INRA/UNSA/CNRS, 400 Route des Chappes, BP 167, 06903 Sophia-Antipolis Cedex, France.

Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next-generation sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11,497 to 34,483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high-quality genetic markers for nonmodel organisms.
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http://dx.doi.org/10.1111/j.1755-0998.2011.02992.xDOI Listing
July 2011

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing.

BMC Genomics 2011 May 19;12:245. Epub 2011 May 19.

Aix-Marseille Université, CNRS, IRD, UMR 6116 - IMEP, Equipe Evolution Génome Environnement, Centre Saint-Charles, Case 36, 3 place Victor Hugo, 13331 Marseille Cedex 3, France.

Background: The rapid evolution of 454 GS-FLX sequencing technology has not been accompanied by a reassessment of the quality and accuracy of the sequences obtained. Current strategies for decision-making and error-correction are based on an initial analysis by Huse et al. in 2007, for the older GS20 system based on experimental sequences. We analyze here the quality of 454 sequencing data and identify factors playing a role in sequencing error, through the use of an extensive dataset for Roche control DNA fragments.

Results: We obtained a mean error rate for 454 sequences of 1.07%. More importantly, the error rate is not randomly distributed; it occasionally rose to more than 50% in certain positions, and its distribution was linked to several experimental variables. The main factors related to error are the presence of homopolymers, position in the sequence, size of the sequence and spatial localization in PT plates for insertion and deletion errors. These factors can be described by considering seven variables. No single variable can account for the error rate distribution, but most of the variation is explained by the combination of all seven variables.

Conclusions: The pattern identified here calls for the use of internal controls and error-correcting base callers, to correct for errors, when available (e.g. when sequencing amplicons). For shotgun libraries, the use of both sequencing primers and deep coverage, combined with the use of random sequencing primer sites should partly compensate for even high error rates, although it may prove more difficult than previous thought to distinguish between low-frequency alleles and errors.
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http://dx.doi.org/10.1186/1471-2164-12-245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116506PMC
May 2011

Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX titanium pyrosequencing.

BMC Genomics 2010 Oct 12;11:560. Epub 2010 Oct 12.

Centre de biologie et de gestion des Populations, Montpellier SupAgro, INRA, IRD, CIRAD, Campus International de Baillarguet, CS30016, Montferrier sur Lez cedex, France.

Background: Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatellites through multiplex-enriched libraries and 454 GS-FLX Titanium pyrosequencing is a promising new tool for the isolation of new markers in unknown genomes. This approach can also be used to evaluate the extent to which microsatellite-enriched libraries are representative of the genome from which they were isolated. In this study, we deciphered potential discrepancies in microsatellite content recovery for two reference genomes (Apis mellifera and Danio rerio), selected on the basis of their extreme heterogeneity in terms of the proportions and distributions of microsatellites on chromosomes.

Results: The A. mellifera genome, in particular, was found to be highly heterogeneous, due to extremely high rates of recombination, with hotspots, but the only bias consistently introduced into pyrosequenced multiplex-enriched libraries concerned sequence length, with the overrepresentation of sequences 160 to 320 bp in length. Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited. Furthermore, no consistent adverse competition between multiplexed probes was observed during the motif enrichment phase.

Conclusions: This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.
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http://dx.doi.org/10.1186/1471-2164-11-560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091709PMC
October 2010

Pin1 allows for differential Tau dephosphorylation in neuronal cells.

Mol Cell Neurosci 2006 May-Jun;32(1-2):155-60. Epub 2006 May 11.

Inserm, U815, Institut de Médecine Prédictive et Recherche Thérapeutique, F-59045 Lille, France.

Neurofibrillary degeneration is likely to be related to abnormal Tau phosphorylation and aggregation. Among abnormal Tau phosphorylation sites, pThr231 is of particular interest since it is associated with early stages of Alzheimer's disease and is a binding site of Pin1, a peptidyl-prolyl cis/trans isomerase mainly involved in cell cycle regulation. In the present work, Pin1 level was found strongly increased during neuronal differentiation and tightly correlated with Tau dephosphorylation at Thr231. Likewise, we showed in cellular model that Pin1 allowed for specific Tau dephosphorylation at Thr231, whereas other phosphorylation sites were unchanged. Moreover, cells displaying Tau phosphorylation at Thr231 did not show any Pin1 nuclear depletion. Altogether, these data indicate that Pin1 has key function(s) in neuron and is at least involved in the regulation of Tau phosphorylation at relevant sites. Hence, Pin1 dysfunction, unlikely by nuclear depletion, may have critical consequences on Tau pathological aggregation and neuronal death.
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http://dx.doi.org/10.1016/j.mcn.2006.03.006DOI Listing
September 2006

Evidence of a balance between phosphorylation and O-GlcNAc glycosylation of Tau proteins--a role in nuclear localization.

Biochim Biophys Acta 2003 Jan;1619(2):167-76

Laboratoire de Chimie Biologique, Unité Mixte de Recherches 8576 du CNRS, Université des Sciences et Technologies de Lille I, F-59655 Villeneuve d'Ascq, France.

Both phosphorylation and O-GlcNAc glycosylation posttranslationally modify microtubule-associated Tau proteins. Whereas the hyperphosphorylation of these proteins that occurs in Alzheimer's disease is well characterized, little is known about the O-GlcNAc glycosylation. The present study demonstrates that a balance exists between phosphorylation and O-GlcNAc glycosylation of Tau proteins, and furthermore that a dysfunction of this balance correlates with reduced nuclear localization. The affinity of Tau proteins for WGA lectin, together with evidence from [3H]-galactose transfer and analysis of beta-eliminated products, demonstrated the presence of O-GlcNAc residues on both cytosolic and nuclear Tau proteins. In addition, our data indicated the existence of a balance between phosphorylation and O-GlcNAc glycosylation events. Indeed, as demonstrated by 2D-electrophoresis and Western blotting, O-GlcNAc residues were mainly located on the less phosphorylated Tau 441 variants, whereas the more phosphorylated forms were devoid of O-GlcNAc residues. Furthermore, the Tau protein hyperphosphorylation induced by cellular okadaic acid treatment was correlated with reduced incorporation of O-GlcNAc residues into Tau proteins and with diminished Tau transfer into the nucleus. Hence, this paper establishes a direct relationship between O-GlcNAc glycosylation, phosphorylation and cellular localization of Tau proteins.
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http://dx.doi.org/10.1016/s0304-4165(02)00477-4DOI Listing
January 2003
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