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Article: In vitro sensitivity of 30 anaerobic bacterial strains of the human intestinal core microbiota to antibiotics: Culture and LC-MS/MS approaches

Ecale, Florine / El Houari, Abdelaziz / Crapart, Stéphanie / Laparre, Jérome / Ramnath, Manilduth / Berjeaud, Jean-Marc / Rodier, Marie-Hélène / Crépin, Alexandre

Anaerobe. 2021 Feb., v. 67

2021

Abstract: We have a vast knowledge on human intestinal microbiota but it can still be regarded incomplete. One of the objectives of scientists using so-called "omics" techniques is to be interested in the consequences that drugs can have on the composition of the ... ...

Abstract	We have a vast knowledge on human intestinal microbiota but it can still be regarded incomplete. One of the objectives of scientists using so-called "omics" techniques is to be interested in the consequences that drugs can have on the composition of the intestinal microbiota and inversely. To date, few publications have reported the effects of drugs on the growth of bacteria composing this microbiota using a "culturomics" approach. We focused on antibiotics commonly prescribed for which the only published are the susceptibility of the pathogenic strains and not that of the commensal strains. The aim of our study was to determine the sensitivity of 30 strains considered to represent the intestinal core microbiota to 8 antibiotics and to study the possible modification of these molecules by bacteria. The 30 bacterial strains were cultured under anaerobic conditions in order to determine their sensitivity to the antibiotics. After 48 h of culture, the supernatants were also analyzed via UHPLC-MS/MS in order to determine if the antibiotics have been chemically modified. Under the current experimental conditions, cefpodoxime, metronidazole, erythromycin, sulfamethozaxole, trimethoprim and the trimethoprim/sulfamethozaxole combination have little impact on the core microbiota strain growth. On the contrary, moxifloxacin and amoxicillin inhibit the growth of numerous strains of our panel. Using UHPLC-MS/MS analyses, we have shown that some antibiotics can be modifed by the bacteria composing the intestinal core microbiome. The bacteria that make up the intestinal microbiota core are impacted by the antibiotics most commonly prescribed in clinics today and inversely.
Keywords	amoxicillin ; anaerobic conditions ; bacteria ; cefpodoxime ; erythromycin ; humans ; intestinal microorganisms ; intestines ; knowledge ; methodology ; metronidazole ; microbiome ; moxifloxacin ; objectives ; publications ; scientists ; trimethoprim ; virulent strains
Language	English
Dates of publication	2021-02
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-light
ZDB-ID	1237621-8
ISSN	1075-9964
ISSN	1075-9964
DOI	10.1016/j.anaerobe.2020.102314
Database	NAL-Catalogue (AGRICOLA)

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Article: Development of an

El Houari, Abdelaziz / Ecale, Florine / Mercier, Anne / Crapart, Stéphanie / Laparre, Jérôme / Soulard, Baptiste / Ramnath, Manilduth / Berjeaud, Jean-Marc / Rodier, Marie-Hélène / Crépin, Alexandre

Frontiers in microbiology

2022 Volume 13, Page(s) 828359

Abstract: Altering the gut microbiota can negatively affect human health. Efforts may be sustained to predict the intended or unintended effects of molecules not naturally produced or expected to be present within the organism on the gut microbiota. Here, culture- ... ...

Abstract	Altering the gut microbiota can negatively affect human health. Efforts may be sustained to predict the intended or unintended effects of molecules not naturally produced or expected to be present within the organism on the gut microbiota. Here, culture-dependent and DNA-based approaches were combined to UHPLC-MS/MS analyses in order to investigate the reciprocal interactions between a constructed Human Gut Microbiota Model (HGMM) and molecules including antibiotics, drugs, and xenobiotics. Our HGMM was composed of strains from the five phyla commonly described in human gut microbiota and belonging to
Language	English
Publishing date	2022-04-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.828359
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Article ; Online: In vitro sensitivity of 30 anaerobic bacterial strains of the human intestinal core microbiota to antibiotics: Culture and LC-MS/MS approaches.

Ecale, Florine / El Houari, Abdelaziz / Crapart, Stéphanie / Laparre, Jérome / Ramnath, Manilduth / Berjeaud, Jean-Marc / Rodier, Marie-Hélène / Crépin, Alexandre

Anaerobe

2020 Volume 67, Page(s) 102314

Abstract	We have a vast knowledge on human intestinal microbiota but it can still be regarded incomplete. One of the objectives of scientists using so-called "omics" techniques is to be interested in the consequences that drugs can have on the composition of the intestinal microbiota and inversely. To date, few publications have reported the effects of drugs on the growth of bacteria composing this microbiota using a "culturomics" approach. We focused on antibiotics commonly prescribed for which the only published are the susceptibility of the pathogenic strains and not that of the commensal strains. The aim of our study was to determine the sensitivity of 30 strains considered to represent the intestinal core microbiota to 8 antibiotics and to study the possible modification of these molecules by bacteria. The 30 bacterial strains were cultured under anaerobic conditions in order to determine their sensitivity to the antibiotics. After 48 h of culture, the supernatants were also analyzed via UHPLC-MS/MS in order to determine if the antibiotics have been chemically modified. Under the current experimental conditions, cefpodoxime, metronidazole, erythromycin, sulfamethozaxole, trimethoprim and the trimethoprim/sulfamethozaxole combination have little impact on the core microbiota strain growth. On the contrary, moxifloxacin and amoxicillin inhibit the growth of numerous strains of our panel. Using UHPLC-MS/MS analyses, we have shown that some antibiotics can be modifed by the bacteria composing the intestinal core microbiome. The bacteria that make up the intestinal microbiota core are impacted by the antibiotics most commonly prescribed in clinics today and inversely.
MeSH term(s)	Amoxicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Chromatography, Liquid/methods ; Gastrointestinal Microbiome/drug effects ; Humans ; Mass Screening ; Metronidazole/pharmacology ; Microbial Sensitivity Tests ; Moxifloxacin/pharmacology ; Sulfamethoxazole/pharmacology ; Tandem Mass Spectrometry/methods
Chemical Substances	Anti-Bacterial Agents ; Metronidazole (140QMO216E) ; Amoxicillin (804826J2HU) ; Sulfamethoxazole (JE42381TNV) ; Moxifloxacin (U188XYD42P)
Language	English
Publishing date	2020-12-30
Publishing country	England
Document type	Journal Article
ZDB-ID	1237621-8
ISSN	1095-8274 ; 1075-9964
ISSN (online)	1095-8274
ISSN	1075-9964
DOI	10.1016/j.anaerobe.2020.102314
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Article ; Online: Comprehensive steroid profiling by liquid chromatography coupled to high resolution mass spectrometry.

Kaabia, Zied / Laparre, Jérôme / Cesbron, Nora / Le Bizec, Bruno / Dervilly-Pinel, Gaud

The Journal of steroid biochemistry and molecular biology

2018 Volume 183, Page(s) 106–115

Abstract: A steroidomics workflow has been developed in the objective of monitoring a wide range (n >150) of steroids in urine. The proposed workflow relies on the optimization of an adequate SPE extraction step followed by an UHPLC-HRMS/MS simultaneous analysis ... ...

Abstract	A steroidomics workflow has been developed in the objective of monitoring a wide range (n >150) of steroids in urine. The proposed workflow relies on the optimization of an adequate SPE extraction step followed by an UHPLC-HRMS/MS simultaneous analysis of both free and conjugated forms of C18, C19 and C21 steroid hormones. On the basis of 44 selected steroids, representative of main classes of steroids constituting the steroidome, the performances of the developed workflow were evaluated in terms of selectivity, repeatability (< 13%) and linearity (R2> 0.985 in the concentration range [0.01-10 ng/mL]). As metabolites identification and characterization constitute the bottleneck of such profiling approaches, a homemade database was created encompassing a large number of characterized free and conjugated steroids (n> 150) for putative steroid-like biomarkers identification purposes. The efficiency of the workflow in highlighting fine modifications within the urinary steroidome was assessed in the frame of an anabolic treatment involving an intra-muscular administration of boldenone undecylenate (2 mg/kg) to veals (n=6) and the investigation of potential steroid biomarkers. Besides monitoring known phase II metabolites of boldenone in the bovine specie, namely, boldenone glucuronide and sulfate, the applied strategy also permitted to observe, upon boldenone administration, a modified profile of epiboldenone glucuronide. Furthermore, 31 signals corresponding to non-identified steroid species could also be highlighted as impacted upon the exogenous steroid treatment. This study is the first to simultaneously investigate both free and conjugated C18, C19 and C21 steroid hormones in their native form using UHPLC-HRMS/MS and allowing their comprehensive profiling. This strategy was probed in-vivo.
MeSH term(s)	Animals ; Biomarkers/urine ; Cattle ; Chromatography, Liquid/methods ; Steroids/urine ; Tandem Mass Spectrometry/methods
Chemical Substances	Biomarkers ; Steroids
Language	English
Publishing date	2018-07-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1049188-0
ISSN	1879-1220 ; 0960-0760
ISSN (online)	1879-1220
ISSN	0960-0760
DOI	10.1016/j.jsbmb.2018.06.003
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Article ; Online: Impact of storage conditions on the urinary metabolomics fingerprint.

Laparre, Jérôme / Kaabia, Zied / Mooney, Mark / Buckley, Tom / Sherry, Mark / Le Bizec, Bruno / Dervilly-Pinel, Gaud

Analytica chimica acta

2017 Volume 951, Page(s) 99–107

Abstract: Urine stability during storage is essential in metabolomics to avoid misleading conclusions or erroneous interpretations. Facing the lack of comprehensive studies on urine metabolome stability, the present work performed a follow-up of potential ... ...

Abstract	Urine stability during storage is essential in metabolomics to avoid misleading conclusions or erroneous interpretations. Facing the lack of comprehensive studies on urine metabolome stability, the present work performed a follow-up of potential modifications in urinary chemical profile using LC-HRMS on the basis of two parameters: the storage temperature (+4 °C, -20 °C, -80 °C and freeze-dried stored at -80 °C) and the storage duration (5-144 days). Both HILIC and RP chromatographies have been implemented in order to globally monitor the urinary metabolome. Using an original data processing associated to univariate and multivariate data analysis, our study confirms that chemical profiles of urine samples stored at +4 °C are very rapidly modified, as observed for instance for compounds such as:N-acetyl Glycine, Adenosine, 4-Amino benzoic acid, N-Amino diglycine, creatine, glucuronic acid, 3-hydroxy-benzoic acid, pyridoxal, l-pyroglutamic acid, shikimic acid, succinic acid, thymidine, trigonelline and valeryl-carnitine, while it also demonstrates that urine samples stored at -20 °C exhibit a global stability over a long period with no major modifications compared to -80 °C condition. This study is the first to investigate long term stability of urine samples and report potential modifications in the urinary metabolome, using both targeted approach monitoring individually a large number (n > 200) of urinary metabolites and an untargeted strategy enabling assessing for global impact of storage conditions.
Language	English
Publishing date	2017-01-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1483436-4
ISSN	1873-4324 ; 0003-2670
ISSN (online)	1873-4324
ISSN	0003-2670
DOI	10.1016/j.aca.2016.11.055
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Article ; Online: Combining metabolomics and gene expression analysis reveals that propionyl- and butyryl-carnitines are involved in late stages of arbuscular mycorrhizal symbiosis.

Laparre, Jérôme / Malbreil, Mathilde / Letisse, Fabien / Portais, Jean Charles / Roux, Christophe / Bécard, Guillaume / Puech-Pagès, Virginie

Molecular plant

2014 Volume 7, Issue 3, Page(s) 554–566

Abstract: The arbuscular mycorrhizal (AM) symbiosis is a widespread mutualistic association between soil fungi (Glomeromycota) and the roots of most plant species. AM fungi are obligate biotrophs whose development is partially under the control of their plant host. ...

Abstract	The arbuscular mycorrhizal (AM) symbiosis is a widespread mutualistic association between soil fungi (Glomeromycota) and the roots of most plant species. AM fungi are obligate biotrophs whose development is partially under the control of their plant host. We explored the possibility to combine metabolomic and transcriptomic approaches to find putative mycorrhiza-associated metabolites regulating AM fungal development. Methanol extracts of Medicago truncatula roots colonized or not with the AM fungus Rhizophagus irregularis were analyzed and compared by ultra-high-performance liquid chromatography (UHPLC), high-resolution mass spectrometry (Q-TOF), and multivariate statistical discrimination. We detected 71 mycorrhiza-associated analytes exclusively present or at least 10-fold more abundant in mycorrhizal roots. To identify among these analytes those that could regulate AM fungal development, we fractionated by preparative and semi-preparative HPLC the mycorrhizal and non-mycorrhizal root extracts and established how the 71 analytes were distributed among the fractions. Then we tested the activity of the fractions on germinating spores of R. irregularis by quantifying the expression of 96 genes known for their diverse in planta expression patterns. These investigations reveal that propionyl- and butyryl-carnitines accumulated in mycorrhizal roots. The results suggest that these two molecules regulate fungal gene expression in planta and represent interesting candidates for further biological characterization.
MeSH term(s)	Carnitine/metabolism ; Gene Expression Regulation, Plant/genetics ; Gene Expression Regulation, Plant/physiology ; Glomeromycota/genetics ; Glomeromycota/physiology ; Mycorrhizae/genetics ; Mycorrhizae/physiology ; Plant Roots/microbiology ; Symbiosis/genetics ; Symbiosis/physiology
Chemical Substances	Carnitine (S7UI8SM58A)
Language	English
Publishing date	2014-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2393618-6
ISSN	1752-9867 ; 1674-2052
ISSN (online)	1752-9867
ISSN	1674-2052
DOI	10.1093/mp/sst136
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Article ; Online: Metabolite profiling of pea roots in response to phosphate availability.

Laparre, Jérôme / Balzergue, Coline / Rochange, Soizic / Ludwiczak, Pascal / Letisse, Fabien / Portais, Jean Charles / Bécard, Guillaume / Puech-Pages, Virginie

Plant signaling & behavior

2011 Volume 6, Issue 6, Page(s) 837–839

Abstract: The arbuscular mycorrhizal (AM) symbiosis is a mutualistic association between soil fungi (Glomeromycota) and roots of most plant species. A recent study showed that high phosphate fertilization could inhibit mycorrhizal colonization at a very early ... ...

Abstract	The arbuscular mycorrhizal (AM) symbiosis is a mutualistic association between soil fungi (Glomeromycota) and roots of most plant species. A recent study showed that high phosphate fertilization could inhibit mycorrhizal colonization at a very early stage, before hyphopodium formation. The authors proposed that inhibiting and/or stimulatory compounds might be present in roots grown under high phosphate or low phosphate, respectively. To further address this question, we performed metabolite profiling analyses of extracts of pea roots grown under low and high phosphate concentrations. Ultra high performance liquid chromatography (UHPLC) was coupled with high resolution (HR) mass spectrometry (Q-TOF) and multivariate statistical analysis. This allowed the detection of 34 ions discriminating the two conditions. A majority (28 ions) were more abundant in roots grown under low phosphate concentration, and among them four were specific of this condition. The results suggest that the regulation of AM symbiosis by phosphate may involve the synthesis or accumulation of stimulatory compounds in roots grown under low phosphate.
MeSH term(s)	Chromatography, High Pressure Liquid ; Discriminant Analysis ; Mass Spectrometry ; Metabolomics/methods ; Pisum sativum/drug effects ; Pisum sativum/growth & development ; Pisum sativum/metabolism ; Phosphates/pharmacology ; Plant Extracts/metabolism ; Plant Roots/drug effects ; Plant Roots/metabolism ; Principal Component Analysis
Chemical Substances	Phosphates ; Plant Extracts
Language	English
Publishing date	2011-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1559-2324
ISSN (online)	1559-2324
DOI	10.4161/psb.6.6.15168
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Article ; Online: Serum profile in preeclampsia and intra-uterine growth restriction revealed by iTRAQ technology.

Auer, Jana / Camoin, Luc / Guillonneau, François / Rigourd, Virginie / Chelbi, Sonia T / Leduc, Marjorie / Laparre, Jérôme / Mignot, Thérèse-Marie / Vaiman, Daniel

Journal of proteomics

2010 Volume 73, Issue 5, Page(s) 1004–1017

Abstract: In order to identify new protein markers modified in placental diseases, high-throughput analysis of proteins in the plasma of pregnant women was carried out for normal and pathological pregnancies (Preeclampsia and/or Intra-Uterine Growth Restriction) ... ...

Abstract	In order to identify new protein markers modified in placental diseases, high-throughput analysis of proteins in the plasma of pregnant women was carried out for normal and pathological pregnancies (Preeclampsia and/or Intra-Uterine Growth Restriction) using iTRAQ technology. We could identify 166 proteins that were modified (p<0.05) and the technique used allowed the detection of previously undetected factors, such as various members of the SERPINA clade. The modifications of two proteins (C reactive protein and antichymotrypsin, SERPINA3) were validated on individual samples. Complement and coagulation cascades proteins were significantly enriched among modified protein clusters in the case of intra-uterine growth restriction (p<2.6.10(-11)). Several proteins were specifically enriched in isolated preeclampsia and depleted when preeclampsia was complicated by intra-uterine growth restriction. These findings suggest that the growth restricted foeto-placental unit is able to moderate some changes in maternal plasma composition. Overall, the use of iTRAQ technology, for the first time on this subject, enabled us to provide a new list of proteins modified in placental diseases, among which proteins expressed at a low level that were not accessible by other methods.
MeSH term(s)	Biomarkers ; Blood Proteins/analysis ; C-Reactive Protein/analysis ; Case-Control Studies ; Female ; Fetal Growth Retardation/blood ; Fetal Growth Retardation/diagnosis ; Humans ; Pre-Eclampsia/blood ; Pre-Eclampsia/diagnosis ; Pregnancy ; Serpins/blood
Chemical Substances	Biomarkers ; Blood Proteins ; SERPINA3 protein, human ; Serpins ; C-Reactive Protein (9007-41-4)
Language	English
Publishing date	2010-03-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2009.12.014
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