Journal of Microbiology

Journal Article

Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities: Edmond Kuete Yimagou , Jean-Pierre Baudoin , Rita Abou Abdallah , Fabrizio Di Pinto , Jacques Yaacoub Bou Khalil , Didier Raoult; J. Microbiol. 2020;58(5):377-386. Published online April 11, 2020; DOI: https://doi.org/10.1007/s12275-020-9365-3

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The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the “microscomics” approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our cultureindependent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect “minimicrobes” Candidate Phyla Radiation (CPR) for the first time in human stool samples. This “microscomics” approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.

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Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease
Sabrina Naud, Ahmad Ibrahim, Camille Valles, Mohamad Maatouk, Fadi Bittar, Maryam Tidjani Alou, Didier Raoult
Clinical Microbiology Reviews.2022;[Epub] CrossRef
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Jing Liu, Chao Liu, Jinbo Yue
Radiation Oncology.2021;[Epub] CrossRef
Host–microbiota maladaptation in colorectal cancer
Alina Janney, Fiona Powrie, Elizabeth H. Mann
Nature.2020; 585(7826): 509. CrossRef

Research Support, Non-U.S. Gov'ts

Pseudomonas aeruginosa MdaB and WrbA are Water-soluble Two-electron Quinone Oxidoreductases with the Potential to Defend against Oxidative Stress: Laura K Green , Anne C La Flamme , David F Ackerley; J. Microbiol. 2014;52(9):771-777. Published online August 2, 2014; DOI: https://doi.org/10.1007/s12275-014-4208-8

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Abstract

Water-soluble quinone oxidoreductases capable of reducing quinone substrates via a concerted two-electron mechanism have been implicated in bacterial antioxidant defence. Twoelectron transfer avoids formation of dangerously reactive semi-quinone intermediates, moreover previous work in Pseudomonas putida indicated a direct protective effect for the quinols generated by an over-expressed oxidoreductase. Here, the Pseudomonas aeruginosa orthologs of five quinone oxidoreductases – MdaB, ChrR, WrbA, NfsB, and NQO1 – were tested for their possible role in defending P. aeruginosa against H2O2 challenge. In in vitro assays, each enzyme was shown to reduce quinone substrates with only minimal semiquinone formation. However, when each was individually over-expressed in P. aeruginosa no overt H2O2-protective phenotype was observed. It was shown that this was due to a masking effect of the P. aeruginosa catalase, KatA; in a katA mutant, H2O2 challenged strains over-expressing the WrbA and MdaB orthologs grew significantly better than the empty plasmid control. A growth advantage was also observed for H2O2 challenged P. putida strains over-expressing P. aeruginosa wrbA, mdaB or katA. Despite not conferring a growth advantage to wild type P. aeruginosa, it is possible that these quinone oxidoreductases defend against H2O2 toxicity at lower concentrations.

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Cyclic Isothiocyanate Goitrin Impairs Lotus japonicus Nodulation, Affects the Proteomes of Nodules and Free Mesorhizobium loti, and Induces the Formation of Caffeic Acid Derivatives in Bacterial Cultures
Seungwoo Jeong, Vadim Schütz, Fatih Demir, Matthias Preusche, Pitter Huesgen, Laurent Bigler, Filip Kovacic, Katharina Gutbrod, Peter Dörmann, Margot Schulz
Plants.2024; 13(20): 2897. CrossRef
Effects of the Quinone Oxidoreductase WrbA on Escherichia coli Biofilm Formation and Oxidative Stress
Federico Rossi, Cristina Cattò, Gianmarco Mugnai, Federica Villa, Fabio Forlani
Antioxidants.2021; 10(6): 919. CrossRef
Enrichment and description of novel bacteria performing syntrophic propionate oxidation at high ammonia level
Abhijeet Singh, Anna Schnürer, Maria Westerholm
Environmental Microbiology.2021; 23(3): 1620. CrossRef
Plasma Membrane MCC/Eisosome Domains Promote Stress Resistance in Fungi
Carla E. Lanze, Rafael M. Gandra, Jenna E. Foderaro, Kara A. Swenson, Lois M. Douglas, James B. Konopka
Microbiology and Molecular Biology Reviews.2020;[Epub] CrossRef
Diazaquinomycin Biosynthetic Gene Clusters from Marine and Freshwater Actinomycetes
Jana Braesel, Jung-Ho Lee, Benoit Arnould, Brian T. Murphy, Alessandra S. Eustáquio
Journal of Natural Products.2019; 82(4): 937. CrossRef
Kinetic Investigation of a Presumed Nitronate Monooxygenase from Pseudomonas aeruginosa PAO1 Establishes a New Class of NAD(P)H:Quinone Reductases
Renata A. G. Reis, Francesca Salvi, Isabella Williams, Giovanni Gadda
Biochemistry.2019; 58(22): 2594. CrossRef
Quantitative Proteomics of the 2016 WHO Neisseria gonorrhoeae Reference Strains Surveys Vaccine Candidates and Antimicrobial Resistance Determinants
Fadi E. El-Rami, Ryszard A. Zielke, Teodora Wi, Aleksandra E. Sikora, Magnus Unemo
Molecular & Cellular Proteomics.2019; 18(1): 127. CrossRef
Escherichia coli Modulator of Drug Activity B (MdaB) Has Different Enzymological Properties to Eukaryote Quinone Oxidoreductases
Clare F. Megarity, David J. Timson
Helvetica Chimica Acta.2019;[Epub] CrossRef
Identification of a Small Molecule Anti-biofilm Agent Against Salmonella enterica
Jasmine Moshiri, Darpan Kaur, Chido M. Hambira, Jenna L. Sandala, Jacob A. Koopman, James R. Fuchs, John S. Gunn
Frontiers in Microbiology.2018;[Epub] CrossRef
Kinetic Characterization of PA1225 from Pseudomonas aeruginosa PAO1 Reveals a New NADPH:Quinone Reductase
Elias Flores, Giovanni Gadda
Biochemistry.2018; 57(21): 3050. CrossRef
Pseudomonas aeruginosa ttcA encoding tRNA-thiolating protein requires an iron-sulfur cluster to participate in hydrogen peroxide-mediated stress protection and pathogenicity
Adisak Romsang, Jintana Duang-nkern, Khwannarin Khemsom, Lampet Wongsaroj, Kritsakorn Saninjuk, Mayuree Fuangthong, Paiboon Vattanaviboon, Skorn Mongkolsuk
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WrpA Is an Atypical Flavodoxin Family Protein under Regulatory Control of the Brucella abortus General Stress Response System
Julien Herrou, Daniel M. Czyż, Jonathan W. Willett, Hye-Sook Kim, Gekleng Chhor, Gyorgy Babnigg, Youngchang Kim, Sean Crosson, A. M. Stock
Journal of Bacteriology.2016; 198(8): 1281. CrossRef
Identification of novel members of the bacterial azoreductase family in Pseudomonas aeruginosa
Vincenzo Crescente, Sinead M. Holland, Sapna Kashyap, Elena Polycarpou, Edith Sim, Ali Ryan
Biochemical Journal.2016; 473(5): 549. CrossRef
Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH:Quinone Reductases
Jacob Ball, Francesca Salvi, Giovanni Gadda
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Nitroreductase gene-directed enzyme prodrug therapy: insights and advances toward clinical utility
Elsie M. Williams, Rory F. Little, Alexandra M. Mowday, Michelle H. Rich, Jasmine V.E. Chan-Hyams, Janine N. Copp, Jeff B. Smaill, Adam V. Patterson, David F. Ackerley
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Molecular Characterization of Chloranilic Acid Degradation in Pseudomonas putida TQ07: Luis G. Treviño-Quintanilla , Julio A. Freyre-González , Rosa A. Guillén-Garcés , Clarita Olvera; J. Microbiol. 2011;49(6):974-980. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1507-1

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Abstract: Pentachlorophenol is the most toxic and recalcitrant chlorophenol because both aspects are directly proportional to the halogenation degree. Biological and abiotic pentachlorophenol degradation generates p-chloranil, which in neutral to lightly alkaline environmental conditions is hydrolyzed to chloranilic acid that present a violet-reddish coloration in aqueous solution. Several genes of the degradation pathway, cadR-cadCDX, as well as other uncharacterized genes (ORF5 and 6), were isolated from a chloranilic acid degrading bacterium, Pseudomonas putida strain TQ07. The disruption by random mutagenesis of the cadR and cadC genes in TQ07 resulted in a growth deficiency in the presence of chloranilic acid, indicating that these genes are essential for TQ07 growth with chloranilic acid as the sole carbon source. Complementation assays demonstrated that a transposon insertion in mutant CAD82 (cadC) had a polar effect on other genes contained in cosmid pLG3562. These results suggest that at least one of these genes, cadD and cadX, also takes part in chloranilic acid degradation. Based on molecular modeling and function prediction, we strongly suggest that CadC is a pyrone dicarboxylic acid hydrolase and CadD is an aldolase enzyme like dihydrodipicolinate synthase. The results of this study allowed us to propose a novel pathway that offers hypotheses on chloranilic acid degradation (an abiotic by-product of pentachlorophenol) by means of a very clear phenotype that is narrowly related to the capability of Pseudomonas putida strain TQ07 to degrade this benzoquinone.

Isolation and Characterization of Ethylbenzene Degrading Pseudomonas putida E41: Lan-Hee Kim , Sang-Seob Lee; J. Microbiol. 2011;49(4):575-584. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0399-4

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Abstract: Pseudomonas putida E41 was isolated from oil-contaminated soil and showed its ability to grow on ethylbenzene as the sole carbon and energy source. Moreover, P. putida E41 show the activity of biodegradation of ethylbenzene in the batch culture. E41 showed high efficiency of biodegradation of ethylbenzene with the optimum conditions (a cell concentration of 0.1 g wet cell weight/L, pH 7.0, 25°C, and ethylbenzene concentration of 50 mg/L) from the results of the batch culture. The maximum degradation rate and specific growth rate (μmax) under the optimum conditions were 0.19±0.03 mg/mg-DCW (Dry Cell Weight)/h and 0.87±0.13 h-1, respectively. Benzene, toluene and ethylbenzene were degraded when these compounds were provided together; however, xylene isomers persisted during degradation by P. putida E41. When using a bioreactor batch system with a binary culture with P. putida BJ10, which was isolated previously in our lab, the degradation rate for benzene and toluene was improved in BTE mixed medium (each initial concentration: 50 mg/L). Almost all of the BTE was degraded within 4 h and 70-80% of m-, p-, and o-xylenes within 11 h in a BTEX mixture (initial concentration: 50 mg/L each). In summary, we found a valuable new strain of P. putida, determined the optimal degradation conditions for this isolate and tested a mixed culture of E41 and BJ10 for its ability to degrade a common sample of mixed contaminants containing benzene, toluene, and xylene.

Application of Free-Flow Electrophoresis/2-Dimentional Gel Electrophoresis for Fractionation and Characterization of Native Proteome of Pseudomonas putida KT2440: Chi-Won Choi , Young S. Hong , Seung Il Kim; J. Microbiol. 2008;46(4):448-455. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0063-9

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Abstract: Free Flow Electrophoresis (FFE) is a liquid-based isoelectric focusing method. Unlike conventional in-gel fractionation of proteins, FFE can resolve proteins in their native forms and fractionation of subcellular compartments of the cell is also possible. To test the efficacy of the FFE method, the native cytosol proteome of a bacterium, Pseudomonas putida KT2440 was fractionated by FFE and the spectrum of protein elutes was characterized in association with 2-dimentional gel electrophoresis (2-DE). Major native proteins of P. putida KT2440 were eluted in the range of pH 4.8~6.0 in FFE, whereas the denatured proteome of P. putida KT2440 was widely distributed in the rage of pH 4~10 in the 2-DE analysis. In addition, one of the three FFE major fractions, which was eluted at pH 5.0, was further analyzed using 2-DE/MS-MS. Then, the pH range of identified proteins eluted in 2-DE/MS-MS was 4.72~5.89, indicating that observed pI values of native cytosolic proteomes in FFE were narrower than those of denatured cytosolic proteome. These results suggest that FFE fractionation and 2-DE/MS analysis may be useful tools for characterization of native proteomes of P. putida KT2440 and comparative analysis between denatured and native proteomes.

Evidence of Indigenous NAH Plasmid of Naphthalene Degrading Pseudomonas putida PpG7 Strain Implicated in Limonin Degradation: Moushumi Ghosh , Abhijit Ganguli , Meenakshi Mallik; J. Microbiol. 2006;44(5):473-479.; DOI: https://doi.org/2451 [pii]

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Abstract: A well characterized naphthalene-degrading strain, Pseudomonas putida PpG7 was observed to utilize limonin, a highly-oxygenated triterpenoid compound as a sole source of carbon and energy. Limonin concentrations evidenced a 64% reduction over 48 h of growth in batch cultures. Attempts were made to acquire a plasmid-less derivative via various methods (viz. Ethidium Bromide, SDS, elevated temperature & mitomycin C), among which the method involving mitomycin C (20 μg/ml) proved successful. Concomitant with the loss of plasmid in P. putida PpG7 strain, the cured derivative was identified as a lim- phenotype. The lim+ phenotype could be conjugally transferred to the cured derivative. Based on the results of curing with mitomycin C, conjugation studies and presence of ndo gene encoding naphthalene 1,2 dioxygenase, it was demonstrated that genes for the limonin utilization were encoded on an 83 kb indigenous transmissible Inc. P9 NAH plasmid in Pseudomonas putida PpG7 strain.

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