Journal of Microbiology

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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
Radiotherapy and the gut microbiome: facts and fiction
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

Characterization of siderophore produced by Pseudomonas syringae BAF.1 and its inhibitory effects on spore germination and mycelium morphology of Fusarium oxysporum: Sumei Yu , Chunying Teng , Jinsong Liang , Tao Song , Liying Dong , Xin Bai , Yu Jin , Juanjuan Qu; J. Microbiol. 2017;55(11):877-884. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7191-z

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Abstract

In this study, an antagonistic bacterium against Fusarium oxysporum was identified and designated as Pseudomonas syringae strain BAF.1 on the basis of 16S rDNA sequence analysis and physiological-biochemical characteristics. It produced catechol-species siderophore at a molecular weight of 488.59 Da and a maximum amount of 55.27 μg/ml with glucose as a carbon source and asparagine as a nitrogen source at a C/N ratio of 10:1, 30°C and pH 7. The siderophore exhibited prominent antagonistic activity against Fusarium oxysporum with a maximum inhibition rate of 95.24% and had also suppressive effects on other kinds of 11 phytopathogenic fungi in the absence of FeCl3·6H2O. Spore germination was completely inhibited by 50 μl of the siderophorecontaining solution, and the ultrastructures of mycelia and spores were also considerably suppressed by siderophore treatment as established by electron microscopy observation. These results indicate that the siderophore produced by Pseudomonas syringae BAF.1 could be potentially used for biocontrol of pathogenic Fusarium oxysporum.

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Phytochemical composition and antifungal effectiveness of Phoenix dactylifera L. rachis extracts
Ahmed Abdelkhalek, Eman A. Abdelwahab, Saad F. Elalem, Abdulaziz A. Al-Askar, Przemysław Ł. Kowalczewski, Said Behiry
Polish Journal of Chemical Technology.2024; 26(3): 76. CrossRef
Unveiling the biocontrol potential of Pseudomonas syringae through seed biopriming against charcoal rot disease in maize
Muhammad Jarrar Ahmed, Amna Shoaib
Physiological and Molecular Plant Pathology.2024; 133: 102370. CrossRef
Exploring the rhizosphere of perennial wheat: potential for plant growth promotion and biocontrol applications
Gianluigi Giannelli, Lorenzo Del Vecchio, Martina Cirlini, Marco Gozzi, Laura Gazza, Gianni Galaverna, Silvia Potestio, Giovanna Visioli
Scientific Reports.2024;[Epub] CrossRef
Torilis arvensis ethanolic extract: Phytochemical analysis, antifungal efficacy, and cytotoxicity properties
Abdallah Khalil, Eman A. Abdelwahab, Omaima A. Sharaf, Abdulaziz A. Al-Askar, Przemysław Kowalczewski, Ahmed Abdelkhalek, Said Behiry
Open Chemistry.2024;[Epub] CrossRef
Rapid and accurate detection of Fusarium oxysporum f. sp. Lycopersici using one-pot, one-step LAMP-CRISPR/Cas12b method
Shijie Dai, Yangsheng Wu, Na Zhu, Yujin Zhao, Mingjiang Mao, Zheming Li, Bo Zhu, Weichun Zhao, Xiaofeng Yuan
Frontiers in Plant Science.2024;[Epub] CrossRef
Anticandidal Activity of a Siderophore from Marine Endophyte Pseudomonas aeruginosa Mgrv7
Essam Kotb, Amira H. Al-Abdalall, Ibtisam Ababutain, Nada F. AlAhmady, Sahar Aldossary, Eida Alkhaldi, Azzah I. Alghamdi, Hind A. S. Alzahrani, Mashael A. Almuhawish, Moudhi N. Alshammary, Asmaa A. Ahmed
Antibiotics.2024; 13(4): 347. CrossRef
Siderophores and metallophores: Metal complexation weapons to fight environmental pollution
Ana F.R. Gomes, Mariana C. Almeida, Emília Sousa, Diana I.S.P. Resende
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Ravinsh Kumar, Ashutosh Singh, Ekta Shukla, Pratika Singh, Azmi Khan, Naveen Kumar Singh, Amrita Srivastava
Journal of Applied Microbiology.2024;[Epub] CrossRef
A Practical Toolkit for the Detection, Isolation, Quantification, and Characterization of Siderophores and Metallophores in Microorganisms
Ana F. R. Gomes, Emília Sousa, Diana I. S. P. Resende
ACS Omega.2024; 9(25): 26863. CrossRef
Production and Antibacterial Activity of Atypical Siderophore from Pseudomonas sp. QCS59 Recovered from Harpachene schimperi
Mashael A. Almuhawish, Essam Kotb, Eida Alkhaldi, Asmaa A. Ahmed
Pharmaceuticals.2024; 17(9): 1126. CrossRef
A comparative study of the antifungal efficacy and phytochemical composition of date palm leaflet extracts
Karrar A. Hamzah, Abdulaziz Al-Askar, Przemysław Kowalczewski, Ahmed Abdelkhalek, Haitham H. Emaish, Said Behiry
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HPLC and GC–MS analyses of phytochemical compounds in Haloxylon salicornicum extract: Antibacterial and antifungal activity assessment of phytopathogens
Said Behiry, Eman A. Abdelwahab, Abdulaziz A. Al-Askar, Przemysław Kowalczewski, Ahmed Abdelkhalek
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Antifungal Activity of Siderophore Isolated from Pantoea brenneri Against Fusarium oxysporum
A. D. Suleimanova, L. V. Sokolnikova, E. A. Egorova, E. S. Berkutova, D. S. Pudova, I. V. Khilyas, M. R. Sharipova
Russian Journal of Plant Physiology.2023;[Epub] CrossRef
Suppression of tomato wilt by cell-free supernatants of Acinetobacter baumannii isolates from wild cacao from the Colombian Amazon
Carolina Pisco-Ortiz, Adriana González-Almario, Liz Uribe-Gutiérrez, Mauricio Soto-Suárez, Carol V. Amaya-Gómez
World Journal of Microbiology and Biotechnology.2023;[Epub] CrossRef
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Shihua Zhou, Qing-Song Yuan, Xiaoai Wang, Weike Jiang, Xiaohong Ou, Changgui Yang, Yanping Gao, Yanhong Wang, Lanping Guo, Luqi Huang, Tao Zhou
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Application of Sophora alopecuroides organic fertilizer changes the rhizosphere microbial community structure of melon plants and increases the fruit sugar content
Ling‐qi Hua, Sheng‐qiang Yang, Zhan‐feng Xia, Hong Zeng
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Characterization of Pseudomonas bacteria of Piper tuberculatum regarding the production of potentially bio-stimulating compounds for plant growth
Danyllo Amaral de OLIVEIRA, Solange da Cunha FERREIRA, Daiany Larissa Ribeiro CARRERA, Cleyson Pantoja SERRÃO, Daihany Moraes CALLEGARI, Nicolle Louise Ferreira BARROS, Francinilson Meireles COELHO, Cláudia Regina Batista de SOUZA
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Siderophore Production by Rhizosphere Biological Control Bacteria Brevibacillus brevis GZDF3 of Pinellia ternata and Its Antifungal Effects on Candida albicans
Miao miao Sheng, Hua ke Jia, Gong you Zhang, Li na Zeng, Ting Ting Zhang, Yao hang Long, Jing Lan, Zu quan Hu, Zhu Zeng, Bing Wang, Hong mei Liu
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Research Support, Non-U.S. Gov'ts

The hrp pathogenicity island of Pseudomonas syringae pv. tomato DC3000 is induced by plant phenolic acids: Jun Seung Lee , Hye Ryun Ryu , Ji Young Cha , Hyung Suk Baik; J. Microbiol. 2015;53(10):725-731. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5256-4

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Abstract

Plants produce a wide array of antimicrobial compounds, such as phenolic compounds, to combat microbial pathogens. The hrp PAI is one of the major virulence factors in the plant pathogen, Pseudomonas syringae. A major role of hrp PAI is to disable the plant defense system during bacterial invasion. We examined the influence of phenolic compounds on hrp PAI gene expression at low and high concentrations. There was approximately 2.5 times more hrpA and hrpZ mRNA in PtoDC3000 that was grown in minimal media (MM) supplemented with 10 μM of ortho-coumaric acid than in PtoDC3000 grown in MM alone. On the other hand, a significantly lower amount of hrpA mRNA was observed in bacteria grown in MM supplemented with a high concentration of phenolic compounds. To determine the regulation pathway for hrp PAI gene expression, we performed qRTPCR using gacS, gacA, and hrpS deletion mutants.

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Liebig review: The role of mineral nutrients in the development of Pseudomonas syringae diseases—Lessons learned and implications for disease control in woody plants
Nathalie Soethe, Michelle T. Hulin, Antje Balasus, Gail Preston, Christoph‐Martin Geilfus
Journal of Plant Nutrition and Soil Science.2024; 187(3): 301. CrossRef
Regulation of the Pseudomonas syringae Type III Secretion System by Host Environment Signals
Megan R. O’Malley, Jeffrey C. Anderson
Microorganisms.2021; 9(6): 1227. CrossRef
Quantification of Viable Cells of Pseudomonas syringae pv. tomato in Tomato Seed Using Propidium Monoazide and a Real-Time PCR Assay
A-li Chai, Hai-yan Ben, Wei-tao Guo, Yan-xia Shi, Xue-wen Xie, Lei Li, Bao-ju Li
Plant Disease.2020; 104(8): 2225. CrossRef
Validation of RT-qPCR Approaches to MonitorPseudomonas syringaeGene Expression During Infection and Exposure to Pattern-Triggered Immunity
Amy Smith, Amelia H. Lovelace, Brian H. Kvitko
Molecular Plant-Microbe Interactions®.2018; 31(4): 410. CrossRef
Multidrug Efflux Pumps at the Crossroad between Antibiotic Resistance and Bacterial Virulence
Manuel Alcalde-Rico, Sara Hernando-Amado, Paula Blanco, José L. Martínez
Frontiers in Microbiology.2016;[Epub] CrossRef
Global Analysis of Type Three Secretion System and Quorum Sensing Inhibition of Pseudomonas savastanoi by Polyphenols Extracts from Vegetable Residues
Carola Biancalani, Matteo Cerboneschi, Francesco Tadini-Buoninsegni, Margherita Campo, Arianna Scardigli, Annalisa Romani, Stefania Tegli, Boris Alexander Vinatzer
PLOS ONE.2016; 11(9): e0163357. CrossRef

Impact of cry1AC-Carrying Brassica rapa subsp. pekinensis on Leaf Bacterial Community: Young Tae Kim , Kang Seon Lee , Moon Jung Kim , Seung Bum Kim; J. Microbiol. 2009;47(1):33-39. Published online February 20, 2009; DOI: https://doi.org/10.1007/s12275-008-0254-4

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Abstract: The effects of Chinese cabbage (Brassica rapa subsp. pekinensis) carrying cry1AC derived from Bacillus thuringiensis (Bt) on leaf bacterial community were examined by analyzing the horizontal transfer of transgene fragments from plants to bacteria. The effect of plant pathogenic bacteria on the gene transfer was also examined using Pseudomonas syringae pathovar. maculicola. The frequency of hygromycin-resistant bacteria did not alter in Bt leaves, though slight increase was observed in Pseudomonas-infected Bt leaves with no statistical significance. The analysis of bacterial community profiles using the denaturing gradient gel electrophoresis (DGGE) fingerprinting indicated that there were slight differences between Bt and control Chinese cabbage, and also that infected tissues were dominated by P. syringae pv. maculicola. However, the cultured bacterial pools were not found to contain any transgene fragments. Thus, no direct evidence of immediate gene transfer from plant to bacteria or acquisition of hygromycin resistance could be observed. Still, long-term monitoring on the possibility of gene transfer is necessary to correctly assess the environmental effects of the Bt crop on bacteria.

Occurrence of the strA-strB Streptomycin Resistance Genes in Pseudomonas Species Isolated from Kiwifruit Plants: Hyo Shim Han , Young Jin Koh , Jae-Seoun Hur , Jae Sung Jung; J. Microbiol. 2004;42(4):365-368.; DOI: https://doi.org/2096 [pii]

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Abstract: The occurrence of strA-strB streptomycin-resistance genes within transposon Tn5393 was examined in Pseudomonas syringae pv. actinidiae, P. syringae pv. syringae, and P. marginalis, isolated from kiwifruit plants in Korea and Japan. PCR amplification with primers specific to strA-strB revealed that three of the tested Pseudomonas species harbored these genes for a streptomycin-resistance determinant. Tn5393, containing strA-strB, was also identified with PCR primers designed to amplify parts of tnpA, res, and tnpR. No IS elements were detected within tnpR, nor were they found in the intergenic region between tnpR and strA. Nucleotide sequence analysis indicated that the strA sequence of P. syringae pv. actinidiae contained a single nucleotide alteration at position 593 (CAA→CGA), as compared to Tn5393a in P. syringae pv. syringae. This resulted in an amino acid change, from Gln to Arg.

Molecular Bases of High-Level Streptomycin Resistance in Pseudomonas marginalis and Pseudomonas syringae pv. actinidiae: Hyo Shim Han^ , Hye Young Nam^ , Young Jin Koh^ , Jae-Seoun Hur^ , Jae Sung Jung^; J. Microbiol. 2003;41(1):16-21.

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Abstract: We have collected eight high-level streptomycin-resistant strains of Pseudomonas marginalis and P. syringae pv. actinidiae which were isolated from kiwifruit orchards in Korea and Japan. The molecular mechanisms of resistance were investigated by the PCR, susceptibility tests, and nucleotide sequence analysis. Of the eight high-level streptomycin-resistant strains, four harbored strA-strB genes, which encode streptomycin-inactivating enzymes. While the three Korean strains of P. marginalis did not have plasmid and carried the resistant genes in the chromosomes, the Japanese strain of P. syringae pv. actinidiae had a plasmid containing strA-strB genes. The myomycin susceptibility test demonstrated that the high-level resistance to streptomycin of the remaining four strains is associated with mutations in the rpsL gene. Nucleotide sequence analyses revealed that they contain a single base-pair mutation in codon 43 of their rpsL gene.

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