Journal of Microbiology

Journal Articles

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

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes: Han Na Oh , Doyoung Park , Hoon Je Seong , Dockyu Kim , Woo Jun Sul; J. Microbiol. 2019;57(10):865-873. Published online September 30, 2019; DOI: https://doi.org/10.1007/s12275-019-9217-1

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Abstract

Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil’s metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.

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Metagenomic insights into the lignocellulose degradation mechanism during short-term composting of peach sawdust: Core microbial community and carbohydrate-active enzyme profile analysis
Wei-Wei Zhang, Yu-Xin Guo, Qing-Jun Chen, Yi-Yang Wang, Qiu-Ying Wang, Ya-Ru Yang, Guo-Qing Zhang
Environmental Technology & Innovation.2025; 37: 103959. CrossRef
Comprehensive characterization and resistome analysis of Antarctic Pseudomonas migulae strain CAS19
Çiğdem Otur, Sezer Okay, Ömer Konuksever, Oğuzhan Duyar, Yılmaz Kaya, Aslıhan Kurt-Kızıldoğan
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Response of carbohydrate-degrading enzymes and microorganisms to land use change in the southeastern Qinghai-Tibetan Plateau, China
Renhuan Zhu, Belayneh Azene, Piotr Gruba, Kaiwen Pan, Yalemzewd Nigussie, Awoke Guadie, Xiaoming Sun, Xiaogang Wu, Lin Zhang
Applied Soil Ecology.2024; 200: 105442. CrossRef
Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland
Mariane Schmidt Thøgersen, Athanasios Zervas, Peter Stougaard, Lea Ellegaard-Jensen
Frontiers in Microbiology.2024;[Epub] CrossRef
Bacterial Diversity, Metabolic Profiling, and Application Potential of Antarctic Soil Metagenomes
Mario Fernández, Salvador Barahona, Fernando Gutierrez, Jennifer Alcaíno, Víctor Cifuentes, Marcelo Baeza
Current Issues in Molecular Biology.2024; 46(11): 13165. CrossRef
Cold adaptation and response genes of Antarctic Cryobacterium sp. SO2 from the Fildes Peninsula, King George Island
Chui Peng Teoh, Marcelo González‑Aravena, Paris Lavin, Clemente Michael Vui Ling Wong
Polar Biology.2024; 47(2): 135. CrossRef
A bacterial cold-active dye-decolorizing peroxidase from an Antarctic Pseudomonas strain
Célica Cagide, Juan José Marizcurrena, Diego Vallés, Beatriz Alvarez, Susana Castro-Sowinski
Applied Microbiology and Biotechnology.2023; 107(5-6): 1707. CrossRef
Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review
Ninian Prem Prashanth Pabbathi, Aditya Velidandi, Tanvi Tavarna, Shreyash Gupta, Ram Sarvesh Raj, Pradeep Kumar Gandam, Rama Raju Baadhe
Biomass Conversion and Biorefinery.2023; 13(2): 1371. CrossRef
Different Response of Plant- and Microbial-Derived Carbon Decomposition Potential between Alpine Steppes and Meadows on the Tibetan Plateau
Yanhong Yuan, Lan Chen, Jieying Wang, Yanfang Liu, Chengjie Ren, Yaoxin Guo, Jun Wang, Ninglian Wang, Fazhu Zhao, Wenying Wang
Forests.2023; 14(8): 1580. CrossRef
Investigation of cold-active and mesophilic cellulases: opportunities awaited
Sambhaji Chavan, Ashvini Shete, Yasmin Mirza, Mahesh S. Dharne
Biomass Conversion and Biorefinery.2023; 13(10): 8829. CrossRef
Cold-Adapted Proteases: An Efficient and Energy-Saving Biocatalyst
Zhengfeng Yang, Zhendi Huang, Qian Wu, Xianghua Tang, Zunxi Huang
International Journal of Molecular Sciences.2023; 24(10): 8532. CrossRef
Reclamation of abandoned saline-alkali soil increased soil microbial diversity and degradation potential
Fating Yin, Fenghua Zhang
Plant and Soil.2022; 477(1-2): 521. CrossRef
Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass
Deepak Kukkar, Pushpender Kumar Sharma, Ki-Hyun Kim
Environmental Research.2022; 215: 114369. CrossRef
Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation
Carlos Andrés Díaz Rodríguez, Laura Díaz-García, Boyke Bunk, Cathrin Spröer, Katherine Herrera, Natalia A Tarazona, Luis M Rodriguez-R, Jörg Overmann, Diego Javier Jiménez
ISME Communications.2022;[Epub] CrossRef
The Use of Response Surface Methodology as a Statistical Tool for the Optimisation of Waste and Pure Canola Oil Biodegradation by Antarctic Soil Bacteria
Khadijah Nabilah Mohd Zahri, Azham Zulkharnain, Claudio Gomez-Fuentes, Suriana Sabri, Khalilah Abdul Khalil, Peter Convey, Siti Aqlima Ahmad
Life.2021; 11(5): 456. CrossRef
Comparison of Gut Microbiota between Gentoo and Adélie Penguins Breeding Sympatrically on Antarctic Ardley Island as Revealed by Fecal DNA Sequencing
Yin-Xin Zeng, Hui-Rong Li, Wei Han, Wei Luo
Diversity.2021; 13(10): 500. CrossRef
Deconstruction of Lignin: From Enzymes to Microorganisms
Jéssica P. Silva, Alonso R. P. Ticona, Pedro R. V. Hamann, Betania F. Quirino, Eliane F. Noronha
Molecules.2021; 26(8): 2299. CrossRef
Molecular Characterization of Novel Family IV and VIII Esterases from a Compost Metagenomic Library
Jong-Eun Park, Geum-Seok Jeong, Hyun-Woo Lee, Hoon Kim
Microorganisms.2021; 9(8): 1614. CrossRef
Illite/smectite clay regulating laccase encoded genes to boost lignin decomposition and humus formation in composting habitats revealed by metagenomics analysis
Qingran Meng, Susu Wang, Qiuqi Niu, Hailong Yan, Gen Li, Qiuhui Zhu, Qunliang Li
Bioresource Technology.2021; 338: 125546. CrossRef
Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer
Ohana Y. A. Costa, Mattias de Hollander, Agata Pijl, Binbin Liu, Eiko E. Kuramae
Microbiome.2020;[Epub] CrossRef
Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools
Gislaine Fongaro, Guilherme Augusto Maia, Paula Rogovski, Rafael Dorighello Cadamuro, Joana Camila Lopes, Renato Simões Moreira, Aline Frumi Camargo, Thamarys Scapini, Fábio Spitza Stefanski, Charline Bonatto, Doris Sobral Marques Souza, Patrícia Hermes
Current Genomics.2020; 21(4): 240. CrossRef

Research Support, Non-U.S. Gov't

Antioxidant Capacity of Novel Pigments from an Antarctic Bacterium: Daniela N. Correa-Llantén , Maximiliano J. Amenábar , Jenny M. Blamey; J. Microbiol. 2012;50(3):374-379. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2029-1

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Abstract: In Antarctica microorganisms are exposed to several conditions that trigger the generation of reactive oxygen species, such as high UV radiation. Under these conditions they must have an important antioxidant defense system in order to prevent oxidative damage. One of these defenses are pigments which are part of the non-enzymatic antioxidant mechanisms. In this work we focused on the antioxidant capacity of pigments from an Antarctic microorganism belonging to Pedobacter genus. This microorganism produces different types of pigments which belong to the carotenoids group. The antioxidant capacity of a mix of pigments was analyzed by three different methods: 1,1-diphenyl-2-picrylhydrazyl, ROS detection and oxygen electrode. The results obtained from these approaches indicate that the mix of pigments has a strong antioxidant capacity. The oxidative damage induced by UVB exposure to liposomes was also analyzed. Intercalated pigments within the liposomes improved its resistance to lipid peroxidation. Based on the analysis carried out along this research we conclude that the antioxidant properties of the mix of pigments protect this bacterium against oxidative damage. These properties make this mix of pigments a powerful antioxidant mixture with potential biotechnological applications.

Journal Article

Psychroflexus lacisalsi sp. nov., a Moderate Halophilic Bacterium Isolated from a Hypersaline Lake (Hunazoko-Ike) in Antarctica: Hongyan Zhang , Shoko Hosoi-Tanabe , Syuhei Ban , Satoshi Imura; J. Microbiol. 2010;48(2):160-164. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-0018-9

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Abstract: A novel Gram-negative, aerobic, moderate halophilic, and psychrotolerant bacterium, designated as strain H7T, was isolated from a hypersaline lake located in Skarvsnes, Antarctica. Cells were filaments with varying lengths. Coccoid bodies developed in old cultures. Growth occurred with 0.5-15% (w/v) NaCl (optimum, 5.8-7.0%), at pH 6.0-10.0 (optimum, pH 7.0-8.0), and at 10-28°C (optimum, 25°C). The strain had a G+C content of 34.9 mol%, which is within the range of 32-36 mol% reported for the genus Psychroflexus. Chemotaxonomic data (major respiratory quinone: MK-6; major fatty acids: aC15:0, iC16:0 3-OH, and aC15: 1 A) supported the classification of strain H7T within the genus Psychroflexus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H7T should be assigned to the genus Psychroflexus and has a homology with Psychroflexus salinarum (98.2%), P. sediminis (96.1%), P. torquis (95.2%), P. tropicus (95.8%), and P. gondwanense (92.2%). Strain H7 is not identified as P. salinarum because that DNA-DNA hybridization data were 8.5% between strain H7T and P. salinarum. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics, and chemotaxonomic differences supported the view that strain H7T represents a novel species of the genus Psychroflexus. The name Psychroflexus lacisalsi is proposed, and the type strain is H7T (=JCM 16231T =KACC 14089T).

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