Journal of Microbiology

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The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria: Ji&# , Chahrazed Mekadim , Radko Pechar , V&# , Eva Vlková; J. Microbiol. 2018;56(10):713-721. Published online September 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8167-3

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In the modern era, molecular genetic techniques are crucial in ecological studies, as well as in the classification, typing, and phylogenetic analysis of prokaryotes. These techniques are mainly aimed at whole genome comparisons and PCRderived experiments, including amplifying the 16S rRNA and other various housekeeping genes used in taxonomy, as well as MLST (multilocus sequence typing) and MLSA (multilocus sequence analysis) of different taxonomic bacterial groups. The gene encoding threonine-tRNA ligase (thrS) is a gene potentially applicable as an identification and phylogenetic marker in bacteria. It is widely distributed in bacterial genomes and is subject to evolutionary selection pressure due to its important function in protein synthesis. In this study, specific primers were used to amplify a thrS gene fragment (~740 bp) in 36 type and 30 wild strains classified under family Bifidobacteriaceae. The full-length gene has not yet been considered as a possible identification, classification, and phylogenetic marker in bifidobacteria. The thrS sequences revealed higher sequence variability (82.7% of pairwise identities) among members of the family than that shown by 16S rRNA gene sequences (96.0%). Although discrepancies were found between the thrS-derived and previously reported whole genome phylogenetic analyses, the main phylogenetic groups of bifidobacteria were properly assigned. Most wild strains of bifidobacteria were better differentiated based on their thrS sequences than on their 16S rRNA gene identities. Phylogenetic confidence of the evaluated gene with respect to other alternative genetic markers widely used in taxonomy of bifidobacteria (fusA, GroELhsp60, pyrG, and rplB genes) was confirmed using the localized incongruence difference - Templeton analysis.

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The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum
Cheng-Shan Jiang, Chun Yan Li, Chun Tao Gu
Current Microbiology.2024;[Epub] CrossRef
Bifidobacterium apicola sp. nov., isolated from the gut of honeybee (Apis mellifera)
Ting-Yu Wang, Hao Wang, Chun Tao Gu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Bifidobacterium apis sp. nov., isolated from the gut of honeybee (Apis mellifera)
Cheng-Shan Jiang, Chun Yan Li, Chun Tao Gu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Bifidobacterium favimelis sp. nov., isolated from black comb honey
Yu Li, Qiujie Song, Haizhu Yang, Yue Wei, Bilege Menghe, Wenjun Liu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Antibacterial Activity of Rainbow Trout Plasma: In Vitro Assays and Proteomic Analysis
Toita Mizaeva, Kalimat Alieva, Eldar Zulkarneev, Stanislav Kurpe, Kseniya Isakova, Svetlana Matrosova, Ekaterina Borvinskaya, Irina Sukhovskaya
Animals.2023; 13(22): 3565. CrossRef
Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera)
Ting Ting Li, Hong Xia Zhang, Chun Tao Gu
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris)
Vera Neuzil-Bunesova, Gabriele Andrea Lugli, Nikol Modrackova, Marie Makovska, Jakub Mrazek, Chahrazed Mekadim, Sarka Musilova, Ivona Svobodova, Roman Spanek, Marco Ventura, Jiri Killer
International Journal of Systematic and Evolutionary Microbiology .2020; 70(9): 5040. CrossRef
Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera
Jiří Killer, Chahrazed Mekadim, Věra Bunešová, Jakub Mrázek, Zuzana Hroncová, Eva Vlková
Folia Microbiologica.2020; 65(1): 143. CrossRef
Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics
Chahrazed Mekadim, Věra Bunešová, Eva Vlková, Zuzana Hroncová, Jiří Killer
Antonie van Leeuwenhoek.2019; 112(12): 1785. CrossRef
Prebiotic potential of natural gums and starch for bifidobacteria of variable origins
Nikol Modrackova, Marie Makovska, Chahrazed Mekadim, Eva Vlkova, Vaclav Tejnecky, Petra Bolechova, Vera Bunesova
Bioactive Carbohydrates and Dietary Fibre.2019; 20: 100199. CrossRef

Genetic variation and phylogenetic relationships of the ectomycorrhizal Floccularia luteovirens on the Qinghai-Tibet Plateau: Rui Xing , Qing-bo Gao , Fa-qi Zhang , Peng-cheng Fu , Jiu-li Wang , Hui-ying Yan , Shi-long -Chen; J. Microbiol. 2017;55(8):600-606. Published online July 4, 2017; DOI: https://doi.org/10.1007/s12275-017-7101-4

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Abstract

Floccularia luteovirens, as an ectomycorrhizal fungus, is widely distributed in the Qinghai-Tibet Plateau. As an edible fungus, it is famous for its unique flavor. Former studies mainly focus on the chemical composition and genetic structure of this species. However, the phylogenetic relationship between genotypes remains unknown. In this study, the genetic variation and phylogenetic relationship between the genotypes of F. luteovirens in Qinghai-Tibet Plateau was estimated through the analysis on two protein-coding genes (rpb1 and ef-1α) from 398 individuals collected from 24 wild populations. The sample covered the entire range of this species during all the growth seasons from 2011 to 2015. 13 genotypes were detected and moderate genetic diversity was revealed. Based on the results of network analysis, the maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) analyses, the genotypes H-1, H-4, H-6, H-8, H-10, and H-11 were grouped into one clade. Additionally, a relatively higher genotype diversity (average h value is 0.722) and unique genotypes in the northeast edge of Qinghai- Tibet plateau have been found, combined with the results of mismatch analysis and neutrality tests indicated that Southeast Qinghai-Tibet plateau was a refuge for F. luteovirens during the historical geological or climatic events (uplifting of the Qinghai-Tibet Plateau or Last Glacial Maximum). Furthermore, the present distribution of the species on the Qinghai-Tibet plateau has resulted from the recent population expansion. Our findings provide a foundation for the future study of the evolutionary history and the speciation of this species.

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Diversity and Multigene Phylogeny of the Genus Floccularia (Agaricales, Basidiomycota)
Zai-Wei Ge, Hua Qu, Malka Saba, Tian Gao, Martin Ryberg
Journal of Fungi.2025; 11(1): 74. CrossRef
Metabolomic Profiling of Floccularia luteovirens from Different Geographical Regions Proposes a Novel Perspective on Their Antioxidative Activities
Chuyu Tang, Yuejun Fan, Tao Wang, Jie Wang, Mengjun Xiao, Min He, Xiyun Chang, Yuling Li, Xiuzhang Li
Antioxidants.2024; 13(5): 620. CrossRef
Selection and validation of reference genes for normalization of gene expression in Floccularia luteovirens
Yanqing Ni, Qin Zhang, Wensheng Li, Luping Cao, Rencai Feng, Zhiqiang Zhao, Xu Zhao
Fungal Biology.2024; 128(1): 1596. CrossRef
Study on Enzyme Activity and Metabolomics during Culture of Liquid Spawn of Floccularia luteovirens
Yanqing Ni, Qiuhong Liao, Siyuan Gou, Tongjia Shi, Wensheng Li, Rencai Feng, Zhiqiang Zhao, Xu Zhao
Journal of Fungi.2024; 10(9): 618. CrossRef
The Research Status and Prospects of Floccularia luteovirens: A Mycorrhizal Fungus with Edible Fruiting Bodies
Yanqing Ni, Luping Cao, Wensheng Li, Qin Zhang, Rencai Feng, Zhiqiang Zhao, Xu Zhao
Journal of Fungi.2023; 9(11): 1071. CrossRef
Polysaccharides of Floccularia luteovirens Alleviate Oxidative Damage and Inflammatory Parameters of Diabetic Nephropathy in db/db Mice
Huan Wang, Yang Yang, Shumin Wang, Changtian Li, Changbao Chen, Xilin Wan, Dan Li, Yu Li
Frontiers in Bioscience-Landmark.2023;[Epub] CrossRef
Structure, stability, and potential function of groundwater microbial community responses to permafrost degradation on varying permafrost of the Qinghai-Tibet Plateau
Sining Zhong, Bin Li, Bowen Hou, Xuming Xu, Jinyun Hu, Rong Jia, Shanqing Yang, Shungui Zhou, Jinren Ni
Science of The Total Environment.2023; 875: 162693. CrossRef
Fine-scale genetic diversity and genet dynamics of the fairy ring fungus Floccularia luteovirens on the Qinghai–Tibet plateau
Rui Xing, Yan-fang Deng, Yu Yao, Qing-bo Gao, Fa-qi Zhang, Jiu-li Wang, Hai-rui Liu, Shi-long Chen
Fungal Ecology.2022; 60: 101194. CrossRef
The Molecular Mechanism of Yellow Mushroom (Floccularia luteovirens) Response to Strong Ultraviolet Radiation on the Qinghai-Tibet Plateau
Jing Guo, Zhanling Xie, Hongchen Jiang, Hongyan Xu, Baolong Liu, Qing Meng, Qingqing Peng, Yongpeng Tang, Yingzhu Duan
Frontiers in Microbiology.2022;[Epub] CrossRef
Chemical Constituents and Molecular Mechanism of the Yellow Phenotype of Yellow Mushroom (Floccularia luteovirens)
Xiaolong Gan, Xuemei Bao, Baolong Liu, Yun Li, Dong Cao, Hg Zhang, Yuan Zong
Journal of Fungi.2022; 8(3): 314. CrossRef
The Genomic and Transcriptomic Analyses of Floccularia luteovirens, a Rare Edible Fungus in the Qinghai–Tibet Plateau, Provide Insights into the Taxonomy Placement and Fruiting Body Formation
Zhengjie Liu, Hongyun Lu, Xinglin Zhang, Qihe Chen
Journal of Fungi.2021; 7(11): 887. CrossRef
Genetic relationships and low diversity among the tea-oil Camellia species in Sect. Oleifera, a bulk woody oil crop in China
Huasha Qi, Xiuxiu Sun, Wuping Yan, Hang Ye, Jiali Chen, Jing Yu, Dai Jun, Chunmei Wang, Tengfei Xia, Xuan Chen, Dongliang Li, Daojun Zheng
Frontiers in Plant Science.2020;[Epub] CrossRef
Draft Genome Assembly of Floccularia luteovirens, an Edible and Symbiotic Mushroom on Qinghai-Tibet Plateau
Xiaolong Gan, Dong Cao, Zhenyu Zhang, Shu Cheng, Le Wei, Shiming Li, Baolong Liu
G3 Genes|Genomes|Genetics.2020; 10(4): 1167. CrossRef
Genetic diversity and its conservation implications ofVitex rotundifolia(Lamiaceae) populations in East Asia
Yiqi Sun, Hong Yang, Qiaoyan Zhang, Luping Qin, Pan Li, Joongku Lee, Shichao Chen, Khalid Rahman, Tingguo Kang, Min Jia
PeerJ.2019; 7: e6194. CrossRef
Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria
Rui Xing, Hui‐ying Yan, Qing‐bo Gao, Fa‐qi Zhang, Jiu‐li Wang, Shi‐long Chen
Journal of Basic Microbiology.2018; 58(6): 554. CrossRef

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

NOTE] Two Novel Talaromyces Species Isolated from Medicinal Crops in Korea: Hyunkyu Sang , Tae-Jin An , Chang Sun Kim , Gyu-Sub Shin , Gi-Ho Sung , Seung Hun Yu; J. Microbiol. 2013;51(5):704-708. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3361-9

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Abstract: Two novel biverticillate Talaromyces species, T. angelicus and T. cnidii, were collected from the medicinal crops Angelica gigas and Cnidium officinale, respectively, in Korea. Phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region and the β-tubulin gene as well as morphological analyses revealed that the two species differ from any known Talaromyces species. Talaromyces angelicus is related to T. flavovirens in the phylogeny of the ITS region, but the new species is grouped together with Penicillium liani and T. pinophilus in terms of its β-tubulin phylogeny, and its growth rate on Czapek yeast autolysate differs from that of T. flavovirens. Talaromyces cnidii is phylogenetically similar to T. siamensis, but exhibits differences in the morphologies of the colony margin, metulae, and conidia.

NOTE] Penicillium daejeonium sp. nov., a New Species Isolated from a Grape and Schisandra Fruit in Korea: Hyunkyu Sang , Tae-Jin An , Chang Sun Kim , Young Phil Choi , Jian-Xin Deng , Narayan Chandra Paul , Gi-Ho Sung , Seung Hun Yu; J. Microbiol. 2013;51(4):536-539. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-3291-6

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Abstract: Two isolates of monoverticillate Penicillium species were collected from a grape and schisandra fruit in Korea. Multigene phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region and genes encoding β-tubulin (benA) and calmodulin (cmd), as well as morphological analyses revealed that the two isolates are members of the P. sclerotiorum complex in Penicillium subgenus Aspergilloides, but different from species of the P. sclerotiorum complex. The isolates are closely related to P. cainii, P. jacksonii, and P. viticola in terms of their multigene phylogeny, but their colony and conidiophore morphologies differ from those of closely related species. The name P. daejeonium is proposed for this unclassified new species belonging to the P. sclerotiorum complex in subgenus Aspergilloides.

Methyl Coenzyme M Reductase (mcrA) Gene Based Phylogenetic Analysis of Methanogens Population in Murrah Buffaloes (Bubalus bubalis): Prem Prashant Chaudhary , Sunil Kumar Sirohi , Dheer Singh , Jyoti Saxena; J. Microbiol. 2011;49(4):558-561. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-1052-y

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Abstract: The aim of the present study was to decipher the diversity of methanogens in rumen of Murrah buffaloes so that effective strategies can be made in order to mitigate methane emission from these methanogens. In the present study diversity of rumen methanogens in Murrah buffaloes (Bubalus bubalis) from North India was evaluated by using mcr-A gene library obtained from the pooled PCR product from four animals and by using MEGA4 software. A total of 104 clones were examined, revealing 26 different mcr-A gene sequences or phylotypes. Of the 26 phylotypes, 16 (64 of 104 clones) were less than 97% similar to any of the cultured strain of methanogens. Seven clone sequences were clustered with Methanomicrobium mobile and three clone sequences were clustered with Methanobrevibacter gottschalkii during the phylogenetic analysis. Uncultured group of methanogens comes out to be the major component of the methanogens community structure in Murrah buffaloes. Methanomicrobium phylotype comes out to be major phylotype among cultured methanogens followed by Methanobrevibacter phylotype. These results help in making effective strategies to check the growth of dominant methanogenic communities in the rumen of this animal which in turn help in the reduction of methane emission in the environment and ultimately helps us in fighting with the problem of global warming.

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