Journal of Microbiology

Research Article

PneusPage: A WEB-BASED TOOL for the analysis of Whole-Genome Sequencing Data of Streptococcus pneumonia: Eunju Hong, Youngjin Shin, Hyunseong Kim, Woo Young Cho, Woo-Hyun Song, Seung-Hyun Jung, Minho Lee; J. Microbiol. 2025;63(1):e.2409020. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2409020

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Abstract PDF Supplementary Material: With the advent of whole-genome sequencing, opportunities to investigate the population structure, transmission patterns, antimicrobial resistance profiles, and virulence determinants of Streptococcus pneumoniae at high resolution have been increasingly expanding. Consequently, a user-friendly bioinformatics tool is needed to automate the analysis of Streptococcus pneumoniae whole-genome sequencing data, summarize clinically relevant genomic features, and further guide treatment options. Here, we developed PneusPage, a web-based tool that integrates functions for species prediction, molecular typing, drug resistance determination, and data visualization of Streptococcus pneumoniae. To evaluate the performance of PneusPage, we analyzed 80 pneumococcal genomes with different serotypes from the Global Pneumococcal Sequencing Project and compared the results with those from another platform, PathogenWatch. We observed a high concordance between the two platforms in terms of serotypes (100% concordance rate), multilocus sequence typing (100% concordance rate), penicillin-binding protein typing (88.8% concordance rate), and the Global Pneumococcal Sequencing Clusters (98.8% concordance rate). In addition, PneusPage offers integrated analysis functions for the detection of virulence and mobile genetic elements that are not provided by previous platforms. By automating the analysis pipeline, PneusPage makes whole-genome sequencing data more accessible to non-specialist users, including microbiologists, epidemiologists, and clinicians, thereby enhancing the utility of whole-genome sequencing in both research and clinical settings. PneusPage is available at https://pneuspage.minholee.net/.

Journal Articles

Characterization and Comparative Genomic Analysis of vB_BceM_CEP1: A Novel Temperate Bacteriophage Infecting Burkholderia cepacia Complex: Momen Askoura, Eslam K Fahmy, Safya E Esmaeel, Wael A H Hegazy, Aliaa Abdelghafar; J. Microbiol. 2024;62(11):1035-1055. Published online November 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00185-2

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Abstract: The increasing prevalence of multidrug-resistant bacteria imminently threatens public health and jeopardizes nearly all aspects of modern medicine. The Burkholderia cepacia complex (Bcc) comprises Burkholderia cepacia and the related species of Gram-negative bacteria. Members of the Bcc group are opportunistic pathogens responsible for various chronic illnesses, including cystic fibrosis and chronic granulomatous disease. Phage therapy is emerging as a potential solution to combat the antimicrobial resistance crisis. In this study, a temperate phage vB_BceM_CEP1 was isolated from sewage and fully characterized. Transmission electron microscopy indicated that vB_BceM_CEP1 belongs to the family Peduoviridae. The isolated phage demonstrated enhanced environmental stability and antibiofilm potential. One-step growth analysis revealed a latent period of 30 min and an average burst size of 139 plaque-forming units per cell. The genome of vB_BceM_CEP1 consists of 32,486 bp with a GC content of 62.05%. A total of 40 open reading frames were annotated in the phage genome, and none of the predicted genes was annotated as tRNA. Notably, genes associated with antibiotic resistance, host virulence factors, and toxins were absent from the vB_BceM_CEP1 genome. Based on its unique phenotype and phylogeny, the isolated phage vB_BceM_CEP1 is classified as a new temperate phage with lytic activity. The findings of this study enhance our understanding of the diversity of Bcc phages.

Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale: Allan de Carvalho, Marcia Giambiagi-deMarval, Ciro César Rossi; J. Microbiol. 2024;62(9):775-784. Published online July 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00156-7

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Abstract: Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.

Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil: Abhilash Bhattacharjee, Anil Kumar Singh; J. Microbiol. 2024;62(7):511-523. Published online June 21, 2024; DOI: https://doi.org/10.1007/s12275-024-00129-w

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Abstract: Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.

Letter

Proposal of Flavihumibacter fluvii sp. nov. as a replacement name for the effectively published but invalidated epithet Flavihumibacter fluminis Park et al. 2022: Miri S. Park , Hyeonuk Sa , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2023;61(6):649-651. Published online June 12, 2023; DOI: https://doi.org/10.1007/s12275-023-00057-1

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Abstract

The name Flavihumibacter fluminis Park et al. 2022, which was effectively published but invalidated, is an illegitimate homonymic epithet of Flavihumibacter fluminis Guo et al. 2023. The low 16S rRNA gene sequence similarity and genomic relatedness between the type strains IMCC34837T and RY-1T of the two homonymic species indicated that they are different species. To avoid further confusion, we propose a new name Flavihumibacter fluvii sp. nov. to replace the effectively published but invalidated homonymic epithet Flavihumibacter fluminis Park et al. 2022.

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Validation List no. 214. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Journal Articles

The Revision of Lichen Flora Around Maxwell Bay, King George Island, Maritime Antarctic: Jae Eun So , Josef P. Halda , Soon Gyu Hong , Jae&# , Ji Hee Kim; J. Microbiol. 2023;61(2):159-173. Published online February 27, 2023; DOI: https://doi.org/10.1007/s12275-023-00015-x

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Abstract

Since the floristic study of lichens at the Barton and Weaver Peninsulas of King George Island in 2006, there have been intense investigations of the lichen flora of the two peninsulas as well as that of Fildes Peninsula and Ardley Island in Maxwell Bay, King George Island, South Shetland Islands, maritime Antarctic. In this study, a total of 104 species belonging to 53 genera, are identified from investigations of lichens that were collected in austral summer seasons from 2008 to 2016. Phenotypic and molecular analyses were incorporated for taxonomic identification. In particular, 31 species are found to be endemic to the Antarctic and 22 species are newly recorded to the Maxwell Bay region. Lepra dactylina, Stereocaulon caespitosum, and Wahlenbergiella striatula are newly recorded in the Antarctic, and the previously reported taxon Cladonia furcata is excluded from the formerly recorded list due to misidentification. We also provide ecological and geographical information about lichen associations and habitat preferences.

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Lichens of Larsemann Hills and adjacent oases in the area of Prydz Bay (Princess Elizabeth Land and MacRobertson Land, Antarctica)
Mikhail Andreev (Mихаил АНДРЕЕВ)
Polar Science.2023; 38: 101009. CrossRef

Varicella‑Zoster Virus ORF39 Transmembrane Protein Suppresses Interferon‑Beta Promoter Activation by Interacting with STING: Gwang Myeong Lee , Shuang Gong , Seong&# , Hyemin Ko , Woo&# , Jihyun Lee , Ok Sarah Shin , Jin&#; J. Microbiol. 2023;61(2):259-270. Published online February 20, 2023; DOI: https://doi.org/10.1007/s12275-023-00019-7

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Abstract: Varicella-Zoster virus (VZV) causes varicella in primary infection of children and zoster during reactivation in adults. Type I interferon (IFN) signaling suppresses VZV growth, and stimulator of interferon genes (STING) plays an important role in anti-VZV responses by regulating type I IFN signaling. VZV-encoded proteins are shown to inhibit STING-mediated activation of the IFN-β promoter. However, the mechanisms by which VZV regulates STING-mediated signaling pathways are largely unknown. In this study, we demonstrate that the transmembrane protein encoded by VZV open reading frame (ORF) 39 suppresses STING-mediated IFN-β production by interacting with STING. In IFN-β promoter reporter assays, ORF39 protein (ORF39p) inhibited STING-mediated activation of the IFN-β promoter. ORF39p interacted with STING in co-transfection assays, and this interaction was comparable to that of STING dimerization. The cytoplasmic N-terminal 73 amino acids region of ORF39P was not necessary for ORF39 binding and suppression of STING-mediated IFN-β activation. ORF39p also formed a complex containing both STING and TBK1. A recombinant VZV expressing HA-tagged ORF39 was produced using bacmid mutagenesis and showed similar growth to its parent virus. During HA-ORF39 virus infection, the expression level of STING was markedly reduced, and HA-ORF39 interacted with STING. Moreover, HA-ORF39 also colocalized with glycoprotein K (encoded by ORF5) and STING at the Golgi during virus infection. Our results demonstrate that the transmembrane protein ORF39p of VZV plays a role in evading the type I IFN responses by suppressing STINGmediated activation of the IFN-β promoter.

Functional analysis of ascP in Aeromonas veronii TH0426 reveals a key role in the regulation of virulence: Yongchao Guan , Meng Zhang , Yingda Wang , Zhongzhuo Liu , Zelin Zhao , Hong Wang , Dingjie An , Aidong Qian , Yuanhuan Kang , Wuwen Sun , Xiaofeng Shan; J. Microbiol. 2022;60(12):1153-1161. Published online November 10, 2022; DOI: https://doi.org/10.1007/s12275-022-2373-8

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Abstract

Aeromonas veronii is a pathogen which can induce diseases in humans, animals and aquatic organisms, but its pathogenic mechanism and virulence factors are still elusive. In this study, we successfully constructed a mutant strain (ΔascP) by homologous recombination. The results showed that the deletion of the ascP gene significantly down-regulated the expression of associated effector proteins in A. veronii compared to its wild type. The adhesive and invasive abilities of ΔascP to EPC cells were 0.82-fold lower in contrast to the wild strain. The toxicity of ΔascP to cells was decreased by about 2.91-fold (1 h) and 1.74-fold (2 h). Furthermore, the LD50 of the mutant strain of crucian carp was reduced by 19.94-fold, and the virulence was considerably attenuated. In contrast to the wild strain, the ΔascP content in the liver and spleen was considerably lower. The titers of serum cytokines (IL-8, TNF-α, and IL-1β) in crucian carp after the infection of the ΔascP strain were considerably lower in contrast to the wild strain. Hence, the ascP gene is essential for the etiopathogenesis of A. veronii TH0426.

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Complete genome sequence and genome-wide transposon mutagenesis enable the determination of genes required for sodium hypochlorite tolerance and drug resistance in pathogen Aeromonas veronii GD2019
Yifan Bu, Chengyu Liu, Yabo Liu, Wensong Yu, Tingjin Lv, Yuanxing Zhang, Qiyao Wang, Yue Ma, Shuai Shao
Microbiological Research.2024; 284: 127731. CrossRef
Construction of the flagellin F mutant of Vibrio parahaemolyticus and its toxic effects on silver pomfret (Pampus argenteus) cells
Yang Li, Chao Liu, Yuechen Sun, Ruijun Wang, Choufei Wu, Hanqu Zhao, Liqin Zhang, Dawei Song, Quanxin Gao
International Journal of Biological Macromolecules.2024; 259: 129395. CrossRef
Ferric uptake regulator (fur) affects the pathogenicity of Aeromonas veronii TH0426 by regulating flagellar assembly and biofilm formation
Jin-shuo Gong, Ying-da Wang, Yan-long Jiang, Di Zhang, Ya-nan Cai, Xiao-feng Shan, He Gong, Hao Dong
Aquaculture.2024; 580: 740361. CrossRef

Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea: Ye Chen , Yu Zhen , Jili Wan , Siqi Li , Jiayin Liu , Guodong Zhang , Tiezhu Mi; J. Microbiol. 2022;60(8):814-822. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2022-2

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Abstract

The differences in methanogen abundance and community composition were investigated between nearshore and offshore sediments in the South Yellow Sea (SYS). Shannon, Simpson, and Chao1 indices revealed a higher diversity of methanogens in the nearshore sediments than in the offshore sediments. The Mann–Whitney U test demonstrated that the relative abundance of Methanococcoides was significantly higher in the offshore sediments, while the relative abundances of Methanogenium, Methanosarcina, Methanosaeta, Methanolinea, and Methanomassiliicoccus were significantly higher in the nearshore sediments (P < 0.05). The abundance of the mcrA gene in the nearshore sediments was significantly higher than that in the offshore sediments. Furthermore, a similar vertical distribution of the methanogen and sulfatereducing bacteria (SRB) abundances was observed in the SYS sediments, implying there is potential cooperation between these two functional microbes in this environment. Finally, total organic carbon (TOC) was significantly correlated with methanogen community composition.

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Methylmercury cycling in the Bohai Sea and Yellow Sea: Reasons for the low system efficiency of methylmercury production
Lufeng Chen, Guoyi Cheng, Zhengwen Zhou, Yong Liang, Zhijia Ci, Yongguang Yin, Guangliang Liu, Yong Cai, Yanbin Li
Water Research.2024; 258: 121792. CrossRef
Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage
Yiming Yuan, Guangyi Zhang, Hongyuan Fang, Haifeng Guo, Yongkang Li, Zezhuang Li, Siwei Peng, Fuming Wang
Environmental Science and Pollution Research.2024; 31(9): 13075. CrossRef
Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples
Agata Anna Cisek, Iwona Bąk, Bożena Cukrowska
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Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead): Seomin Kang , Jae-Yun Lee , Jeong Eun Han , Yun-Seok Jeong , Do-Hun Gim , Jin-Woo Bae; J. Microbiol. 2022;60(9):890-898. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2075-2

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Abstract

Two novel bacterial strains, KSM-R2A25T and KSM-R2A30T, were isolated from intestines of Cyclina sinensis (corb shell) and Channa argus (northern snakehead), respectively. Both specimens were collected in Korea. The strains were Gramstain- negative, non-motile, and strictly aerobic. According to phylogenetic analyses based on 16S rRNA gene sequences, strains belonged to the genus Flavobacterium within the family Flavobacteriaceae. 16S rRNA gene sequences of strains KSMR2A25T and KSM-R2A30T were closely related to Flavobacterium cucumis DSM 18830T and Flavobacterium aquaticum JC164T with sequence similarities of 97.77% and 98.54%, respectively. Further genomic analyses including reconstruction of the UBCG tree and overall genome-related indices suggested them as novel species of the genus Flavobacterium. Both strains contained menaquinone with six isoprene units (MK-6) as a major isoprenoid quinone and iso-C15:1 G, iso- C15:0, and iso-C16:0 as major cellular fatty acids. The major polar lipid in both strains was phosphatidylethanolamine. The genomic G + C contents of strains KSM-R2A25T and KSMR2A30T were 31.7 and 31.9%, respectively. Based on the polyphasic taxonomic study presented here, strains KSM-R2A25T and KSM-R2A30T represent novel species of the genus Flavobacterium, for which the names Flavobacterium cyclinae sp. nov and Flavobacterium channae sp. nov are proposed. The type strains of F. cyclinae sp. nov and F. channae sp. nov are KSM-R2A25T (= KCTC 82978T = JCM 34997T) and KSMR2A30T (= KCTC 82979T = JCM 34998T), respectively.

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Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nihed Ajmi, Enes Said Gunduz, Huban Gocmen, Muhammed Duman
Systematic and Applied Microbiology.2024; 47(4): 126518. CrossRef
The first report of submandibular lymph node infection with Flavobacterium ceti in a horse and its complete genome sequence
Seung-Ho Ryu, Beomsoon Jang, Byung-Sun Kim, Kun Taek Park
Microbial Pathogenesis.2024; 197: 107096. CrossRef
Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Transcriptomic insights into the immune response of the intestine to Aeromonas veronii infection in northern snakehead (Channa argus)
Peng Sun, Di Zhang, Na Li, Xiao-Fei Li, Yi-Han Ma, Hui Li, Ye Tian, Tao Wang, Shahrood Ahmed Siddiquid, Wu-wen Sun, Lei Zhang, Xiao-Feng Shan, Chun-Feng Wang, Ai-Dong Qian, Dong-Xing Zhang
Ecotoxicology and Environmental Safety.2023; 255: 114825. CrossRef
Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef
Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Effects of tryptophan and phenylalanine on tryptophol production in Saccharomyces cerevisiae revealed by transcriptomic and metabolomic analyses: Xiaowei Gong , Huajun Luo , Liu Hong , Jun Wu , Heng Wu , Chunxia Song , Wei Zhao , Yi Han , Ya Dao , Xia Zhang , Donglai Zhu , Yiyong Luo; J. Microbiol. 2022;60(8):832-842. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2059-2

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Abstract

Tryptophol (TOL) is a metabolic derivative of tryptophan (Trp) and shows pleiotropic effects in humans, plants and microbes. In this study, the effect of Trp and phenylalanine (Phe) on TOL production in Saccharomyces cerevisiae was determined, and a systematic interpretation of TOL accumulation was offered by transcriptomic and metabolomic analyses. Trp significantly promoted TOL production, but the output plateaued (231.02−266.31 mg/L) at Trp concentrations ≥ 0.6 g/L. In contrast, Phe reduced the stimulatory effect of Trp, which was strongly dependent on the Phe concentration. An integrated genomic, transcriptomic, and metabolomic analysis revealed that the effect of Trp and Phe on TOL production was mainly related to the transamination and decarboxylation of the Ehrlich pathway. Additionally, other genes, including thiamine regulon genes (this), the allantoin catabolic genes dal1, dal2, dal4, and the transcriptional activator gene aro80, may play important roles. These findings were partly supported by the fact that the thi4 gene was involved in TOL production, as shown by heterologous expression analysis. To the best of our knowledge, this novel biological function of thi4 in S. cerevisiae is reported here for the first time. Overall, our findings provide insights into the mechanism of TOL production, which will contribute to TOL production using metabolic engineering strategies.

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Engineering the L-tryptophan metabolism for efficient de novo biosynthesis of tryptophol in Saccharomyces cerevisiae
Ye Li, Jingzhen Sun, Zhenhao Fu, Yubing He, Xiaorui Chen, Shijie Wang, Lele Zhang, Jiansheng Jian, Weihua Yang, Chunli Liu, Xiuxia Liu, Yankun Yang, Zhonghu Bai
Biotechnology for Biofuels and Bioproducts.2024;[Epub] CrossRef
Evaluating the Atypical Aging Potential Development in Sparkling Wines Can Be Achieved by Assessing the Base Wines at the End of the Alcoholic Fermentation
Simone Delaiti, Tiziana Nardin, Tomas Roman, Stefano Pedò, Roberto Larcher
Journal of Agricultural and Food Chemistry.2024; 72(9): 4918. CrossRef
Tryptophol Improves the Biocontrol Efficacy of Scheffersomyces spartinae against the Gray Mold of Strawberries by Quorum Sensing
Zichang Zhao, Yingying Wei, Xiurong Zou, Shu Jiang, Yi Chen, Jianfen Ye, Feng Xu, Hongfei Wang, Xingfeng Shao
Journal of Agricultural and Food Chemistry.2023; 71(49): 19739. CrossRef
A comprehensive review and comparison of L-tryptophan biosynthesis in Saccharomyces cerevisiae and Escherichia coli
Xinru Ren, Yue Wei, Honglu Zhao, Juanjuan Shao, Fanli Zeng, Zhen Wang, Li Li
Frontiers in Bioengineering and Biotechnology.2023;[Epub] CrossRef

Characterization of a cold-adapted debranching enzyme and its role in glycogen metabolism and virulence of Vibrio vulnificus MO6-24/O: Ah-Reum Han , Haeyoung Kim , Jong-Tae Park , Jung-Wan Kim; J. Microbiol. 2022;60(4):375-386. Published online February 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1507-3

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Abstract

Vibrio vulnificus MO6-24/O has three genes annotated as debranching enzymes or pullulanase genes. Among them, the gene encoded by VVMO6_03032 (vvde1) shares a higher similarity at the amino acid sequence level to the glycogen debranching enzymes, AmyX of Bacillus subtilis (40.5%) and GlgX of Escherichia coli (55.5%), than those encoded by the other two genes. The vvde1 gene encoded a protein with a molecular mass of 75.56 kDa and purified Vvde1 efficiently hydrolyzed glycogen and pullulan to shorter chains of maltodextrin and maltotriose (G3), respectively. However, it hydrolyzed amylopectin and soluble starch far less efficiently, and β-cyclodextrin (β-CD) only rarely. The optimal pH and temperature of Vvde1 was 6.5 and 25°C, respectively. Vvde1 was a cold-adapted debranching enzyme with more than 60% residual activity at 5°C. It could maintain stability for 2 days at 25°C and 1 day at 35°C, but it destabilized drastically at 40°C. The Vvde1 activity was inhibited considerably by Cu2+, Hg2+, and Zn2+, while it was slightly enhanced by Co2+, Ca2+, Ni2+, and Fe2+. The vvde1 knock-out mutant accumulated more glycogen than the wild-type in media supplemented with 1.0% maltodextrin; however, the side chain length distribution of glycogen was similar to that of the wild-type except G3, which was much more abundant in the mutant. Therefore, Vvde1 seemed to debranch glycogen with the degree of polymerization 3 (DP3) as the specific target branch length. Virulence of the pathogen against Caenorhabditis elegans was attenuated significantly by the vvde1 mutation. These results suggest that Vvde1 might be a unique glycogen debranching enzyme that is involved in both glycogen utilization and shaping of glycogen molecules, and contributes toward virulence of the pathogen.

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Characterization of glycogen-related glycoside hydrolase glgX and glgB from Klebsiella pneumoniae and their roles in biofilm formation and virulence
Xinyue Liu, Jialin Li, Ruibing Wu, Liping Bai
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Function of the mdxR gene encoding a novel regulator for carbohydrate metabolism and sporulation in Bacillus subtilis 168
Tianshi Wang, Jung-Wan Kim
Archives of Microbiology.2023;[Epub] CrossRef
Identification of a novel cyclomaltodextrinase annotated as a neopullulanase in the genome of Bacillus cereus
Bo-Ram Park, Davoodbasha MubarakAli, Jung-Wan Kim
Archives of Microbiology.2023;[Epub] CrossRef
Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef
Functional characterization of maltodextrin glucosidase for maltodextrin and glycogen metabolism in Vibrio vulnificus MO6-24/O
Hye-Young Kim, MubarakAli Davoodbasha, Jung-Wan Kim
Archives of Microbiology.2022;[Epub] CrossRef

Review

Coordinated regulation of interferon and inflammasome signaling pathways by SARS-CoV-2 proteins: Na-Eun Kim , Yoon-Jae Song; J. Microbiol. 2022;60(3):300-307. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1502-8

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Abstract

Type I and III interferons (IFNs) and the nucleotide-binding domain (NBD) leucine-rich repeat (LRR)-containing receptor (NLR) family pyrin domain containing 3 (NLRP3) inflammasome play pivotal roles in the pathogenesis of SARS-CoV-2. While optimal IFN and inflammasome responses are essential for limiting SARS-CoV-2 infection, aberrant activation of these innate immune responses is associated with COVID-19 pathogenesis. In this review, we focus our discussion on recent findings on SARS-CoV-2-induced type I and III IFNs and NLRP3 inflammasome responses and the viral proteins regulating these mechanisms.

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The impact of polymorphic variants of interferon receptor genes on COVID-19 severity and antibiotic resistance
E. A. Krieger, O. V. Samodova, O. A. Svitich, R. V. Samoilikov, E. A. Meremianina, L. V. Ivanova, N. A. Bebyakova, E. N. Ilina, A. V. Pavlenko, Yu. I. Esin, A. L. Arkhipova, S. N. Kovalchuk, A. V. Kudryavtsev
Russian Journal of Infection and Immunity.2024; 13(6): 1027. CrossRef
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Journal Articles

Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity: Dongwook Kim , Sein Park , Jongsik Chun; J. Microbiol. 2021;59(5):476-480. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-1154-0

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Abstract

The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and multiple studies have proposed its application in prokaryotic taxonomy and related disciplines. AAI demonstrates better resolution in elucidating taxonomic structure beyond the species rank when compared with average nucleotide identity (ANI), which is a standard criterion in species delineation. However, an efficient and easy-to-use computational tool for AAI calculation in large-scale taxonomic studies is not yet available. Here, we introduce a bioinformatic pipeline, named EzAAI, which allows for rapid and accurate AAI calculation in prokaryote sequences. The EzAAI tool is based on the MMSeqs2 program and computes AAI values almost identical to those generated by the standard BLAST algorithm with significant improvements in the speed of these evaluations. Our pipeline also provides a function for hierarchical clustering to create dendrograms, which is an essential part of any taxonomic study. EzAAI is available for download as a standalone JAVA program at http:// leb.snu.ac.kr/ezaai.

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The Genome of a New Halorubrum distributum Strain ICIS4 Isolated from the Culture of a Microalga Dunaliella salina
E. A. Selivanova, A. S. Balkin, Yu. A. Khlopko, V. Ya. Kataev, A. O. Plotnikov
Microbiology.2024; 93(4): 482. CrossRef
Peteryoungia algae sp. nov. isolated from seaweeds of Gouqi Island, China, and its unique genetic features among Peteryoungia strains
Jun Yin, Min He, Xiao-Xiao Liu, Chang-Bin Ren, Hou-Hong Liu, Hai Luo, Gen Chen, Ze-Fei Wang, Sanjit Chandra Debnath, Pin-Mei Wang, Hai-Xin Chen, Dao-Qiong Zheng
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Methylomonas rivi sp. nov., Methylomonas rosea sp. nov., Methylomonas aurea sp. nov. and Methylomonas subterranea sp. nov., type I methane-oxidizing bacteria isolated from a freshwater creek and the deep terrestrial subsurface
Christopher A. Abin, Christopher T. Garner, Krithivasan Sankaranarayanan, Reid A. Sindelar, Kyrah F. Kotary, Rosa M. Garner, Samantha C. Barclay, Haiyuan Cai, Paul A. Lawson, Lee R. Krumholz
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea
Katherine Bedoya-Urrego, Juan F. Alzate
Frontiers in Microbiology.2024;[Epub] CrossRef
Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina
Amal Khalaf Alghamdi, Sabiha Parween, Heribert Hirt, Maged M. Saad
BMC Genomics.2024;[Epub] CrossRef
Ochrobactrum chromiisoli sp. nov., Isolated from Chromium-Contaminated Soil
Yi Yang, Zhe Xu, Li Yang, Meng-yao Hu, Guang-yang Jiang, Jia Chen, Yi-chen Yang, Yongqiang Tian
Current Microbiology.2024;[Epub] CrossRef
Spartinivicinus poritis sp. nov., a red pigment-producing bacterium isolated from a scleractinian coral Porites lutea
Sumbal Sajid, Guoqiang Zhang, Zongyao Zhang, Yishan Lu, Lianguo Chen, Lin Cai
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Tardiphaga alba sp. nov., a heavy-metal-tolerant bacterium isolated from garden soil
Zhihua Bao, Chaojun Wang, Jiahui Cao, Tingting Zhang, Yong Guo, Yoshinori Sato, Tomoyasu Nishizawa, Hiroyuki Ohta
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments
Yue Zheng, Baozhan Wang, Ping Gao, Yiyan Yang, Bu Xu, Xiaoquan Su, Daliang Ning, Qing Tao, Qian Li, Feng Zhao, Dazhi Wang, Yao Zhang, Meng Li, Mari-K H Winkler, Anitra E Ingalls, Jizhong Zhou, Chuanlun Zhang, David A Stahl, Jiandong Jiang, Willm Martens-H
The ISME Journal.2024;[Epub] CrossRef
Refining the taxonomy of the order Hyphomicrobiales (Rhizobiales) based on whole genome comparisons of over 130 type strains
George C. diCenzo, Yuqi Yang, J. Peter W. Young, Nemanja Kuzmanović
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
Huibin Lu, Li Chen, Yujing Wang, Peng Xing, Qinglong Wu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken
Bibiana Rios-Galicia, Johan S. Sáenz, Timur Yergaliyev, Christoph Roth, Amélia Camarinha-Silva, Jana Seifert
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Parendozoicomonas callyspongiae sp. nov. Isolated from a Marine Sponge, Callyspongia elongate, and Reclassification of Sansalvadorimonas verongulae as Parendozoicomonas verongulae comb. nov.
Soo-Bin Kim, Kyung Hyun Kim, Jin-Sook Park
Current Microbiology.2024;[Epub] CrossRef
Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family
Zuqing Wu, Luyuan Guo, Ying Wu, Mingyu Yang, Sen Du, Jiabing Shao, Zefeng Zhang, Yanlin Zhao, Michael J. Imperiale
mSphere.2024;[Epub] CrossRef
Biochip-Based Identification of Mycobacterial Species in Russia
Danila Zimenkov, Vyacheslav Zhuravlev, Anastasia Ushtanit, Marina Filippova, Uliana Semenova, Natalia Solovieva, Maria Sviridenko, Anastasia Khakhalina, Svetlana Safonova, Marina Makarova, Elizaveta Gordeeva, Elena Guselnikova, Yakov Schwartz, Natalia Sta
International Journal of Molecular Sciences.2024; 25(23): 13200. CrossRef
Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon
Gracee K. Tothero, Rene L. Hoover, Ibrahim F. Farag, Daniel I. Kaplan, Pamela Weisenhorn, David Emerson, Clara S. Chan, Arpita Bose
Applied and Environmental Microbiology.2024;[Epub] CrossRef
Svornostia abyssi gen. nov., sp. nov. isolated from the world’s deepest silver–uranium mine currently devoted to the extraction of radon-saturated water
Gabriela Kapinusova, Jachym Suman, Michal Strejcek, Petr Pajer, Tomas Cajthaml, Pavel Ulbrich, Meina Neumann-Schaal, Ondrej Uhlik
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria
Wouter B. Lenferink, Theo A. van Alen, Mike S. M. Jetten, Huub J. M. Op den Camp, Maartje A. H. J. van Kessel, Sebastian Lücker
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Genome streamlining in Parcubacteria transitioning from soil to groundwater
Narendrakumar M. Chaudhari, Olga M. Pérez-Carrascal, Will A. Overholt, Kai U. Totsche, Kirsten Küsel
Environmental Microbiome.2024;[Epub] CrossRef
Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil
Huijuan Jin, Leitao Huo, Yi Yang, Yan Lv, Jingjing Wang, Julien Maillard, Christof Holliger, Frank E. Löffler, Jun Yan
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Description of Pseudocalidococcus azoricus gen. sp. nov. (Thermosynechococcaceae, Cyanobacteria), a Rare but Widely Distributed Coccoid Cyanobacteria
Rúben Luz, Rita Cordeiro, Jan Kaštovský, Amélia Fonseca, Ralph Urbatzka, Vitor Vasconcelos, Vítor Gonçalves
Diversity.2023; 15(12): 1157. CrossRef
The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea
Ramona Marasco, Grégoire Michoud, Fatmah O. Sefrji, Marco Fusi, Chakkiath P. Antony, Kholoud A. Seferji, Alan Barozzi, Giuseppe Merlino, Daniele Daffonchio
Frontiers in Microbiology.2023;[Epub] CrossRef
Danxiaibacter flavus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from forest soil on Danxia Mountain
Zhuo-Huan Zheng, Chun-Yan Lu, Wen-Hui Lian, Jia-Rui Han, Fang Chen, Ting Zhou, Shuai Li, Lei Dong, Wen-Jun Li
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions
Jinbo Xu, Lu Wang, Weifeng Lv, Xinmin Song, Yong Nie, Xiao-Lei Wu
Frontiers in Microbiology.2023;[Epub] CrossRef
Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum
Ana Marina Pedrolo, Filipe Pereira Matteoli, Cláudio Roberto Fônseca Sousa Soares, Ana Carolina Maisonnave Arisi
Microbial Ecology.2023; 86(1): 563. CrossRef
UACG: Up-to-Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction
Seong-In Na, Michael James Bailey, Mauricio Chalita, Jae Hyoung Cho, Jongsik Chun
Journal of Microbiology.2023; 61(7): 683. CrossRef
Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emend
Kyung Hyun Kim, Dong Min Han, Jae Kyeong Lee, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma
Jiung-Wen Chen, Chao-Jen Shih, Li-Wha Wu, Yen-Chi Wu, Wei-Fan Chiang, Yuh-Ling Chen, Jer-Horng Wu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov.
Samuel Imisi Awala, Joo-Han Gwak, Yongman Kim, Chanmee Seo, Andrea Strazzulli, Song-Gun Kim, Sung-Keun Rhee
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov
Can Cui, Dong Han, Jing Hou, Heng-Lin Cui
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Complete genome sequence analysis of plant growth-promoting bacterium, Isoptericola sp. AK164 isolated from the rhizosphere of Avicennia marina growing at the Red Sea coast
Amal Khalaf Alghamdi, Sabiha Parween, Heribert Hirt, Maged M. Saad
Archives of Microbiology.2023;[Epub] CrossRef
Draft genome sequence of Hahella sp. CR1 and its ability in producing cellulases for saccharifying agricultural biomass
Melvin Chun Yun Tan, Muhammad Ramziuddin Zakaria, Kok Jun Liew, Chun Shiong Chong
Archives of Microbiology.2023;[Epub] CrossRef
Sedimenticola hydrogenitrophicus sp. nov. a chemolithoautotrophic bacterium isolated from a terrestrial mud volcano, and proposal of Sedimenticolaceae fam. nov. in the order Chromatiales
Galina Slobodkina, Alexander Merkel, Nataliya Ratnikova, Alexandra Kuchierskaya, Alexander Slobodkin
Systematic and Applied Microbiology.2023; 46(5): 126451. CrossRef
Comparative genomic assessment of members of genus Tenacibaculum: an exploratory study
Rohit Satyam, Shaban Ahmad, Khalid Raza
Molecular Genetics and Genomics.2023; 298(5): 979. CrossRef
Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species
Mina Bizic, Traian Brad, Danny Ionescu, Lucian Barbu-Tudoran, Luca Zoccarato, Joost W Aerts, Paul-Emile Contarini, Olivier Gros, Jean-Marie Volland, Radu Popa, Jessica Ody, Daniel Vellone, Jean-François Flot, Scott Tighe, Serban M Sarbu
The ISME Journal.2023; 17(3): 340. CrossRef
Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant
Marco A. Lopez Marin, Jachym Suman, Kunal Jani, Pavel Ulbrich, Tomas Cajthaml, Alena Filipova, Petr Pajer, Meina Neumann-Schaal, Michal Strejcek, Ondrej Uhlik
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation
Wen-Bo Nie, Guo-Jun Xie, Xin Tan, Jie Ding, Yang Lu, Yi Chen, Chun Yang, Qiang He, Bing-Feng Liu, Defeng Xing, Nanqi Ren
Environmental Science & Technology.2023; 57(17): 7029. CrossRef
Allocoprobacillus halotolerans gen. nov., sp. nov and Coprobacter tertius sp. nov., isolated from human gut microbiota
Nancy M. Y. Teng, Raymond Kiu, Rhiannon Evans, David J. Baker, Christian Zenner, Stephen D. Robinson, Lindsay J. Hall
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Aridibaculum aurantiacum gen. nov., sp. nov., isolated from the Kumtag Desert soil
Lei Dong, Shuai Li, Guo-Yuan Shi, Jia-Rui Han, Chun-Yan Lu, Wen-Hui Lian, Ling-Xiang Yue, Dalal Hussien M. Alkhalifah, Wael N. Hozzein, Wen-Jun Li
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Acidaminococcus homini s sp. nov., Amedibacillus hominis sp. nov., Lientehia hominis gen. nov. sp. nov., Merdimmobilis hominis gen. nov. sp. nov., and Paraeggerthella hominis sp. nov., isolated from human faeces
Rashidin Abdugheni, Dan-Hua Li, Yu-Jing Wang, Meng-Xuan Du, Nan Zhou, Chang Liu, Shuang-Jiang Liu
International Journal of Systematic and Evolutionary Microbiology.2023;[Epub] CrossRef
Vogesella aquatica sp. nov. and Vogesella margarita sp. nov., isolated from rivers in Southwest China
Huibin Lu, Li Chen, Lingyang Kong, Linpei Huang, Guangjie Chen
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Dermatobacter hominis gen. nov., sp. nov., a new member of the family Iamiaceae, revealed the potential utilisation of skin-derived metabolites
HyungWoo Jo, Chaeyun Baek, Young Mok Heo, Hye-Been Kim, Haeun Lee, Seunghyun Kang, Seyoung Mun, Yunseok Oh, Doyeong Ko, Kyudong Han, Raúl Riesco, Martha E. Trujillo, Dong-Geol Lee
Antonie van Leeuwenhoek.2023; 116(11): 1139. CrossRef
Dynamic Development of Viral and Bacterial Diversity during Grass Silage Preservation
Johan S. Sáenz, Bibiana Rios-Galicia, Bianca Rehkugler, Jana Seifert
Viruses.2023; 15(4): 951. CrossRef
Alteromonas gilva sp. nov. and Erythrobacter fulvus sp. nov., isolated from a tidal mudflat
Sunho Park, Inhyup Kim, Geeta Chhetri, Yoonseop So, Yonghee Jung, Haejin Woo, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Two novel alkalitolerant species Pseudalkalibacillus spartinae sp. nov. and Pseudalkalibacillus sedimenti sp. nov.
Guo-Hong Liu, Shuang Han, Bing Li, Rui-Li Li, Huai Shi, Qian-Qian Chen, Hend A. Alwathnani, Christopher Rensing, Shun-Gui Zhou
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Description of Brachybacterium sillae sp. nov., a thermophilic bacterium isolated from a hot spring
Dariimaa Ganbat, DoKyung Oh, Yong-Jik Lee, Dong-Woo Lee, Seong-Bo Kim, Won-Jae Chi, Ki-Eun Lee, Byoung-Hee Lee, You-Jung Jung, Jung-Sook Lee, Sang-Jae Lee
Antonie van Leeuwenhoek.2023; 116(8): 791. CrossRef
Bacillus mexicanus sp. nov., a biological control bacterium isolated from the common bean (Phaseolus vulgaris L.) crop in Sinaloa, Mexico
Sergio de los Santos Villalobos, Carmen María Félix Pablos, Valeria Valenzuela Ruiz, Fannie I. Parra Cota
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors
Patricia Bovio-Winkler, Leandro D. Guerrero, Leonardo Erijman, Pía Oyarzúa, María Eugenia Suárez-Ojeda, Angela Cabezas, Claudia Etchebehere
BMC Microbiology.2023;[Epub] CrossRef
Potential for homoacetogenesis via the Wood–Ljungdahl pathway in Korarchaeia lineages from marine hydrothermal vents
Francesca Vulcano, Petra Hribovšek, Emily Olesin Denny, Ida H. Steen, Runar Stokke
Environmental Microbiology Reports.2023; 15(6): 698. CrossRef
Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated
James G. Volmer, Rochelle M. Soo, Paul N. Evans, Emily C. Hoedt, Ana L. Astorga Alsina, Benjamin J. Woodcroft, Gene W. Tyson, Philip Hugenholtz, Mark Morrison
BMC Biology.2023;[Epub] CrossRef
Thermomonas mangrovi sp. nov., isolated from soil of a mangrove nature reserve
Shanshan Xu, Junpeng Chen, Si Chen, Qiliang Lai, Zengzhi Liu, Ying Xu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Proposal to transfer Bacillus massiliigorillae to the genus Peribacillus as Peribacillus massiliigorillae comb. nov., and Bacillus sinesaloumensis to the genus Ferdinandcohnia as Ferdinandcohnia sinesaloumensis comb. nov
Awalagaway Dhulappa, Manik Prabhu Narsing Rao, Haijie Wang, Bhagwan Narayan Rekadwad, Ying-Qian Kang
Archives of Microbiology.2023;[Epub] CrossRef
Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L.
Inhyup Kim, Geeta Chhetri, Yoonseop So, Sunho Park, Yonghee Jung, Haejin Woo, Taegun Seo
Microorganisms.2023; 11(8): 1900. CrossRef
Leucobacter edaphi sp. nov., a highly chromate-tolerant bacterium isolated from chromium containing chemical plant soil
Bijun Zheng, Zhe Xu, Li Yang, Guangyang Jiang, Jia Chen, Yichen Yang, Yongqiang Tian
Antonie van Leeuwenhoek.2023; 116(12): 1433. CrossRef
Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov.
Sunho Park, Inhyup Kim, Geeta Chhetri, Yoonseop So, Yonghee Jung, Haejin Woo, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Isolation and Genomic Analysis of 3-Chlorobenzoate-Degrading Bacteria from Soil
Ifat Ara, Ryota Moriuchi, Hideo Dohra, Kazuhide Kimbara, Naoto Ogawa, Masaki Shintani
Microorganisms.2023; 11(7): 1684. CrossRef
Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages
Atena Sadat Sombolestani, Dries Bongaerts, Eliza Depoorter, Ilse Cleenwerck, Anneleen D. Wieme, Scott J. Britton, Stefan Weckx, Luc De Vuyst, Peter Vandamme
Systematic and Applied Microbiology.2023; 46(5): 126440. CrossRef
Complete genome sequence of Vibrio gazogenes PB1: an estuarine bacterium capable of producing prodigiosin from starch or cellulose
Bincy Baby, Dhanya Vijay, Pretty S. Philip, Afra A. Alnuaimi, Hessa M. Almansoori, Sarah O. Areidat, Gulfaraz Khan, Ranjit Vijayan, M. Kalim Akhtar
Frontiers in Marine Science.2023;[Epub] CrossRef
Tianweitania aestuarii sp. nov., isolated from a coastal dune, reclassification of Corticibacterium populi as Tianweitania populi comb. nov., and emended description of the genus Tianweitania
Ji Hyeon Song, Sooyeon Park, Jung-Sook Lee, Wonyong Kim, Jung-Hoon Yoon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Fluviispira vulneris sp. nov., isolated from human wound secretions
Peijuan Tang, Na Peng, Pengwen Ouyang, Sheng Long, Zhenhua Wei, Xingchun Chen, Pinghua Qu, Liangyi Xie
Antonie van Leeuwenhoek.2023; 116(12): 1305. CrossRef
Neorhizobium turbinariae sp. nov., a coral-beneficial bacterium isolated from Turbinaria peltata
Hao Sun, Zhiyuan Miao, Shuai Liu, Xuerui Liu, Bogui Chen, Baolin Liao, Baohua Xiao
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Description of Salinimicrobium tongyeongense sp. nov., isolated from seawater
Dariimaa Ganbat, Dong-Woo Lee, Seong-Bo Kim, Yong-Jik Lee, Gaewon Nam, Won-Jae Chi, Byoung-Hee Lee, You-Jung Jung, Jung-Sook Lee, Sang-Jae Lee
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus
Zefeng Zhang, Zuqing Wu, He Liu, Mingyu Yang, Rui Wang, Yanlin Zhao, Feng Chen
Frontiers in Microbiology.2023;[Epub] CrossRef
PhaGAA: an integrated web server platform for phage genome annotation and analysis
Jiawei Wu, Qingrui Liu, Min Li, Jiliang Xu, Chen Wang, Junyin Zhang, Minfeng Xiao, Yannan Bin, Junfeng Xia, Can Alkan
Bioinformatics.2023;[Epub] CrossRef
Comparative Genomics Reveals Three Genetic Groups of the Whitefly Obligate Endosymbiont Candidatus Portiera aleyrodidarum
Teng Lei, Ning Luo, Chao Song, Junwei Yu, Yuhang Zhou, Xin Qi, Yinquan Liu
Insects.2023; 14(11): 888. CrossRef
Roseobacter insulae sp. nov. and Loktanella gaetbuli sp. nov., isolated from tidal flats in the Yellow Sea in Korea
Eun Bee Lee, Sooyeon Park, Wonyong Kim, Jung-Hoon Yoon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Novosphingobium mangrovi sp. nov., isolated from mangrove sediment
Qian Huang, Zhihui Qian, Tao Peng, Jin Li, Xueying Ye, Tongwang Huang, Zhong Hu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae
Dao-Feng Zhang, Wei He, Zongze Shao, Iftikhar Ahmed, Yuqin Zhang, Wen-Jun Li, Zhe Zhao
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Scleromatobacter humisilvae gen. nov., sp. nov., a novel bacterium isolated from oak forest soil
Sophie Mieszkin, Blandine Trouche, Julien Ancousture, Youssef Raouf, Stéphane Uroz, Karine Alain
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations
Deyong Li, Zhichang Ren, Yangqi Zhou, Lugao Jiang, Min Zheng, Guoqiang Liu, Jennifer B. Glass
Applied and Environmental Microbiology.2023;[Epub] CrossRef
Citrobacter sp. Y3 harbouring novel gene HBCD-hd-1 mineralizes hexabromocyclododecane via new metabolic pathways according to multi-omics characterization
Xingxing Peng, Tianyu Li, Qihang Zheng, Yingyuan Lu, Yuzhe He, Yetao Tang, Rongliang Qiu
Journal of Hazardous Materials.2023; 442: 130071. CrossRef
Opacimonas viscosa gen. nov., sp. nov., a novel bacterium isolated from phycosphere
Xuanru Lin, Runlin Cai, Guanjing Cai, Jianmin Xie, Zhenyuan Zhou, Hui Wang
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Description of Microbacterium neungamense sp. nov. isolated from a hot spring
Dariimaa Ganbat, Ga Eul Jeong, DoKyung Oh, Dong-Woo Lee, Yong-Jik Lee, Seong-Bo Kim, In-Tae Cha, Won-Jae Chi, Seul-Ki Park, Jung-Sook Lee, Sang-Jae Lee
Archives of Microbiology.2023;[Epub] CrossRef
Habitat distribution of the genus Belliella in continental waters and the description of Belliella alkalica sp. nov., Belliella calami sp. nov. and Belliella filtrata sp. nov.
Kristóf Korponai, Sára Szuróczki, Zsuzsanna Márton, Attila Szabó, Paula V. Morais, Diogo Neves Proença, Erika Tóth, Emil Boros, Károly Márialigeti, Tamás Felföldi
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Molecular Characterization of Indigenous Rhizobia from Kenyan Soils Nodulating with Common Beans
Clabe Wekesa, Kelvin Kiprotich, Patrick Okoth, George O. Asudi, John O. Muoma, Alexandra C. U. Furch, Ralf Oelmüller
International Journal of Molecular Sciences.2023; 24(11): 9509. CrossRef
Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field
Petra Hribovšek, Emily Olesin Denny, Håkon Dahle, Achim Mall, Thomas Øfstegaard Viflot, Chanakan Boonnawa, Eoghan P. Reeves, Ida Helene Steen, Runar Stokke, Michael S. Rappe
mSystems.2023;[Epub] CrossRef
Thiovibrio frasassiensis gen. nov., sp. nov., an autotrophic, elemental sulphur disproportionating bacterium isolated from sulphidic karst sediment, and proposal of Thiovibrionaceae fam. nov.
Heidi S. Aronson, Cais Thomas, Maia K. Bhattacharyya, Shaan R. Eckstein, Sophia R. Jensen, Roman A. Barco, Jennifer L. Macalady, Jan P. Amend
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Hufsiella ginkgonis gen. nov., sp. nov. and Hufsiella arboris sp. nov., isolated from tree barks
Heeyoung Kang, Seokhyeon Bae, Haneul Kim, Kiseong Joh
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Phenotypic and genomic characterization of the first alkaliphilic aceticlastic methanogens and proposal of a novel genus Methanocrinis gen.nov. within the family Methanotrichaceae
Maria A. Khomyakova, Alexander Y. Merkel, Alexander I. Slobodkin, Dimitry Y. Sorokin
Frontiers in Microbiology.2023;[Epub] CrossRef
Description of Xanthocytophaga agilis sp. nov. and Xanthocytophaga flavus sp. nov. of the new genus Xanthocytophaga gen. nov and the proposal of Rhodocytophagaceae fam. nov. within the order Cytophagales
Xianjiao Zhang, Guang-Da Feng, Yang Liu, Fan Yang, Yanxuan Li, Xiaoqin Deng, Honghui Zhu, Qing Yao
Archives of Microbiology.2023;[Epub] CrossRef
Draft genome sequence of Joostella atrarenae M1-2T with cellulolytic and hemicellulolytic ability
Kok Jun Liew, Muhammad Ramziuddin Zakaria, Clarine Wan Ling Hong, Melvin Chun Yun Tan, Chun Shiong Chong
3 Biotech.2023;[Epub] CrossRef
Transcriptional Landscapes of Herelleviridae Bacteriophages and Staphylococcus aureus during Phage Infection: An Overview
Maria Kornienko, Dmitry Bespiatykh, Roman Gorodnichev, Narina Abdraimova, Egor Shitikov
Viruses.2023; 15(7): 1427. CrossRef
Tenacibaculum tangerinum sp. nov., isolated from a tidal flat sediment
Sang Hyun Lee, Yeonjae Yoo, Dae Young Kwon, Jong Seong Khim, Xiaoyue Xu, Bogun Kim, In-Geol Choi, Jae-Jin Kim
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
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The synergy effect of arbuscular mycorrhizal fungi symbiosis and exogenous calcium on bacterial community composition and growth performance of peanut (Arachis hypogaea L.) in saline alkali soil: Dunwei Ci , Zhaohui Tang , Hong Ding , Li Cui , Guanchu Zhang , Shangxia Li , Liangxiang Dai , Feifei Qin , Zhimeng Zhang , Jishun Yang , Yang Xu; J. Microbiol. 2021;59(1):51-63. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-021-0317-3

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Abstract

Peanut (Arachis hypogaea. L) is an important oil seed crop. Both arbuscular mycorrhizal fungi (AMF) symbiosis and calcium (Ca2+) application can ameliorate the impact of saline soil on peanut production, and the rhizosphere bacterial communities are also closely correlated with peanut salt tolerance; however, whether AMF and Ca2+ can withstand high-salinity through or partially through modulating rhizosphere bacterial communities is unclear. Here, we used the rhizosphere bacterial DNA from saline alkali soil treated with AMF and Ca2+ alone or together to perform high-throughput sequencing of 16S rRNA genes. Taxonomic analysis revealed that AMF and Ca2+ treatment increased the abundance of Proteobacteria and Firmicutes at the phylum level. The nitrogenfixing bacterium Sphingomonas was the dominant genus in these soils at the genus level, and the soil invertase and urease activities were also increased after AMF and Ca2+ treatment, implying that AMF and Ca2+ effectively improved the living environment of plants under salt stress. Moreover, AMF combined with Ca2+ was better than AMF or Ca2+ alone at altering the bacterial structure and improving peanut growth in saline alkali soil. Together, AMF and Ca2+ applications are conducive to peanut salt adaption by regulating the bacterial community in saline alkali soil.

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