Journal of Microbiology

Journal Articles

Dynamics of Microbial Community Structure, Function and Assembly Mechanism with Increasing Stand Age of Slash Pine (Pinus elliottii) Plantations in Houtian Sandy Area, South China: Xiaoyang Zhang , Si-Yi Xiong , Xiukun Wu , Bei-Bei Zeng , Yang-Mei Mo , Zhi-Cheng Deng , Qi Wei , Yang Gao , Licao Cui , Jianping Liu , Haozhi Long; J. Microbiol. 2023;61(11):953-966. Published online November 29, 2023; DOI: https://doi.org/10.1007/s12275-023-00089-7

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Establishing slash pine plantations is the primary method for restoring sandification land in the Houtian area of South China. However, the microbial variation pattern with increasing stand age remains unclear. In this study, we investigated microbial community structure and function in bare sandy land and four stand age gradients, exploring ecological processes that determine their assembly. We did not observe a significant increase in the absolute abundance of bacteria or fungi with stand age. Bacterial communities were dominated by Chloroflexi, Actinobacteria, Proteobacteria, and Acidobacteria; the relative abundance of Chloroflexi significantly declined while Proteobacteria and Acidobacteria significantly increased with stand age. Fungal communities showed succession at the genus level, with Pisolithus most abundant in soils of younger stands (1- and 6-year-old). Turnover of fungal communities was primarily driven by stochastic processes; both deterministic and stochastic processes influenced the assembly of bacterial communities, with the relative importance of stochastic processes gradually increasing with stand age. Bacterial and fungal communities showed the strongest correlation with the diameter at breast height, followed by soil available phosphorus and water content. Notably, there was a significant increase in the relative abundance of functional groups involved in nitrogen fixation and uptake as stand age increased. Overall, this study highlights the important effects of slash pine stand age on microbial communities in sandy lands and suggests attention to the nitrogen and phosphorus requirements of slash pine plantations in the later stages of sandy management.

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Assembly processes and networks of soil microbial communities along karst forest succession
Wanxia Peng, Min Song, Hu Du, Shanghua Jiang, Fuping Zeng, Huijun Chen, Tongqing Song
CATENA.2025; 248: 108574. CrossRef
Temporal dynamics of soil microbial symbioses in the root zone of wolfberry: deciphering the effects of biotic and abiotic factors on bacterial and fungal ecological networks
Mengyuan He, Qianqian Wang, Yiming Wang, Junhua Zhang
Frontiers in Plant Science.2025;[Epub] CrossRef
Assessing the health of climate-sensitive trees in a subalpine ecosystem through microbial community dynamics
Bo Ram Kang, Soo Bin Kim, Jin-Kyung Hong, Seok Hyun Ahn, Jinwon Kim, Nayeon Lee, Tae Kwon Lee
Science of The Total Environment.2024; 957: 177724. CrossRef
The complex relationships between diatoms, bacterial communities, and dissolved organic matter: Effects of silicon concentration
Xiding Wang, Yang Liu, Yi Zhang, Peng Wu, Xudong Liu, Fangru Nan, Qi Liu, Junping Lv, Jia Feng, Shulian Xie
Algal Research.2024; 79: 103460. CrossRef
Assembly and co-occurrence pattern of microbial communities in bulk and rhizosphere soils of Pinus elliottii plantations on sandy lands in China
Haozhi Long, Si-Yi Xiong, Yang-Mei Mo, Bei-Bei Zeng, Bin-Xuan Shan, Ting Xiao, Yang Gao, Chaoyu Cui
Plant and Soil.2024;[Epub] CrossRef

Alterations of oral microbiota in Chinese children with viral encephalitis and/or viral meningitis: Yijie Li , Jing Liu , Yimin Zhu , Chunying Peng , Yao Dong , Lili Liu , Yining He , Guoping Lu , Yingjie Zheng; J. Microbiol. 2022;60(4):429-437. Published online February 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1560-y

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Abstract

The role of oral microbiota in viral encephalitis and/or viral meningitis (VEVM) remains unclear. In this hospital-based, frequency-matched study, children with clinically diagnosed VEVM (n = 68) and those with other diseases (controls, n = 68) were recruited. Their oral swab samples were collected and the oral microbiota was profiled using 16S rRNA gene sequencing. The oral microbiota of children with VEVM exhibited different beta diversity metrics (unweighted UniFrac distance: P < 0.001, R2 = 0.025, Bray-curtis dissimilarity: P = 0.045, R2 = 0.011, and Jaccard dissimilarity: P < 0.001, R2 = 0.017) and higher relative abundances of taxa identified by Linear discriminant analysis (LDA) with effect size (Enterococcus, Pedobacter, Massilia, Prevotella_9, Psychrobacter, Butyricimonas, Bradyrhizobium, etc., LDA scores > 2.0) when compared with the control group. The higher pathway abundance of steroid hormone biosynthesis predicted by oral microbiota was suggested to be linked to VEVM (q = 0.020). Further, a model based on oral microbial traits showed good predictive performance for VEVM with an area under the receiver operating characteristic curve of 0.920 (95% confidence interval: 0.834–1.000). Similar results were also obtained between children with etiologically diagnosed VEVM (n = 43) and controls (n = 68). Our preliminary study identified VEVM-specific oral microbial traits among children, which can be effective in the diagnosis of VEVM.

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Metagenomic next-generation sequencing and proteomics analysis in pediatric viral encephalitis and meningitis
Yi-Long Wang, Xiao-Tong Guo, Meng-Ying Zhu, Yu-Chen Mao, Xue-Bin Xu, Yi Hua, Lu Xu, Li-Hua Jiang, Cong-Ying Zhao, Xin Zhang, Guo-Xia Sheng, Pei-Fang Jiang, Zhe-Feng Yuan, Feng Gao
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef
Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection
William Bourumeau, Karine Tremblay, Guillaume Jourdan, Catherine Girard, Catherine Laprise
Microorganisms.2023; 11(11): 2703. CrossRef

Review

[MINIREVIEW]The rapid adaptation of SARS-CoV-2–rise of the variants: transmission and resistance: Sandrine M. Soh , Yeongjun Kim , Chanwoo Kim , Ui Soon Jang , Hye-Ra Lee; J. Microbiol. 2021;59(9):807-818. Published online August 27, 2021; DOI: https://doi.org/10.1007/s12275-021-1348-5

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Abstract

The causative factor of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously mutating. Interestingly, identified mutations mainly occur in the spike (S) protein which interacts with the ACE2 receptor and is cleaved via serine protease TMPRSS2. Some mutated strains are becoming dominant in various parts of the globe because of increased transmissibility as well as cell entry efficacy. Remarkably, the neutralizing activity of monoclonal antibodies, convalescent sera, and vaccines against the variants has been reported to be significantly reduced. Therefore, the efficacy of various monoclonal antibodies therapy and vaccines against these variants is becoming a great global concern. We herein summarize the current status of SARS-CoV- 2 with gears shifted towards the recent and most common genetic variants in relation to transmission, neutralizing activity, and vaccine efficacy.

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Understanding the Molecular Actions of Spike Glycoprotein in SARS-CoV-2 and Issues of a Novel Therapeutic Strategy for the COVID-19 Vaccine
Yasunari Matsuzaka, Ryu Yashiro
BioMedInformatics.2024; 4(2): 1531. CrossRef
Complex vaccination strategies prevent the emergence of vaccine resistance
Simon A Rella, Yuliya A Kulikova, Aygul R Minnegalieva, Fyodor A Kondrashov, Ben Ashby, Tim Connallon
Evolution.2024; 78(10): 1722. CrossRef
Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies
Sarah E. Fumagalli, Nigam H. Padhiar, Douglas Meyer, Upendra Katneni, Haim Bar, Michael DiCuccio, Anton A. Komar, Chava Kimchi-Sarfaty
Virology Journal.2023;[Epub] CrossRef
Broad neutralization against SARS-CoV-2 variants induced by ancestral and B.1.351 AS03-Adjuvanted recombinant Plant-Derived Virus-Like particle vaccines
Charlotte Dubé, Sarah Paris-Robidas, Guadalupe Andreani, Cindy Gutzeit, Marc-André D'Aoust, Brian J. Ward, Sonia Trépanier
Vaccine.2022; 40(30): 4017. CrossRef
A tentative tracking of the SARS-Cov2 pandemic in France, based on a corrected SIR model including vaccination effects
Mathilde Varret, François Xavier Martin, François Varret, J.-C.S. Lévy
EPJ Web of Conferences.2022; 263: 01002. CrossRef
Changing Dynamics of SARS-CoV-2: A Global Challenge
Ananya Chugh, Nimisha Khurana, Kangna Verma, Ishita Sehgal, Rajan Rolta, Pranjal Vats, Rajendra Phartyal, Deeksha Salaria, Neha Kaushik, Eun Ha Choi, Mansi Verma, Nagendra Kumar Kaushik
Applied Sciences.2022; 12(11): 5546. CrossRef
The SARS-CoV-2 differential genomic adaptation in response to varying UVindex reveals potential genomic resources for better COVID-19 diagnosis and prevention
Naveed Iqbal, Muhammad Rafiq, Masooma, Sanaullah Tareen, Maqsood Ahmad, Faheem Nawaz, Sumair Khan, Rida Riaz, Ting Yang, Ambrin Fatima, Muhsin Jamal, Shahid Mansoor, Xin Liu, Nazeer Ahmed
Frontiers in Microbiology.2022;[Epub] CrossRef
SARS-CoV-2 Variants of Concern Hijack IFITM2 for Efficient Replication in Human Lung Cells
Rayhane Nchioua, Annika Schundner, Dorota Kmiec, Caterina Prelli Bozzo, Fabian Zech, Lennart Koepke, Alexander Graf, Stefan Krebs, Helmut Blum, Manfred Frick, Konstantin M. J. Sparrer, Frank Kirchhoff, Tom Gallagher
Journal of Virology.2022;[Epub] CrossRef
Viral Load in COVID-19 Patients: Implications for Prognosis and Vaccine Efficacy in the Context of Emerging SARS-CoV-2 Variants
Severino Jefferson Ribeiro da Silva, Suelen Cristina de Lima, Ronaldo Celerino da Silva, Alain Kohl, Lindomar Pena
Frontiers in Medicine.2022;[Epub] CrossRef
Antibody engineering improves neutralization activity against K417 spike mutant SARS-CoV-2 variants
Lili Li, Meiling Gao, Peng Jiao, Shulong Zu, Yong-qiang Deng, Dingyi Wan, Yang Cao, Jing Duan, Saba R Aliyari, Jie Li, Yueyue Shi, Zihe Rao, Cheng-feng Qin, Yu Guo, Genhong Cheng, Heng Yang
Cell & Bioscience.2022;[Epub] CrossRef
Perspectives and Factors Affecting the Preventive Behavior Pertinent to COVID-19 among School Employees in Chiang Mai, Thailand: A Cross-Sectional Study
Pheerasak Assavanopakun, Tharntip Promkutkao, Suchat Promkutkeo, Wachiranun Sirikul
International Journal of Environmental Research and Public Health.2022; 19(9): 5662. CrossRef
Efficacy, safety, and immunogenicity of a booster regimen of Ad26.COV2.S vaccine against COVID-19 (ENSEMBLE2): results of a randomised, double-blind, placebo-controlled, phase 3 trial
Karin Hardt, An Vandebosch, Jerald Sadoff, Mathieu Le Gars, Carla Truyers, David Lowson, Ilse Van Dromme, Johan Vingerhoets, Tobias Kamphuis, Gert Scheper, Javier Ruiz-Guiñazú, Saul N Faust, Christoph D Spinner, Hanneke Schuitemaker, Johan Van Hoof, Macay
The Lancet Infectious Diseases.2022; 22(12): 1703. CrossRef
Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions
Denis Jacob Machado, Richard Allen White, Janice Kofsky, Daniel A. Janies
Antimicrobial Stewardship & Healthcare Epidemiology.2021;[Epub] CrossRef
Daily Physical Activity and Sleep Measured by Wearable Activity Trackers during the Coronavirus Disease 2019 Pandemic: A Lesson for Preventing Physical Inactivity during Future Pandemics
Hidetaka Hamasaki
Applied Sciences.2021; 11(21): 9956. CrossRef
The adaptation of SARS-CoV-2 to humans
Eduardo Tosta
Memórias do Instituto Oswaldo Cruz.2021;[Epub] CrossRef

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

Characterization of Streptococcus pneumoniae N-Acetylglucosamine-6-Phosphate Deacetylase as a Novel Diagnostic Marker: Chi-Won Choi , Hee-Young An , Yong Ju Lee , Yeol Gyun Lee , Sung Ho Yun , Edmond Changkyun Park , Yeonhee Hong , Gun-Hwa Kim , Jae-Eun Park , Sun Jong Baek , Hyun Sik Kim , Seung Il Kim; J. Microbiol. 2013;51(5):659-664. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3451-8

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Abstract

The identification of novel diagnostic markers of pathogenic bacteria is essential for improving the accuracy of diagnoses and for developing targeted vaccines. Streptococcus pneumoniae is a significant human pathogenic bacterium that causes pneumonia. N-acetylglucosamine-6-phosphate deacetylase (NagA) was identified in a protein mixture secreted by S. pneumoniae and its strong immunogenicity was confirmed in an immuno-proteomic assay against the anti-serum of the secreted protein mixture. In this study, recombinant S. pneumoniae NagA protein was expressed and purified to analyze its protein characteristics, immunospecificity, and immunogenicity, thereby facilitating its evaluation as a novel diagnostic marker for S. pneumoniae. Mass spectrometry analysis showed that S. pneumoniae NagA contains four internal disulfide bonds and that it does not undergo posttranslational modification. S. pneumoniae NagA antibodies successfully detected NagA from different S. pneumoniae strains, whereas NagA from other pathogenic bacteria species was not detected. In addition, mice infected with S. pneumoniae generated NagA antibodies in an effective manner. These results suggest that NagA has potential as a novel diagnostic marker for S. pneumoniae because of its high immunogenicity and immunospecificity.

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Multi-omic profiling to assess the effect of iron starvation inStreptococcus pneumoniaeTIGR4
Irene Jiménez-Munguía, Mónica Calderón-Santiago, Antonio Rodríguez-Franco, Feliciano Priego-Capote, Manuel J. Rodríguez-Ortega
PeerJ.2018; 6: e4966. CrossRef
Mycoplasma fermentans deacetylase promotes mammalian cell stress tolerance
Qingzhou Cheng, Lijuan Wu, Rongfu Tu, Jun Wu, Wenqian Kang, Tong Su, Runlei Du, Wenbin Liu
Microbiological Research.2017; 201: 1. CrossRef
Serotype IV Sequence Type 468 Group BStreptococcusNeonatal Invasive Disease, Minnesota, USA
Sarah Teatero, Patricia Ferrieri, Nahuel Fittipaldi
Emerging Infectious Diseases.2016; 22(11): 1937. CrossRef
Mass Spectrometry in Clinical Microbiology and Infectious Diseases
Frank Fleurbaaij, Hans C. van Leeuwen, Oleg I. Klychnikov, Ed J. Kuijper, Paul J. Hensbergen
Chromatographia.2015; 78(5-6): 379. CrossRef

Molecular Detection and Genotyping of Fusarium oxysporum f. sp. psidii Isolates from Different Agro-Ecological Regions of India: Rupesh Kumar Mishra , Brajesh Kumar Pandey , Vijai Singh , Amita John Mathew , Neelam Pathak , Mohammad Zeeshan; J. Microbiol. 2013;51(4):405-412. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2638-3

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Abstract: Twenty one isolates of Fusarium oxysporum f. sp. psidii (Fop), causing a vascular wilt in guava (Psidium guajava L.), were collected from different agro-ecological regions of India. The pathogenicity test was performed in guava seedlings, where the Fop isolates were found to be highly pathogenic. All 21 isolates were confirmed as F. oxysporum f. sp. psidii by a newly developed, species-specific primer against the conserved regions of 28S rDNA and the intergenic spacer region. RAPD and PCR-RFLP were used for genotyping the isolates to determine their genetic relationships. Fifteen RAPD primers were tested, of which five primers produced prominent, polymorphic, and reproducible bands. RAPD yielded an average of 6.5 polymorphic bands per primer, with the amplified DNA fragments ranging from 200–2,000 bp in size. A dendrogram constructed from these data indicated a 22–74% level of homology. In RFLP analysis, two major bands (350 and 220 bp) were commonly present in all isolates of F. oxysporum. These findings provide new insight for rapid, specific, and sensitive disease diagnosis. However, genotyping could be useful in strain-level discrimination of isolates from different agro-ecological regions of India.

Review

MINIREVIEW] Development of Diagnostic and Vaccine Markers Through Cloning, Expression, and Regulation of Putative Virulence-Protein-Encoding Genes of Aeromonas hydrophila: Vijai Singh , Dharmendra Kumar Chaudhary , Indra Mani , Rohan Jain , B.N. Mishra; J. Microbiol. 2013;51(3):275-282. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-2437-x

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Abstract: Aeromonas hydrophila is an opportunistic bacterial pathogen that is associated with a number of diseases in fish, amphibians, reptiles, and humans. In fish it causes several disease symptoms including tail and skin rot, and haemorrhagic septicemia; in human it causes soft-tissue wound infection and diarrhoea. The pathogenesis of A. hydrophila is multifactorial, but the mechanism is unknown so far. It is considered to be mediated by expression and secretion of extracellular proteins such as aerolysin, lipase, chitinase, amylase, gelatinase, hemolysins, and enterotoxins. A number of the putative virulence-protein-encoding genes that are present in the genome of A. hydrophila have been targeted by PCR for molecular diagnosis. These significant genes are also targeted for over-production of proteins by cloning and expression methods. In this review, we emphasize recent progress in the cloning, expression, and regulation of putative virulence-protein-encoding genes of A. hydrophila for a better understanding of the pathogenesis and also help to provide effective strategies for control of diseases.

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

Production of and Applications for a Polyclonal IgY Diagnostic Reagent Specific for Mycobacterium avium subsp. paratuberculosis: Sung Jae Shin , Seung-Sub Lee , Elizabeth J. B. Manning , Michael T. Collins; J. Microbiol. 2009;47(5):600-609. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0052-7

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Abstract: Antibodies specific to the cell surface antigens of Mycobacterium avium subsp. paratuberculosis (MAP) have multiple useful applications, e.g. organism detection, immunoconcentration, and cell visualization. The aim of this study was to produce and compare polyclonal antibodies for such research and diagnostic purposes. Three polyclonal antibodies to MAP were produced using sera from immunized rabbits and chickens plus naturally infected cows. Cross-reactive antibodies in each MAP antibody preparation were removed by absorption with heterologous mycobacterial and non-mycobacterial cells. The specificity of each resulting polyclonal antibody preparation was evaluated by ELISA to multiple bacterial cell wall extract antigens. After absorption, chicken anti-MAP IgY had the highest specificity of the three antibody preparations. FITC-labeled anti-MAP IgY was used to effectively locate MAP in macrophages 12 h post-infection. Also, immuno- magnetic beads coated with anti-MAP IgY enhanced recovery of MAP from bacterial suspensions in comparison with non-antibody coated beads. Anti-MAP IgY provides a novel new reagent with broad diagnostic and research applications requiring specific concentration, detection, and quantification of MAP.

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