Journal of Microbiology

Review

Minor and major circRNAs in virus and host genomes: Zhihao Lou , Rui Zhou , Yinghua Su , Chun Liu , Wenting Ruan , Che Ok Jeon , Xiao Han , Chun Lin , Baolei Jia; J. Microbiol. 2021;59(3):324-331. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1021-z

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As a special type of noncoding RNA, circular RNAs (circRNAs) are prevalent in many organisms. They can serve as sponges for microRNAs and protein scaffolds, or templates for protein translation, making them linked to cellular homeostasis and disease progression. In recent years, circRNAs have been found to be abnormally expressed during the processes of viral infection and pathogenesis, and can help a virus escape the immune response of a host. Thus, they are now considered to play important functions in the invasion and development of viruses. Moreover, the potential application of circRNAs as biomarkers of viral infection or candidates for therapeutic targeting deserves consideration. This review summarizes circRNAs in the transcriptome, including their classification, production, functions, and value as biomarkers. This review paper also describes research progress on circRNAs in viral infection (mainly hepatitis B virus, HIV, and some human herpes viruses) and aims to provide new ideas for antiviral therapies targeting circRNAs.

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Host combats porcine reproductive and respiratory syndrome virus infection at non-coding RNAs level
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Tian Gan, Jianwei Yu, Jun He
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Circ_0138959/miR-495-3p/TRAF6 axis regulates proliferation, wound healing and osteoblastic differentiation of periodontal ligament cells in periodontitis
Wenjuan Deng, Xiaoliang Wang, Jin Zhang, Sainan Zhao
Journal of Dental Sciences.2022; 17(3): 1125. CrossRef
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Yuncong Shi, Huanji Zhang, Suli Huang, Li Yin, Feng Wang, Pei Luo, Hui Huang
Signal Transduction and Targeted Therapy.2022;[Epub] CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
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Journal of Microbiology.2021; 59(3): 229. CrossRef

Journal Article

Influence of dragon bamboo with different planting patterns on microbial community and physicochemical property of soil on sunny and shady slopes: Weiyi Liu , Fang Wang , Yanmei Sun , Lei Yang , Huihai Chen , Weijie Liu , Bin Zhu , Chaomao Hui , Shiwei Wang; J. Microbiol. 2020;58(11):906-914. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0082-8

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Abstract

Dragon bamboo (Dendrocalamus giganteus) is a giant sympodial bamboo species widely distributed in Asia. However, it remains unclear how dragon bamboo and soil microbes interact to affect soil properties. In this study, we investigated the planting patterns (semi-natural and artificial) on different slopes (sunny and shady) to determine the effects on soil properties and microbial community. The results showed that the soil in which dragon bamboo was grown was acidic, with a pH value of ~5. Also, the soil organic matter content, nitrogen hydrolysate concentration, total nitrogen, available potassium, and total potassium of the dragon bamboo seminatural forest significantly improved, especially on the sunny slope. In contrast, the available phosphorus level was higher in the artificial bamboo forest, probably owing to the phosphate fertilizer application. The bacterial and fungal diversity and the bacterial abundance were all higher on the sunny slope of the semi-natural forest than those in the other samples. The microbial operational taxonomic units (OTUs) shared between the shady and sunny slopes accounted for 47.8–62.2%, but the core OTUs of all samples were only 24.4– 30.4% of each sample, suggesting that the slope type had a significant effect on the microbial community. Some acidophilic microbes, such as Acidobacteria groups, Streptomyces and Mortierella, became dominant in dragon bamboo forest soil. A PICRUSt analysis of the bacterial functional groups revealed that post-translational modification, cell division, and coenzyme transport and metabolism were abundant in the semi-natural forest. However, some microorganisms with strong stress resistance might be activated in the artificial forest. Taken together, these results illustrated the influence of dragon bamboo growth on soil physicochemical property and microbial community, which might help understand the growth status of dragon bamboo under different planting patterns.

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Characteristic Analysis of the Soil Bacterial Community Structure of Dendrocalamus brandisii from Seven Geographical Provenances in Yunnan Province
Qian Chen, Manyun Zhang, Negar Omidvar, Zhihong Xu, Shahla Hosseini Bai, Chaomao Hui, Weiyi Liu
Agronomy.2024; 14(9): 2010. CrossRef
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Weixue Luo, Qingyu Zhang, Peng Wang, Jie Luo, Chunyan She, Xuman Guo, Jiajia Yuan, Yuhong Sun, Ruming Guo, Zongfeng Li, Jinchun Liu, Jianping Tao
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Jiayi Hu, Xiaofang Yang, Huajian Chi, Xin Liu, Ning Lu, Ya Liu, Shengchun Yang, Xiaodong Wen
Microchemical Journal.2024; 207: 111958. CrossRef
Microbial control of soil DOM transformation during the vegetation restoration in the Loess Plateau
Wenxin Chen, Qianqian Gao, Huaying Hu, Tingwei Shao, Chuifan Zhou
Plant and Soil.2024; 504(1-2): 385. CrossRef
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Ping Zhu, Wenyan Liu, Zhongyuan Sun, Xinfu Bai, Jianqiang Song, Nan Wu, Yuping Hou
Eurasian Soil Science.2023; 56(5): 599. CrossRef
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Zhijia Cui, Ran Li, Fan Li, Ling Jin, Haixu Wu, Chunya Cheng, Yi Ma, Zhenheng Wang, Yuanyuan Wang
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Effects of different planting durations of Dendrocalamus brandisii on the soil bacterial community
Shuhong Zhu, Xiuting Zhao, Chaomao Hui, Zhongfu Zhang, Ruli Zhang, Weihan Su, Weiyi Liu
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Haoqiang Sun, Binkai Han, Xiaolin Yang, Changfen He, Ke Zhao, Ting Wang, Shujing An, Xiaochang Xue, Jiefang Kang
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Pei Cao, Xuemin Wei, Gang Wang, Xiaochen Chen, Jianping Han, Yuan Li
Chinese Herbal Medicines.2022; 14(1): 58. CrossRef
Heterotrophic Bacteria Play an Important Role in Endemism of Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang, 2007, a Full-Year Shooting Woody Bamboo
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Review

MINIREVIEW] Bacterial persistence: Fundamentals and clinical importance: Sung-Hee Jung , Choong-Min Ryu , Jun-Seob Kim; J. Microbiol. 2019;57(10):829-835. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9218-0

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Abstract

The threat of antibiotic-resistant bacteria is increasing worldwide. Bacteria utilize persistence and resistance to survive antibiotic stress. For a long time, persistence has been studied only under laboratory conditions. Hence, studies of bacterial persistence are limited. Recently, however, the high incidence of infection relapses caused by persister cells in immunocompromised patients has emphasized the importance of persister research. Furthermore, persister pathogens are one of the causes of chronic infectious diseases, leading to the overuse of antibiotics and the emergence of antibiotic-resistant bacteria. Therefore, understanding the precise mechanism of persister formation is important for continued use of available antibiotics. In this review, we aimed to provide an overview of the persister studies published to date and the current knowledge of persister formation mechanisms. Recent studies of the features and mechanisms of persister formation are analyzed from the perspective of the nature of the persister cell.

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

NOTE] Comparative Assessment of the Intracellular Survival of the Burkholderia pseudomallei bopC Mutant: Varintip Srinon , Sunsiree Muangman , Nithima Imyaem , Veerachat Muangsombut , Natalie R. Lazar Adler , Edouard E. Galyov , Sunee Korbsrisate; J. Microbiol. 2013;51(4):522-526. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2557-3

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Abstract: Burkholderia pseudomallei, the causative agent of melioidosis, is a Gram-negative saprophytic bacterium capable of surviving within phagocytic cells. To assess the role of BopC (a type III secreted effector protein) in the pathogenesis of B. pseudomallei, a B. pseudomallei bopC mutant was used to infect J774A.1 macrophage-like cells. The bopC mutant showed significantly reduced intracellular survival in infected macrophages compared to wild-type B. pseudomallei. In addition, the bopC mutant displayed delayed escape from endocytic vesicles compared with the wild-type strain. This indicates that BopC is important, and at least in part, needed for intracellular survival of B. pseudomallei.

Effects of Exopolysaccharide Production on Liquid Vegetative Growth, Stress Survival, and Stationary Phase Recovery in Myxococcus xanthus: Wei Hu , Jing Wang , Ian McHardy , Renate Lux , Zhe Yang , Yuezhong Li , Wenyuan Shi; J. Microbiol. 2012;50(2):241-248. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1349-5

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Abstract: Exopolysaccharide (EPS) of Myxococcus xanthus is a wellregulated cell surface component. In addition to its known functions for social motility and fruiting body formation on solid surfaces, EPS has also been proposed to play a role in multi-cellular clumping in liquid medium, though this phenomenon has not been well studied. In this report, we confirmed that M. xanthus clumps formed in liquid were correlated with EPS levels and demonstrated that the EPS encased cell clumps exhibited biofilm-like structures. The clumps protected the cells at physiologically relevant EPS concentrations, while cells lacking EPS exhibited significant reduction in long-term viability and resistance to stressful conditions. However, excess EPS production was counterproductive to vegetative growth and viable cell recovery declined in extended late stationary phase as cells became trapped in the matrix of clumps. Therefore, optimal EPS production by M. xanthus is important for normal physiological functions in liquid.

Conserved Virulence Factors of Pseudomonas aeruginosa are Required for Killing Bacillus subtilis: Shin-Young Park , Yun-Jeong Heo , Young-Seok Choi , Eric Deziel , You-Hee Cho; J. Microbiol. 2005;43(5):443-450.; DOI: https://doi.org/2277 [pii]

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Abstract: The multi-host pathogen, Pseudomonas aeruginosa, possesses an extraordinary versatility which makes it capable of surviving the adverse conditions provided by environmental, host, and, presumably, competing microbial factors in its natural habitats. Here, we investigated the P. aeruginosa-Bacillus subtilis interaction in laboratory conditions and found that some P. aeruginosa strains can outcompete B. subtilis in mixed planktonic cultures. This is accompanied by the loss of B. subtilis viability. The bactericidal activity of P. aeruginosa is measured on B. subtilis plate cultures. The bactericidal activity is attenuated in pqsA, mvfR, lasR, pilB, gacA, dsbA, rpoS, and phnAB mutants. These results suggest that P. aeruginosa utilizes a subset of conserved virulence pathways in order to survive the conditions provided by its bacterial neighbors.

Journal Article

The Viable But Nonculturable State of Kanagawa Positive and Negative Strains of Vibrio parahaemolyticus: Tonya C. Bates , James D. Oliver; J. Microbiol. 2004;42(2):74-79.; DOI: https://doi.org/2042 [pii]

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Abstract: Ingestion of shellfish-associated Vibrio parahaemolyticus is the primary cause of potentially severe gastroenteritis in many countries. However, only Kanagawa phenomenon (hemolysin) positive (KP^+) strains of V. parahaemolyticus are isolated from patients, whereas >99% of strains isolated from the environment do not produce this hemolysin (i.e. are KP^-). The reasons for these differences are not known. Following a temperature downshift, Vibrio parahaemolyticus enters the viable but nonculturable (VBNC) state wherein cells maintain viability but cannot be cultured on routine microbiological media. We speculated that KP^+ and KP^- strains may respond differently to the temperature and salinity conditions of seawater by entering into this state which might account for the low numbers of culturable KP^+ strains isolated from estuarine waters. The response of eleven KP^+ and KP^- strains of V. parahaemolyticus following exposure to a nutrient and temperature downshift in different salinities, similar to conditions encountered in their environment, was examined. The strains included those from which the KP^+ genes had been selectively removed or added. Our results indicated that the ability to produce hemolysin did not affect entrance into the VBNC state. Further, VBNC cells of both biotypes could be restored to the culturable state following an overnight temperature upshift.

Molecular Cloning of the Superoxide Dismutase Gene from Orientia tsutsugamushi, the Causative Agent of Scrub Typhus: Ji-Hyun Yun , Young-Sang Koh , Se-Jae Kim; J. Microbiol. 2002;40(2):151-155.

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Abstract: A superoxide dismutase (SOD) gene from the obligate intracellular bacterium Orientia tsutsugamushi has been cloned by using the polymerase chain reaction with degenerate oligonucleotide primers corresponding to conserved regions of known SODs. Nucleotide sequencing revealed that the predicted amino acid sequence was significantly more homologous to known iron-containing SODs (FeSOD) than to manganese-containing SODs (MnSOD). Conserved regions in bacterial FeSOD could also be seen. Isolation of the oriential SOD gene may provide an opportunity to examine its role in the intracellular survival of this bacterium.

The Viable but Nonculturable State in Bacteria: James D. Oliver; J. Microbiol. 2005;43(1):93-100.

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Abstract: It had long been assumed that a bacterial cell was dead when it was no longer able to grow on routine culture media. We now know that this assumption is simplistic, and that there are many situations where a cell loses culturability but remains viable and potentially able to regrow. This mini-review defines what the "viable but nonculturable" (VBNC) state is, and illustrates the methods that can be used to show that a bacterial cell is in this physiological state. The diverse environmental factors which induce this state, and the variety of bacteria which have been shown to enter into the VBNC state, are listed. In recent years, a great amount of research has revealed what occurs in cells as they enter and exist in this state, and these studies are also detailed. The ability of cells to resuscitate from the VBNC state and return to an actively metabolizing and culturable form is described, as well as the ability of these cells to retain virulence. Finally, the question of why cells become nonculturable is addressed. It is hoped that this mini-review will encourage researchers to consider this survival state in their studies as an alternative to the conclusion that a lack of culturability indicates the cells they are examining are dead.

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