Journal of Microbiology

Full article

The key pathways and genes related to oncolytic Newcastle disease virus-induced phenotypic changes in ovarian cancer cells: Wei Song, Yuan Yuan, Fangfang Cao, Huazheng Pan, Yaqing Liu; J. Microbiol. 2025;63(4):e2411018. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2411018

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Abstract PDF Supplementary Material: The poor prognosis and high recurrence rate of ovarian cancer highlight the urgent need to develop new therapeutic strategies. Oncolytic Newcastle disease virus (NDV) can kill cancer cells directly and regulate innate and adaptive immunity. In this study, ovarian cancer cells infected with or without velogenic NDV-BJ were subjected to a CCK-8 assay for detecting cell proliferation, flow cytometry for detecting the cell cycle and apoptosis, and wound healing and transwell assays for detecting cell migration and invasion. Transcriptomic sequencing was conducted to identify the differentially expressed genes (DEGs). GO and KEGG enrichment analyses were performed to explore the mechanism underlying the oncolytic effect of NDV on ovarian cancer cells. The results showed that infection with NDV inhibited ovarian cancer cell proliferation, migration, and invasion; disrupted the cell cycle; and promoted apoptosis. Compared with those in negative control cells, the numbers of upregulated and downregulated genes in ovarian cancer cells infected with NDV were 1,499 and 2,260, respectively. Thirteen KEGG pathways related to cell growth and death, cell mobility, and signal transduction were significantly enriched. Among these pathways, 48 DEGs, especially SESN2, HLA B/C/E, GADD45B, and RELA, that may be involved in the oncolytic process were screened, and qPCR analysis verified the reliability of the transcription data. This study discovered some key pathways and genes related to oncolytic NDV-induced phenotypic changes in ovarian cancer cells, which will guide our future research directions and help further explore the specific mechanisms by which infection with NDV suppresses ovarian cancer development.

Research Article

Synbiotic combination of fructooligosaccharides and probiotics ameliorates the metabolic dysfunction-associated steatotic liver disease: Sang Yoon Lee, Su-Been Lee, Goo-Hyun Kwon, Seol Hee Song, Jeong Ha Park, Min Ju Kim, Jung A Eom, Kyeong Jin Lee, Sang Jun Yoon, Hyunjoon Park, Sung-Min Won, Jin-Ju Jeong, Ki-Kwang Oh, Young Lim Ham, Gwang Ho Baik, Dong Joon Kim, Satya Priya Sharma, Ki Tae Suk; J. Microbiol. 2025;63(2):e2411002. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411002

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Abstract PDF: Synbiotics have become a new-age treatment tool for limiting the progression of metabolic dysfunction-associated steatotic liver disease; however, inclusive comparisons of various synbiotic treatments are still lacking. Here, we have explored and evaluated multiple synbiotic combinations incorporating three distinctive prebiotics, lactitol, lactulose and fructooligosaccharides. Of the synbiotic treatments evaluated, a combination of fructooligosaccharides and probiotics (FOS+Pro) exhibited superior protection against western diet-induced liver degeneration. This synbiotic (FOS+Pro) combination resulted in the lowest body weight gains, liver weights and liver/body weight ratios. The FOS+Pro synbiotic combination substantially alleviated liver histopathological markers and reduced serum AST and cholesterol levels. FOS+Pro ameliorated hepatic inflammation by lowering expression of proinflammatory markers including TNF-α, IL-1β, IL-6, and CCL2. FOS+Pro significantly improved steatosis by restricting the expression of lipid metabolic regulators (ACC1, FAS) and lipid transporters (CD36) in the liver. These findings are critical in suggesting that synbiotic treatments are capable of restraining western diet-induced metabolic dysfunction in the liver. Additionally, this study demonstrated that adding probiotic strains amplified the effectiveness of fructooligosaccharides but not all prebiotics.

Journal Article

Lactobacillus gasseri BNR17 and Limosilactobacillus fermentum ABF21069 Ameliorate High Sucrose-Induced Obesity and Fatty Liver via Exopolysaccharide Production and β-oxidation: Yu Mi Jo, Yoon Ji Son, Seul-Ah Kim, Gyu Min Lee, Chang Won Ahn, Han-Oh Park, Ji-Hyun Yun; J. Microbiol. 2024;62(10):907-918. Published online October 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00173-6

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Abstract: Obesity and metabolic dysfunction-associated fatty liver disease (MAFLD) are prevalent metabolic disorders with substantial global health implications that are often inadequately addressed by current treatments and may have side effects. Probiotics have emerged as promising therapeutic agents owing to their beneficial effects on gut health and metabolism. This study investigated the synergistic effects of a probiotic combination of BNR17 and ABF21069 on obesity and MAFLD in C57BL/6 mice fed a high-sucrose diet. The probiotic combination significantly reduced body weight and fat accumulation compared with the high-sucrose diet. It also alleviated elevated serum leptin levels induced by a high-sucrose diet. Histological analysis revealed a significant reduction in white adipose tissue and fatty liver in the mice treated with the probiotic combination. Furthermore, increased expression of genes related to β-oxidation, thermogenesis, and lipolysis suggested enhanced metabolic activity. The probiotic groups, particularly the BNR17 group, showed an increase in fecal exopolysaccharides, along with a tendency toward a lower expression of intestinal sugar transport genes, indicating reduced sugar absorption. Additionally, inflammatory markers in the liver tissue exhibited lower expression in the ABF21069 group than in the HSD group. Despite each strain in the combination group having distinct characteristics and functions, their combined effect demonstrated synergy in mitigating obesity and MAFLD, likely through the modulation of fecal exopolysaccharides content and improvement in lipid metabolism. These findings underscore the potential of probiotic supplementation as a promising assistant therapy for managing obesity and MAFLD and provide valuable insights into its therapeutic mechanisms in metabolic disorders.

Reviews

Microbiome-Mucosal Immunity Nexus: Driving Forces in Respiratory Disease Progression: Young Chae Park, Soo Yeon Choi, Yunah Cha, Hyeong Won Yoon, Young Min Son; J. Microbiol. 2024;62(9):709-725. Published online September 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00167-4

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Abstract

The importance of the complex interplay between the microbiome and mucosal immunity, particularly within the respiratory tract, has gained significant attention due to its potential implications for the severity and progression of lung diseases. Therefore, this review summarizes the specific interactions through which the respiratory tract-specific microbiome influences mucosal immunity and ultimately impacts respiratory health. Furthermore, we discuss how the microbiome affects mucosal immunity, considering tissue-specific variations, and its capacity in respiratory diseases containing asthma, chronic obstructive pulmonary disease, and lung cancer. Additionally, we investigate the external factors which affect the relationship between respiratory microbiome and mucosal immune responses. By exploring these intricate interactions, this review provides valuable insights into the potential for microbiome-based interventions to modulate mucosal immunity and alleviate the severity of respiratory diseases.

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The impact of environmental factors on respiratory tract microbiome and respiratory system diseases
Yutao Ge, Guo Tang, Yawen Fu, Peng Deng, Rong Yao
European Journal of Medical Research.2025;[Epub] CrossRef
Bacteria and fungi of the lung: allies or enemies?
Enrico Garaci, Marilena Pariano, Emilia Nunzi, Claudio Costantini, Marina Maria Bellet, Cinzia Antognelli, Matteo Antonio Russo, Luigina Romani
Frontiers in Pharmacology.2024;[Epub] CrossRef

Application of Microbiome‑Based Therapies in Chronic Respiratory Diseases: Se Hee Lee, Jang Ho Lee, Sei Won Lee; J. Microbiol. 2024;62(3):201-216. Published online April 18, 2024; DOI: https://doi.org/10.1007/s12275-024-00124-1

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Abstract

The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and afected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably diferent, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome infuences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fber diets, for example, present benefcial efects through the production of short-chain fatty acids. Additionally, genetically modifed probiotics to secrete some benefcial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.

Citations

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Bacteria and Allergic Diseases
Svetlana V. Guryanova
International Journal of Molecular Sciences.2024; 25(19): 10298. CrossRef
The emerging roles of microbiome and short-chain fatty acids in the pathogenesis of bronchopulmonary dysplasia
Yuan Gao, Kaixuan Wang, Zupan Lin, Shujing Cai, Aohui Peng, Le He, Hui Qi, Zhigang Jin, Xubo Qian
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Host-Associated Microbiome
Woo Jun Sul
Journal of Microbiology.2024; 62(3): 135. CrossRef

Journal Articles

Fresh Washed Microbiota Transplantation Alters Gut Microbiota Metabolites to Ameliorate Sleeping Disorder Symptom of Autistic Children: Nai-Hua Liu , Hong-Qian Liu , Jia-Yi Zheng , Meng-Lu Zhu , Li-Hao Wu , Hua-Feng Pan , Xing-Xiang He; J. Microbiol. 2023;61(8):741-753. Published online September 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00069-x

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Abstract

Accumulating studies have raised concerns about gut dysbiosis associating autism spectrum disorder (ASD) and its related symptoms. However, the effect of gut microbiota modification on the Chinese ASD population and its underlying mechanism were still elusive. Herein, we enrolled 24 ASD children to perform the first course of fresh washed microbiota transplantation (WMT), 18 patients decided to participate the second course, 13 of which stayed to participate the third course, and there were 8 patients at the fourth course. Then we evaluated the effects of fresh WMT on these patients and their related symptoms. Our results found that the sleeping disorder symptom was positively interrelated to ASD, fresh WMT significantly alleviated ASD and its sleeping disorder and constipation symptoms. In addition, WMT stably and continuously downregulated Bacteroides/ Flavonifractor/Parasutterella while upregulated Prevotella_9 to decrease toxic metabolic production and improve detoxification by regulating glycolysis/myo-inositol/D-glucuronide/D-glucarate degradation, L-1,2-propanediol degradation, fatty acid β-oxidation. Thus, our results suggested that fresh WMT moderated gut microbiome to improve the behavioral and sleeping disorder symptoms of ASD via decrease toxic metabolic production and improve detoxification. Which thus provides a promising gut ecological strategy for ASD children and its related symptoms treatments.

Citations

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Untargeted urine metabolomics and machine learning provide potential metabolic signatures in children with autism spectrum disorder
Xian Liu, Xin Sun, Cheng Guo, Zhi-Fang Huang, Yi-Ru Chen, Fang-Mei Feng, Li-Jie Wu, Wen-Xiong Chen
Frontiers in Psychiatry.2024;[Epub] CrossRef
Washed Microbiota Transplantation Improves the Sleep Quality in Patients with Inflammatory Bowel Disease
Qianqian Li, Yujie Liu, Zulun Zhang, Sheng Zhang, Xiao Ding, Faming Zhang
Nature and Science of Sleep.2024; Volume 16: 1141. CrossRef

Relationship Between Mycotoxin Production and Gene Expression in Fusarium graminearum Species Complex Strains Under Various Environmental Conditions: Wenwen Huang , Ping Zhou , Guanghui Shen , Tao Gao , Xin Liu , Jianrong Shi , Jianhong Xu , Jianbo Qiu; J. Microbiol. 2023;61(5):525-542. Published online May 2, 2023; DOI: https://doi.org/10.1007/s12275-023-00046-4

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Abstract

The Fusarium graminearum species complex (FGSC) can produce various mycotoxins and is a major concern for food quantity and quality worldwide. In this study, we determined the effects of water activity ( aw), temperature, incubation time and their interactions on mycotoxin accumulation and the expression levels of biosynthetic genes in FGSC strains from maize samples in China. The highest deoxynivalenol (DON), 3-acetyldeoxynivalenol(3ADON) and 15-acetyldeoxynivalenol (15ADON) levels of the F. boothii and F. graminearum strains were observed at 0.98 aw/ 30 °C or 0.99 aw/ 25 °C. F. asiaticum and F. meridionale reached maximum nivalenol (NIV) and 4-acetylnivalenol (4ANIV) contents at 0.99 aw and 30 °C. With the extension of the incubation time, the concentrations of DON and NIV gradually increased, while those of their derivatives decreased. F. boothii, F. meridionale and one F. asiaticum strain had the highest zearalenone (ZEN) values at 0.95 aw and 25 °C, while the optimum conditions for the other F. asiaticum strain and F. graminearum were 0.99 aw and 30 °C. Four genes associated with trichothecene and zearalenone synthesis were significantly induced under higher water stress in the early stage of production. The results indicated independence of mycotoxin production and gene expression, as maximum amounts of these toxic metabolites were observed at higher aw in most cases. This study provides useful information for the monitoring and prevention of such toxins entering the maize production chain.

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Geographic variations in the Fusarium species and toxins associated with maize ear rot in China
Jianbo Qiu, Can Jiang, Shufang Wang, Can He, Daoming Chen, Jing Lan, Jianhong Xu, Yin-Won Lee, Jianrong Shi
International Journal of Food Microbiology.2025; 436: 111208. CrossRef
Application of MOX Sensors to Determine the Emission of Volatile Compounds in Corn Groats as a Function of Vertical Pressure in the Silo and Moisture Content of the Bed
Robert Rusinek, Aleksandra Żytek, Mateusz Stasiak, Joanna Wiącek, Marek Gancarz
Sensors.2024; 24(7): 2187. CrossRef

Detection of colistin-resistant populations prior to antibiotic exposure in KPC-2-producing Klebsiella pneumoniae clinical isolates: Jungyu Seo , Yu Mi Wi , Jong Min Kim , Yae-Jean Kim , Kwan Soo Ko; J. Microbiol. 2021;59(6):590-597. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0610-1

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Abstract

Although colistin is frequently regarded as the antibiotic of last resort in treating carbapenem-resistant Klebsiella pneumoniae, colistin heteroresistance may in part be associated with antibiotic treatment failure. However, we do not know how widespread the colistin heteroresistance is in carbapenem- resistant K. pneumoniae isolates. In this study, we performed colistin disc diffusion assays, E-tests, and population analysis profiling for KPC-2-producing K. pneumoniae isolates to identify colistin heteroresistance. Although no colistin- resistant colonies were detected by the disc diffusion test and E-test, a colistin-resistant subpopulation was identified in population analysis profiling in all colistin-susceptible, KPC-2-producing K. pneumoniae isolates. Colistin-resistant subpopulations were also identified even when isolates had no colistin exposure. The ratio of colistin-resistant subpopulations to the total population increased as the exposure concentration of colistin increased. In in vitro time-kill assays, regrowth was observed in all isolates after 2 h upon exposure to colistin. We identified common amino acid alterations in PhoQ, PhoP, and PmrB in colistin-resistant subpopulations from some isolates, but no substitutions were found in most resistant subpopulations from other isolates. In all colistin-resistant subpopulations, overexpression of PhoQ and PbgP was observed. In this study, we demonstrated that colistin heteroresistance may be common in KPC-2-producing K. pneumoniae isolates, which could not be detected in the disc diffusion method and E-test. Colistin heteroresistance may cause colistin treatment failure in part and may evolve into resistance. Thus, development of more reliable diagnostic methods is required to detect colistin heteroresistance.

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High prevalence of polymyxin-heteroresistant carbapenem-resistant Klebsiella pneumoniae and its within-host evolution to resistance among critically ill scenarios
Xiaoli Wang, Tianjiao Meng, Yunqi Dai, Hong-Yu Ou, Meng Wang, Bin Tang, Jingyong Sun, Decui Cheng, Tingting Pan, Ruoming Tan, Hongping Qu
Infection.2024;[Epub] CrossRef
Development of colistin resistance via heteroresistance modeling in Klebsiella pneumoniae: A diagnostic study
Jungyu Seo, Kwan Soo Ko
Precision and Future Medicine.2024; 8(1): 10. CrossRef
Conversion to colistin susceptibility by tigecycline exposure in colistin-resistant Klebsiella pneumoniae and its implications to combination therapy
Suyeon Park, Jihyun Choi, Dongwoo Shin, Ki Tae Kwon, Si-Ho Kim, Yu Mi Wi, Kwan Soo Ko
International Journal of Antimicrobial Agents.2024; 63(1): 107017. CrossRef
Insight into Antibiotic Synergy Combinations for Eliminating Colistin Heteroresistant Klebsiella pneumoniae
Sahaya Glingston Rajakani, Basil Britto Xavier, Adwoa Sey, El Bounja Mariem, Christine Lammens, Herman Goossens, Youri Glupczynski, Surbhi Malhotra-Kumar
Genes.2023; 14(7): 1426. CrossRef
Mechanisms and Clinical Relevance ofPseudomonas aeruginosaHeteroresistance
Zhao Chen
Surgical Infections.2023; 24(1): 27. CrossRef
Heteroresistance Is Associated With in vitro Regrowth During Colistin Treatment in Carbapenem-Resistant Klebsiella pneumoniae
Yifan Wang, Xinqian Ma, Lili Zhao, Yukun He, Wenyi Yu, Shining Fu, Wentao Ni, Zhancheng Gao
Frontiers in Microbiology.2022;[Epub] CrossRef
Prevalence of Mutated Colistin-Resistant Klebsiella pneumoniae: A Systematic Review and Meta-Analysis
Nik Yusnoraini Yusof, Nur Iffah Izzati Norazzman, Siti Nur’ain Warddah Ab Hakim, Mawaddah Mohd Azlan, Amy Amilda Anthony, Fatin Hamimi Mustafa, Naveed Ahmed, Ali A. Rabaan, Souad A. Almuthree, Abdulsalam Alawfi, Amer Alshengeti, Sara Alwarthan, Mohammed G
Tropical Medicine and Infectious Disease.2022; 7(12): 414. CrossRef
Antibiotic Heteroresistance in Klebsiella pneumoniae
Karolina Stojowska-Swędrzyńska, Adrianna Łupkowska, Dorota Kuczyńska-Wiśnik, Ewa Laskowska
International Journal of Molecular Sciences.2021; 23(1): 449. CrossRef
Treatment for carbapenem-resistant Enterobacterales infections: recent advances and future directions
Kathleen Tompkins, David van Duin
European Journal of Clinical Microbiology & Infectious Diseases.2021; 40(10): 2053. CrossRef

Agromyces laixinhei sp. nov. isolated from bat feces in China: Yanpeng Cheng , Yibo Bai , Yuyuan Huang , Jing Yang , Shan Lu , Dong Jin , Ji Pu , Han Zheng , Junqin Li , Ying Huang , Suping Wang , Jianguo Xu; J. Microbiol. 2021;59(5):467-475. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0546-5

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Abstract

Three rod-shaped, Gram-stain-positive, and catalase-positive, phenotypically closely related isolates (HY052T, HY050, and HY045) were obtained from fecal samples collected from bats in Guangxi province and Chongqing city of China. Circular, smooth, light-yellow colonies appeared on brain heart infusion plate after 24–48 h incubation at 28°C. The optimal pH for growth was between 6.0 and 7.5. Based on 16S rRNA, the three isolates were phylogenetically related to Agromyces terreus DS-10T, Agromyces aureus AR33T, Agromyces salentinus 20-5T, Agromyces allii UMS-62T, Agromyces lapidis CD55T, and Agromyces italicus CD1T. Moreover, based on 296 core genes, the phylogenomic tree indicated that the three isolates clustered together, closest to Agromyces cerinus VKM Ac- 1340T and Agromyces fucosus VKM Ac-1345T but separated distantly from other Agromyces species. The average nucleotide identity values between strain HY052T and other Agromyces species ranged from 79.3% to 87.9%, lower than the 95–96% threshold. Furthermore, the genome of strain HY052T contains a circular chromosome of 3,437,203 bp with G + C content of 69.0 mol%. Main fatty acids were anteiso-C15:0 and anteiso-C17:0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Rhamnose, ribose, and glucose were the primary cell wall sugars. The major peptidoglycan amino acids included alanine, glutamic acid, glycine, and 2,4-diaminobutyric acid. An additional remarkable difference from other Agromyces species is that MK-12 was the sole menaquinone in strain HY052T. Based on results from the polyphasic characterizations performed in this study, our isolates are proposed to be members of a novel species in genus Agromyces, named Agromyces laixinhei. The type strain is HY052T (= CGMCC 1.17175T = JCM 33695T).

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Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata
Juan Guzman, Maite Ortúzar, Anja Poehlein, Rolf Daniel, Martha E. Trujillo, Andreas Vilcinskas
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
The Threat of Potentially Pathogenic Bacteria in the Feces of Bats
Yuyuan Huang, Yamin Sun, Qianni Huang, Xianglian Lv, Ji Pu, Wentao Zhu, Shan Lu, Dong Jin, Liyun Liu, Zhengli Shi, Jing Yang, Jianguo Xu, Biao He
Microbiology Spectrum.2022;[Epub] CrossRef
Morphological and genomic characteristics of two novel halotolerant actinomycetes, Tomitella gaofuii sp. nov. and Tomitella fengzijianii sp. nov. isolated from bat faeces
Yuyuan Huang, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Juan Zhou, Sihui Zhang, Qianni Huang, Xianglian Lv, Wentao Zhu, Ji Pu, Ying Huang, Liyun Liu, Jianguo Xu
Systematic and Applied Microbiology.2022; 45(2): 126294. CrossRef
Phenotypic and genomic characteristics of Brevibacterium zhoupengii sp. nov., a novel halotolerant actinomycete isolated from bat feces
Yuyuan Huang, Lingzhi Dong, Jian Gong, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Qianni Huang, Ji Pu, Liyun Liu, Jianguo Xu
Journal of Microbiology.2022; 60(10): 977. CrossRef

Diversity and composition of microbiota during fermentation of traditional Nuodeng ham: Xiao-mei Zhang , Xi-jun Dang , Yuan-bing Wang , Tao Sun , Yao Wang , Hong Yu , Wu-song Yang; J. Microbiol. 2021;59(1):20-28. Published online December 23, 2020; DOI: https://doi.org/10.1007/s12275-021-0219-4

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Abstract

The microbial community is one of the most important factors in shaping the characteristics of fermented food. Nuodeng ham, traditionally produced and subjected to 1–4 years of fermentation, is a dry fermented food product with cultural and economic significance to locals in southwestern China. In this study, we aimed to characterize the microbiota and physicochemical profiles of Nuodeng ham across different stages of fermentation. Ham samples from each of the four years were analyzed by sequencing bacterial 16S rRNA gene and fungal internal transcribed spacer sequence, in order to characterize the diversity and composition of their microflora. A total of 2,679,483 bacterial and 2,983,234 fungal sequences of high quality were obtained and assigned to 514 and 57 genera, respectively. Among these microbes, Staphylococcus and Candida were the most abundant genera observed in the ham samples, though samples from different years showed differences in their microbial abundance. Results of physicochemical properties (pH, water, amino acid, NaCl, nitrate and nitrite contents, and the composition of volatile compounds) revealed differences among the ham samples in the composition of volatile compounds, especially in the third year samples, in which no nitrite was detected. These results suggest that the structure and diversity of microbial communities significantly differed across different stages of fermentation. Moreover, the third year hams exhibits a unique and balanced microbial community, which might contribute to the special flavor in the green and safe food products. Thus, our study lends insights into the production of high quality Nuodeng ham.

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Metabolite and microbial community composition of normal and sensory defect Nuodeng hams characterized based on metabolomics and high-throughput sequencing
Nannan Zhou, Yaying Zhao, Guiying Wang, Guanghui Chen, Zhijie Zheng, Ruwei Ren, Guozhou Liao
Food Chemistry.2025; 463: 141358. CrossRef
Insight into the Relationship between the Causes of Off-Odour and Microorganism Communities in Xuanwei Ham
Haoyi Wang, Xiaoyu Yin, Lu Zhang, Xuejiao Wang, Jiliang Zhang, Rongxin Wen, Jianxin Cao
Foods.2024; 13(5): 776. CrossRef
Study on the Changes and Correlation of Microorganisms and Flavor in Different Processing Stages of Mianning Ham
Yue Huang, Zhengli Wang, Ling Gan, Jiamin Zhang, Wei Wang, Lili Ji, Lin Chen
Foods.2024; 13(16): 2587. CrossRef
Revealing the correlation between small molecule metabolites, volatile compounds and microbial communities during the ripening of Xuanwei ham
Cong Li, Zhijie Zheng, Guiying Wang, Guanghui Chen, Nannan Zhou, Ruwei Ren, Qiongfang Yang, Wenxi Fu, Bo Li, Guozhou Liao
LWT.2024; 211: 116955. CrossRef
Changes in Physicochemical Characteristics and Microbial Diversity of Traditional Fermented Vinasse Hairtail
Yue Zhang, Chuanhai Tu, Huimin Lin, Yuwei Hu, Junqi Jia, Shanshan Shui, Jiaxing Wang, Yi Hu, Bin Zhang
Fermentation.2023; 9(2): 173. CrossRef
Recent developments in off-odor formation mechanism and the potential regulation by starter cultures in dry-cured ham
Changyu Zhou, Qiang Xia, Lihui Du, Jun He, Yangying Sun, Yali Dang, Fang Geng, Daodong Pan, Jinxuan Cao, Guanghong Zhou
Critical Reviews in Food Science and Nutrition.2023; 63(27): 8781. CrossRef
Role of microbiota and its ecological succession on flavor formation in traditional dry-cured ham: a review
Ping Li, Zhijie Bao, Yang Wang, Xinlian Su, Hui Zhou, Baocai Xu
Critical Reviews in Food Science and Nutrition.2023; : 1. CrossRef
Illumina-Based Analysis Yields New Insights Into the Fungal Contamination Associated With the Processed Products of Crataegi Fructus
Jingsheng Yu, Mengyue Guo, Wenjun Jiang, Yujie Dao, Xiaohui Pang
Frontiers in Nutrition.2022;[Epub] CrossRef
Evaluation of protein degradation and flavor compounds during the processing of Xuan'en ham
Rui Li, Cuizhu Geng, Zhemin Xiong, Yingying Cui, E Liao, Lijuan Peng, Weiping Jin, Haibin Wang
Journal of Food Science.2022; 87(8): 3366. CrossRef
Characterization and correlation of dominant bacteria and volatile compounds in post-fermentation process of Ba-bao Douchi
Yan-Zeng Zhang, Xiang-Na Lin, Yan-Qing Ji, Hong-Jun He, Hong-Zhuan Yang, Xiao-Juan Tang, Yun-Guo Liu
Food Research International.2022; 160: 111688. CrossRef
Microbial community composition and soil metabolism in the coexisting Cordyceps militaris and Ophiocordyceps highlandensis
Xiaorong Xu, Xiaomei Zhang, Zhipu Huang, Yuxiao Xu, Dexiang Tang, Bing Zhang, Ketao Zhang, Chaojin Liu, Hong Yu
Journal of Basic Microbiology.2022; 62(10): 1254. CrossRef
Metagenomic Analysis of Suansun, a Traditional Chinese Unsalted Fermented Food
Yaping Hu, Xiaodong Chen, Jie Zhou, Wenxuan Jing, Qirong Guo
Processes.2021; 9(9): 1669. CrossRef

Characterization of the effects of terminators and introns on recombinant gene expression in the basidiomycete Ceriporiopsis subvermispora: Dong Xuan Nguyen , Emi Nishisaka , Moriyuki Kawauchi , Takehito Nakazawa , Masahiro Sakamoto , Yoichi Honda; J. Microbiol. 2020;58(12):1037-1045. Published online September 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0213-2

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Abstract

Terminators and introns are vital regulators of gene expression in many eukaryotes; however, the functional importance of these elements for controlling gene expression in Agaricomycetes remains unclear. In this study, the effects of Ceriporiopsis subvermispora terminators and introns on the expression of a recombinant hygromycin B phosphotransferase gene (hph) were characterized. Using a transient transformation system, we proved that a highly active terminator (e.g., the gpd terminator) is required for the efficient expression of the hph gene. Mutational analyses of the C. subvermispora gpd terminator revealed that hph expression was dictated by an A-rich region, which included a putative positioning element, and polyadenylation sites. In contrast, our results indicated that introns are not required for the expression of hph directed by the Csβ1-tub and Csgpd promoters in C. subvermispora. This study provides insights into the functions and cis-element requirements of transcriptional terminators in Agaricomycetes, which may be relevant for designing recombinant genes for this important fungal class.

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Development of a 2A peptide-based multigene expression system and its application for enhanced production of ganoderic acids in Ganoderma lucidum
Qiong Wang, Hong-Jun Liu, Yan Xu, Zi-Xu Wang, Bin Sun, Jun-Wei Xu
Journal of Biotechnology.2024; 393: 109. CrossRef
CRISPR/Cas9 using a transient transformation system in Ceriporiopsis subvermispora
Takehito Nakazawa, Chikako Inoue, Dong Xuan Nguyen, Moriyuki Kawauchi, Masahiro Sakamoto, Yoichi Honda
Applied Microbiology and Biotechnology.2022; 106(17): 5575. CrossRef
A promoter assay system using gene targeting in agaricomycetes Pleurotus ostreatus and Coprinopsis cinerea
Dong Xuan Nguyen, Takehito Nakazawa, Genki Myo, Chikako Inoue, Moriyuki Kawauchi, Masahiro Sakamoto, Yoichi Honda
Journal of Microbiological Methods.2020; 179: 106053. CrossRef

Evolutionary analysis and protein family classification of chitin deacetylases in Cryptococcus neoformans: Seungsue Lee , Hyun Ah Kang , Seong-il Eyun; J. Microbiol. 2020;58(9):805-811. Published online September 1, 2020; DOI: https://doi.org/10.1007/s12275-020-0288-9

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Abstract

Cryptococcus neoformans is an opportunistic fungal pathogen causing cryptococcal meningoencephalitis. Interestingly, the cell wall of C. neoformans contains chitosan, which is critical for its virulence and persistence in the mammalian host. C. neoformans (H99) has three chitin deacetylases (CDAs), which convert chitin to chitosan. Herein, the classification of the chitin-related protein (CRP) family focused on cryptococcal CDAs was analyzed by phylogenetics, evolutionary pressure (dN/dS), and 3D modeling. A phylogenetic tree of 110 CRPs revealed that they can be divided into two clades, CRP I and II with bootstrap values (> 99%). CRP I clade comprises five groups (Groups 1–5) with a total of 20 genes, while CRP II clade comprises sixteen groups (Groups 6–21) with a total of 90 genes. CRP I comprises only fungal CDAs, including all three C. neoformans CDAs, whereas CRP II comprises diverse CDAs from fungi, bacteria, and amoeba, along with other carbohydrate esterase 4 family proteins. All CDAs have the signal peptide, except those from group 11. Notably, CDAs with the putative O-glycosylation site possess either the glycosylphosphatidylinositol (GPI)-anchor motif for CRP I or the chitin-binding domain (CBD) for CRP II, respectively. This evolutionary conservation strongly indicates that the O-glycosylation modification and the presence of either the GPI-anchor motif or the chitin-binding domain is important for fungal CDAs to function efficiently at the cell surface. This study reveals that C. neoformans CDAs carrying GPI anchors have evolved divergently from fungal and bacterial CDAs, providing new insights into evolution and classification of CRP family.

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Chitin Deacetylase Homologous Gene cda Contributes to Development and Aflatoxin Synthesis in Aspergillus flavus
Xin Zhang, Meifang Wen, Guoqi Li, Shihua Wang
Toxins.2024; 16(5): 217. CrossRef
Effects of altered N-glycan structures of Cryptococcus neoformans mannoproteins, MP98 (Cda2) and MP84 (Cda3), on interaction with host cells
Su-Bin Lee, Catia Mota, Eun Jung Thak, Jungho Kim, Ye Ji Son, Doo-Byoung Oh, Hyun Ah Kang
Scientific Reports.2023;[Epub] CrossRef
Novel Chitin Deacetylase from Thalassiosira weissflogii Highlights the Potential for Chitin Derivative Production
Mengzhen Cheng, Zhanru Shao, Xin Wang, Chang Lu, Shuang Li, Delin Duan
Metabolites.2023; 13(3): 429. CrossRef
Identification and Phylogenetic Analysis of Chitin Synthase Genes from the Deep-Sea Polychaete Branchipolynoe onnuriensis Genome
Hyeongwoo Choi, Sang Lyeol Kim, Man-Ki Jeong, Ok Hwan Yu, Seongil Eyun
Journal of Marine Science and Engineering.2022; 10(5): 598. CrossRef

WasC, a WASP family protein, is involved in cell adhesion and migration through regulation of F-actin polymerization in Dictyostelium: Pyeonghwa Jeon , Taeck Joong Jeon; J. Microbiol. 2020;58(8):696-702. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-0138-9

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Abstract

The actin cytoskeleton is involved in the regulation of cell morphology and migration. Wiskott-Aldrich Syndrome proteins (WASPs) play an important role in controlling actin polymerization by activating the Arp2/3 complex. The present study investigated the roles of WasC, one of the 3 WASPs in Dictyostelium, in cellular processes. Cells lacking WasC displayed strong cell adhesion and approximately 1.5-fold increase in F-actin levels as compared to the wild-type cells. Loss of wasC caused defects in phagocytosis and decreased the migration speed in chemoattractant-mediated cell migration but did not affect directionality. WasC was localized to the protruding region in migrating cells and, transiently and rapidly translocated to the cell cortex in response to chemoattractant stimulation, in an F-actin dependent manner. Our
results
suggest that WasC is involved in cell adhesion and migration by regulating F-actin polymerization at the leading edge of migrating cells, probably as a negative regulator. The increased strength of adhesion in wasC null cells is likely to decrease the migration speed but not the directionality.

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Wiskott-Aldrich syndrome gene as a prognostic biomarker correlated with immune infiltrates in clear cell renal cell carcinoma
Guixin Ding, Tianqi Wang, Shangjing Liu, Zhongbao Zhou, Jian Ma, Jitao Wu
Frontiers in Immunology.2023;[Epub] CrossRef
Dual regulation of the actin cytoskeleton by CARMIL-GAP
Goeh Jung, Miao Pan, Christopher J. Alexander, Tian Jin, John A. Hammer
Journal of Cell Science.2022;[Epub] CrossRef
Regulation of the Actin Cytoskeleton via Rho GTPase Signalling in Dictyostelium and Mammalian Cells: A Parallel Slalom
Vedrana Filić, Lucija Mijanović, Darija Putar, Antea Talajić, Helena Ćetković, Igor Weber
Cells.2021; 10(7): 1592. CrossRef

A histone deacetylase, MoHOS2 regulates asexual development and virulence in the rice blast fungus: Jongjune Lee , Jae-Joon Lee , Junhyun Jeon; J. Microbiol. 2019;57(12):1115-1125. Published online November 22, 2019; DOI: https://doi.org/10.1007/s12275-019-9363-5

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Abstract

Histone acetylation/deacetylation represent a general and efficient epigenetic mechanism through which fungal cells control gene expression. Here we report developmental requirement of MoHOS2-mediated histone deacetylation (HDAC) for the rice blast fungus, Magnaporthe oryzae. Structural similarity and nuclear localization indicated that MoHOS2 is an ortholog of Saccharomyces cerevisiae Hos2, which is a member of class I histone deacetylases and subunit of Set3 complex. Deletion of MoHOS2 led to 25% reduction in HDAC activity, compared to the wild-type, confirming that it is a bona-fide HDAC. Lack of MoHOS2 caused decrease in radial growth and impinged dramatically on asexual sporulation. Such reduction in HDAC activity and phenotypic defects of ΔMohos2 were recapitulated by a single amino acid change in conserved motif that is known to be important for HDAC activity. Expression analysis revealed up-regulation of MoHOS2 and concomitant down-regulation of some of the key genes involved in asexual reproduction under sporulation-promoting condition. In addition, the deletion mutant exhibited defect in appressorium formation from both germ tube tip and hyphae. As a result, ΔMohos2 was not able to cause disease symptoms. Wound-inoculation showed that the mutant is compromised in its ability to grow inside host plants as well. We found that some of ROS detoxifying genes and known effector genes are de-regulated in the mutant. Taken together, our data suggest that MoHOS2-dependent histone deacetylation is pivotal for proper timing and induction of transcription of the genes that coordinate developmental changes and host infection in M. oryzae.

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Glsirt1-mediated deacetylation of GlCAT regulates intracellular ROS levels, affecting ganoderic acid biosynthesis in Ganoderma lucidum
Jing Han, Lingshuai Wang, Xin Tang, Rui Liu, Liang Shi, Jing Zhu, Mingwen Zhao
Free Radical Biology and Medicine.2024; 216: 1. CrossRef
Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology
Yufeng Guan, Joanna Gajewska, Jolanta Floryszak‐Wieczorek, Umesh Kumar Tanwar, Ewa Sobieszczuk‐Nowicka, Magdalena Arasimowicz‐Jelonek
Molecular Plant Pathology.2024;[Epub] CrossRef
FolSas2 is a regulator of early effector gene expression during Fusarium oxysporum infection
Limin Song, Yalei Wang, Fahui Qiu, Xiaoxia Li, Jingtao Li, Wenxing Liang
New Phytologist.2024;[Epub] CrossRef
Regulatory roles of epigenetic modifications in plant-phytopathogen interactions
Zeng Tao, Fei Yan, Matthias Hahn, Zhonghua Ma
Crop Health.2023;[Epub] CrossRef
The additional PRC2 subunit and Sin3 histone deacetylase complex are required for the normal distribution of H3K27me3 occupancy and transcriptional silencing in Magnaporthe oryzae
Chuyu Lin, Zhongling Wu, Huanbin Shi, Jinwei Yu, Mengting Xu, Fucheng Lin, Yanjun Kou, Zeng Tao
New Phytologist.2022; 236(2): 576. CrossRef
Regulatory Roles of Histone Modifications in Filamentous Fungal Pathogens
Yiling Lai, Lili Wang, Weilu Zheng, Sibao Wang
Journal of Fungi.2022; 8(6): 565. CrossRef
Polycomb Repressive Complex 2-Mediated H3K27 Trimethylation Is Required for Pathogenicity in Magnaporthe oryzae
Zhongling Wu, Jiehua Qiu, Huanbin Shi, Chuyu Lin, Jiangnan Yue, Zhiquan Liu, Wei Xie, Naweed I. Naqvi, Yanjun Kou, Zeng Tao
Rice Science.2022; 29(4): 363. CrossRef
Protein acetylation and deacetylation in plant‐pathogen interactions
Jing Wang, Chao Liu, Yun Chen, Youfu Zhao, Zhonghua Ma
Environmental Microbiology.2021; 23(9): 4841. CrossRef
Emerging Roles of Posttranslational Modifications in Plant-Pathogenic Fungi and Bacteria
Wende Liu, Lindsay Triplett, Xiao-Lin Chen
Annual Review of Phytopathology.2021; 59(1): 99. CrossRef
Fungal Lysine Deacetylases in Virulence, Resistance, and Production of Small Bioactive Compounds
Ingo Bauer, Stefan Graessle
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A Histone Deacetylase, Magnaporthe oryzae RPD3, Regulates Reproduction and Pathogenic Development in the Rice Blast Fungus
Song Hee Lee, Mohamed El-Agamy Farh, Jaejoon Lee, Young Taek Oh, Eunbyeol Cho, Jiyeun Park, Hokyoung Son, Junhyun Jeon, Antonio Di Pietro
mBio.2021;[Epub] CrossRef
The Histone Deacetylases MoRpd3 and MoHst4 Regulate Growth, Conidiation, and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae
Chaoxiang Lin, Xue Cao, Ziwei Qu, Shulin Zhang, Naweed I. Naqvi, Yi Zhen Deng, Aaron P. Mitchell
mSphere.2021;[Epub] CrossRef
Histone Acetyltransferases and Deacetylases Are Required for Virulence, Conidiation, DNA Damage Repair, and Multiple Stresses Resistance of Alternaria alternata
Haijie Ma, Lei Li, Yunpeng Gai, Xiaoyan Zhang, Yanan Chen, Xiaokang Zhuo, Yingzi Cao, Chen Jiao, Fred G. Gmitter, Hongye Li
Frontiers in Microbiology.2021;[Epub] CrossRef
Function of PoLAE2, a laeA homolog, in appressorium formation and cAMP signal transduction in Pyricularia oryzae
Pradabrat Prajanket, Kim-Chi Thi Vu, Jun Arai, Worawan Sornkom, Ayumi Abe, Teruo Sone
Bioscience, Biotechnology, and Biochemistry.2020; 84(11): 2401. CrossRef
A Histone Deacetylase, MoHDA1 Regulates Asexual Development and Virulence in the Rice Blast Fungus
Taehyun Kim, Song Hee Lee, Young Taek Oh, Junhyun Jeon
The Plant Pathology Journal.2020; 36(4): 314. CrossRef
Protein Acetylation/Deacetylation: A Potential Strategy for Fungal Infection Control
Junzhu Chen, Qiong Liu, Lingbing Zeng, Xiaotian Huang
Frontiers in Microbiology.2020;[Epub] CrossRef

Cultivable butyrate-producing bacteria of elderly Japanese diagnosed with Alzheimer’s disease: Thi Thuy Tien Nguyen , Yuta Fujimura , Iyo Mimura , Yusuke Fujii , Ngoc Luong Nguyen , Kensuke Arakawa , Hidetoshi Morita; J. Microbiol. 2018;56(10):760-771. Published online August 22, 2018; DOI: https://doi.org/10.1007/s12275-018-8297-7

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Abstract

The group of butyrate-producing bacteria within the human gut microbiome may be associated with positive effects on memory improvement, according to previous studies on dementia- associated diseases. Here, fecal samples of four elderly Japanese diagnosed with Alzheimer’s disease (AD) were used to isolate butyrate-producing bacteria. 226 isolates were randomly picked, their 16S rRNA genes were sequenced, and assigned into sixty OTUs (operational taxonomic units) based on BLASTn results. Four isolates with less than 97% homology to known sequences were considered as unique OTUs of potentially butyrate-producing bacteria. In addition, 12 potential butyrate-producing isolates were selected from the remaining 56 OTUs based on scan-searching against the PubMed and the ScienceDirect databases. Those belonged to the phylum Bacteroidetes and to the clostridial clusters I, IV, XI, XV, XIVa within the phylum Firmicutes. 15 out of the 16 isolates were indeed able to produce butyrate in culture as determined by high-performance liquid chromatography with UV detection. Furthermore, encoding genes for butyrate formation in these bacteria were identified by sequencing of degenerately primed PCR products and included the genes for butyrate kinase (buk), butyryl-CoA: acetate CoAtransferase (but), CoA-transferase-related, and propionate CoA-transferase. The results showed that eight isolates possessed buk, while five isolates possessed but. The CoA-transfer- related gene was identified as butyryl-CoA:4-hydroxybutyrate CoA transferase (4-hbt) in four strains. No strains contained the propionate CoA-transferase gene. The biochemical and butyrate-producing pathways analyses of butyrate producers presented in this study may help to characterize the butyrate-producing bacterial community in the gut of AD patients.

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