Journal of Microbiology

Volume 58(11); November 2020

Journal Articles

[PROTOCOL] High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang: Suhyun Kim , Miri S. Park , Jaeho Song , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2020;58(11):893-905. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0452-2

51 View
0 Download
11 Web of Science
12 Crossref

Multi-omics approaches, including metagenomics and single- cell amplified genomics, have revolutionized our understanding of the hidden diversity and function of microbes in nature. Even in the omics age, cultivation is an essential discipline in microbial ecology since microbial cultures are necessary to assess the validity of an in silico prediction about the microbial metabolism and to isolate viruses infecting bacteria and archaea. However, the ecophysiological characteristics of predominant freshwater bacterial lineages remain largely unknown due to the scarcity of cultured representatives. In an ongoing effort to cultivate the uncultured majority of freshwater bacteria, the most abundant freshwater Actinobacteria acI clade has recently been cultivated from Lake Soyang through catalase-supplemented high-throughput cultivation based on dilution-to-extinction. This method involves physical isolation of target microbes from mixed populations, culture media simulating natural habitats, and removal of toxic compounds. In this protocol, we describe detailed procedures for isolating freshwater oligotrophic microbes, as well as the essence of the dilution-to-extinction culturing. As a case study employing the catalase-supplemented dilution-to-extinction protocol, we also report a cultivation trial using a water sample collected from Lake Soyang. Of the 480 cultivation wells inoculated with a single lake-water sample, 75 new acI strains belonging to 8 acI tribes (acI-A1, A2, A4, A5, A6, A7, B1, B4, C1, and C2) were cultivated, and each representative strain per subclade could be revived from glycerol stocks. These cultivation results demonstrate that the protocol described in this study is efficient in isolating freshwater bacterioplankton harboring streamlined genomes.

Citations

Citations to this article as recorded by

Frontiers of lake microbial ecology opened up by new technologies.
Yusuke OKAZAKI
Japanese Journal of Limnology (Rikusuigaku Zasshi).2024; 85(1): 1. CrossRef
Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria
Minjia Zheng, Linran Wen, Cailing He, Xinlan Chen, Laiting Si, Hao Li, Yiting Liang, Wei Zheng, Feng Guo
Nature Communications.2024;[Epub] CrossRef
Adaptive genetic traits in pelagic freshwater microbes
Maria‐Cecilia Chiriac, Markus Haber, Michaela M. Salcher
Environmental Microbiology.2023; 25(3): 606. CrossRef
Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability
Xavier Rey-Velasco, Ona Deulofeu-Capo, Isabel Sanz-Sáez, Clara Cardelús, Isabel Ferrera, Josep M. Gasol, Olga Sánchez, Vincent J. Denef
Microbiology Spectrum.2023;[Epub] CrossRef
Two-Dimensional Cell Separation: a High-Throughput Approach to Enhance the Culturability of Bacterial Cells from Environmental Samples
Krishna K. Yadav, Yogesh Nimonkar, Bhagyashri J. Poddar, Lochana Kovale, Isita Sagar, Yogesh Shouche, Hemant J. Purohit, Anshuman A. Khardenavis, Stefan J. Green, Om Prakash, Kristen M. DeAngelis
Microbiology Spectrum.2022;[Epub] CrossRef
Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications—a review
Hoda Hosseini, Hareb M. Al‐Jabri, Navid R. Moheimani, Simil A. Siddiqui, Imen Saadaoui
Journal of Basic Microbiology.2022; 62(9): 1030. CrossRef
Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis
Tereza Smrhova, Kunal Jani, Petr Pajer, Gabriela Kapinusova, Tomas Vylita, Jachym Suman, Michal Strejcek, Ondrej Uhlik
Environmental Microbiome.2022;[Epub] CrossRef
Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended descrip
Dong-Wook Hyun, Euon Jung Tak, Pil Soo Kim, Jin-Woo Bae
Journal of Microbiology.2021; 59(2): 132. CrossRef
Metaviromics coupled with phage-host identification to open the viral ‘black box’
Kira Moon, Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 311. CrossRef
Heme auxotrophy in abundant aquatic microbial lineages
Suhyun Kim, Ilnam Kang, Jin-Won Lee, Che Ok Jeon, Stephen J. Giovannoni, Jang-Cheon Cho
Proceedings of the National Academy of Sciences.2021;[Epub] CrossRef
Recent trend, biases and limitations of cultivation-based diversity studies of microbes
Om Prakash, Mrinalini Parmar, Manali Vaijanapurkar, Vinay Rale, Yogesh S Shouche
FEMS Microbiology Letters.2021;[Epub] CrossRef
Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period
Suhyun Kim, Md. Rashedul Islam, Ilnam Kang, Jang-Cheon Cho
Frontiers in Microbiology.2021;[Epub] CrossRef

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

53 View
0 Download
10 Web of Science
10 Crossref

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.

Citations

Citations to this article as recorded by

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
Unveiling the impacts moso bamboo invasion on litter and soil properties: A meta-analysis
Weixue Luo, Qingyu Zhang, Peng Wang, Jie Luo, Chunyan She, Xuman Guo, Jiajia Yuan, Yuhong Sun, Ruming Guo, Zongfeng Li, Jinchun Liu, Jianping Tao
Science of The Total Environment.2024; 909: 168532. CrossRef
Transport, pollution, and health risk of heavy metals in “soil-medicinal and edible plant-human” system: A case study of farmland around the Beiya mining area in Yunnan, China
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
Soil Bacterial Community Response to Fire Varies with Slope Aspect at Zhenshan Mountain, East China
Ping Zhu, Wenyan Liu, Zhongyuan Sun, Xinfu Bai, Jianqiang Song, Nan Wu, Yuping Hou
Eurasian Soil Science.2023; 56(5): 599. CrossRef
Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau
Zhijia Cui, Ran Li, Fan Li, Ling Jin, Haixu Wu, Chunya Cheng, Yi Ma, Zhenheng Wang, Yuanyuan Wang
Frontiers in Microbiology.2023;[Epub] CrossRef
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
Journal of Soils and Sediments.2023; 23(11): 3891. CrossRef
Correlates of Rhizosphere Soil Properties, Fungal Community Composition, and Active Secondary Metabolites in Cornus officinalis in Different Regions of China
Haoqiang Sun, Binkai Han, Xiaolin Yang, Changfen He, Ke Zhao, Ting Wang, Shujing An, Xiaochang Xue, Jiefang Kang
Journal of Soil Science and Plant Nutrition.2023; 23(1): 514. CrossRef
Microbial inoculants and garbage fermentation liquid reduced root-knot nematode disease and As uptake in Panax quinquefolium cultivation by modulating rhizosphere microbiota community
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
Tize Xia, Lushuang Li, Bin Li, Peitong Dou, Hanqi Yang
Forests.2022; 13(1): 121. CrossRef

Occurrence of four waterborne viruses at five typical raw water resources in the Republic of Korea during August 2013 to February 2019: Young Yil Bahk , Min-Ho Kim , Tong-Soo Kim , Sang Jung Park , Jeong-Myeong Kim , Ok-Jae Rhee , Sang-Seob Lee; J. Microbiol. 2020;58(11):915-925. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0231-0

51 View
0 Download
2 Web of Science
2 Crossref

Abstract

Waterborne diseases have critical public health issues and socioeconomic relevancy worldwide. Various viral pathogens are ordinarily associated with waterborne diseases. Six-yearsurveillance (a total of 20 times) of norovirus, hepatitis A virus, group C rotavirus, and enterovirus was conducted at five raw water sampling sites including two lakes (Lakes Soyang and Juam), Hyundo region of Geum River in Daejeon City, and Guui region of Han River in Seoul Metropolitan City and Moolgeum region of Nakdong River in Gimhae City which are located near two water intake plants. In this study, we routinely investigated virus contamination in water samples through reverse transcription polymerase chain reaction (RTPCR) and integrated cell culture RT-PCR with high sensitivity and specificity. A total 100 samples were tested. Most of the targeted viruses were found in 32% of the samples and at least one of the indicator bacteria was detected in 65% of these occurrences. Among all the detected viruses, enterovirus was the most prevalent with a detection frequency of 12% and 2.71 MPN/10 L on average, while hepatitis A virus was the least prevalent with a detection frequency of 4%. Nearly all of the analyzed viruses (except for group C rotavirus) were present in samples from Han River (the Guui region), Geum River (the Hyundo region), Lake Juam, and Nakdong River (the Moolgeum region), while group C rotavirus was detected in those from the Guui region. During the six-year sampling period, the targeted waterborne viruses in water samples exhibited seasonal patterns in their occurrence that were different from the indicator bacteria levels in the water samples. The fact that they were detected in the five representative Korean water environments makes it necessary to establish the chemical and biological analysis systems for waterborne viruses and sophisticated management systems.

Citations

Citations to this article as recorded by

Occurrence characteristics, removal efficiencies and potential health risks of typical viruses in rural domestic sewage: A review
Yingming Zhu, Su Xu, Yu Zhou, Xuesong Guo, Yunping Han, Jun Zhan, Lin Li, Junxin Liu
Journal of Water Process Engineering.2025; 69: 106611. CrossRef
Occurrence of Hepatitis A Virus in Water Matrices: A Systematic Review and Meta-Analysis
Guy Roussel Takuissu, Sebastien Kenmoe, Jean Thierry Ebogo-Belobo, Cyprien Kengne-Ndé, Donatien Serge Mbaga, Arnol Bowo-Ngandji, Juliette Laure Ndzie Ondigui, Raoul Kenfack-Momo, Serges Tchatchouang, Josiane Kenfack-Zanguim, Robertine Lontuo Fogang, Elisa
International Journal of Environmental Research and Public Health.2023; 20(2): 1054. CrossRef

The effects of cigarettes and alcohol on intestinal microbiota in healthy men: Renbin Lin , Yawen Zhang , Luyi Chen , Yadong Qi , Jiamin He , Mengjia Hu , Ying Zhang , Lina Fan , Tao Yang , Lan Wang , Misi Si , Shujie Chen; J. Microbiol. 2020;58(11):926-937. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0006-7

49 View
0 Download
27 Web of Science
30 Crossref

Abstract

Human intestinal microbiota is affected by the exogenous microenvironment. This study aimed to determine the effects of cigarettes and alcohol on the gut microbiota of healthy men. In total, 116 healthy male subjects were enrolled and divided into four groups: non-smoking and non-drinking (Group A), smoking only (Group B), drinking only (Group C), and smoking and drinking combined (Group D). Fecal samples were collected and sequenced using 16S rRNA to analyze the microbial composition. Short-chain fatty acid (SCFAs) levels in feces were determined by gas chromatography. We found that cigarette and alcohol consumptions can alter overall composition of gut microbiota in healthy men. The relative abundances of phylum Bacteroidetes and Firmicutes and more than 40 genera were changed with cigarette and alcohol consumptions. SCFAs decreased with smoking and alcohol consumption. Multivariate analysis indicated that when compared with group A, group B/C/D had higher Bacteroides, and lower Phascolarctobacterium, Ruminococcaceae_ UCG-002, Ruminococcaceae_UCG-003, and Ruminiclostridium_ 9 regardless of BMI and age. Additionally, the abundance of Bacteroides was positively correlated with the smoking pack-year (r = 0.207, p < 0.05), the abundance of predicted pathway of bacterial toxins (r = 0.3672, p < 0.001) and the level of carcinoembryonic antigen in host (r = 0.318, p < 0.01). Group D shared similar microbial construction with group B, but exerted differences far from group C with lower abundance of Haemophilus. These results demonstrated that cigarette and alcohol consumption separately affected the intestinal microbiota and function in healthy men; furthermore, the co-occurrence of cigarette and alcohol didn’t exacerbate the dysbiosis and cigarette played the predominated role on the alteration.

Citations

Citations to this article as recorded by

Potential roles of cigarette smoking on gut microbiota profile among Chinese men
Jiayao Fan, Fangfang Zeng, Haili Zhong, Jun Cai, Wentao Shen, Chunxiao Cheng, Chunfeng He, Yuanjiao Liu, Yuan Zhou, Shujie Chen, Yimin Zhu, Tao Liu, Ju-Sheng Zheng, Lan Wang, Yu-Ming Chen, Wenjun Ma, Dan Zhou
BMC Medicine.2025;[Epub] CrossRef
Gut Microbiota at the Crossroad of Hepatic Oxidative Stress and MASLD
Fabrizio Termite, Sebastiano Archilei, Francesca D’Ambrosio, Lucrezia Petrucci, Nicholas Viceconti, Roberta Iaccarino, Antonio Liguori, Antonio Gasbarrini, Luca Miele
Antioxidants.2025; 14(1): 56. CrossRef
A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design
Sun-Young Kim, So-Youn Woo, Hyung-Lae Kim, Yoosoo Chang, Seungho Ryu, Han-Na Kim
Journal of Affective Disorders.2025; 376: 26. CrossRef
An Investigation into the Relationship of Circulating Gut Microbiome Molecules and Inflammatory Markers with the Risk of Incident Dementia in Later Life
Kolade Oluwagbemigun, Andrea Anesi, Urska Vrhovsek, Fulvio Mattivi, Pamela Martino Adami, Michael Pentzek, Martin Scherer, Steffi G. Riedel-Heller, Siegfried Weyerer, Horst Bickel, Birgitt Wiese, Matthias Schmid, John F. Cryan, Alfredo Ramirez, Michael Wa
Molecular Neurobiology.2024; 61(12): 9776. CrossRef
Effect of chronic alcohol consumption on oral microbiota in rats with periodontitis
Zirui Zhao, Xiao Zhang, Wanqing Zhao, Jianing Wang, Yanhui Peng, Xuanning Liu, Na Liu, Qing Liu
PeerJ.2024; 12: e17795. CrossRef
Altered interaction network in the gut microbiota of current cigarette smokers
Zhouhai Zhu, Meng Wang, Ying Guan, Meng Li, Qiyuan Peng, Ning Zheng, Wenbin Ma
Engineering Microbiology.2024; 4(2): 100138. CrossRef
The role of the gut microbiome in the development of hepatobiliary cancers
Neil Daniel, Flavia Genua, Mazda Jenab, Ana-Lucia Mayén, Anastasia Chrysovalantou Chatziioannou, Pekka Keski-Rahkonen, David J. Hughes
Hepatology.2024; 80(5): 1252. CrossRef
The role and mechanism of gut-lung axis mediated bidirectional communication in the occurrence and development of chronic obstructive pulmonary disease
Xiaofan Song, Xina Dou, Jiajing Chang, Xiaonan Zeng, Qinhong Xu, Chunlan Xu
Gut Microbes.2024;[Epub] CrossRef
The interplay between microbiome and host factors in pathogenesis and therapy of head and neck cancer
Martina Raudenská, Maria Bugajová, David Kalfeřt, Jan Plzák, Adam Šubrt, Petra Tesařová, Michal Masařík
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2024; 1879(6): 189216. CrossRef
The Crucial Roles of Diet, Microbiota, and Postbiotics in Colorectal Cancer
Rüya Kuru-Yaşar, Özlem Üstün-Aytekin
Current Nutrition Reports.2024; 13(2): 126. CrossRef
Relationship between dietary live microbe intake and the prevalence of COPD in adults: a cross-sectional study of NHANES 2013–2018
Dongbo Zhou, Baimei He, Qiong Huang, Siqi Li, Wenbin Nan, Qiong Chen, Qiao Yu
BMC Pulmonary Medicine.2024;[Epub] CrossRef
When smoke meets gut: deciphering the interactions between tobacco smoking and gut microbiota in disease development
Bo Chen, Guangyi Zeng, Lulu Sun, Changtao Jiang
Science China Life Sciences.2024; 67(5): 854. CrossRef
Preliminary exploratory research on the application value of oral and intestinal meta-genomics in predicting subjects' occupations–A case study of the distinction between students and migrant workers
Shujie Dou, Guanju Ma, Yu Liang, Guangping Fu, Jie Shen, Lihong Fu, Qian Wang, Tao Li, Bin Cong, Shujin Li
Frontiers in Microbiology.2024;[Epub] CrossRef
A Comparative Study of Serum Butyric Acid in Subjects with Tongue Cancer
P. C. Suhasini, Shilpa S. Shetty, Vijith Vittal Shetty, Vadisha Bhat, P. G. Roopashree, N. Suchetha Kumari
Journal of Datta Meghe Institute of Medical Sciences University.2024; 19(1): 104. CrossRef
What are the common downstream molecular events between alcoholic and nonalcoholic fatty liver?
Giovanni Tarantino, Vincenzo Citro
Lipids in Health and Disease.2024;[Epub] CrossRef
Scarring the early-life microbiome: its potential life-long effects on human health and diseases
Hyunji Park, Na-Young Park, Ara Koh
BMB Reports.2023; 56(9): 469. CrossRef
Influence of Microbiota on Vaccine Effectiveness: “Is the Microbiota the Key to Vaccine-induced Responses?”
So-Hee Hong
Journal of Microbiology.2023; 61(5): 483. CrossRef
Cross-talks between gut microbiota and tobacco smoking: a two-sample Mendelian randomization study
Jiayao Fan, Yuan Zhou, Ran Meng, Jinsong Tang, Jiahao Zhu, Melinda C. Aldrich, Nancy J. Cox, Yimin Zhu, Yingjun Li, Dan Zhou
BMC Medicine.2023;[Epub] CrossRef
Changes in Gut Microbiota and Multiple Sclerosis: A Systematic Review
Alba Ordoñez-Rodriguez, Pablo Roman, Lola Rueda-Ruzafa, Ana Campos-Rios, Diana Cardona
International Journal of Environmental Research and Public Health.2023; 20(5): 4624. CrossRef
Checkpoint inhibitor responses can be regulated by the gut microbiota – A systematic review
Mariam Zeriouh, Hans Raskov, Lasse Kvich, Ismail Gögenur, Astrid Louise Bjørn Bennedsen
Neoplasia.2023; 43: 100923. CrossRef
Probiotic Bifidobacterium longum subsp. longum Protects against Cigarette Smoke-Induced Inflammation in Mice
Kurtis F. Budden, Shaan L. Gellatly, Annalicia Vaughan, Nadia Amorim, Jay C. Horvat, Nicole G. Hansbro, David L. A. Wood, Philip Hugenholtz, Paul G. Dennis, Peter A. B. Wark, Philip M. Hansbro
International Journal of Molecular Sciences.2022; 24(1): 252. CrossRef
Cigarette Smoking and Human Gut Microbiota in Healthy Adults: A Systematic Review
Martina Antinozzi, Monica Giffi, Nicolò Sini, Francesca Gallè, Federica Valeriani, Corrado De Vito, Giorgio Liguori, Vincenzo Romano Spica, Maria Sofia Cattaruzza
Biomedicines.2022; 10(2): 510. CrossRef
The Protective Effects of Ganoderic Acids from Ganoderma lucidum Fruiting Body on Alcoholic Liver Injury and Intestinal Microflora Disturbance in Mice with Excessive Alcohol Intake
Ying-Jia Cao, Zi-Rui Huang, Shi-Ze You, Wei-Ling Guo, Fang Zhang, Bin Liu, Xu-Cong Lv, Zhan-Xi Lin, Peng-Hu Liu
Foods.2022; 11(7): 949. CrossRef
Serum Short-Chain Fatty Acids and Associations With Inflammation in Newly Diagnosed Patients With Multiple Sclerosis and Healthy Controls
Anna Olsson, Stefan Gustavsen, Thao Duy Nguyen, Margareta Nyman, Annika R. Langkilde, Tue H. Hansen, Finn Sellebjerg, Annette B. Oturai, Helle Bach Søndergaard
Frontiers in Immunology.2021;[Epub] CrossRef
Preoperative Microbiomes and Intestinal Barrier Function Can Differentiate Prodromal Alzheimer’s Disease From Normal Neurocognition in Elderly Patients Scheduled to Undergo Orthopedic Surgery
Mei Duan, Fangyan Liu, Huiqun Fu, Shibao Lu, Tianlong Wang
Frontiers in Cellular and Infection Microbiology.2021;[Epub] CrossRef
Optimization of lactate production from co-fermentation of swine manure with apple waste and dynamics of microbial communities
Tianjing Lian, Wanqin Zhang, Qitao Cao, Shunli Wang, Fubin Yin, Yongxin Chen, Tanlong Zhou, Hongmin Dong
Bioresource Technology.2021; 336: 125307. CrossRef
Probiotics-induced changes in gut microbial composition and its effects on cognitive performance after stress: exploratory analyses
Mirjam Bloemendaal, Joanna Szopinska-Tokov, Clara Belzer, David Boverhoff, Silvia Papalini, Franziska Michels, Saskia van Hemert, Alejandro Arias Vasquez, Esther Aarts
Translational Psychiatry.2021;[Epub] CrossRef
Microbiology of the American Smokeless Tobacco
A. J. Rivera, R. E. Tyx
Applied Microbiology and Biotechnology.2021; 105(12): 4843. CrossRef
The Immune System through the Lens of Alcohol Intake and Gut Microbiota
Javier Calleja-Conde, Victor Echeverry-Alzate, Kora-Mareen Bühler, Pedro Durán-González, Jose Morales-García, Lucía Segovia-Rodríguez, Fernando Rodríguez de Fonseca, Elena Giné, Jose López-Moreno
International Journal of Molecular Sciences.2021; 22(14): 7485. CrossRef
Mining microbes for mental health: Determining the role of microbial metabolic pathways in human brain health and disease
Simon Spichak, Thomaz F.S. Bastiaanssen, Kirsten Berding, Klara Vlckova, Gerard Clarke, Timothy G. Dinan, John F. Cryan
Neuroscience & Biobehavioral Reviews.2021; 125: 698. CrossRef

Iron interferes with quorum sensing-mediated cooperation in Pseudomonas aeruginosa by affecting the expression of ppyR and mexT, in addition to rhlR: Feng Sun , Na Li , Lijia Wang , Huajun Feng , Dongsheng Shen , Meizhen Wang; J. Microbiol. 2020;58(11):938-944. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0264-4

56 View
0 Download
4 Web of Science
4 Crossref

Abstract

The stabilization of quorum sensing (QS) is vital for bacterial survival in various environments. Although the mechanisms of QS stabilization in certain conditions have been well studied, the impact of environmental factors has received much less attention. In this study, we show that the supplementation of 25 μM iron in competition experiments and 50 μM in evolution experiments to casein growth cultures significantly increased the possibility of population collapse by affecting elastase production. However, the expression of lasI and lasR remained constant regardless of iron concentration and hence this effect was not through interference with the LasIR circuit, which mainly regulates the secretion of elastase in Pseudomonas aeruginosa. However, the expression of rhlR was significantly inhibited by iron treatment, which could affect the production of elastase. Further, based on both reverse transcription quantitative polymerase chain reaction and gene knock-out assays, we show that iron inhibits the transcription of ppyR and enhances the expression of mexT, both of which decrease elastase production and correspondingly interfere with QS stabilization. Our findings show that environmental factors can affect the genes of QS circuits, interfering with QS stabilization. These findings are not only beneficial in understanding the mechanistic effect of iron on QS stabilization, but also demonstrate the complexity of QS stabilization by linking non-QS-related genes with QS traits.

Citations

Citations to this article as recorded by

Effect of LuxS/AI-2-mediated quorum sensing system on bacteriocin production of Lactobacillus plantarum NMD-17
Li-Li Man, Dian-Jun Xiang
Folia Microbiologica.2023; 68(6): 855. CrossRef
PtsN in Pseudomonas aeruginosa Is Phosphorylated by Redundant Upstream Proteins and Impacts Virulence-Related Genes
Simon A. M. Underhill, Somalisa Pan, Mary Erdmann, Matthew T. Cabeen, Joseph Bondy-Denomy
Journal of Bacteriology.2023;[Epub] CrossRef
The immune responses to different Uropathogens call individual interventions for bladder infection
Linlong Li, Yangyang Li, Jiali Yang, Xiang Xie, Huan Chen
Frontiers in Immunology.2022;[Epub] CrossRef
Design of Polymeric Thin Films to Direct Microbial Biofilm Growth, Virulence, and Metabolism
Trevor Franklin, Yinan Wu, Jiayan Lang, Sijin Li, Rong Yang
Biomacromolecules.2021; 22(12): 4933. CrossRef

Similarities and differences between 6S RNAs from Bradyrhizobium japonicum and Sinorhizobium meliloti: Olga Y. Burenina , Daria A. Elkina , Anzhela Y. Migur , Tatiana S. Oretskaya , Elena Evguenieva-Hackenberg , RolK. Hartmann , Elena A. Kubareva; J. Microbiol. 2020;58(11):945-956. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0283-1

48 View
0 Download
5 Web of Science
6 Crossref

Abstract

6S RNA, a conserved and abundant small non-coding RNA found in most bacteria, regulates gene expression by inhibiting RNA polymerase (RNAP) holoenzyme. 6S RNAs from α-proteobacteria have been studied poorly so far. Here, we present a first in-depth analysis of 6S RNAs from two α-proteobacteria species, Bradyrhizobium japonicum and Sinorhizobium meliloti. Although both belong to the order Rhizobiales and are typical nitrogen-fixing symbionts of legumes, their 6S RNA expression profiles were found to differ: B. japonicum 6S RNA accumulated in the stationary phase, thus being reminiscent of Escherichia coli 6S RNA, whereas S. meliloti 6S RNA level peaked at the transition to the stationary phase, similarly to Rhodobacter sphaeroides 6S RNA. We demonstrated in vitro that both RNAs have hallmarks of 6S RNAs: they bind to the σ70-type RNAP holoenzyme and serve as templates for de novo transcription of so-called product RNAs (pRNAs) ranging in length from ~13 to 24 nucleotides, with further evidence of the synthesis of even longer pRNAs. Likewise, stably bound pRNAs were found to rearrange the 6S RNA structure to induce its dissociation from RNAP. Compared with B. japonicum 6S RNA, considerable conformational heterogeneity was observed for S. meliloti 6S RNA and its complexes with pRNAs, even though the two 6S RNAs share ~75% sequence identity. Overall, our findings suggest that the two rhizobial 6S RNAs have diverged with respect to their regulatory impact on gene expression throughout the bacterial life cycle.

Citations

Citations to this article as recorded by

Bacteria Adaptation Mechanisms to Stress Conditions with Small Non-Coding RNAs Participation
A. S. Karpov, D. A. Elkina, T. S. Oretskaya, E. A. Kubareva
Биоорганическая химия.2023; 49(6): 555. CrossRef
Bacterial Adaptation Mechanisms to Stress Conditions with Small Non-Coding RNAs Participation (A Review)
A. S. Karpov, D. A. Elkina, T. S. Oretskaya, E. A. Kubareva
Russian Journal of Bioorganic Chemistry.2023; 49(6): 1198. CrossRef
Structural and Functional Insight into the Mechanism of Bacillus subtilis 6S-1 RNA Release from RNA Polymerase
Sweetha Ganapathy, Philipp G. Hoch, Marcus Lechner, Malte Bussiek, Roland K. Hartmann
Non-Coding RNA.2022; 8(1): 20. CrossRef
Involvement of E. coli 6S RNA in Oxidative Stress Response
Olga Y. Burenina, Daria A. Elkina, Anna Ovcharenko, Valeria A. Bannikova, M. Amri C. Schlüter, Tatiana S. Oretskaya, Roland K. Hartmann, Elena A. Kubareva
International Journal of Molecular Sciences.2022; 23(7): 3653. CrossRef
Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
Viola Vaňková Hausnerová, Olga Marvalová, Michaela Šiková, Mahmoud Shoman, Jarmila Havelková, Milada Kambová, Martina Janoušková, Dilip Kumar, Petr Halada, Marek Schwarz, Libor Krásný, Jarmila Hnilicová, Josef Pánek
Frontiers in Microbiology.2022;[Epub] CrossRef
Detection of Small Products of Transcription from 6S RNA (pRNA) by “Mirror-Like” Northern Blot Hybridization
O. Y. Burenina, T. S. Oretskaya, E. A. Kubareva
Russian Journal of Bioorganic Chemistry.2021; 47(2): 478. CrossRef

Analyses of DNA double-strand break repair pathways in tandem arrays of HXT genes of Saccharomyces cerevisiae: Ju-Hee Choi , Ye-Seul Lim , Min-Ku Kim , Sung-Ho Bae; J. Microbiol. 2020;58(11):957-966. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0461-1

47 View
0 Download
4 Web of Science
4 Crossref

Abstract

Eukaryotic genomes contain numerous homologous repeat sequences including redundant genes with divergent homology that can be potential recombination targets. Recombination between divergent sequences is rare but poses a substantial threat to genome stability. The hexose transporter (HXT) gene family shares high sequence similarities at both protein and DNA levels, and some members are placed close together in tandem arrays. In this study, we show that spontaneous interstitial deletions occur at significantly high rates in HXT gene clusters, resulting in chimeric HXT sequences that contain a single junction point. We also observed that DNA double-strand breaks created between HXT genes produce primarily interstitial deletions, whereas internal cleavage of the HXT gene resulted in gene conversions as well as deletion products. Interestingly, interstitial deletions were less constrained by sequence divergence than gene conversion. Moreover, recombination-defective mutations differentially affected the survival frequency. Mutations that impair single-strand annealing (SSA) pathway greatly reduced the survival frequency by 10–1,000-fold, whereas disruption of Rad51-dependent homologous recombination exhibited only modest reduction. Our results indicate that recombination in the tandemly repeated HXT genes occurs primarily via SSA pathway.

Citations

Citations to this article as recorded by

Deletion of IRC19 Causes Defects in DNA Double-Strand Break Repair Pathways in Saccharomyces cerevisiae
Ju-Hee Choi, Oyungoo Bayarmagnai, Sung-Ho Bae
Journal of Microbiology.2024; 62(9): 749. CrossRef
A novel CRISPR/Cas9 system with high genomic editing efficiency and recyclable auxotrophic selective marker for multiple-step metabolic rewriting in Pichia pastoris
Xiang Wang, Yi Li, Zhehao Jin, Xiangjian Liu, Xiang Gao, Shuyuan Guo, Tao Yu
Synthetic and Systems Biotechnology.2023; 8(3): 445. CrossRef
Enhancing Homologous Recombination Efficiency in Pichia pastoris for Multiplex Genome Integration Using Short Homology Arms
Jucan Gao, Cuifang Ye, Jintao Cheng, Lihong Jiang, Xinghao Yuan, Jiazhang Lian
ACS Synthetic Biology.2022; 11(2): 547. CrossRef
Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae
Ye-Seul Lim, Ju-Hee Choi, Kyu-Jin Ahn, Min-Ku Kim, Sung-Ho Bae
Journal of Microbiology.2021; 59(4): 401. CrossRef

1Medical Convergence Materials Commercialization Center, Gyeongsan: JaeJin An , Eun-Mi Ha; J. Microbiol. 2020;58(11):967-977. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0375-y

57 View
0 Download
20 Web of Science
17 Crossref

Abstract

Lactobacillus plantarum-derived metabolites (LDMs) increase drug sensitivity to 5-FU and antimetastatic effects in 5-FUresistant colorectal cancer cells (HCT-116/5FUR). In this study, we evaluated the effects of LDMs on the regulation of genes and proteins involved in HCT-116/5-FUR cell proliferation and metastasis. HCT-116/5-FUR cells showed high metastatic potential, significantly reduced tight junction (TJ) integrity, including increased migration and paracellular permeability, and upregulation of claudin-1 (CLDN-1). The genetic silencing of CLDN-1 increased the sensitivity of HCT- 116/5FUR to 5-FU and inhibited its metastatic potential by regulating the expression of epithelial-mesenchymal transition (EMT) related genes. Co-treatment of HCT-116/5FUR with LDMs and 5-FU suppressed chemoresistant and metastatic behavior by downregulating CLDN-1 expression. Finally, we designed LDMs-based therapeutic strategies to treatment for metastatic 5-FU-resistant colorectal cancer cells. These
results
suggested that LDMs and 5-FU cotreatments can synergistically target 5-FU-resistant cells, making it a candidate strategy to overcome 5-FU chemoresistance improve anticancer drug efficacy.

Citations

Citations to this article as recorded by

Targeting the gut and tumor microbiome in cancer treatment resistance
Sona Ciernikova, Aneta Sevcikova, Michal Mego
American Journal of Physiology-Cell Physiology.2024; 327(6): C1433. CrossRef
Tight Junctions and Cancer: Targeting Claudin-1 and Claudin-4 in Thyroid Pathologies
Jędrzej Borowczak, Dariusz Łaszczych, Katarzyna Olejnik, Jakub Michalski, Anna Gutowska, Monika Kula, Anita Bator, Marta Sekielska-Domanowska, Roman Makarewicz, Andrzej Marszałek, Łukasz Szylberg, Magdalena Bodnar
Pharmaceuticals.2024; 17(10): 1304. CrossRef
Modulation of hypoxia-inducible factor-1 signaling pathways in cancer angiogenesis, invasion, and metastasis by natural compounds: a comprehensive and critical review
Sajad Fakhri, Seyed Zachariah Moradi, Farahnaz Faraji, Leila Kooshki, Kassidy Webber, Anupam Bishayee
Cancer and Metastasis Reviews.2024; 43(1): 501. CrossRef
Claudins in Cancer: A Current and Future Therapeutic Target
Caroline Hana, Nyein Nyein Thaw Dar, Michael Galo Venegas, Michel Vulfovich
International Journal of Molecular Sciences.2024; 25(9): 4634. CrossRef
Probiotic-Derived Bioactive Compounds in Colorectal Cancer Treatment
Christina Thoda, Maria Touraki
Microorganisms.2023; 11(8): 1898. CrossRef
Microbiota-Derived Natural Products Targeting Cancer Stem Cells: Inside the Gut Pharma Factory
Valentina Artusa, Luana Calabrone, Lorenzo Mortara, Francesco Peri, Antonino Bruno
International Journal of Molecular Sciences.2023; 24(5): 4997. CrossRef
Lactobacillus rhamnosus GG ameliorates radiation-induced lung fibrosis via lncRNASNHG17/PTBP1/NICD axis modulation
Zhao Ju, Huiji Pan, Can Qu, Liang Xiao, Meiling Zhou, Yin Wang, Jinhua Luo, Liangfang Shen, Pingkun Zhou, Ruixue Huang
Biology Direct.2023;[Epub] CrossRef
Gut microbiota in colorectal cancer development and therapy
Chi Chun Wong, Jun Yu
Nature Reviews Clinical Oncology.2023; 20(7): 429. CrossRef
Mechanisms by which the intestinal microbiota affects gastrointestinal tumours and therapeutic effects
Jikai He, Haijun Li, Jiaqi Jia, Yang Liu, Ning Zhang, Rumeng Wang, Wenhao Qu, Yanqi Liu, Lizhou Jia
Molecular Biomedicine.2023;[Epub] CrossRef
Role of lactobacillus strains in the management of colorectal cancer: An overview of recent advances
Elnaz Ghorbani, Amir Avan, Mikhail Ryzhikov, Gordon Ferns, Majid Khazaei, Saman Soleimanpour
Nutrition.2022; 103-104: 111828. CrossRef
Patient-Derived Organoid Model in the Prediction of Chemotherapeutic Drug Response in Colorectal Cancer
Minglu Hao, Zhipeng Cao, Zhiwei Wang, Jianjun Xin, Biao Kong, Jing Xu, Lei Zhang, Pu Chen
ACS Biomaterials Science & Engineering.2022; 8(8): 3515. CrossRef
The beneficial effects of Lacticaseibacillus casei on the small intestine and colon of Swiss mice against the deleterious effects of 5-fluorouracil
Stphannie Jamyla de Araújo Barbosa, Maisie Mitchele Barbosa Oliveira, Susana Barbosa Ribeiro, Caroline Addison Carvalho Xavier de Medeiros, Maria Laura de Souza Lima, Gerlane Coelho Bernardo Guerra, Raimundo Fernandes de Araújo Júnior, Francisco Caninde d
Frontiers in Immunology.2022;[Epub] CrossRef
Lactobacillus plantarum-derived metabolites sensitize the tumor-suppressive effects of butyrate by regulating the functional expression of SMCT1 in 5-FU-resistant colorectal cancer cells
Hye-Ju Kim, JaeJin An, Eun-Mi Ha
Journal of Microbiology.2022; 60(1): 100. CrossRef
Extracellular vesicles derived from Lactobacillus plantarum restore chemosensitivity through the PDK2-mediated glucose metabolic pathway in 5-FU-resistant colorectal cancer cells
JaeJin An, Eun-Mi Ha
Journal of Microbiology.2022; 60(7): 735. CrossRef
Therapeutic applications and biological activities of bacterial bioactive extracts
Zainab Abdelghani, Nancy Hourani, Zahraa Zaidan, Ghassan Dbaibo, Marguerite Mrad, Rouba Hage-Sleiman
Archives of Microbiology.2021; 203(8): 4755. CrossRef
Active Enhancer Assessment by H3K27ac ChIP-seq Reveals Claudin-1 as a Biomarker for Radiation Resistance in Colorectal Cancer
Zu-Xuan Chen, He-Qing Huang, Jia-Ying Wen, Li-Sha Qin, Yao-Dong Song, Ye-Ying Fang, Da-Tong Zeng, Wei-Jian Huang, Xin-Gan Qin, Ting-Qing Gan, Jie Luo, Jian-Jun Li
Dose-Response.2021;[Epub] CrossRef
GABA-producing Lactobacillus plantarum inhibits metastatic properties and induces apoptosis of 5-FU-resistant colorectal cancer cells via GABAB receptor signaling
JaeJin An, Heon Seok, Eun-Mi Ha
Journal of Microbiology.2021; 59(2): 202. CrossRef

First
Prev
Page of 1
Next
Last

Previous issues