Journal of Microbiology

Journal Articles

Chemokine CCL6 Plays Key Role in the Inhibitory Effect of Vitamin A on Norovirus Infection: Heetae Lee , Giljae Lee , You-Hee Cho , Youngcheon Song , GwangPyo Ko; J. Microbiol. 2023;61(5):579-587. Published online May 26, 2023; DOI: https://doi.org/10.1007/s12275-023-00047-3

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Abstract: Norovirus (NoV) is the most common viral cause of acute gastroenteritis worldwide. Vitamin A has demonstrated the potential to protect against gastrointestinal infections. However, the effects of vitamin A on human norovirus (HuNoV) infections remain poorly understood. This study aimed to investigate how vitamin A administration affects NoV replication. We demonstrated that treatment with retinol or retinoic acid (RA) inhibited NoV replication in vitro based on their effects on HuNoV replicon-bearing cells and murine norovirus-1 (MNV-1) replication in murine cells. MNV replication in vitro showed significant transcriptomic changes, which were partially reversed by retinol treatment. RNAi knockdown of CCL6, a chemokine gene that was downregulated by MNV infection but upregulated by retinol administration, resulted in increased MNV replication in vitro. This suggested a role of CCL6 in the host response to MNV infections. Similar gene expression patterns were observed in the murine intestine after oral administration of RA and/or MNV-1.CW1. CCL6 directly decreased HuNoV replication in HG23 cells, and might indirectly regulate the immune response against NoV infection. Finally, relative replication levels of MNV-1.CW1 and MNV-1.CR6 were significantly increased in CCL6 knockout RAW 264.7 cells. This study is the first to comprehensively profile transcriptomes in response to NoV infection and vitamin A treatment in vitro, and thus may provide new insights into dietary prophylaxis and NoV infections.

The type II histidine triad protein HtpsC facilitates invasion of epithelial cells by highly virulent Streptococcus suis serotype 2: Yunjun Lu , Shu Li , Xiaodong Shen , Yan Zhao , Dongming Zhou , Dan Hu , Xushen Cai , Lixia Lu , Xiaohui Xiong , Ming Li , Min Cao; J. Microbiol. 2021;59(10):949-957. Published online September 7, 2021; DOI: https://doi.org/10.1007/s12275-021-1129-1

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Streptococcus suis serotype 2 (S. suis 2) is an important zoonotic pathogen that presents a significant threat both to pigs and to workers in the pork industry. The initial steps of S. suis 2 pathogenesis are unclear. In this study, we found that the type II histidine triad protein HtpsC from the highly virulent Chinese isolate 05ZYH33 is structurally similar to internalin A (InlA) from Listeria monocytogenes, which plays an important role in mediating listerial invasion of epithelial cells. To determine if HtpsC and InlA function similarly, an isogenic htpsC mutant (ΔhtpsC) was generated in S. suis by homologous recombination. The htpsC deletion strain exhibited a diminished ability to adhere to and invade epithelial cells from different sources. Double immunofluorescence microscopy also revealed reduced survival of the ΔhtpsC mutant after cocultivation with epithelium. Adhesion to epithelium and invasion by the wild type strain was inhibited by a monoclonal antibody against E-cadherin. In contrast, the htpsC-deficient mutant was unaffected by the same treatment, suggesting that E-cadherin is the host-cell receptor that interacts with HtpsC and facilitates bacterial internalization. Based on these results, we propose that HtpsC is involved in the process by which S. suis 2 penetrates host epithelial cells, and that this protein is an important virulence factor associated with cell adhesion and invasion.

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Genomic and phenotypic analysis of invasive Streptococcus suis isolated in Spain reveals genetic diversification and associated virulence traits
Cristina Uruén, Ana Fernandez, José Luis Arnal, Mateo del Pozo, Maria Casas Amoribieta, Ignacio de Blas, Paula Jurado, Jorge Hugo Calvo, Marcelo Gottschalk, Luis Daniel González-Vázquez, Miguel Arenas, Clara M. Marín, Jesús Arenas
Veterinary Research.2024;[Epub] CrossRef
A rapid colloidal gold immunochromatographic assay based on polyclonal antibodies against HtpsC protein for the detection of Streptococcus suis
Yawei Lu, Sibo Wang, Xushen Cai, Min Cao, Qingyu Lu, Dan Hu, Qiong Chen, Xiaohui Xiong
Frontiers in Microbiology.2023;[Epub] CrossRef

Review

Omics in gut microbiome analysis: Tae Woong Whon , Na-Ri Shin , Joon Yong Kim , Seong Woon Roh; J. Microbiol. 2021;59(3):292-297. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1004-0

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Abstract

Our understanding of the interactions between microbial communities and their niche in the host gut has improved owing to recent advances in environmental microbial genomics. Integration of metagenomic and metataxonomic sequencing data with other omics data to study the gut microbiome has become increasingly common, but downstream analysis after data integration and interpretation of complex omics data remain challenging. Here, we review studies that have explored the gut microbiome signature using omics approaches, including metagenomics, metataxonomics, metatranscriptomics, and metabolomics. We further discuss recent analytics programs to analyze and integrate multi-omics datasets and further utilization of omics data with other advanced techniques, such as adaptive immune receptor repertoire sequencing, microbial culturomics, and machine learning, to evaluate important microbiome characteristics in the gut.

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Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery
Hye Seon Song, Yeon Bee Kim, Joon Yong Kim, Seong Woon Roh, Tae Woong Whon
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Deciphering the microbial map and its implications in the therapeutics of neurodegenerative disorder
Shrutikirti Vashishth, Rashmi K. Ambasta, Pravir Kumar
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Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology
Parul Mehra, Anil Kumar
Cell Biochemistry and Function.2024;[Epub] CrossRef
Gut microbiota and metabolic modulation by supplementation of polysaccharide-producing Bacillus licheniformis from Tibetan Yaks: A comprehensive multi-omics analysis
Zhibo Zeng, Chuxian Quan, Shimeng Zhou, Saisai Gong, Mudassar Iqbal, Muhammad Fakhar-e-Alam Kulyar, Shah Nawaz, Kewei Li, Jiakui Li
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In-Young Chung, Jihyun Kim, Ara Koh
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Deciphering the gut microbiome: The revolution of artificial intelligence in microbiota analysis and intervention
Mohammad Abavisani, Alireza Khoshrou, Sobhan Karbas Foroushan, Negar Ebadpour, Amirhossein Sahebkar
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Should Routine Diagnostics Implement Gut Microbiota Analysis?
Giuseppe Guido Maria Scarlata, Ludovico Abenavoli
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Microbiome and pancreatic cancer: time to think about chemotherapy
Juliana de Castilhos, Katharina Tillmanns, Jana Blessing, Arnelyn Laraño, Vadim Borisov, Christoph K. Stein-Thoeringer
Gut Microbes.2024;[Epub] CrossRef
Microbiota in Irritable Bowel Syndrome and Endometriosis: Birds of a Feather Flock Together—A Review
Noemi Salmeri, Emanuele Sinagra, Carolina Dolci, Giovanni Buzzaccarini, Giulio Sozzi, Miriam Sutera, Massimo Candiani, Federica Ungaro, Luca Massimino, Silvio Danese, Francesco Vito Mandarino
Microorganisms.2023; 11(8): 2089. CrossRef
Revelation of the sciences of traditional foods
Zhen Jia, Boce Zhang, Arnav Sharma, Nathalie S. Kim, Sonia M. Purohit, Madison M. Green, Michelle R. Roche, Emma Holliday, Hongda Chen
Food Control.2023; 145: 109392. CrossRef
The gut microbiota: A new perspective for tertiary prevention of hepatobiliary and gallbladder diseases
Xiaoyu Huang, Yi Yang, Xueli Li, Xiaoya Zhu, Dan Lin, Yueran Ma, Min Zhou, Xiangyi Cui, Bingyu Zhang, Dongmei Dang, Yuhong Lü, Changwu Yue
Frontiers in Nutrition.2023;[Epub] CrossRef
Environmental factors and gut microbiota: Toward better conservation of deer species
Yu Wang, Bo Xu, Huan Chen, Fang Yang, Jinlin Huang, Xin’an Jiao, Yunzeng Zhang
Frontiers in Microbiology.2023;[Epub] CrossRef
Potential role of gut microbes in the efficacy and toxicity of immune checkpoints inhibitors
Jingxin Ma, Qi Wei, Xin Cheng, Jie Zhang, Zhongtao Zhang, Jianrong Su
Frontiers in Pharmacology.2023;[Epub] CrossRef
Microbiota-Gut-Brain Axis in Neurological Disorders: From Leaky Barriers Microanatomical Changes to Biochemical Processes
Irene Neri, Elisa Boschetti, Matilde Yung Follo, Roberto De Giorgio, Lucio Ildebrando Cocco, Lucia Manzoli, Stefano Ratti
Mini-Reviews in Medicinal Chemistry.2023; 23(3): 307. CrossRef
Effects of microbial-derived biotics (meta/pharma/post-biotics) on the modulation of gut microbiome and metabolome; general aspects and emerging trends
Alireza Sadeghi, Maryam Ebrahimi, Mohammad Saeed Kharazmi, Seid Mahdi Jafari
Food Chemistry.2023; 411: 135478. CrossRef
Interkingdom interactions between Pseudomonas aeruginosa and Candida albicans affect clinical outcomes and antimicrobial responses
Lisa J Kahl, Nina Stremmel, M Alejandra Esparza-Mora, Rachel M Wheatley, R Craig MacLean, Markus Ralser
Current Opinion in Microbiology.2023; 75: 102368. CrossRef
Molecular Insights Into the Role of Gut Microbiota in Antibiotic Therapy Selection and Resistance Mitigation
Mihaela Andreescu
Cureus.2023;[Epub] CrossRef
Gut Microbiota Composition and Cardiovascular Disease: A Potential New Therapeutic Target?
Martina Belli, Lucy Barone, Susanna Longo, Francesca Romana Prandi, Dalgisio Lecis, Rocco Mollace, Davide Margonato, Saverio Muscoli, Domenico Sergi, Massimo Federici, Francesco Barillà
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Old Folks, Bad Boon: Antimicrobial Resistance in the Infant Gut Microbiome
Silvia Saturio, Alejandra Rey, Anna Samarra, Maria Carmen Collado, Marta Suárez, Laura Mantecón, Gonzalo Solís, Miguel Gueimonde, Silvia Arboleya
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A New Biomarker Profiling Strategy for Gut Microbiome Research: Valid Association of Metabolites to Metabolism of Microbiota Detected by Non-Targeted Metabolomics in Human Urine
Sijia Zheng, Lina Zhou, Miriam Hoene, Andreas Peter, Andreas L. Birkenfeld, Cora Weigert, Xinyu Liu, Xinjie Zhao, Guowang Xu, Rainer Lehmann
Metabolites.2023; 13(10): 1061. CrossRef
Causal discovery for the microbiome
Jukka Corander, William P Hanage, Johan Pensar
The Lancet Microbe.2022; 3(11): e881. CrossRef
Play the plug: How bacteria modify recognition by host receptors?
Suma Tiruvayipati, Dharjath S. Hameed, Niyaz Ahmed
Frontiers in Microbiology.2022;[Epub] CrossRef
Intestinal virome: An important research direction for alcoholic and nonalcoholic liver diseases
Yan Li, Wen-Cheng Liu, Bing Chang
World Journal of Gastroenterology.2022; 28(26): 3279. CrossRef
Regulator of RNase E activity modulates the pathogenicity of Salmonella Typhimurium
Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
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Long-term high loading intensity of aerobic exercise improves skeletal muscle performance via the gut microbiota-testosterone axis
Lidong Zhang, Hedong Lang, Li Ran, Guoliang Tian, Hui Shen, Jundong Zhu, Qianyong Zhang, Long Yi, Mantian Mi
Frontiers in Microbiology.2022;[Epub] CrossRef
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Jang-Cheon Cho
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Journal Articles

Parabacteroides chongii sp. nov., isolated from blood of a patient with peritonitis: Hyunsoo Kim , Wan-Taek Im , Myungsook Kim , Dokyun Kim , Young Hee Seo , Dongeun Yong , Seok Hoon Jeong , Kyungwon Lee; J. Microbiol. 2018;56(10):722-726. Published online September 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8122-3

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Abstract

An obligate anaerobic, Gram-reaction-negative, non-sporeforming, non-motile, rod shaped bacterium designated YMC B3181T was isolated from the blood of a patient with peritonitis. Strain B3181T grew at 20 to 40°C with optimum growth at 37°C. 16S rRNA gene sequence similarity showed strain B3181T belongs to the genus Parabacteroides and is closely related to Parabacteroides faecis 157T (97.3%), Parabacteroides gordonii MS-1T (96.6%), and Parabacteroides goldsteinii DSM 19448T (95.7%). The G + C content of the genomic DNA was 42.3 mol%. The major cellular fatty acids were anteiso- C15:0 and iso-C17:0 3-OH, and the predominant respiratory quinones were MK-9 and MK-10 menaquinones. Genomic and chemotaxonomic data supported affiliation of B3181T with the genus Parabacteroides. Strain B3181T was phylogenetically and phenotypically different from recognized species of the genus Parabacteroides. Accordingly, this isolate belongs to a novel species for which the name Parabacteroides chongii sp. nov. (type strain YMC B3181T = LMG 30065T = KACC 19034T) is proposed.

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Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina
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Bacteroides sedimenti sp. nov., isolated from a chloroethenesdechlorinating consortium enriched from river sediment: Mohamed Ismaeil , Naoko Yoshida , Arata Katayama; J. Microbiol. 2018;56(9):619-627. Published online August 23, 2018; DOI: https://doi.org/10.1007/s12275-018-8187-z

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Abstract

A Gram-negative, anaerobic, non-motile, non-spore-forming bacterial strain, designated YN3PY1T, was isolated from a chloroethene-dechlorinating consortium originally enriched from river sediment. The strain enhanced the dechlorination of cis-dichloroethene to ethene by Dehalococcoides, especially at the early stages of cultivation. Strain YN3PY1T was the first isolate of the genus Bacteroides, obtained from animal- independent environments, and its 16S rRNA gene had the highest sequence similarity (97.1%) with Bacteroides luti JCM 19020T in the ‘Coprosuis’ clade of the genus Bacteroides. Strain YN3PY1T formed a phylogenetic cluster with other phylotypes detected from sediments and paddy soil, and the cluster was affiliated with a linage of so-called free-living Bacteroides detected from animal-independent environments, suggesting specific adaptations to sediment-like environments. The strain showed typical phenotypes of Bacteroides, i.e., polysaccharolytic anaerobe having anteiso-C15:0 as the most abundant fatty acid and MK-11 as one of the major respiratory quinones. Additionally, the strain uniquely transforms glucose to lactate and malate, has MK-12 as another major respiratory quinone, and grows at comparatively low temperatures, i.e. 10–40°C, with an optimum at 28°C. Based on the presented data, strain YN3PY1T (= KCTC 15656T = NBRC 113168T) can be proposed as a novel species of the genus Bacteroides and named as Bacteroides sedimenti sp. nov.

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Yunho Lee, Sang Eun Jeong, Moonsuk Hur, Sunghwan Ko, Che Ok Jeon
Frontiers in Microbiology.2018;[Epub] CrossRef

Bile salt hydrolase-mediated inhibitory effect of Bacteroides ovatus on growth of Clostridium difficile: Soobin Yoon , Junsun Yu , Andrea McDowell , Sung Ho Kim , Hyun Ju You , GwangPyo Ko; J. Microbiol. 2017;55(11):892-899. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7340-4

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Abstract

Clostridium difficile infection (CDI) is one of the most common nosocomial infections. Dysbiosis of the gut microbiota due to consumption of antibiotics is a major contributor to CDI. Recently, fecal microbiota transplantation (FMT) has been applied to treat CDI. However, FMT has important limitations including uncontrolled exposure to pathogens and standardization issues. Therefore, it is necessary to evaluate alternative treatment methods, such as bacteriotherapy, as well as the mechanism through which beneficial bacteria inhibit the growth of C. difficile. Here, we report bile acid-mediated inhibition of C. difficile by Bacteroides strains which can produce bile salt hydrolase (BSH). Bacteroides strains are not commonly used to treat CDI; however, as they comprise a large proportion of the intestinal microbiota, they can contribute to bile acid-mediated inhibition of C. difficile. The inhibitory effect on C. difficile growth increased with increasing bile acid concentration in the presence of Bacteroides ovatus SNUG 40239. Furthermore, this inhibitory effect on C. difficile growth was significantly attenuated when bile acid availability was reduced by cholestyramine, a bile acid sequestrant. The findings of this study are important due to the discovery of a new bacterial strain that in the presence of available bile acids inhibits growth of C. difficile. These
results
will facilitate development of novel bacteriotherapy strategies to control CDI.

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Molecular Identification of Fecal Pollution Sources in Water Supplies by Host-Specific Fecal DNA Markers and Terminal Restriction Fragment Length Polymorphism Profiles of 16S rRNA Gene: Ju-Yong Jeong , Kyung-Ik Gil , Kyong-Hee Lee , Jong-Ok Ka; J. Microbiol. 2008;46(6):599-607. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0174-3

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Abstract: Specific fecal DNA markers were investigated for major pollution sources, cow, human, and pig, and occurrence of the identified markers was analyzed in river waters using Terminal Restriction Fragment Length Polymorphism (T-RFLP) techniques and sequencing of 16S rDNA of Bacteroides-Prevotella. The unique and specific DNA markers for cow and human were identified as a 222 bp and 60 bp peak in HaeIII T-RFLP profiles, respectively, and the pig-specific marker was not identified but the unique T-RFLP profile of pig could be used as a substitution. Human-specific marker was detected in most of the river waters tested (92.1%) and T-RFLP profiles of river waters were shown to be similar to those of human feces. Cluster analysis of T-RFLP data showed that the fecal sources were multiple (human plus cow and human plus dairy cow) in most of the river waters. The phylogenetic analysis for the clones recovered from the fecal and water samples showed that the clones from cow formed a discreet cluster from those of other sources. The other clones from human, pig, and river water formed two groups all together. The results of this study could be used to identify and control the fecal pollution source in the bodies of water in Korea.

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