Journal of Microbiology

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

Current status and perspectives on vaccine development against dengue virus infection: Jisang Park , Ju Kim , Yong-Suk Jang; J. Microbiol. 2022;60(3):247-254. Published online February 14, 2022; DOI: https://doi.org/10.1007/s12275-022-1625-y

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Abstract

Dengue virus (DENV) consists of four serotypes in the family Flaviviridae and is a causative agent of dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. DENV is transmitted by mosquitoes, Aedes aegypti and A. albopictus, and is mainly observed in areas where vector mosquitoes live. The number of dengue cases reported by the World Health Organization increased more than 8-fold over the last two decades from 505,430 in 2000 to over 2.4 million in 2010 to 5.2 million in 2019. Although vaccine is the most effective
method
against DENV, only one commercialized vaccine exists, and it cannot be administered to children under 9 years of age. Currently, many researchers are working to resolve the various problems hindering the development of effective dengue vaccines; understanding of the viral antigen configuration would provide insight into the development of effective vaccines against DENV infection. In this review, the current status and perspectives on effective vaccine development for DENV are examined. In addition, a plausible direction for effective vaccine development against DENV is suggested.

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Nanoparticle and virus-like particle vaccine approaches against SARS-CoV-2: Chulwoo Kim , Jae-Deog Kim , Sang-Uk Seo; J. Microbiol. 2022;60(3):335-346. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1608-z

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Abstract

The global spread of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has provoked an urgent need for prophylactic measures. Several innovative vaccine platforms have been introduced and billions of vaccine doses have been administered worldwide. To enable the creation of safer and more effective vaccines, additional platforms are under development. These include the use of nanoparticle (NP) and virus-like particle (VLP) technology. NP vaccines utilize self-assembling scaffold structures designed to load the entire spike protein or receptor-binding domain of SARS-CoV-2 in a trimeric configuration. In contrast, VLP vaccines are genetically modified recombinant viruses that are considered safe, as they are generally replication-defective. Furthermore, VLPs have indigenous immunogenic potential due to their microbial origin. Importantly, NP and VLP vaccines have shown stronger immunogenicity with greater protection by mimicking the physicochemical characteristics of SARS-CoV-2. The study of NPand VLP-based coronavirus vaccines will help ensure the development of rapid-response technology against SARS-CoV-2 variants and future coronavirus pandemics.

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Journal Articles

Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola: Yurim Bae , Sujin Lee , Kitae Kim , Hyun-Kwon Lee , Soon-Kyeong Kwon , Jihyun F. Kim; J. Microbiol. 2021;59(11):1010-1018. Published online November 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1452-6

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Abstract

The actinobacterial group is regarded as a reservoir of biologically active natural products and hydrolytic enzymes with the potential for biomedical and industrial applications. Here, we present the complete genome sequence of Isoptericola dokdonensis DS-3 isolated from soil in Dokdo, small islets in the East Sea of Korea. This actinomycete harbors a large number of genes encoding carbohydrate-degrading enzymes, and its activity to degrade carboxymethyl cellulose into glucose was experimentally evaluated. Since the genus Isoptericola was proposed after reclassification based on phylogenetic analysis, strains of Isoptericola have been continuously isolated from diverse environments and the importance of this genus in the ecosystem has been suggested by recent culturomic or metagenomic studies. The phylogenic relationships of the genus tended to be closer among strains that had been isolated from similar habitats. By analyzing the properties of published genome sequences of seven defined species in the genus, a large number of genes for carbohydrate hydrolysis and utilization, as well as several biosynthetic gene clusters for secondary metabolites, were identified. Genomic information of I. dokdonensis DS-3 together with comparative analysis of the genomes of Isoptericola provides insights into understanding this actinobacterial group with a potential for industrial applications.

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Yu Duan, Limei Chen, Longxue Ma, Farrukh Raza Amin, Yida Zhai, Guofu Chen, Demao Li
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Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments: Shengxiang Pei , Siwen Niu , Fuquan Xie , Wenjing Wang , Shuang Zhang , Gaiyun Zhang; J. Microbiol. 2021;59(10):898-910. Published online September 7, 2021; DOI: https://doi.org/10.1007/s12275-021-1235-0

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Abstract

During a study of the marine actinobacterial biodiversity, a large number of Brevibacterium strains were isolated. Of these, five that have relatively low 16S rRNA gene similarity (98.5– 99.3%) with validly published Brevibacterium species, were chosen to determine taxonomic positions. On the basis of 16S rRNA gene sequence analysis and BOX-PCR fingerprinting, strains o2T, YB235T, and WO024T were selected as representative strains. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly differentiated the three strains from each other and from their closest relatives, with values ranging from 82.8% to 91.5% for ANI and from 26.7% to 46.5% for dDDH that below the threshold for species delineation. Strains YB235T, WO024T, and o2T all exhibited strong and efficient decolorization activity in congo red (CR) dyes, moderate decolorization activity in toluidine blue (TB) dyes and poor decolorization in reactive blue (RB) dyes. Genes coding for peroxidases and laccases were identified and accounted for these strains’ ability to effectively oxidize a variety of dyes with different chemical structures. Mining of the whole genome for secondary metabolite biosynthesis gene clusters revealed the presence of gene clusters encoding for bacteriocin, ectoine, NRPS, siderophore, T3PKS, terpene, and thiopeptide. Based on the phylogenetic, genotypic and phenotypic data, strains o2T, YB235T and WO024T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2T = JCM 33844T = MCCC 1A09961T), Brevibacterium pigmenatum sp. nov. (type strain YB235T = JCM 33843T = MCCC 1A09842T) and Brevibacterium atlanticum sp. nov. (type strain WO024T = JCM 33846T = MCCC 1A16743T) are proposed.

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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
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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

Stenotrophomonas maltophilia outer membrane protein A induces epithelial cell apoptosis via mitochondrial pathways: Xin Wang , Yan Li , Xueping Tang , Xueyi Shang , Zunquan Zhao , Yongqiang Jiang , Yan Li; J. Microbiol. 2020;58(10):868-877. Published online September 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0235-9

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Abstract

Stenotrophomonas maltophilia (S. maltophilia) is a common opportunistic pathogen in intensive care units and causes infections most often after surgeries in immune-compromised patients such as those undergoing chemotherapy. Outer membrane protein A (OmpA) is the most abundant of the outer membrane proteins in S. maltophilia. Previous studies on OmpA usually focus on its interaction with the host cells and its role in vaccine development. However, the impact of OmpA on the virulence of S. maltophilia to host cells and the effects on apoptosis remain unclear. In this study, we exposed purified recombinant S. maltophilia OmpA (rOmpA) to HEp-2 cells and investigated the effects of OmpA on epithelial cell apoptosis. Morphologic and flow cytometric analyses revealed that HEp-2 cells stimulated with rOmpA multiple apoptosis features, including nuclear roundness and pyknosis, chromatin aggregation, and phosphatidylserine eversion. We found that rOmpA regulated the protein levels of Bax and Bcl-xL in HEp-2 cells, leading to changes in mitochondria permeability and the release of cytochrome c and apoptosis-inducing factors into the cytoplasm. These subsequently activate the caspase-9/caspase-3 pathway that promote apoptosis. We also observed that rOmpA enhanced the generation of reactive oxygen species and increased intracellular Ca2+ levels in HEp-2 cells. Collectively, our data suggested that rOmpA induced epithelial cells apoptosis via mitochondrial pathways.

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Comparative genomics of Lactobacillus species as bee symbionts and description of Lactobacillus bombintestini sp. nov., isolated from the gut of Bombus ignitus: Jun Heo , Soo-Jin Kim , Jeong-Seon Kim , Seung-Beom Hong , Soon-Wo Kwon; J. Microbiol. 2020;58(6):445-455. Published online March 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9596-3

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Abstract

The Lactobacillus genus is widely used for fermentation of plant materials and dairy products. These species are typically found in highly specialized environments, with the bee gut serving as one of the niche locations in which Lactobacillus is detected. Lactobacillus species isolated from the bee gut and bee-related habitats were phylogenetically classified into three distinct groups, Lactobacillus kunkeei, Firm-4, and Firm-5. The L. kunkeei group was clearly differentiated from other members of the Lactobacillus buchneri group isolated from non-bee habitats. In comparison with non-bee members of the L. buchneri group, three bee-symbiotic Lactobacillus groups had a small-sized genome with low G + C content and showed a sharp reduction in the number of genes involved in energy production, carbohydrate transport and metabolism, and amino acid transport and metabolism. In addition, all three groups lacked the mutY gene, which encodes A/G-specific adenine glycosylase. The phylogenetic dendrogram based on the presence or absence of 1,199 functional genes indicated that these bee-symbiotic groups experienced convergent evolution. The occurrence of convergent evolution is thought to stem from the three bee-symbiotic groups sharing a similar habitat, i.e., the bee gut. The causative factor underlying genomic reduction was postulated to be mutY, which was absent in all three groups. Here, a novel strain, BHWM-4T, isolated from the gut of Bombus ignites was studied using polyphasic taxonomy and classified as a new member of the L. kunkeei group. The strain was Gram-positive, facultative anaerobic, and rod-shaped. The 16S ribosomal RNA gene sequence and genome analysis revealed that strain BHWM-4T was clustered into the L. kunkeei group, forming a compact cluster with L. kunkeei and Lactobacillus apinorum. Biochemical, chemotaxonomic, and genotypic data of strain BHWM-4T supports the proposal of a novel species, Lactobacillus bombintestini sp. nov., whose type strain is BHWM-4T (= KACC 19317T = NBRC 113067T).

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Reviews

[MINIREVIEW] Modulation of gut microbiome in nonalcoholic fatty liver disease: pro-, pre-, syn-, and antibiotics: Min Seok Cho , Sang Yeol Kim , Ki Tae Suk , Byung-Yong Kim; J. Microbiol. 2018;56(12):855-867. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8346-2

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Abstract

Nonalcoholic fatty liver disease (NAFLD) is one of the most common types of liver diseases worldwide and its incidence continues to increase. NAFLD occurs when the body can no longer effectively store excess energy in the adipose tissue. Despite the increasing prevalence of NAFLD, making lifestyle changes, including increased exercise, is often an elusive goal for patients with NAFLD. The liver directly connects to the gut-gastrointestinal milieu via the portal vein, which are all part of the gut-liver axis. Therefore, the gut-microbiome and microbial products have been actively studied as likely key factors in NAFLD pathophysiology. Hence, dysbiosis of the gut microbiome and therapeutic manipulation of the gut-liver axis are being investigated. Novel therapeutic approaches for modulating gut microbiota through the administration of probiotics, prebiotics, synbiotics, and antibiotics have been proposed with numerous promising initial reports on the effectiveness and clinical applications of these approaches. This review delves into the current evidence on novel therapies that modulate gut microbiota and discusses ongoing clinical trials targeting the gut-liver axis for the management and prevention of NAFLD.

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[MINIREVIEW] Probiotics in human health and disease: from nutribiotics to pharmabiotics: Eun-Sook Lee , Eun-Ji Song , Young-Do Nam , So-Young Lee; J. Microbiol. 2018;56(11):773-782. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8293-y

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Abstract

Probiotics are the most useful tools for balancing the gut microbiota and thereby influencing human health and disease. Probiotics have a range of effects, from those on nutritional status to medical conditions throughout the body from the gut to non-intestinal body sites such as the brain and skin. Research interest in probiotics with nutritive claims (categorized as nutribiotics) has evolved into interest in therapeutic and pharmacological probiotics with health claims (pharmabiotics). The concept of pharmabiotics emerged only two decades ago, and the new categorization of probiotics to nutribiotics and pharmabiotics was recently suggested, which are under the different regulation depending on that they are food or drug. Information of the gut microbiome has been continuously accumulating, which will make possible the gut microbiome-based healthcare in the future, when nutribiotics show potential for maintaining health while pharmabiotics are effective therapeutic tools for human diseases. This review describes the current understanding in the conceptualization and classification of probiotics. Here, we reviewed probiotics as nutribiotics with nutritional functions and pharmabiotics with pharmaceutic functions in different diseases.

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REVIEW] Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease: Taekil Eom , Yong Sung Kim , Chang Hwan Choi , Michael J. Sadowsky , Tatsuya Unno; J. Microbiol. 2018;56(3):189-198. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8049-8

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Abstract

Inflammatory bowel disease (IBD) is a result of chronic inflammation caused, in some part, by dysbiosis of intestinal microbiota, mainly commensal bacteria. Gut dysbiosis can be caused by multiple factors, including abnormal immune responses which might be related to genetic susceptibility, infection, western dietary habits, and administration of antibiotics. Consequently, the disease itself is characterized as having multiple causes, etiologies, and severities. Recent studies have identified > 200 IBD risk loci in the host. It has been postulated that gut microbiota interact with these risk loci
result
ing in dysbiosis, and this subsequently leads to the development of IBD. Typical gut microbiota in IBD patients are characterized with decrease in species richness and many of the commensal, and beneficial, fecal bacteria such as Firmicutes and Bacteroidetes and an increase or bloom of Proteobacteria. However, at this time, cause and effect relationships have not been rigorously established. While treatments of IBD usually includes medications such as corticosteroids, 5-aminosalicylates, antibiotics, immunomodulators, and anti- TNF agents, restoration of gut dysbiosis seems to be a safer and more sustainable approach. Bacteriotherapies (now called microbiota therapies) and dietary interventions are effective way to modulate gut microbiota. In this review, we summarize factors involved in IBD and studies attempted to treat IBD with probiotics. We also discuss the potential use of microbiota therapies as one promising approach in treating IBD. As therapies based on the modulation of gut microbiota becomes more common, future studies should include individual gut microbiota differences to develop personalized therapy for IBD.

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REVIEW] Mind-altering with the gut: Modulation of the gut-brain axis with probiotics: Namhee Kim , Misun Yun , Young Joon Oh , Hak-Jong Choi; J. Microbiol. 2018;56(3):172-182. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8032-4

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Abstract

It is increasingly evident that bidirectional interactions exist among the gastrointestinal tract, the enteric nervous system, and the central nervous system. Recent preclinical and clinical trials have shown that gut microbiota plays an important role in these gut-brain interactions. Furthermore, alterations in gut microbiota composition may be associated with pathogenesis of various neurological disorders, including stress, autism, depression, Parkinson’s disease, and Alzheimer’s disease. Therefore, the concepts of the microbiota-gut-brain axis is emerging. Here, we review the role of gut microbiota in bidirectional interactions between the gut and the brain, including neural, immune-mediated, and metabolic mechanisms. We highlight recent advances in the understanding of probiotic modulation of neurological and neuropsychiatric disorders via the gut-brain axis.

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Journal Articles

Effects of heat-killed Lactobacillus plantarum against influenza viruses in mice: Sehee Park , Jin Il Kim , Joon-Yong Bae , Kirim Yoo , Hyunung Kim , In-Ho Kim , Man-Seong Park , Ilseob Lee; J. Microbiol. 2018;56(2):145-149. Published online February 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7411-1

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Abstract

The potential use of dietary measures to treat influenza can be an important alternative for those who lack access to influenza vaccines or antiviral drugs. Lactobacillus plantarum (Lp) is one of many lactic acid bacteria that grow in ‘kimchi’, an essential part of Korean meal, and several strains of Lp reportedly show protective effects against influenza. Using heat-killed Lp (nF1) isolated from kimchi, which is known for its immunomodulatory effects, we investigated whether regular oral intake of nF1 could influence the outcome of influenza virus infection in a mouse model. In a lethal challenge with influenza A (H1N1 and H3N2 subtypes) and influenza B (Yamagata lineage) viruses, daily oral administration of nF1 delayed the mean number of days to death of the infected mice and resulted in increased survival rates compared with those of the non-treated mice. Consistent with these observations, nF1 treatment also significantly reduced viral replication in the lungs of the infected mice. Taken together, our results might suggest the remedial potential of heatkilled Lactobacillus probiotics against influenza.

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Probiotic potential of novel Lactobacillus strains isolated from salted-fermented shrimp as antagonists for Vibrio parahaemolyticus: Bao Le , Seung Hwan Yang; J. Microbiol. 2018;56(2):138-144. Published online February 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7407-x

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Abstract

Lactobacillus strains have been considered good candidates as biological control agents for prevention or treatment of plant and animal infections. One L. plantarum strain FB003 and three strains (FB011, FB081, and FB110) which closed to L. sakei were isolated from fermented and salted shrimp and their abilities in inhibiting growth of Vibrio parahaemolyticus were characterized. These strains were selected as potential probiotics based on their oro-gastro-intestinal resistance, gut colonization, adhesion to Caco-2 cells, antimicrobial activities, antibiotic resistance, and safety aspects.
Results
of this study revealed that these isolates possessed high aggregation activities against pathogens in host intestines. Strain FB011 strain showed higher coaggregation and immunomodulatory activity in the gastro-intestinal tract than L. plantarum. These difference effects of Lactobacillus strains provide valuable information about using them to prevent Vibrio infections in the aquaculture industry.

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