Journal of Microbiology

Volume 56(12); December 2018

Review

[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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31 Citations

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.

Journal Articles

Zunongwangia flava sp. nov., belonging to the family Flavobacteriaceae, isolated from Salicornia europaea: Eui-Sang Cho , In-Tae Cha , Hak-Jong Choi , Seong Woon Roh , Young-Do Nam , Sung Man Seo , Myung-Ji Seo; J. Microbiol. 2018;56(12):868-873. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8231-z

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Abstract: A yellow pigmented bacterium designated strain MBLN094T within the family Flavobacteriaceae was isolated from a halophyte Salicornia europaea on the coast of the Yellow Sea. This strain was a Gram-stain negative, aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain MBLN094T was found to be related to the genus Zunongwangia, exhibiting 16S rRNA gene sequence similarity values of 97.0, 96.8, 96.4, and 96.3% to Zunongwangia mangrovi P2E16T, Z. profunda SM-A87T, Z. atlantica 22II14-10F7T, and Z. endophytica CPA58T, respectively. Strain MBLN094T grew at 20‒37°C (optimum, 25‒ 30°C), at pH 6.0‒10.0 (optimum, 7.0‒8.0), and with 0.5‒15.0% (w/v) NaCl (optimum, 2.0‒5.0%). Menaquinone MK-6 was the sole respiratory quinone. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, and four unidentified lipids. Major fatty acids were iso-C17:0 3-OH, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), and iso-C15:0. The genomic DNA G + C content was 37.4 mol%. Based on these polyphasic taxonomic data, strain MBLN094T is considered to represent a novel species of the genus Zunongwangia, for which the name Zunongwangia flava sp. nov. is proposed. The type strain is MBLN094T (= KCTC 62279T = JCM 32262T).

Paenibacillus seodonensis sp. nov., isolated from a plant of the genus Campanula: Myung-Suk Kang , Ki-Eun Lee , Eun-Young Lee , Soo-Je Park; J. Microbiol. 2018;56(12):874-879. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8455-y

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Abstract: Strain DCT-19T, representing a Gram-stain-positive, rodshaped, aerobic bacterium, was isolated from a native plant belonging to the genus Campanula on Dokdo, the Republic of Korea. Comparative analysis of the 16S rRNA gene sequence showed that this strain was closely related to Paenibacillus amylolyticus NRRL NRS-290T (98.6%, 16S rRNA gene sequence similarity), Paenibacillus tundrae A10bT (98.1%), and Paenibacillus xylanexedens NRRL B-51090T (97.6%). DNADNA hybridization indicated that this strain had relatively low levels of DNA-DNA relatedness with P. amylolyticus NRRL NRS-290T (30.0%), P. xylanexedens NRRL B-51090T (29.0%), and P. tundrae A10bT (24.5%). Additionally, the genomic DNA G + C content of DCT-19T was 44.8%. The isolated strain grew at pH 6.0–8.0 (optimum, pH 7.0), 0–4% (w/v) NaCl (optimum, 0%), and a temperature of 15–45°C (optimum 25–30°C). The sole respiratory quinone in the strain was menaquinone-7, and the predominant fatty acids were C15:0 anteiso, C16:0 iso, and C16:0. In addition, the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. Based on its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain DCT-19T is proposed as a novel species in the genus Paenibacillus, for which the name Paenibacillus seodonensis sp. nov. is proposed (=KCTC 43009T =LMG 30888T). The type strain of Paenibacillus seodonensis is DCT-19T.

Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi: Ja-Young Jang , Young Joon Oh , Seul Ki Lim , Hyo Kyeong Park , Changsu Lee , Joon Yong Kim , Mi-Ai Lee , Hak-Jong Choi; J. Microbiol. 2018;56(12):880-885. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8518-0

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Abstract: A moderately halophilic and alkalitolerant bacterial strain NKC1-1T was isolated from commercial kimchi in Korea. Strain NKC1-1T was Gram-stain-positive, aerobic, rod-shaped, non-motile, and contained diaminopimelic acid-type murein. Cell growth was observed in a medium containing 0–25% (w/v) NaCl (optimal at 10% [w/v]), at 20–40°C (optimal at 37°C) and pH 6.5–10.0 (optimal at pH 9.0). The major isoprenoid quinone of the isolate was menaquinone-7, and the major polar lipids were phosphatidylglycerol and unidentified phospholipids. Cell membrane of the strain contained iso-C17:0 and anteiso-C15:0 as the major fatty acids. Its DNA G + C content was 45.2 mol%. Phylogenetic analysis indicated the strain to be most closely related to Geomicrobium halophilum with 92.7–92.9% 16S rRNA gene sequence similarity. Based on polyphasic taxonomic evaluation with phenotypic, phylogenetic, and chemotaxonomic analyses, the strain represents a novel species in a new genus, for which the name Salicibibacter kimchii gen. nov., sp. nov. is proposed (= CECT 9537T; KCCM 43276T).

Comparative analysis of the gut microbiota in distinct statin response patients in East China: Baoqing Sun , Luming Li , Xinfu Zhou; J. Microbiol. 2018;56(12):886-892. Published online November 27, 2018; DOI: https://doi.org/10.1007/s12275-018-8152-x

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26 Citations

Abstract: Statin response shows great interindividual variations. Recently, emerging studies have shown that gut microbiota is linked to therapeutic responses to drugs, including statins. However, the association between the gut bacteria composition and statin response is still unclear. In this study, gut microbiota of 202 hyperlipidemic patients with statin sensitive (SS) response and statin resistant (SR) response in East China were investigated by high throughput sequencing to compare the gut bacteria composition and biodiversity in distinct statin response patients. Higher biodiversity was detected in Group SS than Group SR. Specifically, group SS showed significantly increased proportion of genera Lactobacillus (P = 0.001), Eubacterium (P = 0.004), Faecalibacterium (P = 0.005), and Bifidobacterium (P = 0.002) and decreased proportion of genus Clostridium (P = 0.001) compared to Group SR. The results indicated that higher gut biodiversity was associated with statin sensitive response. The increased genera Lactobacillus, Eubacterium, Faecalibacterium, Bifidobacterium, and decreased genus Clostridium in patient gut microbiota may predict patient's statin response, and hence may guide statin dosage adjustments.

Characterization of the velvet regulators in Aspergillus flavus: Tae-Jin Eom , Heungyun Moon , Jae-Hyuk Yu , Hee-Soo Park; J. Microbiol. 2018;56(12):893-901. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8417-4

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Abstract: Fungal development and secondary metabolism are closely associated via the activities of the fungal NK-kB-type velvet regulators that are highly conserved in filamentous fungi. Here, we investigated the roles of the velvet genes in the aflatoxigenic fungus Aspergillus flavus. Distinct from other Aspergillus species, the A. flavus genome contains five velvet genes, veA, velB, velC, velD, and vosA. The deletion of velD blocks the production of aflatoxin B1, but does not affect the formation of sclerotia. Expression analyses revealed that vosA and velB mRNAs accumulated at high levels during the late phase of asexual development and in conidia. The absence of vosA or velB decreased the content of conidial trehalose and the tolerance of conidia to the thermal and UV stresses. In addition, double mutant analyses demonstrated that VosA and VelB play an inter-dependent role in trehalose biosynthesis and conidial stress tolerance. Together with the findings of previous studies, the results of the present study suggest that the velvet regulators play the conserved and vital role in sporogenesis, conidial trehalose biogenesis, stress tolerance, and aflatoxin biosynthesis in A. flavus.

Antibiofilm effect of biofilm-dispersing agents on clinical isolates of Pseudomonas aeruginosa with various biofilm structures: Soo-Kyoung Kim , Xi-Hui Li , Hyeon-Ji Hwang , Joon-Hee Lee; J. Microbiol. 2018;56(12):902-909. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8336-4

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Abstract: Pseudomonas aeruginosa, an opportunistic human pathogen, causes many biofilm-mediated chronic infections. In this study, biofilm structures of various clinical strains of P. aeruginosa isolated from hospitalized patients were examined and their influence on the biofilm-dispersing effects of chemicals was investigated. The clinical isolates formed structurally distinct biofilms that could be classified into three different groups: 1) mushroom-like, 2) thin flat, and 3) thick flat structures. A dispersion of these differently structured biofilms was induced using two biofilm-dispersing agents, anthranilate and sodium nitroprusside (SNP). Although both SNP and anthranilate could disperse all types of biofilms, the thick flat biofilms were dispersed less efficiently than the biofilms of other structures. This suggests that biofilm-dispersing agents have higher potency on the biofilms of porous structures than on densely packed biofilms.

Water-based extracts of Zizania latifolia inhibit Staphylococcus aureus infection through the induction of human beta-defensin 2 expression in HaCaT cells: Bo Yeon Kang , Seung-Su Lee , Myun-Ho Bang , Hyoik Jeon , Hangeun Kim , Dae Kyun Chung; J. Microbiol. 2018;56(12):910-916. Published online November 27, 2018; DOI: https://doi.org/10.1007/s12275-018-8307-9

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Abstract: Zizania latifolia is a perennial herb belonging to the family Gramineae that has been used as a health food in Asian countries. In this study, we investigated the antimicrobial effect of Z. latifolia, which increased human beta-defensin 2 (hBD2) expression in HaCaT cells. hBD2 expression was further increased in cells treated with Z. latifolia extracts and subsequently infected with Staphylococcus aureus. Inversely, S. aureus infection decreased after treatment. The induction of hBD2 in HaCaT cells was mediated by the Toll-like receptor 2 (TLR2) signaling pathway, including the activation of extracellular signal-regulated kinase (ERK) and activator protein 1 (AP-1). Further study using siRNA revealed that hBD2 played an important role in the inhibition of S. aureus infection in HaCaT cells. Our data suggest that Z. latifolia extracts can be used as an antimicrobial ingredient for skin treatment formulas.

Characterization of a Salmonella Enteritidis bacteriophage showing broad lytic activity against Gram-negative enteric bacteria: Shukho Kim , Sung-Hun Kim , Marzia Rahman , Jungmin Kim; J. Microbiol. 2018;56(12):917-925. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8310-1

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24 Citations

Abstract: In this study, we sought to isolate Salmonella Enteritidis-specific lytic bacteriophages (phages), and we found a lytic phage that could lyse not only S. Enteritidis but also other Gramnegative foodborne pathogens. This lytic phage, SS3e, could lyse almost all tested Salmonella enterica serovars as well as other enteric pathogenic bacteria including Escherichia coli, Shigella sonnei, Enterobacter cloacae, and Serratia marcescens. This SS3e phage has an icosahedral head and a long tail, indicating belong to the Siphoviridae. The genome was 40,793 base pairs, containing 58 theoretically determined open reading frames (ORFs). Among the 58 ORFs, ORF49, and ORF25 showed high sequence similarity with tail spike protein and lysozyme-like protein of Salmonella phage SE2, respectively, which are critical proteins recognizing and lysing host bacteria. Unlike SE2 phage whose host restricted to Salmonella enterica serovars Enteritidis and Gallinarum, SS3e showed broader host specificity against Gram-negative enteric bacteria; thus, it could be a promising candidate for the phage utilization against various Gram-negative bacterial infection including foodborne pathogens.

Prevalence of human Norovirus by genotype in contaminated groundwater in Korea over the last decade (2007–2016): Siwon Lee , Junhyeong Jang , Kyungseon Bae , Wonseok Lee , Hyenmi Chung , Sangjung Park; J. Microbiol. 2018;56(12):926-931. Published online November 27, 2018; DOI: https://doi.org/10.1007/s12275-018-8340-8

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Abstract: This study investigated the occurrence of human Norovirus (HuNoV) by genotype in 1,486 groundwater samples collected from 843 groundwater wells suspected of contamination during 2007–2016, in South Korea. We identified and genotyped 186 HuNoV sequences in 178 HuNoV-positive samples using the RIVM-NoroNet norovirus genotyping tool (NGT) and phylogenetic tree analysis based on RIVM-NoroNet reference sequences. HuNoV GII was more prevalent than GI. The major genotypes detected were HuNoV GII.4 (43.0%), GII.22 (15.6%), GI.5 (10.2%), and GI.1 (8.6%); several genotypes accounted for < 5.0% of all HuNoVs, including GII.17, GI.6, GI.4, GII.6, GI.8, GII.3, GII.13, GI.3, GI.7, GI.2, GI.9, GII.1, GII.8, and GII.10. The prevalence of HuNoVs and number of genotypes detected has drastically decreased over the last decade. HuNoV GII.17, the emerging genotype worldwide including Europe and Asia, appeared in Korean groundwater from 2010, dominated in 2013–2014, and continued to be observed. HuNoV GII.4, the major type occurred last decade from Korean groundwater except 2013–2014, continued to be detected and prevalent similar to HuNoV GII.17 in 2016.

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