Journal of Microbiology

Volume 56(11); November 2018

Review

[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.

Journal Articles

Roseovarius tibetensis sp. nov., a halophilic bacterium isolated from Lake LongmuCo on Tibetan Plateau: Hui-bin Lu , Xiao-feng Xue , Dorji Phurbu , Peng Xing , Qing-long Wu; J. Microbiol. 2018;56(11):783-789. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8178-0

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Abstract: Two Gram-stain negative halophilic strains, designated as LM2T and LM4, were isolated from Lake LongmuCo on Tibetan Plateau. These two strains were aerobic, catalaseand oxidase- positive, nonmotile and rod-shaped organisms. Phylogenetic analysis based on 16S rRNA gene sequences indicated that LM2T and LM4 belong to the genus Roseovarius, with Roseovarius tolerans EL-172T (97.3% and 97.4% 16S rRNA gene sequence similarity, respectively) and Roseovarius azorensis SSW084T (95.5% and 95.6% 16S rRNA gene sequence similarity, respectively) as their closest neighbors. Q-10 was the sole respiratory quinone of these two strains. The major fatty acids were C18:1 ω7c/C18:1 ω6c, C16:0, C19:0 cyclo ω8c, and 11-methyl C18:1 ω7c. The polar lipids included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phospholipid of unknown structure containing glucosamine, and unidentified aminolipid. The DNA G + C content was between 64.2 and 64.5 mol%. DNA-DNA hybridization showed 96.7% relatedness between LM2T and LM4, 24.9% relatedness between LM2T and R. tolerans EL-172T, and 36.3% relatedness between LM4 and R. tolerans EL-172T. Based on phylogenetic analysis, DNA-DNA hybridization, a range of physiological and biochemical characteristics, LM2T and LM4 belong to the same species and were clearly distinguished from the type strains of the genus Roseovarius. It was evident that LM2T and LM4 could be classified as a novel species of the genus Roseovarius, for which the name Roseovarius tibetensis sp. nov. is proposed. The type strain is LM2T (= CGMCC 1.16230T = KCTC 62028T).

Circular pellicles formed by Pseudomonas alkylphenolica KL28 are a sophisticated architecture principally designed by matrix substance: Myeong Mi Song , Yaligara Veeranagouda , Munkhtsatsral Ganzorig , Kyoung Lee; J. Microbiol. 2018;56(11):790-797. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8252-7

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Abstract: The colonization of liquid surfaces as floating biofilms or pellicles is a bacterial adaptation to optimally occupy the airliquid (A-L) niche. In aerobic heterotrophs, pellicle formation is beneficial for the utilization of O2 and nonpolar organic compounds. Pseudomonas alkylphenolica KL28, an alkylphenol degrader, forms flat circular pellicles that are 0.3– 0.5 mm in diameter. In this study, we first monitored the pellicle developmental patterns of multicellular organization from the initial settlement stage. The pellicles developed by clonal growth and mutants for flagella and pilus formation established normal pellicles. In contrast, the mutants of an epm gene cluster for biosynthesis of alginate-like polymer were incompetent in cell alignment for initial two-dimensional (2D) pellicle growth, suggesting the role of the Epm polymer as a structural scaffold for pellicle biofilms. Microscopic observation revealed that the initial 2D growth transited to multilayers by an accumulated self-produced extracellular polymeric substance that may exert a constraint force. Electron microscopy and confocal laser scanning microscopy revealed that the fully matured pellicle structures were densly packed with matrix-encased cells displaying distinct arrangements. The cells on the surface of the pellicle were relatively flat, and those inside were longitudinally cross-packed. The extracellular polysaccharide stained by Congo red was denser on the pellicle rim and a thin film was observed in the open spaces, indicative of its role in pellicle flotation. Our results demonstrate that P. alkylphenolica KL28 coordinately dictates the cell arrangements of pellicle biofilms by the controlled growth of constituent cells that accumulate extracellular polymeric substances.

Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation: Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha; J. Microbiol. 2018;56(11):798-804. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8372-0

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24 Citations

Abstract: The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.

Identification and heterologous reconstitution of a 5-alk(en)ylresorcinol synthase from endophytic fungus Shiraia sp. Slf14: Huiwen Yan , Lei Sun , Jinge Huang , Yixing Qiu , Fuchao Xu , Riming Yan , Du Zhu , Wei Wang , Jixun Zhan; J. Microbiol. 2018;56(11):805-812. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8278-x

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Abstract: A new type III polyketide synthase gene (Ssars) was discovered from the genome of Shiraia sp. Slf14, an endophytic fungal strain from Huperzia serrata. The intron-free gene was cloned from the cDNA and ligated to two expression vectors pET28a and YEpADH2p-URA3 for expression in Escherichia coli BL21(DE3) and Saccharomyces cerevisiae BJ5464, respectively. SsARS was efficiently expressed in E. coli BL21(DE3), leading to the synthesis of a series of polyketide products. Six major products were isolated from the engineered E. coli and characterized as 1,3-dihydroxyphenyl- 5-undecane, 1,3-dihydroxyphenyl-5-cis-6􍿁-tridecene,1,3-dihydroxyphenyl- 5-tridecane, 1,3-dihydroxyphenyl-5-cis-8􍿁- pentadecene, 1,3-dihydroxyphenyl-5-pentadecane, and 1,3- dihydroxyphenyl-5-cis-10􍿁-heptadecene, respectively, based on the spectral data and biosynthetic origin. Expression of SsARS in the yeast also led to the synthesis of the same polyketide products, indicating that this enzyme can be reconstituted in both heterologous hosts. Supplementation of soybean oil into the culture of E. coli BL21(DE3)/SsARS increased the production titers of 1–6 and led to the synthesis of an additional product, which was identified as 5-(8􍿁Z,11􍿁Z-heptadecadienyl) resorcinol. This work thus allowed the identification of SsARS as a 5-alk(en)ylresorcinol synthase with flexible substrate specificity toward endogenous and exogenous fatty acids. Desired resorcinol derivatives may be synthesized by supplying corresponding fatty acids into the culture medium.

Genetic variation of Colletotrichum magnum isolated from Carica papaya as revealed by DNA fingerprinting: Daisy Pérez-Brito , Alberto Cortes-Velázquez , Teresita Valencia-Yah , Anuar Magaña-Álvarez , Cuauhtémoc Navarro , Blanca Moreno , Steven Quiroga , Raúl Tapia-Tussell; J. Microbiol. 2018;56(11):813-821. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8215-z

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Abstract: Mexico is one of the five largest producers of papaya worldwide, but losses caused by pathogens, mainly fungus, at the pre- and post-harvest stages are often more than 50% of the crop. Papaya anthracnose, caused by three different species of the Colletotrichum genus in Mexico, occupies a preponderant place in this problem. Although two of these species, C. gloeosporiodes and C. truncatum, have been characterized morphologically and genotypically, this has not occurred with C. magnum, the third species involved, about which there is very little information. Because of this, it is vital to know its genetic characterization, much more so considering that the studies carried out on the other two species reveal a wide genetic diversity, differences in pathogenicity and in the response to fungicides of the different strains characterized. In this work, Colletotrichum spp. isolates were collected at different papaya orchards in the south-southeast of Mexico. C. magnum isolates identified by species-specific primers were characterized by morphological and molecular approaches. Differences in colony characteristics resulted in five morphological groups. AP-PCR, DAMD and ISSR markers were found to be very efficient for revealing the interspecific variability of this species. The high genetic variability found in the accessions of C. magnum was linked to the geographical area where they were collected. Isolates from Chiapas State were the most variable, showing point mutations in the ITS1- ITS2 region. These results will enable a better phytosanitary management of anthracnose in papaya in this region of Mexico.

Spectral and structural analysis of large Stokes shift fluorescent protein dKeima570: Yongbin Xu , Kwang Yeon Hwang , Ki Hyun Nam; J. Microbiol. 2018;56(11):822-827. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8319-5

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Abstract: The Keima family comprises large Stokes shifts fluorescent proteins, which are useful for dual-color fluorescence crosscorrelation spectroscopy and multicolor imaging. dKeima570 belongs to the Keima family. It has a unique chromophore sequence composed of CYG with an emission peak at 570 nm, but its molecular properties are unclear. We report the spectral analysis of dKeima570 and its crystal structure at 2.0 Å resolution. The dKeima570 chromophore is mainly in the protonation state in the entire pH range. The pH-induced non-fluorescence state was observed below pH 4.0. The crystal structure of the dKeima570 chromophore has a cis conformation at pH 6.5. The chromophore is surrounded by a unique hydrogen bonding network containing a water bridge between Glu212 and Arg194. The analysis of the dimeric interface of dKeima570 revealed the key residues that maintain the oligomerization of Keima family. Structural comparisons of dKeima570 and mKeima provided insights into the unique large Stokes shifts characteristics of the Keima family.

Photodynamic antimicrobial activity of new porphyrin derivatives against methicillin resistant Staphylococcus aureus: Hüseyin Ta&# , Ay&# , Nermin Topalo&# , Vildan Alptüzün; J. Microbiol. 2018;56(11):828-837. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8244-7

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26 Citations

Abstract: Methicillin resistant Staphylococcus aureus (MRSA) with multiple drug resistance patterns is frequently isolated from skin and soft tissue infections that are involved in chronic wounds. Today, difficulties in the treatment of MRSA associated infections have led to the development of alternative approaches such as antimicrobial photodynamic therapy. This study aimed to investigate photoinactivation with cationic porphyrin derivative compounds against MRSA in in-vitro conditions. In the study, MRSA clinical isolates with different antibiotic resistance profiles were used. The newly synthesized cationic porphyrin derivatives (PM, PE, PPN, and PPL) were used as photosensitizer, and 655 nm diode laser was used as light source. Photoinactivation experiments were performed by optimizing energy doses and photosensitizer concentrations. In photoinactivation experiments with different energy densities and photosensitizer concentrations, more than 99% reduction was achieved in bacterial cell viability. No decrease in bacterial survival was observed in control groups. It was determined that there was an increase in photoinactivation efficiency by increasing the energy dose. At the energy dose of 150 J/cm2 a survival reduction of over 6.33 log10 was observed in each photosensitizer type. While 200 μM PM concentration was required for this photoinactivation, 12.50 μM was sufficient for PE, PPN, and PPL. In our study, antimicrobial photodynamic therapy performed with cationic porphyrin derivatives was found to have potent antimicrobial efficacy against multidrug resistant S. aureus which is frequently isolated from wound infections.

Astragaloside IV reversed the autophagy and oxidative stress induced by the intestinal microbiota of AIS in mice: Nan Xu , Pengcheng Kan , Xiuhua Yao , Ping Yang , Jiwei Wang , Lei Xiang , Yu Zhu; J. Microbiol. 2018;56(11):838-846. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8327-5

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44 Citations

Abstract: Acute ischaemic stroke (AIS) seriously affects patient quality of life. We explored the role of the intestinal microbiota on oxidative stress and autophagy in stroke, and Astragaloside IV (AS-IV) reversed the changes induced by intestinal microbiota. We determined the characteristics of the intestinal microbiota of AIS and transient ischaemic attack (TIA) patients by 16S sequencing and found that the structure and diversity of the intestinal microbiota in patients with AIS and TIA were significantly different from those in healthy subjects. Specifically, the abundance of genus Bifidobacterium, Megamonas, Blautia, Holdemanella, and Clostridium, content of homocysteine and triglyceride was increased significantly, thus it may be as a potential mechanism of AIS and TIA. Furthermore, germ-free mice were infused intracolonically with fecal supernatants of TIA and AIS with/without feed AS-IV for 12 weeks, and we found that the feces of AIS up-regulated the autophagy markers Beclin-1, light chain 3 (LC3)-II and autophagy-related gene (Atg)12, and the expression of reactive oxygen species (ROS) and NADPH oxidase 2/4 (NOX2/4), malondialdehyde (MDA), however, the expression of total antioxidant capacity (T-AOC) and activity of superoxide dismutase (SOD) and glutathione (GSH) was down-regulated in brain tissue, the content of homocysteine and free fatty acids (FFA) in serum of the mice. Meanwhile, AS-IV could reverse the above phenomenon, however, it does not affect the motor function of mice. AS-IV reversed these changes and it may be a potential drug for AIS therapeutics.

Diagnosis and molecular characteristics of human infections caused by Anaplasma phagocytophilum in South Korea: Seung Hun Lee , Sungdo Park , Yeong Seon Lee , Hae Kyung Lee , Seon Do Hwang; J. Microbiol. 2018;56(11):847-853. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8385-8

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Abstract: Human granulocytic anaplasmosis (HGA) is a tick borne infection caused by Anaplasma phagocytophilum. HGA cases in South Korea have been identified since the first report in 2014. In this study, we investigated the serological response in 594 clinical samples of patients with acute febrile illness and molecular characteristics of A. phagocytophilum clinical isolates obtained from HGA patients. In serological test for A. phagocytophilum, 7.91% (47/594 cases) were positive for IgG and Ig M and 13 of 47 cases showed seroconversion. In the detection rate of the 16S rRNA, msp2(p44), and ankA, genes were showed 3.68% (14/380 cases) for A. phagocytophilum- specific 16S rRNA gene. Phylogenetic analysis of three clinical isolates demonstrated high sequence similarity (98.58– 100%) with A. phagocytophilum 16S rRNA sequences identified from public databases. Analysis of the msp2(p44) gene showed highly variable similarity rates (7.24–98.85%) even within isolated countries and host ranges. These results provide clues into the bacterial characterization of A. phagocytophilum originating from Korean patients, providing useful guidance for treatment and improving clinical outcomes.

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