Journal of Microbiology

Review

Transmissibility and pathogenicity of SARS-CoV-2 variants in animal models: Young-Il Kim , Mark Anthony B. Casel , Young Ki Choi; J. Microbiol. 2022;60(3):255-267. Published online March 2, 2022; DOI: https://doi.org/10.1007/s12275-022-2033-z

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8 Citations

Abstract: As of February 2022, SARS-CoV-2 is still one of the most serious public health threats due to its high mortality rate and rapid spread of novel variants. Since the first outbreak in 2019, general understanding of SARS-CoV-2 has been improved through basic and clinical studies; however, knowledge gaps still exist in our understanding of the emerging novel SARSCoV- 2 variants, which impacts the corresponding development of vaccines and therapeutics. Especially, accumulation of mutations in SARS-CoV-2 and rapid spread in populations with previous immunity has resulted in selection of variants that evade the host immune response. This phenomenon threatens to render current SARS-CoV-2 vaccines ineffective for controlling the pandemic. Proper animal models are essential for detailed investigations into the viral etiology, transmission and pathogenesis mechanisms, as well as evaluation of the efficacy of vaccine candidates against recent SARS-CoV-2 variants. Further, the choice of animal model for each research topic is important for researchers to gain better knowledge of recent SARS-CoV-2 variants. Here, we review the advantages and limitations of each animal model, including mice, hamsters, ferrets, and non-human primates, to elucidate variant SARS-CoV-2 etiology and transmission and to evaluate therapeutic and vaccine efficacy.

Journal Article

Fungal diversity in soils across a gradient of preserved Brazilian Cerrado: Ademir Sergio Ferreira de Araujo , Walderly Melgaço Bezerra , Vilma Maria dos Santos , Luis Alfredo Pinheiro Leal Nunes , Maria do Carmo Catanho Pereira de Lyra , Marcia do Vale Barreto Figueiredo , Vania Maria Maciel Melo; J. Microbiol. 2017;55(4):273-279. Published online January 27, 2017; DOI: https://doi.org/10.1007/s12275-017-6350-6

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26 Citations

Abstract: The preserved Cerrado from Northeastern Brazil presents different physicochemical properties and plant diversity, which can influence the fungal communities. Therefore, we evaluated the fungal diversity in preserved sites, at Sete Ci-dades National Park, across a gradient of vegetation that in-cluded Campo graminoide, Cerrado stricto sensu, Cerradao, and Floresta decidual. Of all of the operational taxonomic units (OTUs) obtained, the Floresta decidual presented the highest richness. Ascomycota were the most abundant phy-lum (45%), followed by Basidiomycota (32%). Basal fungi and other phyla accounted for 23% of the total dataset. Agaricomycetes, Eurotiomycetes, Lecanoromycetes, Basi-diobolus, Dothideomycetes, and Taphrinomycetes were the most abundant classes of fungi found across the gradient of Cerrado vegetation. In conclusion, our study suggests that the Brazilian Cerrado from Sete Cidades National Park pre-sents a high fungal diversity and includes sources of new fungal species for biotechnological purposes.

Research Support, U.S. Gov't, Non-P.H.S.

Identification of Enriched Conjugated Linoleic Acid Isomers in Cultures of Ruminal Microorganisms after Dosing with 1-13C-Linoleic Acid: Yong-Jae Lee , Thomas C. Jenkins; J. Microbiol. 2011;49(4):622-627. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0415-8

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9 Citations

Abstract: Most studies of linoleic acid biohydrogenation propose that it converts to stearic acid through the production of cis-9 trans-11 CLA and trans-11 C18:1. However, several other CLA have been identified in ruminal contents, suggesting additional pathways may exist. To explore this possibility, this research investigated the linoleic acid biohydrogenation pathway to identify CLA isomers in cultures of ruminal microorganisms after dosing with a 13C stable isotope. The 13C enrichment was calculated as [(M+1/M)×100] in labeled minus unlabeled cultures. After 48 h incubation, significant 13C enrichment was observed in seven CLA isomers, indicating their formation from linoleic acid. All enriched CLA isomers had double bonds in either the 9,11 or 10,12 position except for trans-9 cis-11 CLA. The cis-9 trans-11 CLA exhibited the highest enrichment (30.65%), followed by enrichments from 21.06 to 23.08% for trans-10 cis-12, cis-10 trans-12, trans-9 trans-11, and trans-10 trans-12 CLA. The remaining two CLA (cis-9 cis-11 and cis-10 cis-12 CLA) exhibited enrichments of 18.38 and 19.29%, respectively. The results of this study verified the formation of cis-9 trans-11 and trans-10 cis-12 CLA isomers from linoleic acid biohydrogenation. An additional five CLA isomers also contained carbons originating from linoleic acid, indicating that pathways of linoleic acid biohydrogenation are more complex than previously described.

Research Support, Non-U.S. Gov'ts

Characterization of a Novel β-Glucosidase-Like Activity from a Soil Metagenome: Chengjian Jiang , Gefei Ma , Shuangxi Li , Tingting Hu , Zhiqun Che , Peihong Shen , Bing Yan , Bo Wu; J. Microbiol. 2009;47(5):542-548. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0024-y

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38 Citations

Abstract: We report the cloning of a novel β-glucosidase-like gene by function-based screening of a metagenomic library from uncultured soil microorganisms. The gene was named bgl1C and has an open reading frame of 1,443 base pairs. It encodes a 481 amino acid polypeptide with a predicted molecular mass of about 57.8 kDa. The deduced amino acid sequence did not show any homology with known β-glucosidases. The putative β-glucosidase gene was subcloned into the pETBlue-2 vector and overexpressed in E. coli Tuner (DE3) pLacІ; the recombinant protein was purified to homogeneity. Functional characterization with a high performance liquid chromatography method demonstrated that the recombinant Bgl1C protein hydrolyzed D-glucosyl-β-(1-4)-D-glucose to glucose. The maximum activity for Bgl1C protein occurred at pH 8.0 and 42°C using p-nitrophenyl-β-D-glucoside as the substrate. A CaCl2 concentration of 1 mM was required for optimal activity. The putative β-glucosidase had an apparent Km value of 0.19 mM, a Vmax value of 4.75 U/mg and a kcat value of 316.7/min under the optimal reaction conditions. The biochemical characterization of Bgl1C has enlarged our understanding of the novel enzymes that can be isolated from the soil metagenome.

Reductive Dechlorination of Polychlorinated Biphenyls as Affected by Natural Halogenated Aromatic Compounds: Jongseol Kim , Ahmi Lee , Yong-Suk Moon , Jae-Seong So , Sung-Cheol Koh; J. Microbiol. 2006;44(1):23-28.; DOI: https://doi.org/2341 [pii]

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Abstract: We investigated the effects of halogenated aromatic compounds (HACs) including naturally occurring ones (L-thyroxine, 3-chloro-L-tyrosine, 5-chloroindole, 2-chlorophenol, 4-chlorophenol and chlorobenzene) on polychlorinated biphenyl (PCB) dechlorination in sediment cultures. A PCB-dechlorinating enrichment culture of sediment microorganisms from the St. Lawrence River was used as an initial inoculum. When the culture was inoculated into Aroclor 1248 sediments amended with each of the six HACs, the extent of dechlorination was not enhanced by amendment with HACs. The dechlorination patterns in the HAC-amended sediments were nearly identical to that of the HAC-free sediments except the 3-chloro-L-tyrosine-amended ones where no dechlorination activity was observed. When these sediment cultures were transferred into fresh sediments with the same HACs, the dechlorination specificities remained the same as those of the initial inoculations. Thus, in the present study, the substrate range of the highly selected enrichment culture could not be broadened by the HACs. It appears that HACs affect PCB dechlorination mainly through population selection rather than enzyme induction of single population.

Effects of Sulfate Concentration on the Anaerobic Dechlorination of Polychlorinated Biphenyls in Estuarine Sediments: Young-Cheol Cho , Kyoung-Hee Oh; J. Microbiol. 2005;43(2):166-171.; DOI: https://doi.org/2167 [pii]

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Abstract: In order to determine the effects of sulfate concentration on the anaerobic dechlorination of polychlorinated biphenyls, sediments spiked with Aroclor 1242 were made into slurries using media which had various sulfate concentrations ranging from 3 to 23 mM. The time course of dechlorination clearly demonstrated that dechlorination was inhibited at high concentration of sulfate due to less dechlorination of meta-substituted congeners. When the dechlorination patterns were analyzed by the calculation of Euclidean distance, the dechlorination pathway in the 3 mM sulfate samples was found to be different from that observed in the 13 mM samples, although the extent of dechlorination in these two samples was similar. It is possible that the dechlorination in the high sulfate concentration samples is inhibited by the suppression of growth of methanogen, which have been shown to be meta-dechlorinating microorganisms.

Introductory Journal Article

[Editorial]Omics-based microbiome analysis in microbial ecology: from sequences to information: Jang-Cheon Cho; J. Microbiol. 2021;59(3):229-232.; DOI: https://doi.org/10.1007/s12275-021-0698-3

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5 Citations

Abstract: Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics
methods
triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.

Distribution of airborne microorganisms in yellow sands of Korea: Choi, Dae Sung , Park, Yong Keun , Oh, Sang Kon , Yoon, Hee Ju , Kim, Jee Cheon , Seo, Won Jun , Cha, Seung Hee; J. Microbiol. 1997;35(1):1-9.

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Abstract: Distribution of airborne microorganisms was determined with two different types of air samplers, the Anderson cascade sampler and the Aerobioscope sampler, in the vicinity of Taejon. The size distribution of particles carrying bacteria and fungi was concurrently measured. The concentration of detected viable airborne particles was greatly varied. It was observed that the number of microbial particles increased in April and October. The most size of particles carrying bacteria was larger than 4.7 um in mean aerodiameter, which made up 69.8% of the total particle fraction. About 63.2% of fungi-carrying particles were smaller than 4.7 um in aerodiameter. The distribution of particles on Yellow Sand Phenomena days was also analyzed. The number of fine particles having mass median aero-diameter from 1.0 to 10.mu.m increased on Yellow Sand Phenomena days to about 6 times that on normal days and the n umber of colony forming unit (CFU/㎥) of airborne bacteria also increased by 4.3 times in April. The results from the Anderson sampler showed that the concentration of bacteria increased greatly on the fraction of fine particles ranging from 0.6 um to 4.7 um in diameter. Unlike the increase in bacterial floraon Yellow Sand Phenomena days, the fungal concentration slightly decreased and showed a normal size distribution pattern. This study suggests that a long-range transmission of bacteria results form bacteria adsorbing onto the fine particles during the Yellow Sand Phenomena.

Microbial Degradation of Monohydroxybenzoic Acids: Timmanagouda B. Karegoudar , Chi-Kyung Kim; J. Microbiol. 2000;38(2):53-61.

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Abstract: Hydroxybenzoic acids are the most important intermediates in the degradative pathways of various aromatic compounds. Microorganisms catabolize aromatic compounds by converting them to hydroxylated intermediates and then cleave the benzene nucleus with ring dioxygenases. Hydroxylation of the benzene nucleus of an aromatic compound is an essential step for the initiation and subsequent disintegration of the benzene ring. The incorporation of two hydroxyl groups is essential for the labilization of the benzene nucleus. Monohydroxybenzoic acids such as 2-hydroxybenzoic acid, 3-hydroxybenzoic acid, and 4-hydroxybenzoic acid through hydroxylation yield terminal aromatic intermediates like catechol, protocatechuic acid, gentisic acid, or pyrocatechuic acid that are susceptible for subsequent oxygenative cleavage of the benzene ring. These terminal aromatic intermediates are further degraded to cellular components through ortho-and /or meta-cleavage pathways and finally lead to the formation of constituents of the TCA cycle. Many groups of microorganisms have been isolated as degraders of hydroxybenzoic acids with diverse degradative routes and specific enzymes involved in their metabolic pathways. Various microorganisms carry out unusual non-oxidative decarboxylation of aromatic acids and convert them to respective phenols which have been documented. Further, Pseudomonas and Bacillus spp. are the most ubiquitous microorganisms, being the principal components of microflora of most soil and water environments.

Effect of Moisture Content on Reductive Dechlorination of Polychlorinated Biphenyls and Population Dynamics of Dechlorinating Microorganisms: O-Seob Kwon , Young Eui Kim , Jong Gyu Park; J. Microbiol. 2001;39(3):195-201.

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Abstract: The effect of moisture content on the reductive dechlorination of polychlorinated biphenyls and population dynamics of dechlorinating microorganisms was investigated in sediments spiked with Aroclor 1248. In sediment slurry with an overlying water layer, dechlorination ensued after a 4-week lag period and reduced the average number of chlorines per biphenyl from 3.91 to 3.15 after 48 weeks. In the sediments of reduced moisture content, however, dechlorination occurred after a lag period of 12 weeks and decreased the average number of chlorines per biphenyl to only 3.62, and the dechlorination rate was also slower. When the population size of dechlorinators, methanogens, and sulfate-reducing bacteria was determined by the most probable number techniques, however, no difference was found between the slurry and the low-moisture sediments, except for methanogens. The growth of dechlorinating populations coincided with the end of the lag period and they then increased by 3 orders of magnitude in two conditions. Specific growth rate of dechlorinators showed little difference between the slurry and the low-moisture sediments; however, growth yield was high in the sediments of reduced moisture content. The reduction of sediment moisture decreased the dechlorination rate and extent of PCBs but did not inhibit the growth of PCB dechlorinators.

Morphological Diversity of Marine Microorganisms on Different Isolation Media: Shin Hye Park , Kae Kyoung Kwon , Deuk-Soo Lee , Hong Kum Lee; J. Microbiol. 2002;40(2):161-165.

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Abstract: Isolation frequency of microorganisms from marine sources was examined with different media and samples collected from the coastal area of Cheju Island. From sea water samples, about 1% of microorganisms from the total number of bacteria were recovered. Microorganisms were cultured at the much lower frequency of 10^-4 ?0^-6 from other marine sources, such as sediment, sponges and corals. The frequency of duplicated isolation was examined with 140 morphologically different colonies isolated on different media. Fourteen percent of them exhibited the same morphology on two different media. The duplication frequency of the isolates among three different media was 33%.

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