Journal of Microbiology

Journal Articles

Flavivirga spongiicola sp. nov. and Flavivirga abyssicola sp. nov., Isolated from Marine Environments: Sung-Hyun Yang , Mi-Jeong Park , Hyun-Myung Oh , Yeong-Jun Park , Kae Kyoung Kwon; J. Microbiol. 2024;62(1):11-19. Published online February 6, 2024; DOI: https://doi.org/10.1007/s12275-023-00102-z

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Two novel Gram-stain-negative, strictly-aerobic, rod-shaped (1.2 ± 3.4 μm × 0.3 ± 0.7 μm), and non-motile marine bacterial species, designated MEBiC05379T and MEBiC07777T, were isolated from a marine sponge Pseudaxinella sp. in Gangneung City and deep-sea sediments of the Ulleung basin in the East Sea of Korea, respectively. The 16S rRNA gene sequence analysis revealed high levels of similarities between these strains and members of the genus Flavivirga (97.0–98.4% sequence identities). Both novel strains revealed as mesophilic, neutrophilic in pH and slightly halophilic. Similar to those of other Flavivirga members, the primary cellular fatty acids of both strains were iso-C15:0, iso-C15:1 G, iso-C15:03-OH, and iso-C17:0 3-OH, with MEBiC05379T and MEBiC07777T containing relatively higher proportions of C12: 0 and summed feature 3 ( C16:1ω7c and/or C16: 1ω6c). In both taxa, the major isoprenoid quinone was MK-6. The DNA G + C contents of MEBiC05379T and MEBiC07777T genomes were 32.62 and 32.46 mol%, respectively. Compared to other members of Flavivirga, both strains exhibited similar DNA G + C ratio and fatty acids pattern, yet enzyme expression and carbon sources utilization pattern were different. Genomes of the genus Flavivirga showed enzyme preferences to fucoidan and sulfated galactans. Considering the monophyly rule, AAI values delineate the genus Flavivirga from adjacent genera calculated to be 76.0–78.7%. Based on the phenotypic, genomic and biochemical data, strains for MEBiC05379T and MEBiC07777T thus represent two novel species in the genus Flavivirga, for which the names Flavivirga spongiicola sp. nov. ( MEBiC05379T [= KCTC 92527 T = JCM 16662 T]), and Flavivirga abyssicola sp. nov. ( MEBiC07777T [= KCTC 92563 T = JCM 36477 T]) are proposed.

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Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef
Validation List no. 220. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Optimization of Culture Medium for the Production of an Exopolysaccharide (p-CY02) with Cryoprotective Activity by Pseudoalteromonas sp. RosPo-2 from the Antarctic Sea
Pilsung Kang, Sung Jin Kim, Ha Ju Park, Il Chan Kim, Se Jong Han, Joung Han Yim
Journal of Microbiology and Biotechnology.2024; 34(5): 1135. CrossRef

Deletion of lacD gene affected stress tolerance and virulence of Streptococcus suis serotype 2: Xiaowu Jiang , Lexin Zhu , Dongbo Zhan; J. Microbiol. 2022;60(9):948-959. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2146-4

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Abstract

Streptococcus suis type 2 (S. suis type 2, SS2), an infectious pathogen which is zoonotic and can induce severely public health concern. Our previous research identified a newly differential secreted effector of tagatose-bisphosphate aldolase (LacD) mediated by VirD4 factor within the putative type IV secretion system of SS2, whereas the functional basis and roles in virulence of LacD remain elusive. Here in this study, the LacD was found enzymatic and can be activated to express under oxidative stress. Gene mutant and its complemental strain (ΔlacD and cΔlacD) were constructed to analyze the phenotypes, virulence and transcriptomic profiles as compared with the parental strain. The lacD gene deletion showed no effect on growth capability and cells morphology of SS2. However, reduced tolerance to oxidative and heat stress conditions, increased antimicrobial susceptibility to ciprofloxacin and kanamycin were found in ΔlacD strain. Further, the LacD deficiency led to weakened invasion and attenuated virulence since an easier phagocytosed and more prone to be cleared of SS2 in macrophages were shown in ΔlacD mutant. Distinctive transcriptional profiling in ΔlacD strain and typical downregulated genes with significant mRNA changes including alcohol dehydrogenase, GTPase, integrative and conjugative elements, and iron ABC transporters which were mainly involved in cell division, stress response, antimicrobial susceptibility and virulence regulation, were examined and confirmed by RNA sequencing and real time qPCR. In summary, the
results
demonstrated for the first time that LacD was a pluripotent protein mediated the metabolic, stress and virulent effect of SS2.

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Investigation of choline-binding protein of CbpD in the pathogenesis of Streptococcus suis type 2
Lexin Zhu, Mengqing Li, Guijun Yu, Dongbo Zhan, Wenzhen Zeng, Nanyan Fu, Xiaowu Jiang
Frontiers in Veterinary Science.2024;[Epub] CrossRef

Evidence of the genetic diversity and clonal population structure of Oenococcus oeni strains isolated from different wine-making regions of China: Dongliang Yu , Kan Shi , Xiangyuan Wen , Fangshu Xie , Tao Wang , Shuwen Liu , Ling He; J. Microbiol. 2018;56(8):556-564. Published online July 25, 2018; DOI: https://doi.org/10.1007/s12275-018-7568-7

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Abstract

Studies of the genetic diversity and population structure of Oenococcus oeni (O. oeni) strains from China are lacking compared to other countries and regions. In this study, amplified fragment length polymorphism (AFLP) and multilocus sequence typing (MLST) methods were used to investigate the genetic diversity and regional evolutionary patterns of 38 O. oeni strains isolated from different wine-making regions in China. The results indicated that AFLP was markedly more efficient than MLST for typing O. oeni strains. AFLP distinguished 37 DNA patterns compared to 7 sequence types identified using MLST, corresponding to discriminatory indices of 0.999 and 0.602, respectively. The AFLP results revealed a high level of genetic diversity among the O. oeni strains from different regions of China, since two subpopulations and an intraspecific homology higher than 60% were observed. Phylogenetic analysis of the O. oeni strains using the MLST method also identified two major phylogroups, which were differentiated into two distinct clonal complexes by minimum spanning tree analysis. Neither intragenic nor intergenic recombination verified the existence of the clonal population structure of the O. oeni strains.

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Impact of indigenous Oenococcus oeni and Lactiplantibacillus plantarum species co-culture on Cabernet Sauvignon wine malolactic fermentation: Kinetic parameters, color and aroma
Biying Zhang, Doudou Liu, Hui Liu, Jiaxin Shen, Jiaxuan Zhang, Ling He, Jin Li, Penghui Zhou, Xueqiang Guan, Shuwen Liu, Kan Shi
Food Chemistry: X.2024; 22: 101369. CrossRef
Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects
Haitam Lahmamsi, Samir Ananou, Rachid Lahlali, Abdessalem Tahiri
Folia Microbiologica.2024; 69(3): 465. CrossRef
Molecular and Physiological Properties of Indigenous Strains of Oenococcus oeni Selected from Nero di Troia Wine (Apulia, Italy)
Maria Stella Cappello, Vittorio Falco, Rosita Curcio, Giovanni Mita, Giacomo Zapparoli
Microorganisms.2022; 10(4): 795. CrossRef
Molecular typing tools for identifying and characterizing lactic acid bacteria: a review
Anshul Sharma, Sulhee Lee, Young-Seo Park
Food Science and Biotechnology.2020; 29(10): 1301. CrossRef

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

NOTE] Anaerobic Cellulolytic Rumen Fungal Populations in Goats Fed with and without Leucaena leucocephala Hybrid, as Determined by Real-Time PCR: Ching Mun Kok , Chin Chin Sieo , Hui Yin Tan , Wan Zuhainis Saad , Juan Boo Liang , Yin Wan Ho; J. Microbiol. 2013;51(5):700-703. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-2540-z

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Abstract: The effect of Leucaena leucocephala hybrid-Bahru (LLB), which contains a high concentration of condensed tannins, on cellulolytic rumen fungal population in goats was investigated using real-time PCR. The fungal population in goats fed LLB was inhibited during the first 10 days of feeding, but after 15 days of feeding, there was a tremendous increase of fungal population (157.0 μg/ml), which was about fourfold more than that in control goats (39.7 μg/ml). However, after this period, the fungal population decreased continuously, and at 30 days of feeding, the fungal population (50.6 μg/ml) was not significantly different from that in control goats (55.4 μg/ml).

NOTE] The Microbial Population in the Air of Cultivation Facility of Oyster Mushrooms: Se Chul Chun , Yu Na Ahn , Sajid Mohamad Khan , Il Min Chung , Hyang Yoen Won , Chang Sung Jhune , Yool Jin Park; J. Microbiol. 2012;50(6):1053-1057. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2195-1

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Abstract: The microbial population in the air of mushroom cultivation facility was studied to understand the population structure and size depending on the cultivation methods and regions. The air contents of ten farmers’ oyster mushroom cultivation facilities in Kyunggi province were sampled. The results indicated that there was no difference in population size depending on the regions of mushroom cultivation. In addition, the population size of bacteria in the growth room was bigger than that of the cooling room and outside of the mushroom house, but the fungal population was similar in size between cultivation stages. With regard to population structure, Pseudomonas and Penicillium species were most frequently isolated from the air of oyster mushroom cultivation facility.

Journal Article

Detecting Nonculturable Bacteria in the Active Mycorrhizal Zone of the Pine Mushroom Tricholoma matsutake: Ryota Kataoka , Zaki Anwar Siddiqui , Junichi Kikuchi , Masaki Ando , Rina Sriwati , Ai Nozaki , Kazuyoshi Futai; J. Microbiol. 2012;50(2):199-206. Published online April 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1371-7

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Abstract: The fungus Tricholoma matsutake forms an ectomycorrhizal relationship with pine trees. Its sporocarps often develop in a circle, which is commonly known as a fairy ring. The fungus produces a solid, compact, white aggregate of mycelia and mycorrhizae beneath the fairy ring, which in Japanese is called a ‘shiro’. In the present study, we used soil dilution plating and molecular techniques to analyze the bacterial communities within, beneath, and outside the T. matsutake fairy ring. Soil dilution plating confirmed previous reports that bacteria and actinomycetes are seldom present in the soil of the active mycorrhizal zone of the T. matsutake shiro. In addition, the results showed that the absence of bacteria was strongly correlated with the presence of T. matsutake mycorrhizae. The results demonstrate that bacteria, especially aerobic and heterotrophic forms, and actinomycetes, are strongly inhibited by T. matsutake. Indeed, neither bacteria nor actinomycetes were detected in 11.3% of 213 soil samples from the entire shiro area by culture-dependent
methods
. However, molecular techniques demonstrated that some bacteria, such as individual genera of Sphingomonas and Acidobacterium, were present in the active mycorrhizal zone, even though they were not detected in soil assays using the dilution plating technique.

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

Deciphering the Biodiversity of Listeria monocytogenes Lineage III Strains by Polyphasic Approaches: Hanxin Zhao , Jianshun Chen , Chun Fang , Ye Xia , Changyong Cheng , Lingli Jiang , Weihuan Fang; J. Microbiol. 2011;49(5):759-767. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1006-4

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Abstract: Listeria monocytogenes is a foodborne pathogen of humans and animals. The majority of human listeriosis cases are caused by strains of lineages I and II, while lineage III strains are rare and seldom implicated in human listeriosis. We revealed by 16S rRNA sequencing the special evolutionary status of L. monocytogenes lineage III, which falls between lineages I and II strains of L. monocytogenes and the non-pathogenic species L. innocua and L. marthii in the dendrogram. Thirteen lineage III strains were then characterized by polyphasic approaches. Biochemical reactions demonstrated 8 biotypes, internalin profiling identified 10 internalin types clustered in 4 groups, and multilocus sequence typing differentiated 12 sequence types. These typing schemes show that lineage III strains represent the most diverse population of L. monocytogenes, and comprise at least four subpopulations IIIA-1, IIIA-2, IIIB, and IIIC. The in vitro and in vivo virulence assessments showed that two lineage IIIA-2 strains had reduced pathogenicity, while the other lineage III strains had comparable virulence to lineages I and II. The IIIB strains are phylogenetically distinct from other subpopulations, providing additional evidence that this sublineage represents a novel lineage. The two biochemical reactions L-rhamnose and L-lactate alkalinization, and 10 internalins were identified as potential markers for lineage III subpopulations. This study provides new insights into the biodiversity and population structure of lineage III strains, which are important for understanding the evolution of the L. monocytogenes-L. innocua clade.

Genetic Diversity and Population Structure of Escherichia coli from Neighboring Small-Scale Dairy Farms: Jesús Andrei Rosales-Castillo , Ma. Soledad Vázquez-Garcidueñas , Hugo Álvarez-Hernández , Omar Chassin-Noria , Alba Irene Varela-Murillo , María Guadalupe Zavala-Páramo , Horacio Cano-Camacho , Gerardo Vázquez-Marrufo; J. Microbiol. 2011;49(5):693-702. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-0461-2

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Abstract: The genetic diversity and population structure of Escherichia coli isolates from small-scale dairy farms were used to assess the ability of E. coli to spread within the farm environment and between neighboring farms. A total of 164 E. coli isolates were obtained from bovine feces, bedding, cow teats and milk from 6 small-scale dairy farms. Ward’s clustering grouped the isolates into 54 different random amplified polymorphic DNA (RAPD) types at 95% similarity, regardless of either the sample type or the farm of isolation. This suggests that RAPD types are shared between bovine feces, bedding, cow teats, and milk. In addition, transmission of RAPD types between the studied farms was suggested by the Ward grouping pattern of the isolates, Nei’s and AMOVA population analyses, and genetic landscape shape analysis. For the first time, the latter analytical tool was used to assess the ability of E. coli to disseminate between small-scale dairy farms within the same producing region. Although a number of dispersal mechanisms could exist between farms, the genetic landscape shape analysis associated the flow of E. coli RAPD types with the movement of forage and milking staff between farms. This study will aid in planning disease prevention strategies and optimizing husbandry practices.

Microbial Community Response to a Simulated Hydrocarbon Spill in Mangrove Sediments: Rodrigo Gouvêa Taketani , Natália Oliveira Franco , Alexandre Soares Rosado , Jan Dirk van Elsas; J. Microbiol. 2010;48(1):7-15. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0147-1

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Abstract: In this study, we examined the hypothesis that the microbial communities in mangrove sediments with different chemical and historical characteristics respond differently to the disturbance of a hydrocarbon spill. Two different mangrove sediments were sampled, one close to an oil refinery that had suffered a recent oil spill and another that had not been in contact with oil. Based on the sampled sediment, two sets of mesocosms were built, and oil was added to one of them. They were subjected to mimicked mangrove conditions and monitored for 75 days. Archaeal and bacterial communities were evaluated through PCRDGGE. Both communities showed the emergence of small numbers of novel bands in response to oil pollution. 16S rRNA gene clone libraries were constructed from both mesocosms before the addition of oil and at day 75 after oil addition. LIBSHUFF analysis showed that both mangrove-based mesocosms contained similar communities at the start of the experiment and that they were different from the initial one, as well as from each other, after 75 days. These results hint at a role of environmental history that is not obvious from community diversity indicators, but is apparent from the response to the applied stress.

NOTE] Microbial Population Dynamics and Temperature Changes during Fermentation of Kimjang Kimchi: Dongyun Lee , Sunjoo Kim , Jinhee Cho , Jeongho Kim; J. Microbiol. 2008;46(5):590-593. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0156-5

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Abstract: A distinct subset of lactic acid bacteria that are greatly influenced by temperature play an important role during kimchi fermentation. However, microbial population dynamics and temperature control during kimjang kimchi fermentation, which is traditionally fermented underground, are not known. Here we show that Lactobacillus sakei predominates in kimjang kimchi, perhaps due to suitable fermentation (5~9°C) and storage (-2°C) temperatures. The temperature of this kimchi gradually decreased to 3.2°C during the first 20 days of fermentation (-0.3°C/day) and then was stably maintained around 1.6°C, indicating that this simple approach is very efficient both for fermentation and storage. These findings provide important information towards the development of temperature controlling systems for kimchi fermentation.

Journal Article

Prevalence of Antibodies in Response to Legionella Species, Analysis of a Healthy Population from Jeollanam-do Province, Korea: Hae Kyung Lee , Mi Kyeong Woo , Yong In Ju , Soo Jin Baek , Hyeon Je Song , Jin Su Choi , Sun Seog Kweon , Doo Young Jeon , Yeon Ho Kang; J. Microbiol. 2008;46(2):160-164. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0181-9

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Abstract: Seroepidemological investigation of antibodies to Legionella species in 500 healthy individuals from a single geographical location in Korea was conducted by indirect fluorescent antibody assay (IFA). Considering an antibody titer of ≥1:128 as positive reaction, 15.2% of total sera were positive. In males and females older than 40 years old, levels of IgM and IgG were 1.2% and 14%, respectively. The sera with antibody titers of ≥1:128 to Legionella species accounted for 85 sera, and 9 sera of these were reacted to more than one Legionella species. Reactivity to L. bozemanii, L. micdadei, L. longbeachae, L. pneumophila sg 6, and L. gormanii were 32.9%, 20%, 15%, 10.6%, and 8%, respectively. However, L. pneumophila sg 1, sg 2, and sg 3 did not react to any sera. Serological analysis revealed that the level of antibody in response to L. bozemanii was more prevalent than L. pneumophila. Our results suggest that the antibodies of non-L. pneumophila species, such as L. bozemanii, may be highly prevalent in healthy population within Korea. Although conclusions based on the findings of this study must be cautiously considered given that the population sampled were sourced from a single province, we have added to the knowledge base of serodiagnosis of infections due to non-L. pneumophila species in Korea.

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

Immunological Roles of Pasteurella multocida Toxin (PMT) Using a PMT Mutant Strain: Tae Jung Kim , Nguyen Tat Toan , Eun Jin Jang , Bock Gie Jung , Jae Il Lee , Bong Joo Lee; J. Microbiol. 2007;45(4):364-366.; DOI: https://doi.org/2559 [pii]

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Abstract: The immunological role of the Pasteurella multocida toxin (PMT) in mice was examined using a PMT mutant strain. After a nasal inoculation, the mutant strain failed to induce interstitial pneumonia. Moreover, PMT had no significant effect on the populations of CD4+, CD8+, CD3+, and CD19+ immunocytes in blood or on the populations of CD4+ and CD8+ splenocytes (P<0.01). However, there was a significant increase in the total number of cells in the BAL samples obtained from the wild-type P. multocida-inoculated mice. On the other hand, the level of IL-1 expression decreased when the macrophages from the bronchio-alveolar lavage were stimulated with PMT. Overall, PMT appears to play some role (stimulating and/or inhibiting) in the immunological responses but further studies will be required to confirm this.

Effects of Hydrogen Ions on Aquatic Microbial Populations in Korea: Ahn, Young Beom , Cho, Hong Bum , Choi, Yong Keel; J. Microbiol. 1995;33(3):184-190.

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Abstract: From July 1994 to March 1995, eighteen variables of physico-chemical factors including heavy metals, and of bacteria in the four reservoirs of Kyonggi-Do were investigated to examine the effects of acidic precipitation to bacterial population. The pH range in the study area is from 6.56 to 10.24, which also showed seasonal change extensively compared to other factors. The correlation analysis showed that pH has a significant positive correlation (mean 79%) with the microbial populations in Wangsong reservoir. By multiple regression analysis on all of the seasons and stations, good explanation was obtained for the variation in total direct count of bacteria (71% and 88%, respectively), and the plate count of heterotrophic bacteria (76% and 88%, respectively). In the surface water of Wansong reservoir, the variation of total count of bacteria was affected by the S/O (soluble sugar/total organic matter ratio) value and the pH, and that of the plate count of heterotrophic bacteria was explained as 63% by pH. However, in other stations they were explained by the NO₂, total organic matter (TOM), soluble sugar (SS), temperature, and dissolved oxygen as 21~91%. On the basis of the results, the bacterial populations on the media at pH 3.0, 4.0, 5.0, 6.0 and 7.0 were compared to determine the effects of acidic proceeding. All the colonies grew the best on the media of pH 7.0, but started to decrease from pH 5.0.

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