Journal of Microbiology

Journal Articles

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea: Wenhui Li, Yu Zhen, Yuhong Yang, Daling Wang, Hui He; J. Microbiol. 2024;62(10):845-858. Published online August 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00166-5

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This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 10² to 2.17 × 10⁶ copies per gram of sediment and from 6.6 × 10¹ to 7.65 × 10⁴ copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50 °C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

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Metabolism diversification of ammonia-oxidizing archaea and bacteria under different precipitation gradients and land legacies
Soumyadev Sarkar, Anna Kazarina, Paige M. Hansen, Kaitlyn Ward, Christopher Hargreaves, Nicholas Reese, Qinghong Ran, Willow Kessler, Ligia F.T. de Souza, Terry D. Loecke, Marcos V.M. Sarto, Charles W. Rice, Lydia H. Zeglin, Benjamin A. Sikes, Sonny T.M.
Applied Soil Ecology.2025; 206: 105831. CrossRef

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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Abstract

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

Review

Manganese Transporter Proteins in Salmonella enterica serovar Typhimurium: Nakyeong Ha , Eun-Jin Lee; J. Microbiol. 2023;61(3):289-296. Published online March 2, 2023; DOI: https://doi.org/10.1007/s12275-023-00027-7

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Abstract

The metal cofactors are essential for the function of many enzymes. The host restricts the metal acquisition of pathogens for their immunity and the pathogens have evolved many ways to obtain metal ions for their survival and growth. Salmonella enterica serovar Typhimurium also needs several metal cofactors for its survival, and manganese has been found to contribute to Salmonella pathogenesis. Manganese helps Salmonella withstand oxidative and nitrosative stresses. In addition, manganese affects glycolysis and the reductive TCA, which leads to the inhibition of energetic and biosynthetic metabolism. Therefore, manganese homeostasis is crucial for full virulence of Salmonella. Here, we summarize the current information about three importers and two exporters of manganese that have been identified in Salmonella. MntH, SitABCD, and ZupT have been shown to participate in manganese uptake. mntH and sitABCD are upregulated by low manganese concentration, oxidative stress, and host NRAMP1 level. mntH also contains a Mn2+- dependent riboswitch in its 5′ UTR. Regulation of zupT expression requires further investigation. MntP and YiiP have been identified as manganese efflux proteins. mntP is transcr!ptionally activated by MntR at high manganese levels and repressed its activity by MntS at low manganese levels. Regulation of yiiP requires further analysis, but it has been shown that yiiP expression is not dependent on MntS. Besides these five transporters, there might be additional transporters that need to be identified.

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Functional characterization of a TerC family protein of Riemerella anatipestifer in manganese detoxification and virulence
Qinyuan Chen, Fang Guo, Li Huang, Mengying Wang, Chunfeng Shi, Shutong Zhang, Yizhou Yao, Mingshu Wang, Dekang Zhu, Renyong Jia, Shun Chen, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Bin Tian, Juan Huang, Xumin Ou, Qun Gao, Di Sun, Ling Zhang, Yanling
Applied and Environmental Microbiology.2024;[Epub] CrossRef
NO enhances the adaptability to high-salt environments by regulating osmotic balance, antioxidant defense, and ion homeostasis in eelgrass based on transcriptome and metabolome analysis
Xianyan Wang, Tongtong Wang, Pei Yu, Yuchun Li, Xinfang Lv
Frontiers in Plant Science.2024;[Epub] CrossRef
High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection
Benjamin X. Wang, Dmitry Leshchiner, Lijuan Luo, Miles Tuncel, Karsten Hokamp, Jay C. D. Hinton, Denise M. Monack
Nature Genetics.2024; 56(6): 1288. CrossRef
Biological characteristics of manganese transporter MntP in Klebsiella pneumoniae
Wei Peng, Yafei Xu, Yilin Yin, Jichen Xie, Renhui Ma, Guoyuan Song, Zhiqiang Zhang, Qiuhang Quan, Qinggen Jiang, Moran Li, Bei Li, Michael David Leslie Johnson
mSphere.2024;[Epub] CrossRef
Exploring resource competition by protective lactic acid bacteria cultures to control Salmonella in food: an Achilles’ heel to target?
Ludovico Screpanti, Nathalie Desmasures, Margot Schlusselhuber
Critical Reviews in Food Science and Nutrition.2024; : 1. CrossRef
Substrate-Induced Structural Dynamics and Evolutionary Linkage of Siderophore-Iron ABC Transporters of Mycobacterium tuberculosis
Aisha Farhana, Abdullah Alsrhani, Hasan Ejaz, Muharib Alruwaili, Ayman A. M. Alameen, Emad Manni, Zafar Rasheed, Yusuf Saleem Khan
Medicina.2024; 60(11): 1891. CrossRef
Structures and coordination chemistry of transporters involved in manganese and iron homeostasis
Shamayeeta Ray, Rachelle Gaudet
Biochemical Society Transactions.2023; 51(3): 897. CrossRef
Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
Jin-Won Lee
Journal of Microbiology.2023; 61(3): 273. CrossRef

Journal Articles

Expression and purification of intracrine human FGF 11 and study of its FGFR-dependent biological activity: Kyeong Won Lee , Young Jun An , Janet Lee , Ye-Eun Jung , In Young Ko , Jonghwa Jin , Ji Hoon Park , Won Kyu Lee , Kiweon Cha , Sun-Shin Cha , Jung-Hyun Lee , Hyung-Soon Yim; J. Microbiol. 2022;60(11):1086-1094. Published online November 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2406-3

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Abstract

Fibroblast growth factor 11 (FGF11) is one of intracrine FGFs (iFGFs), which function within cells. Unlike canonical FGFs, FGF11 remains intracellularly and plays biological roles in FGF receptor (FGFR)-independent manner. Here, we established an expression system of recombinant FGF11 proteins in E. coli and investigated whether the extracellular administration of FGF11 can activate cellular signaling. Human FGF11 has two isoforms, FGF11a and FGF11b, depending on the presence of nuclear localization sequences (NLSs) in the N-terminus. Because these two isoforms are unstable, we prepared an FGF11a-Mut by substituting three cysteine residues in the NLS with serine and FGF11b-ΔC with C-terminal truncation. The introduction of mutation in the NLS improved the solubility of FGF11 prepared from E. coli. Exogenous addition of FGF11b and FGF11b-ΔC to BALB3T3 increased cell proliferation, while FGF11a-Mut exerted no effect. FGF11b-ΔC showed higher cell proliferation activity and FGFR signaling than FGF11b. The cell-proliferating activities of FGF11b and FGF11b-ΔC were blocked by an FGFR1 inhibitor or a recombinant FGFR1, confirming the FGFR1- dependent extracellular activity of FGF11b. The analysis of circular dichroism suggested that the C-terminus of FGF11 has an α-helical structure, which may affect its interaction with FGFR1. These results suggest that the N-and C-terminus of recombinant FGF11 are involved in the activation of FGFR1. The above results provide novel insights into the function and mechanism of FGF11 that may aid the development of useful ligands for FGFR regulation.

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Glycosylation of FGF/FGFR: An underrated sweet code regulating cellular signaling programs
Aleksandra Gędaj, Paulina Gregorczyk, Dominika Żukowska, Aleksandra Chorążewska, Krzysztof Ciura, Marta Kalka, Natalia Porębska, Łukasz Opaliński
Cytokine & Growth Factor Reviews.2024; 77: 39. CrossRef
FGF homologous factors are secreted from cells to induce FGFR‐mediated anti‐apoptotic response
Martyna Biadun, Martyna Sochacka, Radoslaw Karelus, Karolina Baran, Aleksandra Czyrek, Jacek Otlewski, Daniel Krowarsch, Lukasz Opalinski, Malgorzata Zakrzewska
The FASEB Journal.2023;[Epub] CrossRef
FGF/FGFR1 system in paired breast tumor-adjacent and tumor tissues, associations with mammographic breast density and tumor characteristics
Öykü Boraka, Marie Klintman, Johan Vallon-Christersson, Sophia Zackrisson, Per Hall, Signe Borgquist, Ann H. Rosendahl
Frontiers in Oncology.2023;[Epub] CrossRef

Genomic and physiological analysis of C50 carotenoid-producing novel Halorubrum ruber sp. nov.: Chi Young Hwang , Eui-Sang Cho , Won Jong Rhee , Eunjung Kim , Myung-Ji Seo; J. Microbiol. 2022;60(10):1007-1020. Published online August 26, 2022; DOI: https://doi.org/10.1007/s12275-022-2173-1

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Abstract

A novel haloarchaeal species designated as MBLA0099T was isolated from seawater near Yeongheung Island. Cells were Gram-negative, non-motile, red-pigmented, and rod-shaped. They grew at 10–45°C, within pH 5.5–9.0, and between 7.5% and 30% NaCl concentrations. Cells were able to grow without Mg2+ and were lysed in distilled water. The size of the whole-genome and G + C content of DNA was 3.02 Mb and 68.9 mol%, respectively. Phylogenetic analysis shows that the strain MBLA0099T belongs to the genus Halorubrum. The average nucleotide and amino acid identity, and in silico DNA-DNA hybridization values were below the species delineation threshold. Pan-genomic analysis revealed that 3.2% of all genes present in strain MBLA0099T were unique to the strain. The red carotenoid produced by strain MBLA0099T was subjected to spectrometric and chromatographic analyses and confirmed to be bacterioruberin as C50 carotenoid. Mevalonic acid, terpenoid backbone, and carotenoid biosynthesis pathway were annotated for strain MBLA0099T. The C50 carotenoid production by strain MBLA0099T was also enhanced under various stress conditions including relatively netural pH, high oxidative and salinity conditions. Additionally, the strain MBLA0099T-derived bacterioruberin showed the antioxidant activity with EC50 value of 12.29 μg/ml, based on the evaluation of DPPH free radical scavenging activity. The present study would be the first report on the identification of C50 carotenoid from the strain MBLA0099T representing a novel species of the genus Halorubrum, for which the name Halorubrum ruber sp. nov. is proposed. The typestrain used was MBLA0099T (= KCTC 4296T = JCM 34701T).

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Optimization of bacterioruberin production from Halorubrum ruber and assessment of its antioxidant potential
Chi Young Hwang, Eui-Sang Cho, Sungjun Kim, Kyobum Kim, Myung-Ji Seo
Microbial Cell Factories.2024;[Epub] CrossRef
Microbial Bacterioruberin: A Comprehensive Review
Mouliraj Palanisamy, Sathishkumar Ramalingam
Indian Journal of Microbiology.2024; 64(4): 1477. CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India
Devika. N. Nagar, Kabilan Mani, Judith M. Braganca
Scientific Reports.2024;[Epub] CrossRef
Microbial bacterioruberin: The new C50 carotenoid player in food industries
Cassamo U. Mussagy, Angie V. Caicedo-Paz, Fabiane O. Farias, Leonardo M. de Souza Mesquita, Daniele Giuffrida, Laurent Dufossé
Food Microbiology.2024; 124: 104623. CrossRef
Evaluation of Various Escherichia coli Strains for Enhanced Lycopene Production
Jun Ren, Junhao Shen, Thi Duc Thai, Min-gyun Kim, Seung Ho Lee, Wonseop Lim, Dokyun Na
Journal of Microbiology and Biotechnology.2023; 33(7): 973. CrossRef
Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications
Jamseel Moopantakath, Madangchanok Imchen, V. T. Anju, Siddhardha Busi, Madhu Dyavaiah, Rosa María Martínez-Espinosa, Ranjith Kumavath
Frontiers in Microbiology.2023;[Epub] CrossRef

Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons): Qian Liu , Guoying Fan , Kui Wu , Xiangning Bai , Xi Yang , Wentao Song , Shengen Chen , Yanwen Xiong , Haiying Chen; J. Microbiol. 2022;60(7):668-677. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2089-9

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Abstract

Two novel Gram-positive, non-spore-forming, facultatively anaerobic, non-motile, and short rods to coccoid strains were isolated from the feces of the greater white-fronted geese (Anser albifrons) at Poyang Lake. The 16S rRNA gene sequences of strains 4H37-19T and 3HC-13 shared highest identity to that of Corynebacterium uropygiale Iso10T (97.8%). Phylogenetic and phylogenomic analyses indicated that strains 4H37-19T and 3HC-13 formed an independent clade within genus Corynebacterium and clustered with Corynebacterium uropygiale Iso10T. The average nucleotide identity and digital DNA-DNA hybridization value between strains 4H37-19T and 3HC-13 and members within genus Corynebacterium were all below 95% and 70%, respectively. The genomic G + C content of strains 4H37-19T and 3HC-13 was 52.5%. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), phosphatidylcholine, and phosphatidyl inositol mannosides (PIM) were the major polar lipids, with C18:1ω9c, C16:0, and C18:0 as the major fatty acids, and MK-8 (H4), MK-8(H2), and MK-9(H2) as the predominant respiratory quinones. The major whole cell sugar was arabinose, and the cell wall included mycolic acids. The cell wall peptidoglycan contained meso-diaminopimelic acid (meso-DAP). The polyphasic taxonomic data shows that these two strains represent a novel species of the genus Corynebacterium, for which the name Corynebacterium poyangense sp. nov. is proposed. The type strain of Corynebacterium poyangense is 4H37-19T (=GDMCC 1.1738T = KACC 21671T).

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Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023
Erik Munson, Claire R. Burbick, Sara D. Lawhon, Trinity Krueger, Elena Ruiz-Reyes, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Keratokonjunktivitisli bir tavuktan Corynebacterium spp. ve Arcanobacterium spp. izolasyonu
Hüban GÖÇMEN, Banur BOYNUKARA
Veteriner Hekimler Derneği Dergisi.2023; 94(2): 161. CrossRef

The periplasmic chaperone protein Psg_2795 contributes to the virulence of Pseudomonas savastanoi pv. glycinea: the causal agent of bacterial blight of soybean: Xiuhua Wang , Xiaoyan Zhang , Bao-Hui Lu , Jie Gao; J. Microbiol. 2022;60(5):478-487. Published online March 4, 2022; DOI: https://doi.org/10.1007/s12275-022-1469-5

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Abstract

Pseudomonas savastanoi pv. glycinea (Psg, also named P. syringae pv. glycinea and P. amygdali pv. glycinea) is the causative agent of bacterial blight in soybean. The identification of virulence factors is essential for understanding the pathogenesis of Psg. In this study, a mini-Tn5 transposon mutant library of Psg strain PsgNC12 was screened on soybean, and one low-virulent mini-Tn5 mutant, designated as 4573, was identified. Sequence analysis of the 4573-mutant revealed that the mini-Tn5 transposon was inserted in the Psg_2795 gene. Psg_2795 encodes a FimC-domain protein that is highly conserved in Pseudomonas. Further analysis revealed that the mutation and knockout of Psg_2795 results in a reduced virulence phenotype on soybean, decreased motility, weakened bacterial attachment to a glass surface and delayed the population growth within soybean leaves. The phenotype of the 4573-mutant could be complemented nearly to wild-type levels using an intact Psg_2795 gene. Collectively, our results demonstrate that Psg_2795 plays an important role in the virulence, motility, attachment and the population growth of PsgNC12 in soybean. This finding provides a new insight into the function of periplasmic chaperone proteins in a type I pilus and provides reference information for identifying Psg_2795 homologues in P. savastanoi and other bacteria.

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Vt35 antitoxin plays a central regulatory role in virulence of Pseudomonas savastanoi pv. glycinea on soybean
Viet Tru Nguyen, Nanami Sakata, Takako Ishiga, Giyu Usuki, Yoshiteru Hashimoto, Yasuhiro Ishiga
Journal of General Plant Pathology.2023; 89(4): 211. CrossRef

Characterization and validation of an alternative reference bacterium Korean Pharmacopoeia Staphylococcus aureus strain: Ye Won An , Young Sill Choi , Mi-ran Yun , Chihwan Choi , Su Yeon Kim; J. Microbiol. 2022;60(2):187-191. Published online January 7, 2022; DOI: https://doi.org/10.1007/s12275-022-1335-5

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Abstract

The National Culture Collection of Pathogens (NCCP) is a microbial resource bank in Korea that collects pathogen resources causing infectious disease in human and distributes them for research and education. The NCCP bank attempts to discover strains with various characteristics and specific purposes to provide diverse resources to researchers. Staphylococcus aureus American Type Culture Collection (ATCC) 6538P is used as a reference strain in the microbial assay for antibiotics in the Korean and in the United States Pharmacopoeias. We aimed to analyze domestically isolated microbial resources from the NCCP to replace the S. aureus reference strain. Staphylococcus aureus strains were identified using matrix- assisted laser desorption/ionization time-of-flight mass spectrometry and the VITEK-2 system and characterized by multilocus sequence typing, 16S rRNA sequencing, and antibiotic susceptibility testing. Several candidate strains had similar characteristics as the reference strain. Among them, the nucleotide sequence of the 16S rRNA region of NCCP 16830 was 100% identical to that of the reference strain; it was sensitive to six types of antibiotics and showed results most similar to the reference strain. A validity evaluation was conducted using the cylinder-plate method. NCCP 16830 presented valid results and had the same performance as ATCC 6538P; therefore, it was selected as an alternative candidate strain.

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Bacterial composition of refrigerators in households and inactivation of airborne Staphylococcus aureus using a TiO2-UVLED module in a 512 L aerobiology chamber
So-Seum Yong, Jae-Ik Lee, Dong-Hyun Kang
Food Microbiology.2023; 114: 104274. CrossRef

Constantimarinum furrinae gen. nov., sp. nov., a marine bacterium isolated from saline volcanic rock aquifer (lava seawater) at Jeju Island, Republic of Korea: Sung-Hyun Yang , Hyun-Myung Oh , Mi-Jeong Park , Dongil Jang , Kae Kyoung Kwon; J. Microbiol. 2022;60(1):11-17. Published online December 29, 2021; DOI: https://doi.org/10.1007/s12275-022-1468-6

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Abstract

A Gram-stain-negative, aerobic, rod-shaped (0.3–0.5 × 1.0– 1.9 μm), non-motile marine bacterium designated as ALE3EIT was isolated from a saline volcanic rock aquifer (lava seawater) on Jeju Island, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain ALE3EIT showed high similarity to ‘Altibacter lentus’ JLT2010T (97.2%), followed by Marixanthomonas ophiurae KMM 3046T (94.5%). Growth was observed at 10–41°C (optimum, 30°C), at pH 6.0–8.5 (optimum, pH 7.5) and at 0.5–8% (optimum, 4.0%) NaCl. The predominant cellular fatty acids were iso-C15:0 (23.5%), iso-C16:0 (10.2%), iso-C16:0 3OH (10.5%), and iso-C17:0 3OH (16.8%). The DNA G + C contents was 40.4 mol%. The major respiratory quinone was MK-6. The major polar lipids were determined to be phosphatidylethanolamine, two unidentified glycolipids, and two unidentified aminolipids. Several phenotypic characteristics such as production of acetoin, activities of arginine dihydrolase and acid phosphatase, and utilization pattern of carbon sources differentiate strain ALE3EIT from ‘A. lentus’ JLT2010T. Activities of the lipase, trypsin, α- chymotrypsin and gelatinase and utilization pattern of carbon sources differentiate strain ALE3EIT from M. ophiurae KMM 3046T. The genome of strain ALE3EIT is 3.0 Mbp long and its ANI and AAI values against ‘A. lentus’ JLT2010T were 76.58 and 72.76, respectively, however, AAI values against members in other genera were lower than 72%. The phylogenomic tree inferred by PhyloPhlAn clearly differentiated the strain ALE3EIT together with strain JLT2010T from other genera in the Falvobacteriaceae. This polyphasic taxonomic data indicates that strain ALE3EIT should be identified as a novel species in the genus ‘Altibacter’, however, the name has not been validated. Therefore, the strain is classified as a novel genus and is proposed as Constantimarinum furrinae gen. nov., sp. nov. The type strain is ALE3EIT (= KCCM 43303T = JCM 33022T).

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Comparison of the anti-inflammatory effects of carotenoids-rich product from microalgal mass-cultured between natural seawater and magma seawater
Jayeon Cheon, Eun-A Kim, Nalae Kang, Taeho Kim, Lei Wang, Soo-Jin Heo, Seon-Heui Cha
Biocatalysis and Agricultural Biotechnology.2024; 62: 103420. CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Comparative genomics analysis of Pediococcus acidilactici species: Zhenzhen Li , Qi Song , Mingming Wang , Junli Ren , Songling Liu , Shancen Zhao; J. Microbiol. 2021;59(6):573-583. Published online May 15, 2021; DOI: https://doi.org/10.1007/s12275-021-0618-6

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Abstract

Pediococcus acidilactici is a reliable bacteriocin producer and a promising probiotic species with wide application in the food and health industry. However, the underlying genetic features of this species have not been analyzed. In this study, we performed a comprehensive comparative genomic analysis of 41 P. acidilactici strains from various ecological niches. The bacteriocin production of 41 strains were predicted and three kinds of bacteriocin encoding genes were identified in 11 P. acidilactici strains, namely pediocin PA-1, enterolysin A, and colicin-B. Moreover, whole-genome analysis showed a high genetic diversity within the population, mainly related to a large proportion of variable genomes, mobile elements, and hypothetical genes obtained through horizontal gene transfer. In addition, comparative genomics also facilitated the genetic explanation of the adaptation for host environment, which specify the protection mechanism against the invasion of foreign DNA (i.e. CRISPR/Cas locus), as well as carbohydrate fermentation. The 41 strains of P. acidilactici can metabolize a variety of carbon sources, which enhances the adaptability of this species and survival in different environments. This study evaluated the antibacterial ability, genome evolution, and ecological flexibility of P. acidilactici from the perspective of genetics and provides strong supporting evidence for its industrial development and application.

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Pediococcus acidilactici Y01 reduces HFD-induced obesity via altering gut microbiota and metabolomic profiles and modulating adipose tissue macrophage M1/M2 polarization
Yujing Wang, Yu Xue, Huan Xu, Qian Zhu, Kaili Qin, Zhonglei He, Aixiang Huang, Min Mu, Xinrong Tao
Food & Function.2025;[Epub] CrossRef
Draft genome sequence of Pediococcus acidilactici 3G3 isolated from Philippine fermented pork
Zachary B. Lara, Mia Beatriz C. Amoranto, Francisco B. Elegado, Leslie Michelle M. Dalmacio, Marilen Parungao Balolong, Catherine Putonti
Microbiology Resource Announcements.2024;[Epub] CrossRef
The Potential of Pediococcus acidilactici Cell-Free Supernatant as a Preservative in Food Packaging Materials
Katherine Kho, Adinda Darwanti Kadar, Mario Donald Bani, Ihsan Tria Pramanda, Leon Martin, Matthew Chrisdianto, Ferren Pratama, Putu Virgina Partha Devanthi
Foods.2024; 13(5): 644. CrossRef
The complete genome sequences of the two novel probiotics were isolated from the human gut microbiota: Pediococcus acidilactici WNYM01 and Pediococcus acidilactici WNYM02, vitamin B9, and B2-producers
Wagiha S. Elkalla, Yasser M. Ragab, Mohamed A. Ramadan, Nahla M. Mansour
Egyptian Pharmaceutical Journal.2024; 23(4): 702. CrossRef
Effects of Pediococcus acidilactici and Rhizopus Oryzae on protein degradation and flavor formation in fermented mutton sausages
Zihan Li, Wei Su, Yingchun Mu, Qi Qi, Li Jiang
LWT.2024; 213: 117075. CrossRef
Putative Probiotic Ligilactobacillus salivarius Strains Isolated from the Intestines of Meat-Type Pigeon Squabs
Shaoqi Tian, Yinhong Jiang, Qiannan Han, Chuang Meng, Feng Ji, Bin Zhou, Manhong Ye
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Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase: Jisub Hwang , Chang-Sook Jeong , Chang Woo Lee , Seung Chul Shin , Han-Woo Kim , Sung Gu Lee , Ui Joung Youn , Chang Sup Lee , Tae-Jin Oh , Hak Jun Kim , Hyun Park , Hyun Ho Park , Jun Hyuck Lee; J. Microbiol. 2020;58(7):606-613. Published online April 22, 2020; DOI: https://doi.org/10.1007/s12275-020-0089-1

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Abstract

Crystal structures of enoyl-coenzyme A (CoA) isomerase from Bosea sp. PAMC 26642 (BoECI) and enoyl-CoA hydratase from Hymenobacter sp. PAMC 26628 (HyECH) were determined at 2.35 and 2.70 Å resolution, respectively. BoECI and HyECH are members of the crotonase superfamily and are enzymes known to be involved in fatty acid degradation. Structurally, these enzymes are highly similar except for the orientation of their C-terminal helix domain. Analytical ultracentrifugation was performed to determine the oligomerization states of BoECI and HyECH revealing they exist as trimers in solution. However, their putative ligand-binding sites and active site residue compositions are dissimilar. Comparative sequence and structural analysis revealed that the active site of BoECI had one glutamate residue (Glu135), this site is occupied by an aspartate in some ECIs, and the active sites of HyECH had two highly conserved glutamate residues (Glu118 and Glu138). Moreover, HyECH possesses a salt bridge interaction between Glu98 and Arg152 near the active site. This interaction may allow the catalytic Glu118 residue to have a specific conformation for the ECH enzyme reaction. This salt bridge interaction is highly conserved in known bacterial ECH structures and ECI enzymes do not have this type of interaction. Collectively, our comparative sequential and structural studies have provided useful information to distinguish and classify two similar bacterial crotonase superfamily enzymes.

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User guide for the discovery of potential drugs via protein structure prediction and ligand docking simulation: Bilal Shaker , Myung-Sang Yu , Jingyu Lee , Yongmin Lee , Chanjin Jung , Dokyun Na; J. Microbiol. 2020;58(3):235-244. Published online February 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9563-z

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Abstract

Due to accumulating protein structure information and advances in computational methodologies, it has now become possible to predict protein-compound interactions. In biology, the classic strategy for drug discovery has been to manually screen multiple compounds (small scale) to identify potential drug compounds. Recent strategies have utilized computational drug discovery methods that involve predicting target protein structures, identifying active sites, and finding potential inhibitor compounds at large scale. In this protocol article, we introduce an in silico drug discovery protocol. Since multi-drug resistance of pathogenic bacteria remains a challenging problem to address, UDP-N-acetylmuramate- L-alanine ligase (murC) of Acinetobacter baumannii was used as an example, which causes nosocomial infection in hospital setups and is responsible for high mortality worldwide. This protocol should help microbiologists to expand their knowledge and research scope.

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Garden microbiomes of Apterostigma dentigerum and Apterostigma pilosum fungus-growing ants (Hymenoptera: Formicidae): Cely T. González , Kristin Saltonstall , Hermógenes Fernández-Marín; J. Microbiol. 2019;57(10):842-851. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-8639-0

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Abstract

Fungus-growing ants share a complex symbiosis with microbes, including fungal mutualists, antibiotic-producing bacteria, and fungal pathogens. The bacterial communities associated with this symbiosis are poorly understood but likely play important roles in maintaining the health and function of fungal gardens. We studied bacterial communities in gardens of two Apterostigma species, A. dentigerum, and A. pilosum, using next-generation sequencing to evaluate differences between the two ant species, their veiled and no-veiled fungal garden types, and across three collection locations. We also compared different parts of nests to test for homogeneity within nests. Enterobacteriaceae dominated gardens of both species and common OTUs were shared across both species and nest types. However, differences in community diversity were detected between ant species, and in the communities of A. dentigerum veiled and no-veiled nests within sites. Apterostigma pilosum had a higher proportion of Phyllobacteriaceae and differed from A. dentigerum in the proportions of members of the order Clostridiales. Within A. dentigerum, nests with veiled and no-veiled fungus gardens had similar taxonomic profiles but differed in the relative abundance of some groups, with veiled gardens having more Rhodospirillaceae and Hyphomicrobiaceae, and no-veiled having more Xanthomonadaceae and certain genera in the Enterobacteriaceae C. However, bacterial communities in Apterostigma fungal gardens are highly conserved and resemble those of the nests of other attine ants with dominant taxa likely playing a role in biomass degradation and defense. Further work is required to understand and explain how bacterial community composition of fungus-growing nests is maintained.

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Review

REVIEW] Recent paradigm shift in the assembly of bacterial tripartite efflux pumps and the type I secretion system: Inseong Jo , Jin-Sik Kim , Yongbin Xu , Jaekyung Hyun , Kangseok Lee , Nam-Chul Ha; J. Microbiol. 2019;57(3):185-194. Published online February 26, 2019; DOI: https://doi.org/10.1007/s12275-019-8520-1

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Abstract

Tripartite efflux pumps and the type I secretion system of Gram-negative bacteria are large protein complexes that span the entire cell envelope. These complexes expel antibiotics and other toxic substances or transport protein toxins from bacterial cells. Elucidating the binary and ternary complex structures at an atomic resolution are crucial to understanding the assembly and working mechanism. Recent advances in cryoelectron microscopy along with the construction of chimeric proteins drastically shifted the assembly models. In this review, we describe the current assembly models from a historical perspective and emphasize the common assembly mechanism for the assembly of diverse tripartite pumps and type I secretion systems.

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Journal Article

Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables: Joon Yong Kim , Juseok Kim , In-Tae Cha , Min Young Jung , Hye Seon Song , Yeon Bee Kim , Changsu Lee , Seung-Yeon Kang , Jin-Woo Bae , Yoon-E Choi , Tae-Woon Kim , Seong Woon Roh; J. Microbiol. 2019;57(1):30-37. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-019-8487-y

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Abstract

White colony-forming yeasts (WCFYs) often appear in fermented foods, depending on the storage method. Despite the ongoing research on fermented foods, the community and genome features of WCFYs have not been well studied. In this study, the community structures of WCFYs on fermented vegetables (kimchi) prepared with various raw materials were investigated using deep sequencing. Only eight operational taxonomic units (OTUs) were detected, indicating that the community structure of WCFYs on kimchi is very simple. The five most abundant OTUs represented Pichia kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl- tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables.

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Mi-Ju Kim, Sung-gi Min, So Won Shin, Jiyong Shin, Hae-Yeong Kim
Food Control.2021; 125: 107984. CrossRef
Yarrowia lipolytica: a multitalented yeast species of ecological significance
Dmitry Mamaev, Renata Zvyagilskaya
FEMS Yeast Research.2021;[Epub] CrossRef
ODFM, an omics data resource from microorganisms associated with fermented foods
Tae Woong Whon, Seung Woo Ahn, Sungjin Yang, Joon Yong Kim, Yeon Bee Kim, Yujin Kim, Ji-Man Hong, Hojin Jung, Yoon-E Choi, Se Hee Lee, Seong Woon Roh
Scientific Data.2021;[Epub] CrossRef
Growth Inhibitory Effect of Garlic Powder and Cinnamon Extract on White Colony-Forming Yeast in Kimchi
Mi-Ju Kim, Seong-Eun Kang, Chang Hee Jeong, Sung-Gi Min, Sung Wook Hong, Seong Woon Roh, Deok-Young Jhon, Tae-Woon Kim
Foods.2021; 10(3): 645. CrossRef
Halotolerant Yeasts: Biodiversity and Potential Application
O.D. Ianieva
Mikrobiolohichnyi Zhurnal.2020; 82(5): 65. CrossRef
Impact of fermentation conditions on the diversity of white colony-forming yeast and analysis of metabolite changes by white colony-forming yeast in kimchi
Mi-Ju Kim, Hae-Won Lee, Joon Yong Kim, Seong Eun Kang, Seong Woon Roh, Sung Wook Hong, Seung Ran Yoo, Tae-Woon Kim
Food Research International.2020; 136: 109315. CrossRef
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María Laura Raymond Eder, Alberto Luis Rosa
Molecular Genetics and Genomics.2020; 295(3): 685. CrossRef
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Se Hee Lee, Tae Woong Whon, Seong Woon Roh, Che Ok Jeon
Applied Microbiology and Biotechnology.2020; 104(18): 7731. CrossRef
Draft Genome Sequences of Two Isolates of the Yeast Kazachstania servazzii Recovered from Soil in Ireland
Lynne Faherty, Clifton Lewis, Matt McElheron, Niall Garvey, Róisín Duggan, Ben Shovlin, Tadhg Ó Cróinín, Kevin P. Byrne, Caoimhe E. O’Brien, Kenneth H. Wolfe, Geraldine Butler, Antonis Rokas
Microbiology Resource Announcements.2019;[Epub] CrossRef
Effect of lactic acid bacteria on phenyllactic acid production in kimchi
Sera Jung, Hyelyeon Hwang, Jong-Hee Lee
Food Control.2019; 106: 106701. CrossRef

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