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- Volume 60(2); February 2022
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Journal Articles
- Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
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Wentao Zhu , Juan Zhou , Shan Lu , Jing Yang , Xin-He Lai , Dong Jin , Ji Pu , Yuyuan Huang , Liyun Liu , Zhenjun Li , Jianguo Xu
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J. Microbiol. 2022;60(2):137-146. Published online November 26, 2021
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DOI: https://doi.org/10.1007/s12275-022-1428-1
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Abstract
- Four novel Gram-negative, mesophilic, aerobic, motile, and
cocci-shaped strains were isolated from tick samples (strains
546T and 573) and respiratory tracts of marmots (strains 1318T
and 1311). The 16S rRNA gene sequencing revealed that strains
546T and 573 were 97.8% identical to Roseomonas wenyumeiae
Z23T, whereas strains 1311 and 1318T were 98.3% identical
to Roseomonas ludipueritiae DSM 14915T. In addition,
a 98.0% identity was observed between strains 546T and 1318T.
Phylogenetic and phylogenomic analyses revealed that strains
546T and 573 clustered with R. wenyumeiae Z23T, whereas
strains 1311 and 1318T grouped with R. ludipueritiae DSM
14915T. The average nucleotide identity between our isolates
and members of the genus Roseomonas was below 95%. The
genomic G+C content of strains 546T and 1318T was 70.9% and
69.3%, respectively. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine
(PE) were the major polar lipids, with
Q-10 as the predominant respiratory quinone. According to
all genotypic, phenotypic, phylogenetic, and phylogenomic
analyses, the four strains represent two novel species of the
genus Roseomonas, for which the names Roseomonas haemaphysalidis
sp. nov. and Roseomonas marmotae sp. nov. are
proposed, with 546T (= GDMCC 1.1780T = JCM 34187T) and
1318T (= GDMCC 1.1781T = JCM 34188T) as type strains,
respectively.
- Changpingibacter yushuensis gen. nov., sp. nov., isolated from fluvial sediment in Qinghai Tibet Plateau of China
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Yifan Jiao , Sihui Zhang , Jing Yang , Xin-He Lai , Kui Dong , Yanpeng Cheng , Mingchao Xu , Wentao Zhu , Shan Lu , Dong Jin , Ji Pu , Ying Huang , Liyun Liu , Suping Wang , Jianguo Xu
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J. Microbiol. 2022;60(2):147-155. Published online January 7, 2022
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DOI: https://doi.org/10.1007/s12275-022-1199-8
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Abstract
- Two facultatively anaerobic, short rod-shaped, non-motile,
Gram-stain-positive, unknown bacterial strains (JY-X040T
and JY-X174) were isolated from fluvial sediments of Tongtian
River in Yushu Tibetan Autonomous Prefecture, Qinghai
province, China. Cells formed translucent, gray, round and
convex colonies, with a diameter of less than 0.5 mm after 5
days of incubation at 30°C on brain heart infusion-5% sheep
blood agar. The 16S rRNA gene sequence similarity between
strain JY-X040T and Fudania jinshanensis 313T is 93.87%.
In the four phylogenetic trees constructed based on the 16S
rRNA gene and 423 core genes, the two isolates form an independent
branch, phylogenetically closest to F. jinshanensis
313T, but could not be classified as a member of the genus
Fudania or any other genus of the family Arcanobacteriaceae.
The DNA G + C content of strain JY-X040T was 57.8%. Calculation
results
of average nucleotide identity, digital DNADNA
hybridization value and amino acid identity between
strain JY-X040T and F. jinshanensis 313T are 69.9%, 22.9%,
and 64.1%. The major cellular fatty acids were C16:0 (23%)
and C18:1ω9c (22%). The cell-wall peptidoglycan type was A5α
(L-Lys-L-Ala-L-Lys-D-Glu). The polar lipids comprised diphosphatidylglycerol,
phosphatidylglycerol, phosphatidylinositol,
phosphatidylinositol mannoside and four unidentified components.
The whole-cell sugars contained rhamnose and ribose.
MK-10(H4) was the sole respiratory quinone. The minimum
inhibitory concentration of streptomycin was 32 μg/ml. All
physiological, biochemical, chemotaxonomic and genomic
characteristics support that strains JY-X040T and JY-X174
represent members of a novel species in a new genus, Changpingibacter
yushuensis gen. nov., sp. nov. The type strain is
JY-X040T (GDMCC 1.1996T = KCTC 49514T).
- Potato tillage method is associated with soil microbial communities, soil chemical properties, and potato yield
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Haiyan Ma , Chen Xie , Shunlin Zheng , Peihua Li , Hafsa Nazir Cheema , Jing Gong , Zhuqing Xiang , Juanjuan Liu , Jiahao Qin
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J. Microbiol. 2022;60(2):156-166. Published online January 7, 2022
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DOI: https://doi.org/10.1007/s12275-022-1060-0
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Abstract
- Intensive potato continuous cropping (IPCC) results in low
potato yields compared with non-intensive potato continuous
cropping (PCC) and potato-maize rotation (PMRC). However,
it is still unclear whether the degree of potato continuous cropping
obstacle is related to the soil environment formed by the
previous crop. To investigate the effect of planting potatoes
and planting maize after harvesting the spring potatoes on
soil chemical properties and soil microbial community structure,
an experiment was carried out in the same origin soil
environment over a period of seven years: (a) PCC, i.e., spring
planting; (b) IPCC, i.e., autumn and spring planting (IPCC);
(c) PMRC, i.e., spring potatoes and summer maize (PMRC),
and (d) fallow (CK). We confirmed that the potato yield under
PMRC was significantly higher than that under PCC and
IPCC. Under IPCC, soil total phosphorus content was significantly
higher than other treatments, whereas ammonium
nitrogen content was the lowest. Compared with PCC and
IPCC, PMRC had a higher ammonium nitrogen content and
lower total phosphorus content. The significantly different
fungal taxa in IPCC (Glomerellales, Plectosphaerella, Thelebolales)
may threaten the health of the plant and positive correlated
with soil total phosphorus, while other microbial taxa
in PMRC (Bacillales, Polythrincium, Helotiales) can mainly
promotes plant nitrogen uptake and protects plants against
diseases. The PMRC-promoting taxa were positively correlated
with the ammonium nitrogen content and negative correlated
with soil total phosphorus content. In summary, the
cropping systems might have affected potato yields by changed
soil microorganism community structures – especially fungal
community structures – and by the chemical properties of the
soils that also depends on microbes.
- Whole genome and RNA sequencing of oral commensal bacterium Streptococcus anginosus subsp. anginosus with vancomycin tolerance
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Kyu Hwan Kwack , Jae-Hyung Lee , Ji-Hoi Moon
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J. Microbiol. 2022;60(2):167-176. Published online January 7, 2022
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DOI: https://doi.org/10.1007/s12275-022-1425-4
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Abstract
- “Antibiotic tolerance” promotes the rapid subsequent evolution
of “antibiotic resistance,” however, it is often overlooked
because it is difficult to distinguish between tolerant
and susceptible organisms. A commensal bacterium S. anginosus
subsp. anginosus strain KHUD_S1, isolated from dental
biofilm was found to exhibit a high MBC/MIC ratio of 32
against vancomycin. We observed KHUD_S1 cells exposed
to vancomycin did not grow but maintained viability. Transmission
electron microscope showed KHUD_S1 cells possessed
a dense, thick capsule and maintained the cell wall integrity
upon vancomycin exposure. To infer the underlying
mechanisms of the vancomycin tolerance in KHUD_S1, we
performed whole genome sequencing and RNA sequencing.
The KHUD_S1 genome carried three genes encoding branching
enzymes that can affect peptidoglycan structure through
interpeptide bridge formation. Global gene expression profiling
revealed that the vancomycin-induced downregulation
of carbohydrate and inorganic ion transport/metabolism as
well as translation is less prominent in KHUD_S1 than in the
vancomycin susceptible strain KHUD_S3. Based on the transcriptional
levels of genes related to peptidoglycan synthesis,
KHUD_S1 was determined to have a 3D peptidoglycan architecture
distinct from KHUD_S3. It was found that, under
vancomycin exposure, the peptidoglycan was remodeled
through changes in the interpeptide bridge and transpeptidation
reactions. Collectively, these features of S. anginosus
KHUD_S1, including a dense capsule and differential gene
expression in peptidoglycan synthesis, may contribute to vancomycin
tolerance. Our results showing the occurrence of
vancomycin tolerance amongst oral commensal bacteria highlight
the need for considering future strategies for screening
of antibiotic tolerance as an effort to reduce antibiotic resistance.
- Meiotic prophase roles of Pds5 in recombination and chromosome condensation in budding yeast
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Jeong Hwan Joo , Hyun Ah Kang , Keun Pil Kim , Soogil Hong
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J. Microbiol. 2022;60(2):177-186. Published online February 1, 2022
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DOI: https://doi.org/10.1007/s12275-022-1635-9
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Abstract
- Genetic variation in eukaryotes is mediated during meiosis by
the exchange of genetic material between homologous chromosomes
to produce recombinant chromosomes. Cohesin is
essential to promote proper chromosome segregation, chromosome
morphogenesis, and recombination in meiotic cells.
Cohesin consists of three main subunits–Smc1, Smc3, and the
kleisin subunit Mcd1/Scc1 (Rec8 in meiosis)–and cohesin accessory
factors. In Saccharomyces cerevisiae, the cohesin regulatory
subunit Pds5 plays a role in homolog pairing, meiotic
axis formation, and interhomolog recombination. In this
study, we examine the prophase functions of Pds5 by performing
physical analysis of recombination and three-dimensional
high-resolution microscopy analysis to identify its roles in
meiosis-specific recombination and chromosome morphogenesis.
To investigate whether Pds5 plays a role in mitoticlike
recombination, we inhibited Mek1 kinase activity, which
result
ed in switching to sister template bias by Rad51-dependent
recombination. Reductions in double-strand breaks
and crossover products and defective interhomolog recombination
occurred in the absence of Pds5. Furthermore, recombination
intermediates, including single-end invasion
and double-Holliday junction, were reduced in the absence
of Pds5 with Mek1 kinase inactivation compared to Mek1
kinase inactivation cells. Interestingly, the absence of Pds5
result
ed in increasing numbers of chromosomes with hypercompaction
of the chromosome axis. Thus, we suggest that
Pds5 plays an essential role in recombination by suppressing
the pairing of sister chromatids and abnormal compaction
of the chromosome axis.
- Characterization and validation of an alternative reference bacterium Korean Pharmacopoeia Staphylococcus aureus strain
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Ye Won An , Young Sill Choi , Mi-ran Yun , Chihwan Choi , Su Yeon Kim
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J. Microbiol. 2022;60(2):187-191. Published online January 7, 2022
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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.
- Functional characterization of HigBA toxin-antitoxin system in an Arctic bacterium, Bosea sp. PAMC 26642
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Eunsil Choi , Ahhyun Huh , Changmin Oh , Jeong-Il Oh , Ho Young Kang , Jihwan Hwang
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J. Microbiol. 2022;60(2):192-206. Published online February 1, 2022
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DOI: https://doi.org/10.1007/s12275-022-1619-9
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Abstract
- Toxin-antitoxin (TA) systems are growth-controlling genetic
elements consisting of an intracellular toxin protein and its
cognate antitoxin. TA systems have been spread among microbial
genomes through horizontal gene transfer and are
now prevalent in most bacterial and archaeal genomes. Under
normal growth conditions, antitoxins tightly counteract the
activity of the toxins. Upon stresses, antitoxins are inactivated,
releasing activated toxins, which induce growth arrest or cell
death. In this study, among nine functional TA modules in
Bosea sp. PAMC 26642 living in Arctic lichen, we investigated
the functionality of BoHigBA2. BohigBA2 is located close to
a genomic island and adjacent to flagellar gene clusters. The
expression of BohigB2 induced the inhibition of E. coli growth
at 37°C, which was more manifest at 18°C, and this growth
defect was reversed when BohigA2 was co-expressed, suggesting
that this BoHigBA2 module might be an active TA
module in Bosea sp. PAMC 26642. Live/dead staining and
viable count analyses revealed that the BoHigB2 toxin had
a bactericidal effect, causing cell death. Furthermore, we demonstrated
that BoHigB2 possessed mRNA-specific ribonuclease
activity on various mRNAs and cleaved only mRNAs
being translated, which might impede overall translation and
consequently lead to cell death. Our study provides the insight
to understand the cold adaptation of Bosea sp. PAMC 26642
living in the Arctic.
- Characterization of East-Asian Helicobacter pylori encoding Western EPIYA-ABC CagA
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Kavinda Tissera , Myeong-A Kim , Jing Lai , Sacheera Angulmaduwa , Aeryun Kim , D. Scott Merrell , Ji-Hye Kim , Hanfu Su , Jeong-Heon Cha
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J. Microbiol. 2022;60(2):207-214. Published online November 10, 2021
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DOI: https://doi.org/10.1007/s12275-022-1483-7
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Abstract
- The polymorphic bacterial oncoprotein, CagA shows geography-
dependent variation in the C-terminal Glu-Pro-Ile-
Tyr-Ala (EPIYA) motifs; East-Asian H. pylori isolates carry
the ABD type while Western isolates carry the ABC type. In
Western isolates, the EPIYA-C motif is sometimes found in
multi-copy and this genotype is associated with disease severity.
Interestingly, a small number of East-Asian H. pylori
isolates have been found to carry Western ABC-type CagA.
To gain a better understanding of these unusual isolates, the
genomes of four Korean H. pylori clinical isolates carrying
ABC-type CagA were sequenced via third generation (Pac-
Bio SMRT) sequencing technology. The obtained data were
utilized for phylogenetic analysis as well as comparison of
additional virulence factors that are known to show geographic-
dependent polymorphisms. Three of four isolates indeed
belonged to the hpEastAsia group and showed typical East-
Asian polymorphism in virulence factors such as homA/B/C,
babA/B/C, and oipA. One isolate grouped to HpAfrica and
showed typical Western polymorphism of virulence factors
such as cagA, homA/B/C, and oipA. To understand the occurrence
of the multi-copy EPIYA-C motif genotype in an East-
Asian H. pylori background, the Korean clinical isolate, K154
was analyzed; this strain belonged to hpEastAsia but encoded
CagA EPIYA-ABCCCC. Based on DNA sequence homology
within the CagA multimerization (CM) sequence that flanked
the EPIYA-C motifs, we predicted that the number of C motifs
might change via homologous recombination. To test this
hypothesis, K154 was cultured for one generation and 287
single colonies were analyzed for the number of EPIYA-C
motifs using PCR-based screening and DNA sequencing verification.
Three out of 284 (1%) single colony isolates showed
changes in the number of EPIYA-C motifs in vitro; one isolate
increased to five EPIYA-C motifs, one decreased to three
EPIYA-C motifs, and one completely deleted the EPIYA-C
motifs. The capacity for dynamic changes in the number of
EPIYA-C repeats of CagA may play a role in generating important
intraspecies diversity in East-Asian H. pylori.
- A mucin-responsive hybrid two-component system controls Bacteroides thetaiotaomicron colonization and gut homeostasis
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Ju-Hyung Lee , Soo-Jeong Kwon , Ji-Yoon Han , Sang-Hyun Cho , Yong-Joon Cho , Joo-Hong Park
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J. Microbiol. 2022;60(2):215-223. Published online February 1, 2022
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DOI: https://doi.org/10.1007/s12275-022-1649-3
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Abstract
- The mammalian intestinal tract contains trillions of bacteria.
However, the genetic factors that allow gut symbiotic bacteria
to occupy intestinal niches remain poorly understood. Here,
we identified genetic determinants required for Bacteroides
thetaiotaomicron colonization in the gut using transposon
sequencing analysis. Transposon insertion in BT2391, which
encodes a hybrid two-component system, increased the competitive
fitness of B. thetaiotaomicron. The BT2391 mutant
showed a growth advantage in a mucin-dependent manner
and had an increased ability to adhere to mucus-producing
cell lines. The increased competitive advantage of the BT2391
mutant was dependent on the BT2392–2395 locus containing
susCD homologs. Deletion of BT2391 led to changes in
the expression levels of B. thetaiotaomicron genes during gut
colonization. However, colonization of the BT2391 mutant
promoted DSS colitis in low-fiber diet-fed mice. These results
indicate that BT2391 contributes to a sustainable symbiotic
relationship by maintaining a balance between mucosal
colonization and gut homeostasis.
- Vibrio vulnificus PlpA facilitates necrotic host cell death induced by the pore forming MARTX toxin
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Changyi Cho , Sanghyeon Choi , Myung Hee Kim , Byoung Sik Kim
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J. Microbiol. 2022;60(2):224-233. Published online February 1, 2022
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DOI: https://doi.org/10.1007/s12275-022-1448-x
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Abstract
- Opportunistic pathogen Vibrio vulnificus causes severe systemic
infection in humans with high mortality. Although multiple
exotoxins have been characterized in V. vulnificus, their
interactions and potential synergistic roles in pathogen-induced
host cell death have not been investigated previously.
By employing a series of multiple exotoxin deletion mutants,
we investigated whether specific exotoxins of the pathogen
functioned together to achieve severe and rapid necrotic cell
death. Human epithelial cells treated with V. vulnificus with
a plpA deletion background exhibited an unusually prolonged
cell blebbing, suggesting the importance of PlpA, a phospholipase
A2, in rapid necrotic cell death by this pathogen. Additional
deletion of the rtxA gene encoding the multifunctional
autoprocessing repeats-in-toxin (MARTX) toxin did not result
in necrotic cell blebs. However, if the rtxA gene was engineered
to produce an effector-free MARTX toxin, the cell
blebbing was observed, indicating that the pore forming activity
of the MARTX toxin is sufficient, but the MARTX toxin
effector domains are not necessary, for the blebbing. When
a recombinant PlpA was treated on the blebbed cells, the blebs
were completely disrupted. Consistent with this, MARTX
toxin-pendent rapid release of cytosolic lactate dehydrogenase
was significantly delayed in the plpA deletion background.
Mutations in other exotoxins such as elastase, cytolysin/hemolysin,
and/or extracellular metalloprotease did not affect
the bleb formation or disruption. Together, these findings indicate
that the pore forming MARTX toxin and the phospholipase
A2, PlpA, cooperate sequentially to achieve rapid necrotic
cell death by inducing cell blebbing and disrupting the
blebs, respectively.
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