Journal of Microbiology

Volume 60(8); August 2022

Review

[MINIREVIEW]Glaciers as microbial habitats: current knowledge and implication: Soyeon Kim , Hanbyul Lee , Soon-Do Hur , Woo Jun Sul , Ok-Sun Kim; J. Microbiol. 2022;60(8):767-779. Published online July 29, 2022; DOI: https://doi.org/10.1007/s12275-022-2275-9

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Abstract: Glaciers, formed from the gradual accumulation of snow, can be continuous records representing past environments and recognized as a time capsule of our planetary evolution. Due to extremely harsh conditions, glacial ice has long been considered an uninhabitable ecosystem for microorganisms to sustain their life. However, recent developments in microbiological analysis techniques revealed the presence of unexpectedly diverse microbial strains. Glacial microorganisms could also provide valuable information, including not only biological diversity and structure but also molecular systematics, metabolic profiles, and evolutionary changes from the past climate and ecosystem. However, there are several obstacles in investigating the glacier environment, such as low regional accessibility, technical difficulties of ice coring, potential contamination during the sampling process, and low microbial biomass. This review aims to summarize recent knowledge on decontamination methods, biomass, diversity based on culture-dependent and -independent methods, application of biological proxies, greenhouse gas production and adaptive strategies in glaciers from various regions and to imply further directions for a comprehensive understanding of habitatility in an icy world including outer of our planet.

Journal Articles

Dynamic colonization of gut microbiota and its influencing factors among the breast-feeding infants during the first two years of life: Ping Li , Xuelian Chang , Xiaoyu Chen , Tiantian Tang , Yajing Liu , Yu Shang , Kemin Qi; J. Microbiol. 2022;60(8):780-794. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-1641-y

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Abstract: The maturation of infant gut microbiota has lifelong implications on health, which has been proposed as the major events during the first year of life. However, little is known about their dynamic colonization and influencing elements among the first two-year infancy as well as into the adulthood. So based on the 16S rRNA sequencing data among 30 healthy breast-feeding mother-infant pairs with normal ranges of growth and development indicators from birth to two years old, the dynamic colonization of gut microbiota and its influencing factors were discussed using this birth cohort. Among these, we identified that the diversity of gut microbiota was significantly increased from six-month to two-year subgroups. The significantly dynamic trends of gut microbiota at the phylum (genus) level were that the percents of Firmicutes (Faecalibacterium, Blautia, Enterococcus, Subdoligranulum, Agathobacter, unidentified_Erysipelotrichaceae, Staphylococcus, unidentified_Ruminococcaceae, and Fusicatenibacter), Bacteroidetes and Verrucomicrobia were increased, while Actinobacteria (Bifidobacterium) and Proteobacteria (unidentified- Enterobacteriaceae and Klebsiella) were decreased with the increased ages from six months to two years old, which might simultaneously modulate the host pathways, such as the higher percents of chemoheterotrophy and fermentation, and lower percentages of nitrate_reduction, aerobic_chemoheterotrophy and so on. Furthermore, there were significant associations between maternal (milk microbiota, pre-pregnancy BMI, BMI increment during the pregnancy)/infant characteristics (BMI at birth and BMI gain), and the compositions of gut microbiota. However, no differences of gut microbiota were shown between the different sex and productive mode subgroups. Overall, the colonization of gut microbiota is significantly matured into the adulthood with the increased ages to two-years old and regulated by the above maternal/infant characteristics, which will provide a new direction for the host-gut microbiota interplay during the first two years of life.

Analysis of phylogenetic markers for classification of a hydrogen peroxide producing Streptococcus oralis isolated from saliva by a newly devised differential medium: Ha Pham , Thi Dieu Thuy Tran , Youri Yang , Jae-Hyung Ahn , Hor-Gil Hur , Yong-Hak Kim; J. Microbiol. 2022;60(8):795-805. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2261-2

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Abstract: Hydrogen peroxide (H2O2) is produced by alpha-hemolytic streptococci in aerobic conditions. However, the suitable method for detection of H2O2-producing streptococci in oral microbiota has not been setup. Here we show that o-dianisidine dye and horseradish peroxidase were useful in tryptic soy agar medium to detect and isolate H2O2-producing bacteria with the detection limit of one target colony in > 106 colony-forming units. As a proof, we isolated the strain HP01 (KCTC 21190) from a saliva sample using the medium and analyzed its characteristics. Further tests showed that the strain HP01 belongs to Streptococcus oralis in the Mitis group and characteristically forms short-chain streptococcal cells with a high capacity of acid tolerance and biofilm formation. The genome analysis revealed divergence of the strain HP01 from the type strains of S. oralis. They showed distinctive phylogenetic distances in their ROS-scavenging proteins, including superoxide dismutase SodA, thioredoxin TrxA, thioredoxin reductase TrxB, thioredoxin-like protein YtpP, and glutaredoxin- like protein NrdH, as well as a large number of antimicrobial resistance genes and horizontally transferred genes. The concatenated ROS-scavenging protein sequence can be used to identify and evaluate Streptococcus species and subspecies based on phylogenetic analysis.

Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov., isolated from a freshwater stream: Miri S. Park , Hyeonuk Sa , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2022;60(8):806-813. Published online July 29, 2022; DOI: https://doi.org/10.1007/s12275-022-2298-2

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Abstract: Two Gram-stain-positive, aerobic, chemoheterotrophic, nonmotile, rod-shaped, and yellow-pigmented bacterial strains, designated IMCC34837T and IMCC34838T, were isolated from a freshwater stream. Results of 16S rRNA gene-based phylogenetic analyses showed that strains IMCC34837T and IMCC- 34838T shared 96.3% sequence similarity and were most closely related to Flavihumibacter profundi Chu64-6-1T (99.6%) and Flavihumibacter cheonanensis WS16T (96.4%), respectively. Complete whole-genome sequences of strains IMCC- 34837T and IMCC34838T were 5.0 Mbp and 4.3 Mbp of genome size with 44.5% and 47.9% of DNA G + C contents, respectively. Average nucleotide identity (ANI) and digital DNA- DNA hybridization (dDDH) values between the two strains were 70.0% and 17.9%, repectively, revealing that they are independent species. The two strains showed ≤ 75.2% ANI and ≤ 19.3% dDDH values to each closely related species of the genus Flavihumibacter, indicating that the two strains represent each novel species. Major fatty acid constituents of strain IMCC34837T were iso-C15:0, iso-C15:1 G and anteiso-C15:0 and those of strain IMCC34838T were iso-C15:0 and iso-C15:1 G. The predominant isoprenoid quinone detected in both strains was menaquinone-7 (MK-7). Major polar lipids of both strains were phosphatidylethanolamine, aminolipids, and glycolipids. Based on the phylogenetic and phenotypic characterization, strains IMCC34837T and IMCC34838T were considered to represent two novel species within the genus Flavihumibacter, for which the names Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov. are proposed with IMCC34837T (= KACC 21752T = NBRC 115292T) and IMCC34838T (= KACC 21753T = NBRC 115293T) as the type strains, respectively.

Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea: Ye Chen , Yu Zhen , Jili Wan , Siqi Li , Jiayin Liu , Guodong Zhang , Tiezhu Mi; J. Microbiol. 2022;60(8):814-822. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2022-2

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Abstract: The differences in methanogen abundance and community composition were investigated between nearshore and offshore sediments in the South Yellow Sea (SYS). Shannon, Simpson, and Chao1 indices revealed a higher diversity of methanogens in the nearshore sediments than in the offshore sediments. The Mann–Whitney U test demonstrated that the relative abundance of Methanococcoides was significantly higher in the offshore sediments, while the relative abundances of Methanogenium, Methanosarcina, Methanosaeta, Methanolinea, and Methanomassiliicoccus were significantly higher in the nearshore sediments (P < 0.05). The abundance of the mcrA gene in the nearshore sediments was significantly higher than that in the offshore sediments. Furthermore, a similar vertical distribution of the methanogen and sulfatereducing bacteria (SRB) abundances was observed in the SYS sediments, implying there is potential cooperation between these two functional microbes in this environment. Finally, total organic carbon (TOC) was significantly correlated with methanogen community composition.

Pat- and Pta-mediated protein acetylation is required for horizontallyacquired virulence gene expression in Salmonella Typhimurium: Hyojeong Koo , Eunna Choi , Shinae Park , Eun-Jin Lee , Jung-Shin Lee; J. Microbiol. 2022;60(8):823-831. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2095-y

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Abstract: Salmonella Typhimurium is a Gram-negative facultative pathogen that causes a range of diseases, from mild gastroenteritis to severe systemic infection in a variety of animal hosts. S. Typhimurium regulates virulence gene expression by a silencing mechanism using nucleoid-associated proteins such as Histone-like Nucleoid Structuring protein (H-NS) silencing. We hypothesize that the posttranslational modification, specifically protein acetylation, of proteins in gene silencing systems could affect the pathogenic gene expression of S. Typhimurium. Therefore, we created acetylation-deficient mutant by deleting two genes, pat and pta, which are involved in the protein acetylation pathway. We observed that the pat and pta deletion attenuates mouse virulence and also decreases Salmonella’s replication within macrophages. In addition, the Δpat Δpta strain showed a decreased expression of the horizontally-acquired virulence genes, mgtC, pagC, and ugtL, which are highly expressed in low Mg2+. The decreased virulence gene expression is possibly due to higher H-NS occupancy to those promoters because the pat and pta deletion increases H-NS occupancy whereas the same mutation decreases occupancy of RNA polymerase. Our results suggest that Pat- and Pta-mediated protein acetylation system promotes the expression of virulence genes by regulating the binding affinity of H-NS in S. Typhimurium.

Effects of tryptophan and phenylalanine on tryptophol production in Saccharomyces cerevisiae revealed by transcriptomic and metabolomic analyses: Xiaowei Gong , Huajun Luo , Liu Hong , Jun Wu , Heng Wu , Chunxia Song , Wei Zhao , Yi Han , Ya Dao , Xia Zhang , Donglai Zhu , Yiyong Luo; J. Microbiol. 2022;60(8):832-842. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2059-2

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Abstract: Tryptophol (TOL) is a metabolic derivative of tryptophan (Trp) and shows pleiotropic effects in humans, plants and microbes. In this study, the effect of Trp and phenylalanine (Phe) on TOL production in Saccharomyces cerevisiae was determined, and a systematic interpretation of TOL accumulation was offered by transcriptomic and metabolomic analyses. Trp significantly promoted TOL production, but the output plateaued (231.02−266.31 mg/L) at Trp concentrations ≥ 0.6 g/L. In contrast, Phe reduced the stimulatory effect of Trp, which was strongly dependent on the Phe concentration. An integrated genomic, transcriptomic, and metabolomic analysis revealed that the effect of Trp and Phe on TOL production was mainly related to the transamination and decarboxylation of the Ehrlich pathway. Additionally, other genes, including thiamine regulon genes (this), the allantoin catabolic genes dal1, dal2, dal4, and the transcriptional activator gene aro80, may play important roles. These findings were partly supported by the fact that the thi4 gene was involved in TOL production, as shown by heterologous expression analysis. To the best of our knowledge, this novel biological function of thi4 in S. cerevisiae is reported here for the first time. Overall, our findings provide insights into the mechanism of TOL production, which will contribute to TOL production using metabolic engineering strategies.

Fus3 and Tpk2 protein kinases regulate the phosphorylation-dependent functions of RNA helicase Dhh1 in yeast mating and Ste12 protein expression: Jaehee Hwang , Daehee Jung , Jinmi Kim; J. Microbiol. 2022;60(8):843-848. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2213-x

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Abstract: Decapping of mRNA is a key regulatory step for mRNA decay and translation. The RNA helicase, Dhh1, is known as a decapping activator and translation repressor in yeast Saccharomyces cerevisiae. Dhh1 also functions as a gene-specific positive regulator in the expression of Ste12, a mating-specific transcription factor. A previous study showed that the Nerminal phosphorylation of Dhh1 regulates its association with the mRNA-binding protein, Puf6, to affect the protein translation of Ste12. Here, we investigated the roles of the phosphorylated residues of Dhh1 in yeast mating process and Ste12 expression. The phospho-deficient mutation, DHH1- T10A, was associated with decreased diploid formation during mating and decreased level of the Ste12 protein in response to α-mating pheromone. A kinase overexpression analysis revealed that Ste12 protein expression was affected by overexpression of Fus3 MAP kinase or Tpk2 kinase. Tpk2 was shown to be responsible for phosphorylation of Dhh1 at Thr10. Our study shows that overexpression of Fus3 or Tpk2 alters the Dhh1-Puf6 protein interaction and thereby affects Ste12 protein expression.

Helicobacter pylori-mediated gastric pathogenesis is attenuated by treatment of 2-deoxyglucose and metformin: Hanfu Su , Eun-Jung Bak , Aeryun Kim , Kavinda Tissera , Jeong-Heon Cha , Sungil Jang; J. Microbiol. 2022;60(8):849-858. Published online June 22, 2022; DOI: https://doi.org/10.1007/s12275-022-2130-z

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Abstract: Helicobacter pylori infection causes chronic inflammation in the stomach, which is linked to the development of gastric cancer. The anti-inflammatory and anticancer effects of a glycolysis inhibitor 2-deoxyglucose (2DG) and an antidiabetic medication metformin (Met) have gotten attention. Using a Mongolian gerbil animal model, we investigated H. pylorimediated gastric pathogenesis and how this pathogenesis is influenced by 2DG and Met. Five-week-old male gerbils were infected with H. pylori strain 7.13. After 2 weeks of infection, gerbils were fed 2DG-containing food (0.03% w/w), Met-containing water (0.5% w/v), or both (Combi) for 2 (short-term) or 10 weeks (long-term). Gastric pathogenesis and host response to H. pylori infection were examined by macroscopic and histopathologic analysis of gerbils’ stomach. As a result, indicators of gastric pathogenesis by H. pylori infection including infiltration of polymorphonuclear neutrophils and lymphocytes, intestinal metaplasia, atrophy, and proliferation of gastric epithelial cells were attenuated by short-term administration of 2DG, Met, or Combi. When the infection was sustained for long-term, gastric pathogenesis in drug-treated gerbils was equivalent to that in untreated gerbils, with the exception that the infiltration of neutrophil was reduced by 2DG. Colonization of H. pylori in stomach was unaffected by both short- and long-term treatments. Our findings demonstrate that the progression of gastric pathogenesis induced by H. pylori infection can be attenuated by the shortterm individual or combinational treatment of 2DG and Met, implying that 2DG or Met could be considered as a treatment option for gastric diseases in the early stages of infection.

Eradication of drug-resistant Acinetobacter baumannii by cell-penetrating peptide fused endolysin: Jeonghyun Lim , Jaeyeon Jang , Heejoon Myung , Miryoung Song; J. Microbiol. 2022;60(8):859-866. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2107-y

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Abstract: Antimicrobial agents targeting peptidoglycan have shown successful results in eliminating bacteria with high selective toxicity. Bacteriophage encoded endolysin as an alternative antibiotics is a peptidoglycan degrading enzyme with a low rate of resistance. Here, the engineered endolysin was developed to defeat multiple drug-resistant (MDR) Acinetobacter baumannii. First, putative endolysin PA90 was predicted by genome analysis of isolated Pseudomonas phage PBPA. The His-tagged PA90 was purified from BL21(DE3) pLysS and tested for the enzymatic activity using Gram-negative pathogens known for having a high antibiotic resistance rate including A. baumannii. Since the measured activity of PA90 was low, probably due to the outer membrane, cell-penetrating peptide (CPP) DS4.3 was introduced at the N-terminus of PA90 to aid access to its substrate. This engineered endolysin, DS-PA90, completely killed A. baumannii at 0.25 μM, at which concentration PA90 could only eliminate less than one log in CFU/ml. Additionally, DS-PA90 has tolerance to NaCl, where the ~50% of activity could be maintained in the presence of 150 mM NaCl, and stable activity was also observed with changes in pH or temperature. Even MDR A. baumannii strains were highly susceptible to DS-PA90 treatment: five out of nine strains were entirely killed and four strains were reduced by 3–4 log in CFU/ml. Consequently, DS-PA90 could protect waxworm from A. baumannii-induced death by ~70% for ATCC 17978 or ~44% for MDR strain 1656-2 infection. Collectively, our data suggest that CPP-fused endolysin can be an effective antibacterial agent against Gramnegative pathogens regardless of antibiotics resistance mechanisms.

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