Facemask acne attenuation through modulation of indirect microbiome interactions.

During the COVID-19 pandemic, facemasks played a pivotal role in preventing person-person droplet transmission of viral particles. However, prolonged facemask wearing causes skin irritations colloquially referred to as 'maskne' (mask + acne), which manifests as acne and contact dermatitis and is mostly caused by pathogenic skin microbes. Previous studies revealed that the putative causal microbes were anaerobic bacteria, but the pathogenesis of facemask-associated skin conditions remains poorly defined. We therefore characterized the role of the facemask-associated skin microbiota in the development of maskne using culture-dependent and -independent methodologies. Metagenomic analysis revealed that the majority of the facemask microbiota were anaerobic bacteria that originated from the skin rather than saliva. Previous work demonstrated direct interaction between pathogenic bacteria and antagonistic strains in the microbiome. We expanded this analysis to include indirect interaction between pathogenic bacteria and other indigenous bacteria classified as either 'pathogen helper (PH)' or 'pathogen inhibitor (PIn)' strains. In vitro screening of bacteria isolated from facemasks identified both strains that antagonized and promoted pathogen growth. These data were validated using a mouse skin infection model, where we observed attenuation of symptoms following pathogen infection. Moreover, the inhibitor of pathogen helper (IPH) strain, which did not directly attenuate pathogen growth in vitro and in vivo, functioned to suppress symptom development and pathogen growth indirectly through PH inhibitory antibacterial products such as phenyl lactic acid. Taken together, our study is the first to define a mechanism by which indirect microbiota interactions under facemasks can control symptoms of maskne by suppressing a skin pathogen.

Glucose Transport through N-Acetylgalactosamine Phosphotransferase System in Escherichia coli C Strain.

When ptsG, a glucose-specific phosphotransferase system (PTS) component, is deleted in Escherichia coli, growth can be severely poor because of the lack of efficient glucose transport. We discovered a new PTS transport system that could transport glucose through the growth-coupled experimental evolution of ptsG-deficient E. coli C strain under anaerobic conditions. Genome sequencing revealed mutations in agaR, which encodes a repressor of N-acetylgalactosamine (Aga) PTS expression in evolved progeny strains. RT-qPCR analysis showed that the expression of Aga PTS gene increased because of the loss-of-function of agaR. We confirmed the efficient Aga PTS-mediated glucose uptake by genetic complementation and anaerobic fermentation. We discussed the discovery of new glucose transporter in terms of different genetic backgrounds of E. coli strains, and the relationship between the pattern of mixed-acids fermentation and glucose transport rate.

Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design.

BACKGROUND: As the rapidly evolving characteristic of SARS-CoV-2 could result in false negative diagnosis, the use of as much sequence data as possible is key to the identification of conserved viral sequences. However, multiple alignment of massive genome sequences is computationally intensive. OBJECTIVE: To extract conserved sequences from SARS-CoV-2 genomes for the design of diagnostic PCR primers using a bioinformatics approach that can handle massive genomic sequences efficiently. METHODS: A total of 230,163 full-length viral genomes were retrieved from the NCBI SARS-CoV-2 Resources and GISAID EpiCoV database. This number was reduced to 14.11% following removal of 5'-/3'-untranslated regions and sequence dereplication. Fast, reference-based, multiple sequence alignments identified conserved sequences and specific primer sets were designed against these regions using a conventional tool. Primer sets chosen among the candidates were evaluated by in silico PCR and RT-qPCR. RESULTS: Out of 17 conserved sequences (totaling 4.3 kb), two primer sets targeting the nsp2 and ORF3a genes were picked that exhibited > 99.9% in silico amplification coverage against the original dataset (230,163 genomes) when a 5% mismatch between the primers and target was allowed. In addition, the primer sets successfully detected nine SARS-CoV-2 variant RNA samples (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Iota, and Kappa) in experimental RT-qPCR validations. CONCLUSION: In addition to the RdRp, E, N, and S genes that are targeted commonly, our approach can be used to identify novel primer targets in SARS-CoV-2 and should be a priority strategy in the event of novel SARS-CoV-2 variants or other pandemic outbreaks.

Genome Sequence of Ralstonia pseudosolanacearum SL1931, a Causal Phytopathogen of Bacterial Wilt Disease in Capsicum annuum and Nicotiana benthamiana.

Here, we report the genome sequence of Ralstonia pseudosolanacearum (R. solanacearum phylotype I) strain SL1931 (KACC10711), isolated from pepper (Capsicum annuum L.) stems; R. solanacearum is the causal pathogen of bacterial wilt. Strain SL1931 had a different type III effector profile than that of the reference genome strain GMI1000.

Visualization and Quantification of Genetically Adapted Microbial Cells During Preculture.

As culture history is known to affect the length of the lag phase and microbial cell growth, precultures are often grown in the same medium as the main culture for physiological adaptation and to reduce a prolonged lag time in some microbial cells. To understand the adaptation process of microbial cells during transfer from Luria-Bertani medium to minimal medium, we used the growth of Escherichia coli BL21(DE3) in succinate minimal medium as a model system. We observed that only one or two sequential transfers from minimal medium to fresh minimal medium accelerated the growth rate of BL21(DE3) cells. In addition, the number of large colonies (diameter ≥0.1 cm) on succinate agar increased with the number of transfers. Genome and transcript analyses showed that the C-to-T point mutation in large colony cells converted the inactive promoter of kgtP (known to encode α-ketoglutarate permease) to the active form, allowing efficient uptake of exogenous succinate. Moreover, we visualized the occurrence of genetically adapted cells with better fitness in real time and quantified the number of those cells in the microbial population during transfer to the same medium. Fluorescence microscopy showed the occurrence and increase of adapted mutant cells, which contain intracellular KgtP-fused green fluorescent proteins, as a result of the C-to-T mutation in the promoter of a fused kgtP-sfgfp during transfer to fresh medium. Flow cytometry revealed that the proportion of mutant cells increased from 1.75% (first transfer) to 12.16% (second transfer) and finally 70.79% (third transfer), explaining the shortened lag time and accelerated growth rate of BL21(DE3) cells during adaptation to the minimal medium. This study provides new insights into the genetic heterogeneity of microbial populations that aids microbial adaptability in new environments.

Heminiphilus faecis gen. nov., sp. nov., a member of the family Muribaculaceae, isolated from mouse faeces and emended description of the genus Muribaculum.

The novel strain AM35T was isolated from the faeces of C57BL/6 mice. These cells are strictly anaerobic, gram negative, oxidase negative, catalase positive, rod-shaped and non-motile. The strain produced creamy yellowish colonies on brain heart infusion (BHI) agar with hemin. Growth was investigated at 30-41 °C in the presence of 0.5-1.5% (w/v) NaCl at pH 6.5-8.5. Taxonomic analysis based on 16S rRNA gene sequencing revealed that strain AM35T is affiliated with the family Muribaculaceae and closely related to the genus Muribaculum. The genomic DNA G + C content of strain AM35T was 47.8 mol%. We detected the whole-cell sugars ribose and galactose; meso-2,6-diaminopimelic acid was absent. The major fatty acids (> 10%) were anteiso-C15:0 and iso-C15:0; the major polar lipid was phosphatidylethanolamine. The major respiratory quinones were MK-10 and MK-11. Based on our phylogenetic, phenotypic and chemotaxonomic analyses, strain AM35T represents a novel genus within the family Muribaculaceae, for which we propose the name Heminiphilus faecis gen. nov., sp. nov. The type strain of Heminiphilus faecis gen. nov., sp. nov. is AM35T (= KCTC 15907 T = DSM 110151 T).

When should retailers increase prices during a crisis? A longitudinal inquiry during the COVID-19 pandemic.

The consumer price index in the United States has increased since the COVID-19 outbreak. Little is known about how consumers perceive price increases during such a crisis. Our research focuses on how consumers' price fairness perceptions change at different time points of the COVID-19 pandemic. Results from a longitudinal study (April-May, 2020, N = 271) suggest that when the lockdown restrictions were eased, consumers experienced changes in affect and perceived price increases to be less unfair. Our analysis reveals that such an effect was driven by changes in positive affect rather than negative affect. This research advances pricing literature by showing that affect, triggered by external situations such as a crisis, influences price fairness perceptions over and above the negative affect induced by the price increase.

Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications.

Acinetobacter baumannii is a highly potent nosocomial pathogen that is associated with increased in-hospital mortality. Here, we investigated the changes in molecular characteristics of carbapenem-resistant A. baumannii (CRAB) isolated from the blood samples of patients admitted to a tertiary hospital in South Korea from January 2009 to July 2015. Whole genome sequencing using the Illumina MiSeq platform and multi-locus sequence typing (MLST) were performed for 98 CRAB clinical isolates. In silico analyses for the prediction of antimicrobial resistance and virulence factor genes were performed. Plasmid sequences, including complete forms, were reconstructed from the sequence reads. Epidemiologic data were collected from the hospital database. MLST using the Oxford scheme revealed 10 sequence types of CRAB, of which ST191 was the dominant type (n = 59). Although blaOXA-23 was shared by most analysed strains, the compositions of antimicrobial resistance determinants differed among sequence types. ST447 and ST451/ST1809 with a few resistance genes were isolated during the later years of the study period. The number of virulence genes increased, while that of ST191 did not change significantly over the investigation period. Intriguingly MLST types, compositions of antimicrobial resistance genes, and virulence genes had no association with clinical outcomes of CRAB bacteraemia. In conclusion, active changes in or accumulations of antimicrobial resistance determinants and virulence genes in CRAB were not observed during the research period. Molecular characteristics of CRAB had no association with clinical outcomes of CRAB bacteraemia.

Short-Term Adaptation Modulates Anaerobic Metabolic Flux to Succinate by Activating ExuT, a Novel D-Glucose Transporter in Escherichia coli.

The sugar phosphotransferase system (PTS) is an essential energy-saving mechanism, particularly under anaerobic conditions. Since the PTS consumes equimolar phosphoenolpyruvate to phosphorylate each molecule of internalized glucose in the process of pyruvate generation, its absence can adversely affect the mixed acid fermentation profile and cell growth under anaerobic conditions. In this study, we report that the ΔptsG mutant cells of Escherichia coli K-12 strain exhibited inefficient glucose utilization, produced a significant amount of succinate, and exhibited a low growth rate. However, cells adapted soon after and started to grow rapidly in the same batch culture. As a result, the adapted ΔptsG cells showed the same mixed acid fermentation profiles as the wild-type cells, which was attributed to the mutation of the mlc gene, a repressor of the D-mannose PTS, another transporter for D-glucose. Similar adaptations were observed in the cells with ΔptsGΔmanX and the cells with ΔptsI that resulted in the production of a substantial amount of succinate and fast growth rate. The genome sequencing showed the presence of null mutations in the exuR gene, which encodes a modulator of exuT-encoded non-PTS sugar transporter, in adapted ΔptsGΔmanX and ΔptsI strains. Results from the RT-qPCR analysis and genetic test confirmed that the enhanced expression of ExuT, a non-PTS sugar transporter, was responsible for the uptake of D-glucose, increased succinate production, and fast growth of adapted cells. In conclusion, our study showed that the regulatory network of sugar transporters can be modulated by short-term adaptation and that downstream metabolic flux could be significantly determined by the choice of sugar transporters.

An Outbreak of KPC-Producing Klebsiella pneumoniae Linked with an Index Case of Community-Acquired KPC-Producing Isolate: Epidemiological Investigation and Whole Genome Sequencing Analysis.

Aims: A hospital outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPN) linked with an index case of community-acquired infection occurred in an urban tertiary care hospital in Seoul, South Korea. Therefore, we performed an outbreak investigation and whole genome sequencing (WGS) analysis to trace the outbreak and investigate the molecular characteristics of the isolates. Results: From October 2014 to January 2015, we identified a cluster of three patients in the neurosurgery ward with sputum cultures positive for carbapenem-resistant KPN. An epidemiological investigation, including pulsed-field gel electrophoresis analysis was performed to trace the origins of this outbreak. The index patient's infection was community acquired. Active surveillance cultures using perirectal swabbing from exposed patients, identified one additional patient with KPC-producing KPN colonization. WGS analyses using PacBio RSII instruments were performed for four linked isolates. WGS revealed a genetic linkage of the four isolates belonging to the same sequence type (ST307). All KPN isolates harbored conjugative resistance plasmids, which has blaKPC-2 carbapenemase genes contained within the Tn4401 "a" isoform and other resistance genes. However, WGS showed only three isolates among four KPC-producing KPN were originated from a common origin. Conclusions: This report demonstrates the challenge that KPC-2-producing KPN with the conjugative resistance plasmid may spread not only in hospitals but also in community, and WGS can help to accurately characterize the outbreak.

Complete Genome Sequence of Lactobacillus crispatus AB70, Isolated from a Vaginal Swab from a Healthy Pregnant Korean Woman.

The vaginal bacterial strain AB70, belonging to the species Lactobacillus crispatus, was isolated from a vaginal swab from a healthy pregnant Korean woman. Here, we report the 2.37-Mb complete genome sequence of this strain.

Chronicle of a Soil Bacterium: Paenibacillus polymyxa E681 as a Tiny Guardian of Plant and Human Health.

The Gram-positive rhizosphere bacterium Paenibacillus polymyxa promotes plant growth and produces various antibiotics. Herein, we review research on this species over the past two and a half decades, and focus on the mechanisms of P. polymyxa strain E681, isolated from barley roots in the South Korea in 1995. Strain E681 has outstanding growth-promoting effects on barley, cucumber, pepper, sesame, and Arabidopsis thaliana and produces antimicrobial compounds that protect plants against pathogenic fungi, oomycetes, and bacteria. Induced systemic resistance elicited by treating seeds or roots with strain E681 is a possible mechanism for protecting systemic plant tissues from biotic and other environmental stresses. Genome sequencing has broadened our horizons for antibiotic development and other industrial applications beyond agricultural use. At least six gene clusters for the biosynthesis of antibiotics have been discovered, including polymyxin (pmx), which was recently re-instated as an antibiotic of last resort against Gram-negative drug-resistant bacteria. Three groups of antibiotic synthetases include the gene clusters that encode one for the non-ribosomal peptide polymyxin, fusaricidin, and tridecaptin, another for the lantibiotic paenilan, and the third for a polyketide. We successfully introduced the pmx gene cluster into the surrogate host Bacillus subtilis and created polymyxin derivatives by domain swapping. Furthermore, various E681 derivatives, including a high fusaricidin producer and strains lacking multi-antibiotics production, have been constructed by random mutagenesis and genome engineering. Thus, E681 is an important bacterium that contributes to both plant and human health.

Draft Genome Sequence of Atopobacter sp. Strain AH10, Isolated from a Vaginal Swab from Macaca fascicularis.

A bacterial strain belonging to the genus Atopobacter was isolated from a vaginal swab from a crab-eating macaque (Macaca fascicularis). Here, we report the draft genome sequence of this strain, AH10.

Genome Sequence of the Probiotic Strain Bacillus velezensis Variant polyfermenticus GF423.

The genome sequence of the commercial probiotic strain "Bacillus polyfermenticus" GF423 was determined. Comparison of the 4.1-Mb genome sequence revealed Bacillus velezensis FZB42 as its closest relative. Based on the genome sequence, we propose that this probiotic strain be renamed Bacillus velezensis variant polyfermenticus.

Complete Genome Sequence of Bacillus subtilis Strain WB800N, an Extracellular Protease-Deficient Derivative of Strain 168.

Bacillus subtilis WB800N is a genetically engineered variant of B. subtilis 168, such that all extracellular proteases are disrupted, which enables WB800N to be widely used for the expression of secretory proteins. Here, we report the 4.2-Mb complete genome sequence of WB800N and present all of the disrupted gene structure.

Complete Genome Sequence of the Soil Bacterium Pseudomonas kribbensis Strain 46-2T.

Pseudomonas kribbensis is a novel species belonging to the Pseudomonas fluorescens intrageneric group of the genus Pseudomonas. Herein, we report the complete genome sequence of strain 46-2T, isolated from garden soil in Daejeon, South Korea. The 6.32-Mb chromosome contains 5,626 coding sequences with a G+C content of 60.55%.

Genome Sequences of Two Cyanobacterial Strains, Toxic Green Microcystis aeruginosa KW (KCTC 18162P) and Nontoxic Brown Microcystis sp. Strain MC19, under Xenic Culture Conditions.

Bloom-forming cyanobacteria pose concerns for the environment and the health of humans and animals by producing toxins and thus lowering water quality. Here, we report near-complete genome sequences of two Microcystis strains under xenic culture conditions, which were originally isolated from two separate freshwater reservoirs from the Republic of Korea.

Genome Variations of Evolved Escherichia coli ET8 With a Rhodopsin-Based Phototrophic Metabolism.

We reported that the phototrophic metabolism via plasmid-originated Gloeobacter rhodopsin(GR)-expression is improved in Escherichia coli ET5 harboring pKJ606-GR by a genomic point mutation (dgcQC1082A ) encoding a transmembrane cell signaling protein (Microb. Cell Fact. 16:111, 2017). Another evolved descendant is isolated from the chemostat, and the genome variation of the strain named ET8 harboring pKJ606-GR is investigated in this study. Whole genome sequencing analysis identifies a single point mutation (C3831976A) located in the non-coding upstream region of kdtA and an IS4 insertional mutation at galUG706 without any mutations in the plasmid. ET8 strain shows enhanced kdtA transcription and no growth in the D-galactose or lactose sole carbon sourced minimal media. Size of ET8 strain are almost identical to that of the ancestor. Phototrophic growth and proton pumping in ET8 expressing GR (ET8 + GR) are increased 1.5-fold and threefold, respectively, compared with those in the ancestor (W3110 + GR). To verify the effects of the genomic mutations, either the kdtA-upregulation or the galU-disruption is conducted in the ancestor. Both the kdtA-upregulation and the galU-disruption result in the drastic increases of proton-pumping. The physiological properties arising from the genomic variations of the evolved host with the new phototrophic metabolism are further discussed.

Complete Genome Sequence of Methanobrevibacter smithii Strain KB11, Isolated from a Korean Fecal Sample.

The archaeon Methanobrevibacter smithii is a major colonizer of the human gut. Methanobrevibacter smithii strain KB11 was newly isolated from a Korean fecal sample. Here, we present the complete genome sequence of strain KB11 and a brief comparison with that of M. smithii type strain ATCC 35061T.

Complete Genome Sequences of Enterobacter cancerogenus CR-Eb1 and Enterococcus sp. Strain CR-Ec1, Isolated from the Larval Gut of the Greater Wax Moth, Galleria mellonella.

Enterobacter cancerogenus CR-Eb1 and Enterococcus sp. CR-Ec1 were isolated from the larval gut of Galleria mellonella, the greater wax moth. Here, we report the completed and annotated genome sequences of insect gut-dwelling bacteria.