Details of a Researcher - Tomita, Masaru

Papers - Tomita, Masaru

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Peptide Synthesis under the Alkaline Hydrothermal Conditions on Enceladus

Takahagi W., Seo K., Shibuya T., Takano Y., Fujishima K., Saitoh M., Shimamura S., Matsui Y., Tomita M., Takai K.

ACS Earth and Space Chemistry 3 ( 11 ) 2559 - 2568 2019.11

Chemical evolution is an abiotic reaction process in which complex organic molecules arise from a combination of simple inorganic and organic chemical compounds. To assess the possible ongoing chemical evolution in the subsurface ocean of Saturn's icy satellite Enceladus, we explored the water-rock aqueous reactions and the peptide formation capability under a hydrothermal environment similar to that on Enceladus. It has been suggested that the core of Enceladus has not experienced high temperatures from the time of satellite formation to the present. The major components of the core are assumed to be carbonaceous chondrites; thus, simple organic substances, including amino acids, are likely present in the alkaline seawater of Enceladus. In this study, we conducted a laboratory-based simulation experiment to describe the chemical alteration of six prebiotically abundant amino acids over 147 days under high pressure with thermal cycling (30 to 100 °C) to simulate the water-rock interface of the ocean on Enceladus. As a result, we detected 28 out of 36 possible dipeptide species during the entire reaction period. We propose that peptide-bond formation is coupled to rock surface chemisorption of amino acids under alkaline condition, which was further supported by the elemental analysis showing carbon and nitrogen signature on the rock surface only when amino acids are added. The above result suggests that ongoing chemical evolution on Enceladus is likely producing short abiotic peptides on the porous core surface.

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Association between dyslipidemia and plasma levels of branched-chain amino acids in the Japanese population without diabetes mellitus

Fukushima K., Harada S., Takeuchi A., Kurihara A., Iida M., Fukai K., Kuwabara K., Kato S., Matsumoto M., Hirata A., Akiyama M., Tomita M., Hirayama A., Sato A., Suzuki C., Sugimoto M., Soga T., Sugiyama D., Okamura T., Takebayashi T.

Journal of Clinical Lipidology (Journal of Clinical Lipidology) 13 ( 6 ) 932 - 939.e2 2019.11

ISSN 19332874

Background: Branched-chain amino acids (BCAAs) play a key role in energy homeostasis. Objective: We aimed to investigate the association between plasma BCAA levels and dyslipidemia in the Japanese population without diabetes mellitus. Methods: This cross-sectional study included 4952 participants without diabetes mellitus, enrolled in the Tsuruoka Metabolomic Cohort Study. Plasma BCAA levels were measured by capillary electrophoresis–mass spectrometry. Correlations between lipid and BCAA profiles were evaluated by sex-stratified multiple linear regression analyses, after adjusting for confounders. Logistic regression was used to identify associations between BCAAs and metabolic dyslipidemia (MD) defined as triglyceride levels ≥150 mg/dL, high-density lipoprotein cholesterol levels ≤40 mg/dL for men and ≤50 mg/dL for women, or low-density lipoprotein cholesterol (LDL-C) levels ≥140 mg/dL. Results: In both sexes, the levels of individual BCAAs and the total BCAA levels correlated positively with triglyceride levels and negatively with high-density lipoprotein cholesterol levels. Valine, leucine, and total BCAA levels were weakly and positively correlated with LDL-C levels. Increased BCAA levels showed positive associations with MD. However, associations between BCAAs and elevated LDL-C levels were unclear. Furthermore, the associations between BCAA levels and MD regardless of fasting blood sugar (FBS) levels (high or low). Although valine, leucine, and total BCAA levels were weakly associated with elevated LDL-C levels in the high-FBS group, no such association was observed in the low-FBS group. Conclusions: BCAAs might be associated with MD independently of the FBS level and might play an important role in lipid metabolism and dyslipidemia.

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Draft Genome Sequences of Enterococcus faecalis Strains Isolated from Healthy Japanese Individuals

Tanaka K., Watabe T., Kato K., Tsukimi T., Sato M.P., Odamaki T., Tomita M., Fukuda S.

Microbiology Resource Announcements (Microbiology Resource Announcements) 8 ( 40 ) 2019.10

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Salivary metabolomics with alternative decision tree-based machine learning methods for breast cancer discrimination

Murata T., Yanagisawa T., Kurihara T., Kaneko M., Ota S., Enomoto A., Tomita M., Sugimoto M., Sunamura M., Hayashida T., Kitagawa Y., Jinno H.

Breast Cancer Research and Treatment (Breast Cancer Research and Treatment) 177 ( 3 ) 591 - 601 2019.10

ISSN 01676806

© 2019, Springer Science+Business Media, LLC, part of Springer Nature. Purpose: The aim of this study is to explore new salivary biomarkers to discriminate breast cancer patients from healthy controls. Methods: Saliva samples were collected after 9 h fasting and were immediately stored at − 80 °C. Capillary electrophoresis and liquid chromatography with mass spectrometry were used to quantify hundreds of hydrophilic metabolites. Conventional statistical analyses and artificial intelligence-based methods were used to assess the discrimination abilities of the quantified metabolites. A multiple logistic regression (MLR) model and an alternative decision tree (ADTree)-based machine learning method were used. The generalization abilities of these mathematical models were validated in various computational tests, such as cross-validation and resampling methods. Results: One hundred sixty-six unstimulated saliva samples were collected from 101 patients with invasive carcinoma of the breast (IC), 23 patients with ductal carcinoma in situ (DCIS), and 42 healthy controls (C). Of the 260 quantified metabolites, polyamines were significantly elevated in the saliva of patients with breast cancer. Spermine showed the highest area under the receiver operating characteristic curves [0.766; 95% confidence interval (CI) 0.671–0.840, P ' 0.0001] to discriminate IC from C. In addition to spermine, polyamines and their acetylated forms were elevated in IC only. Two hundred each of two-fold, five-fold, and ten-fold cross-validation using different random values were conducted and the MLR model had slightly better accuracy. The ADTree with an ensemble approach showed higher accuracy (0.912; 95% CI 0.838–0.961, P ' 0.0001). These prediction models also included spermine as a predictive factor. Conclusions: These data indicated that combinations of salivary metabolomics with the ADTree-based machine learning methods show potential for non-invasive screening of breast cancer.

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Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life

Saito M., Sato A., Nagata S., Tamaki S., Tomita M., Suzuki H., Kanai A.

Genome Biology and Evolution (Genome Biology and Evolution) 11 ( 10 ) 2713 - 2726 2019.09

© 2019 The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Clp1, a polyribonucleotide 5′-hydroxyl kinase in eukaryotes, is involved in pretRNA splicing and mRNA 3′-end formation. Enzymes similar in amino acid sequence to Clp1, Nol9, and Grc3, are present in some eukaryotes and are involved in prerRNA processing. However, our knowledge of how these Clp1 family proteins evolved and diversified is limited. We conducted a large-scale molecular evolutionary analysis of the Clp1 family proteins in all living organisms for which protein sequences are available in public databases. The phylogenetic distribution and frequencies of the Clp1 family proteins were investigated in complete genomes of Bacteria, Archaea and Eukarya. In total, 3,557 Clp1 family proteins were detected in the three domains of life, Bacteria, Archaea, and Eukarya. Many were from Archaea and Eukarya, but a few were found in restricted, phylogenetically diverse bacterial species. The domain structures of the Clp1 family proteins also differed among the three domains of life. Although the proteins were, on average, 555 amino acids long (range, 196-2,728), 122 large proteins with >1,000 amino acids were detected in eukaryotes. These novel proteins contain the conserved Clp1 polynucleotide kinase domain and various other functional domains. Of these proteins, >80% were from Fungi or Protostomia. The polyribonucleotide kinase activity of Thermus scotoductus Clp1 (Ts-Clp1) was characterized experimentally. Ts-Clp1 preferentially phosphorylates single-stranded RNA oligonucleotides (Km value for ATP, 2.5 μM), or single-stranded DNA at higher enzyme concentrations. We propose a comprehensive assessment of the diversification of the Clp1 family proteins and the molecular evolution of their functional domains.

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Chlorococcum turfosum comb. nov. (Volvocales, Chlorophyceae) and visualization of chimeric sequences

Nakada T., Watanabe S., Lewis L., Tomita M.

Phycological Research 67 ( 3 ) 239 - 243 2019.07

ISSN 13220829

© 2019 Japanese Society of Phycology Parachlorococcum turfosum was previously described based on morphological studies of a culture collection strain originally identified as ‘Chlorococcum elkhartiense’ and on an 18S rRNA gene phylogeny of a strain derived from the same original strain but from a different culture collection. However, a subsequently published 18S rRNA gene sequence was inconsistent with the original sequence. Therefore, a new 18S rRNA gene sequence was obtained from the strain from which the holotype was derived. Comparative analyses of the new sequence using the basic local alignment search tool and a newly written Perl code, ChimViewP, which visualizes nucleotide signature shifts characteristic of chimeric sequences, revealed that the sequence used in the original description was of a chimeric nature. Similar analyses also indicated that two published ‘Chlamydomonas acidophila’ sequences are chimeric. Phylogenetic analyses excluding all putative chimeras showed that P. turfosum belongs to Chlorococcum, and thus Chlorococcum turfosum comb. nov. is proposed.

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Genomic analysis of Pseudomonas sp. Strain SCT, an iodate-reducing bacterium isolated from marine sediment, reveals a possible use for bioremediation

Harada M., Ito K., Nakajima N., Yamamura S., Tomita M., Suzuki H., Amachi S.

G3: Genes, Genomes, Genetics (G3: Genes, Genomes, Genetics) 9 ( 5 ) 1321 - 1329 2019.05

Copyright © 2019 Harada et al. Strain SCT is an iodate-reducing bacterium isolated from marine sediment in Kanagawa Prefecture, Japan. In this study, we determined the draft genome sequence of strain SCT and compared it to complete genome sequences of other closely related bacteria, including Pseudomonas stutzeri. A phylogeny inferred from concatenation of core genes revealed that strain SCT was closely related to marine isolates of P. stutzeri. Genes present in the SCT genome but absent from the other analyzed P. stutzeri genomes comprised clusters corresponding to putative prophage regions and possible operons. They included pil genes, which encode type IV pili for natural transformation; the mer operon, which encodes resistance systems for mercury; and the pst operon, which encodes a Pi-specific transport system for phosphate uptake. We found that strain SCT had more prophage-like genes than the other P. stutzeri strains and that the majority (70%) of them were SCT strain-specific. These genes, encoded on distinct prophage regions, may have been acquired after branching from a common ancestor following independent phage transfer events. Thus, the genome sequence of Pseudomonas sp. strain SCT can provide detailed insights into its metabolic potential and the evolution of genetic elements associated with its unique phenotype.

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Stable and efficient delivery of DNA to Bacillus subtilis (natto) using pLS20 conjugational transfer plasmids

Itaya M., Nagasaku M., Shimada T., Ohtani N., Shiwa Y., Yoshikawa H., Kaneko S., Tomita M., Sato M.

FEMS Microbiology Letters (FEMS Microbiology Letters) 366 ( 4 ) 2019.02

ISSN 03781097

© FEMS 2019. Bacillus subtilis (natto) is generally regarded as a safe bacterium and used as a host for the production of several materials. However, genetic engineering of B. subtilis (natto) is not well established because of poor DNA delivery methods and the lack of a standard strain for the aim. Here, we developed a genetic delivery tool in B. subtilis (natto) using the pLS20 conjugational plasmid (65 kbp). Transmission of pLS20 from B. subtilis 168 to wild-type B. subtilis (natto) did not occur via established mating protocols. We isolated B. subtilis (natto) mutants showing dramatically increased recipient activity. Whole-genome sequence analyses revealed three common alterations: mutations in the restriction endonuclease gene and in the methyl-accepting chemotaxis protein gene, and a 43-kbp deletion at the genome replication termination locus. A representative strain named NEST116 was generated as the first B. subtilis (natto) strain suitable for exploring pLS20-based genetic engineering.

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Effects of inter-day and intra-day variation on salivary metabolomic profiles

Kawanishi N., Hoshi N., Masahiro S., Enomoto A., Ota S., Kaneko M., Soga T., Tomita M., Kimoto K.

Clinica Chimica Acta (Clinica Chimica Acta) 489 41 - 48 2019.02

ISSN 00098981

© 2018 Elsevier B.V. Background: Salivary secretion is an important parameter reflecting the health status of an individual and has been used clinically for the diagnosis of various oral diseases, such as xerostomia. Salivary metabolomic profiling is considered an emerging potential tool for the detection of various systemic diseases. To our knowledge, this is the first study to investigate the quantitative relationship between salivary secretion volume and salivary metabolomic profile. Methods: To evaluate inter- and intra-day variations in salivary secretion, 234 saliva samples were collected three times per day for three days from 13 subjects and analyzed. Capillary electrophoresis-mass spectrometry was used for non-targeted quantification of water-soluble metabolites. Results: No significant inter- or intra-day variations were observed in salivary secretion volume. No significant inter-day variations were observed in metabolomic patterns. In contrast, significant intra-day variations were observed in salivary metabolomic profiles. The difference was more obvious for stimulated saliva than for unstimulated saliva. These profile changes were independent of salivary secretion volume. Conclusions: Our results indicated that diurnal change had a greater effect on salivary metabolomic profiles than the other factors. Hence, sampling time should be tightly controlled to minimize unexpected bias in the clinical use of salivary metabolomics.

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Perioperative serum and urine metabolome analyses in patients with hepatocellular carcinoma undergoing partial hepatectomy

Kajiura D., Yamanaka-Okumura H., Hirayama A., Tatano H., Endo K., Honma M., Igarashi K., Shoji F., Ikeda S., Yamaguchi N., Katayama T., Morine Y., Imura S., Utsunomiya T., Soga T., Tomita M., Shimada M.

Nutrition (Nutrition) 58 110 - 119 2019.02

ISSN 08999007

© 2018 Elsevier Ltd Objectives: Perioperative nutritional management is essential for early recovery after liver surgery. The aim of this study was to assess changes in amino acid levels in serum and urine after hepatectomy. Methods: Serum samples were collected from 16 patients with hepatocellular carcinoma before and 1, 3, and 14 d after hepatectomy (S0, S1, S3, and S14, respectively). Spot urine samples were collected before and 3 d after the hepatectomy (U0 and U3). Metabolites in the serum and urine were analyzed. Results: Compared with S0, insulin levels significantly increased in the S1 and S3 samples. Valine levels significantly decreased in S1 and S14, and leucine levels significantly decreased in S14. Phenylalanine levels significantly increased in S1 and S3, and tyrosine levels significantly increased in S1. The Fischer ratio (branched-chain/aromatic amino acids) significantly decreased in S1 and S3. In multiple regression analysis, changes in serum taurine levels were related to the white blood cell count in S1 and S3, and inversely related to alanine aminotransferase levels in S14. Changes in serum glutamine levels were negatively related to C-reactive protein levels in S3. Serum glutamine levels decreased in S3 and S14, and tended to increase in U3, suggesting a deficiency of glutamate resulting from the invasive surgical procedure. Conclusions: These findings highlight the usefulness of metabolome analysis for characterizing perioperative patterns after liver resection. The observed amino acid pattern, including the reduction in Fischer ratio, underscores the need for specialized nutritional support.

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Comparative genomics of Bacteria commonly identified in the built environment

Merino N., Zhang S., Tomita M., Suzuki H.

BMC Genomics (BMC Genomics) 20 ( 1 ) 92 2019.01

© 2019 The Author(s). Background: The microbial community of the built environment (BE) can impact the lives of people and has been studied for a variety of indoor, outdoor, underground, and extreme locations. Thus far, these microorganisms have mainly been investigated by culture-based methods or amplicon sequencing. However, both methods have limitations, complicating multi-study comparisons and limiting the knowledge gained regarding in-situ microbial lifestyles. A greater understanding of BE microorganisms can be achieved through basic information derived from the complete genome. Here, we investigate the level of diversity and genomic features (genome size, GC content, replication strand skew, and codon usage bias) from complete genomes of bacteria commonly identified in the BE, providing a first step towards understanding these bacterial lifestyles. Results: Here, we selected bacterial genera commonly identified in the BE (or "Common BE genomes") and compared them against other prokaryotic genera ("Other genomes"). The "Common BE genomes" were identified in various climates and in indoor, outdoor, underground, or extreme built environments. The diversity level of the 16S rRNA varied greatly between genera. The genome size, GC content and GC skew strength of the "Common BE genomes" were statistically larger than those of the "Other genomes" but were not practically significant. In contrast, the strength of selected codon usage bias (S value) was statistically higher with a large effect size in the "Common BE genomes" compared to the "Other genomes." Conclusion: Of the four genomic features tested, the S value could play a more important role in understanding the lifestyles of bacteria living in the BE. This parameter could be indicative of bacterial growth rates, gene expression, and other factors, potentially affected by BE growth conditions (e.g., temperature, humidity, and nutrients). However, further experimental evidence, species-level BE studies, and classification by BE location is needed to define the relationship between genomic features and the lifestyles of BE bacteria more robustly.

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Fast and global detection of periodic sequence repeats in large genomic resources

Mori H., Evans-Yamamoto D., Ishiguro S., Tomita M., Yachie N.

Nucleic acids research (Nucleic Acids Research) 47 ( 2 ) e8 2019.01

ISSN 03051048

Periodically repeating DNA and protein elements are involved in various important biological events including genomic evolution, gene regulation, protein complex formation, and immunity. Notably, the currently used genome editing tools such as ZFNs, TALENs, and CRISPRs are also all associated with periodically repeating biomolecules of natural organisms. Despite the biological importance of periodically repeating sequences and the expectation that new genome editing modules could be discovered from such periodical repeats, no software that globally detects such structured elements in large genomic resources in a high-throughput and unsupervised manner has been developed. We developed new software, SPADE (Search for Patterned DNA Elements), that exhaustively explores periodic DNA and protein repeats from large-scale genomic datasets based on k-mer periodicity evaluation. With a simple constraint, sequence periodicity, SPADE captured reported genome-editing-associated sequences and other protein families involving repeating domains such as tetratricopeptide, ankyrin and WD40 repeats with better performance than the other software designed for limited sets of repetitive biomolecular sequences, suggesting the high potential of this software to contribute to the discovery of new biological events and new genome editing modules.

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Metabolomics Platform with Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Plasma Analysis

Sasaki K., Sagawa H., Suzuki M., Yamamoto H., Tomita M., Soga T., Ohashi Y.

Analytical Chemistry (Analytical Chemistry) 91 ( 2 ) 1295 - 1301 2019.01

ISSN 00032700

© 2018 American Chemical Society. Metabolome analysis using capillary electrophoresis (CE) coupled with high-resolution mass spectrometry (HRMS) has the potential to improve coverage of metabolite detection because of its high selectivity and sensitivity. Configuration of the interface between CE and HRMS to meet the ground connection is essential for enabling independent regulation of the electrical currents in the CE and electrospray field. In the present study, we applied an electrospray-ionization adapter equipped with a grounded nebulizer to CE-HRMS and tested the analytical performance for 34 charged compounds. The extracted-ion electropherograms, consisting of seven sets of isomers, showed reasonable peak shapes and separation for the annotation of each metabolite. The levels of 34 target analytes in a standard mixture were determined with a dynamic range of at least 10 2 , maintaining linearity with r 2 > 0.9. The repeatability and intermediate precision above the lower limit of quantification showed the relative standard deviation to be lower than 20%. In the spike-recovery experiment, 27 of the 34 metabolites in plasma extract were recovered at a rate of 80 to 120%, suggesting high accuracy. Furthermore, we assessed the feasibility of our platform in metabolome analysis using human-plasma extract. The results showed successful detection of 270 metabolites, indicating the potential of our platform to yield higher coverage of the metabolome. In addition, analysis of dilution integrity demonstrated the quantitative ability of metabolome analysis with CE-HRMS, although the existence of saturation or matrix effects were seen in the case of 33 of the metabolites. This study indicates that our platform has great potential for large-scale metabolome analysis of plasma for biological studies and clinical biomarker screening.

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Reconsidering plasmid maintenance factors for computational plasmid design

Yano H., Shintani M., Tomita M., Suzuki H., Oshima T.

Computational and Structural Biotechnology Journal (Computational and Structural Biotechnology Journal) 17 70 - 81 2019.01

ISSN 2001-0370

© 2018 The Authors Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.

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Improved taxon sampling and multigene phylogeny of unicellular chlamydomonads closely related to the colonial volvocalean lineage Tetrabaenaceae-Goniaceae-Volvocaceae (Volvocales, Chlorophyceae)

Nakada T., Tsuchida Y., Tomita M.

Molecular Phylogenetics and Evolution (Molecular Phylogenetics and Evolution) 130 1 - 8 2019.01

ISSN 10557903

© 2018 Elsevier Inc. In the green algal order Volvocales (Chlorophyceae), flagellate colonial forms have evolved at least four times. One of these colonial lineages, Tetrabaenaceae-Goniaceae-Volvocaceae (TGV), which belongs to the clade Reinhardtinia, is closely related to several unicellular chlamydomonads in the genera Chlamydomonas and Vitreochlamys. However, the unicellular sister of TGV has not been specified. Here, the largest ever 18S rRNA phylogenetic tree of Reinhardtinia was constructed including several newly isolated chlamydomonads, and a clade (core-Reinhardtinia) including 32 unicellular lineages and three colonial families were recognized. Interrelationships within core-Reinhardtinia were barely resolved in the tree, and therefore combined 18S-atpB-psaA-psaB-psbC-rbcL gene phylogenetic analyses were performed with selected representatives of 29 of the 32 unicellular lineages and three colonial families. The 29 unicellular lineages were clustered into five metaclades and an unassigned lineage; the metaclade that includes Chlamydomonas pila was resolved, with moderate support, as the sister clade to TGV. To examine possible biases from specific gene(s), long-branch taxa, and the heterogeneous base composition, phylogenetic analyses using several smaller data sets were also performed. Light microscopy of C. pila and its relatives indicated that any early steps towards colony evolution appeared after divergence of TGV from the C. pila lineage.

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Metabolome profiling of various seaweed species discriminates between brown, red, and green algae

Hamid S., Wakayama M., Ichihara K., Sakurai K., Ashino Y., Kadowaki R., Soga T., Tomita M.

Planta (Planta) 249 ( 6 ) 1921 - 1947 2019

ISSN 00320935

© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. Main Conclusion: Among seaweed groups, brown algae had characteristically high concentrations of mannitol, and green algae were characterised by fructose. In red algae, metabolite profiles of individual species should be evaluated. Seaweeds are metabolically different from terrestrial plants. However, general metabolite profiles of the three major seaweed groups, the brown, red, and green algae, and the effect of various extraction methods on metabolite profiling results have not been comprehensively explored. In this study, we evaluated the water-soluble metabolites in four brown, five red, and two green algae species collected from two sites in northern Japan, located in the Sea of Japan and the Pacific Ocean. Freeze-dried seaweed samples were processed by methanol–water extraction with or without chloroform and analysed by capillary electrophoresis- and liquid chromatography-mass spectrometry for metabolite characterisation. The metabolite concentration profiles showed distinctive characteristic depends on species and taxonomic groups, whereas the extraction methods did not have a significant effect. Taxonomic differences between the various seaweed metabolite profiles were well defined using only sugar metabolites but no other major compound types. Mannitol was the main sugar metabolites in brown algae, whereas fructose, sucrose, and glucose were found at high concentrations in green algae. In red algae, individual species had some characteristic metabolites, such as sorbitol in Pyropia pseudolinearis and panose in Dasya sessilis. The metabolite profiles generated in this study will be a resource and provide guidance for nutraceutical research studies because the information about metabolites in seaweeds is still very limited compared to that of terrestrial plants.

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Manufacturing of biomimetic silicone rubber films for experimental fluid mechanics: 3D printed shark skin molds

Yasuda Y., Zhang K., Sasaki O., Tomita M., Rival D., Galipon J.

Journal of the Electrochemical Society 166 ( 9 ) B3302 - B3308 2019

ISSN 00134651

The skin is at the interface of living organisms and their environment, and has evolved interesting structural properties usually over the course of millions of years, providing clues for the design of manmade biomimetic surfaces with favorable fluid mechanics properties. Here, we describe steps to produce silicone rubber films based on microscopy data from shark skin denticles, from data acquisition and manufacturing to attachment to an airfoil for experimental fluid dynamics in large towing tanks. This method is relatively low-cost, may be generalized to other types of patterned micro-structured surfaces, and the manufacturing process may be reproduced by anyone equipped with a 3D printer.

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Cutibacterium acnes (Propionibacterium acnes) 16S rRNA genotyping of microbial samples from possessions contributes to owner identification

Yang J., Tsukimi T., Yoshikawa M., Suzuki K., Takeda T., Tomita M., Fukuda S.

mSystems (mSystems) 4 ( 6 ) 2019

ISSN 2379-5077

The human skin surface harbors huge numbers of microbes. The skin microbiota interacts with its host and forms a skin microbiome profile that is specific for each individual. It has been reported that the skin microbiota that is left on an individual’s possessions can act as a sort of “fingerprint” and be used for owner identification. However, this approach needs to be improved to take into account any long-term instability of skin microbiota and contamination from nonspecific bacteria. Here, we took advantage of single-nucleotide polymorphisms (SNPs) in the 16S-encoding rRNA gene of Cutibacterium acnes, the most common and abundant bacterium on human skin, to perform owner identification. We first developed a high-throughput genotyping method based on next-generation sequencing to characterize the SNPs of the C. acnes 16S rRNA gene and found that the genotype composition of C. acnes 16S rRNA is individual specific. Owner identification accuracy of around 90% based on random forest machine learning was achieved by using a combination of C. acnes 16S rRNA genotype and skin microbiome profile data. Furthermore, our study showed that the C. acnes 16S rRNA genotype remained more stable over time than the skin microbiome profile. This characteristic of C. acnes was further confirmed by the analysis of publicly available human skin metagenome data. Our approach, with its high precision, good reproducibility, and low costs, thus provides new possibilities in the field of microbiome-based owner identification and forensics in general. IMPORTANCE Cutibacterium acnes is the most common and abundant bacterial species on human skin, and the gene that encodes its 16S rRNA has multiple single-nucleotide polymorphisms. In this study, we developed a method to efficiently determine the C. acnes 16S rRNA genotype composition from microbial samples taken from the hands of participants and from their possessions. Using the C. acnes 16S rRNA genotype composition, we could predict the owner of a possession with around 90% accuracy when the 16S rRNA gene-based microbiome profile was included. We also showed that the C. acnes 16S rRNA genotype composition was more stable over time than the skin microbiome profile and thus is more suitable for owner identification.

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Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coli genomes

Masuda T, Kono N, Tomita M, Arakawa K.

Bio-protocol (Bio-protocol) 9 ( 15 ) e3329 2019

Most bacterial genomes have biased nucleotide composition, and the asymmetry is considered to be caused by a single-stranded DNA (ssDNA) deamination arising from the bacterial replication machinery. In order to evaluate the relationship experimentally, the position and frequency of ssDNA formed during replication must be verified clearly. Although many ssDNA detection technologies exist, almost all methods have been developed for eukaryotic genomes. To apply these to bacterial genomes, which harbor a smaller amount of DNA than those of eukaryotes, more efficient, new methods are required. Therefore, we developed a novel strand-specific ssDNA sequencing method, called 4S-seq, for the bacterial genome. The 4S-seq method enriches ssDNA in the extracted genomic DNA by a dsDNA-specific nuclease and implements a strand-specific library using a biotin label with a customized tag. As a result, the 4S-seq is able to calculate the ssDNA content in each strand (Watson/Crick) at each position of the genome efficiently.

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Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert

Ii KM, Kono N, Paulino-Lima IG, Tomita M, Rothschild LJ, Arakawa K.

Journal of genomics 7 18 - 25 2019

ISSN 1839-9940

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