Article
Multidisciplinary Sciences
Martijn G. H. Sanders, Tamar Nijsten, Joost Verlouw, Robert Kraaij, Luba M. Pardo
Summary: The study found differences in the microbiome composition between patients with seborrheic dermatitis (SD) and individuals without diseases, mainly in the genus Staphylococcus.
Article
Biochemistry & Molecular Biology
Hubiao Jiang, Luqiong Lv, Temoor Ahmed, Shaomin Jin, Muhammad Shahid, Muhammad Noman, Hosam-Eldin Hussein Osman, Yanli Wang, Guochang Sun, Xuqing Li, Bin Li
Summary: This study found that metal oxide nanoparticles can reduce the incidence of tomato bacterial wilt and alter the composition and structure of the rhizosphere bacterial community. Among them, the application of CuO nanoparticles significantly affected the abundance of beneficial Streptomyces bacteria. This research provides evidence and strategies for using metal oxide nanoparticles to prevent and control soil-borne disease tomato bacterial wilt.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Ahmed Saeedi, Nicola J. Cummings, Denise McLean, Ian F. Connerton, Phillippa L. Connerton
Summary: ASxL5(T) is a novel Gram-stain negative bacterium with unique growth characteristics and morphology, closely related to members of the Oceanospirillaceae.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Miranda K. Stotz, Darren D. Henry, Whitney L. Crossland
Summary: Bovine liver abscesses have been characterized by both cultural and DNA methods, with non-abscessed livers showing presence of potentially pathogenic bacteria in apparently healthy tissue.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Environmental Sciences
Zdravko Baruch, Craig Liddicoat, Christian Cando-Dumancela, Mark Laws, Hamish Morelli, Philip Weinstein, Jennifer M. Young, Martin F. Breed
Summary: The management of urban green spaces has a significant impact on soil bacterial communities, with plant species richness positively associated with soil bacterial diversity. These trends are not influenced by geographical proximity of sample sites, highlighting the importance of understanding the effects of urban green space management on the soil microbiome for informing policy development.
ENVIRONMENTAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Lina Hamouche, Leonora Poljak, Agamemnon J. Carpousis
Summary: Rifampicin treatment causes a decrease in cell size and total RNA content in E. coli, primarily due to a decrease in 23S and 16S rRNA levels. While rRNA degradation is not complete, growth can be reinitiated after removal of rifampicin. Analysis of mutant strains suggests RNase E, PNPase, and RNase R are involved in rifampicin-induced rRNA degradation, potentially impacting mRNA degradation rates as well.
Article
Immunology
Laura Sheehy, James Cutler, Gareth D. Weedall, Robbie Rae
Summary: In this study, a metagenomic approach was used to analyze the bacterial communities associated with several different strains of nematodes after killing their slug hosts. The results showed that these nematodes are not exclusively associated with one bacterium, but have variable and diverse bacterial communities. Additionally, the commercial strain of nematodes was found to have a specific association with Psychrobacter spp.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marta Soszynska-Jozwiak, Maciej Pszczola, Julita Piasecka, Jake M. Peterson, Walter N. Moss, Katarzyna Taras-Goslinska, Ryszard Kierzek, Elzbieta Kierzek
Summary: In this study, RNA secondary structures of influenza A virus were determined using chemical mapping and 4-thiouridine (4sU) crosslinking, revealing both universal and unique features of different strains. The method highlighted the three-dimensional properties and allowed for proposing long-range interactions in the RNA secondary structure. The combination of 4sU mapping with chemical mapping and bioinformatic analysis could enhance RNA structure determination and target recognition for antisense strategies or viral RNA detection.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Food Science & Technology
Devin A. A. Bowes, Erin M. M. Driver, Sonja Savic, Qiwen Cheng, Corrie M. M. Whisner, Rosa Krajmalnik-Brown, Rolf U. U. Halden
Summary: This study demonstrates that wastewater-based epidemiology can be used for near real-time population dietary assessments, providing a promising tool for actionable and cost-effective data collection to support public health nutrition at the population scale.
Article
Microbiology
Yue Wu, Jian Sun, Pengcheng Yu, Weiliang Zhang, Youze Lin, Dianrong Ma
Summary: Our study found differences in the rhizosphere bacterial community structures of weedy rice and cultivated rice. The rhizosphere bacterial community and co-occurrence network of cultivated rice changed when disturbed by weedy rice. These differences give weedy rice a nutritional competitive advantage in paddy soils.
Article
Agriculture, Dairy & Animal Science
Raghavendra G. Amachawadi, Wesley A. Tom, Michael P. Hays, Samodha C. Fernando, Philip R. Hardwidge, T. G. Nagaraja
Summary: Liver abscesses in feedlot cattle are polymicrobial infections, primarily caused by Fusobacterium necrophorum. This study used 16S ribosomal RNA amplicon sequence analyses to identify bacterial composition in liver abscesses, finding a dominance of Gram-negative bacteria and Fusobacterium followed by Pseudomonas. Differences in bacterial community composition were not observed between crossbred and Holstein steers fed finishing diets with or without tylosin.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Limnology
Qiuwen Chen, Yuchen Chen, Jun Yang, Stephen C. Maberly, Jianyun Zhang, Jinren Ni, Gangsheng Wang, Daniele Tonina, Lin Xiao, Honghai Ma
Summary: This study found that water temperature, rather than the presence of dams, is the main factor influencing the geographical distribution of bacterial communities in cascade reservoirs. There are significant spatial differences in sediment bacterial communities within a reservoir, potentially forming hotspots for biogeochemical cycling. Unlike in deep lakes and deep single reservoirs, the bacterioplankton community composition in deep cascade reservoirs does not have distinctly layered features due to density-induced underwater currents and convection.
LIMNOLOGY AND OCEANOGRAPHY
(2021)
Article
Environmental Sciences
Benjamin Makimilua Tiimub, Zhen-chao Zhou, Lin Zhu, Yang Liu, Xin-Yi Shuai, Lan Xu, Christophe Niyungeko, Ling-Xuan Meng, Yu-Jie Sun, Hong Chen
Summary: This study found that adding sulfanilamide and copper II sulfate in aquaculture can reduce the absolute abundance of 16S rRNA bacteria in fish tanks, while revealing related biomarkers. This offers new perspectives for innovative environmental microbiological and biotechnological studies.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Plant Sciences
Chitose Honsho, Koichiro Ushijima, Misa Anraku, Shuji Ishimura, Qibin Yu, Frederick G. Gmitter, Takuya Tetsumura
Summary: This study identified genes regulating self-incompatibility in Japanese citrus cultivars through RNA-seq, revealing that six T2 RNase genes were S-RNases. The findings support the notion that citrus self-incompatibility is based on S-RNase. Further homology comparisons with S-RNases from Chinese citrus led to the conclusion that three of the T2 RNases were novel citrus S-RNases involved in self-incompatibility.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
D. Vinu, K. Govindaraju, R. Vasantharaja, S. Amreen Nisa, M. Kannan, K. Vijai Anand
Summary: This study investigated the biogenic preparation of ZnO, CuO, and Se nanoparticles using the marine brown alga Sargassum swartzii. The nanoparticles were characterized and their antibacterial activity against V. parahaemolyticus was studied, showing strong inhibition at dose-dependent manner. The results suggest the potential use of these nanomaterials for managing aquatic diseases when incorporated with shrimp feed in the future.
JOURNAL OF NANOSTRUCTURE IN CHEMISTRY
(2021)
Article
Microbiology
Kentaro Miyazaki, Natsuko Tokito
Summary: The complete genome of Thermus thermophilus strain TMY was resequenced using a hybrid assembly of long-read data from Oxford Nanopore Technologies and short-read data from MGI. Correction of errors in the previously reported genome sequence obtained solely from PacBio technology enabled high-quality comparative genomic analysis of closely related T. thermophilus genomes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki, Natsuki Tomariguchi, Yuko Ueno
Summary: The four Thermus thermophilus strains isolated from Arima Hot Spring in Japan showed high nucleotide identity to each other and those from the same spot, but lower identity to strains from geographically different spots, indicating habitat-specific genomic conservation.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki
Summary: In this study, extremely thermophilic strains belonging to the genus Thermus were isolated from Senami Hot Spring in Japan. The complete genome sequences of these strains, including five Thermus thermophilus strains and one Thermus brockianus strain, were obtained using a combination of Oxford Nanopore long-read and DNBSEQ or Illumina short-read sequencing data.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Kentaro Miyazaki, Kae Hosoya
Summary: Four Parageobacillus strains were isolated from soil in Japan and their genomes were fully sequenced. Three of the strains showed high nucleotide identity (>=98.9%) to Parageobacillus caldoxylosilyticus 51812, while one strain, designated KH3-4, showed the highest nucleotide identity (91%) to Parageobacillus thermantarcticus M1, suggesting the novelty of the species KH3-4.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Chemistry, Multidisciplinary
Morito Sakuma, Shingo Honda, Hiroshi Ueno, Kazuhito V. Tabata, Kentaro Miyazaki, Nobuhiko Tokuriki, Hiroyuki Noji
Summary: Enzymes display heterogeneity in their conformational and functional states, which is crucial for the evolution of new functions. A single-molecule enzyme assay was used to analyze functional substates in wild-type and mutant alkaline phosphatase. Mutant enzymes exhibited significantly heterogeneous functional substates, while the wild-type enzyme showed a highly homogeneous substate. The degree of functional substates correlated with the improvement in promiscuous activities. The findings highlight the importance of functional substates in enzyme evolution.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Shunsuke Kato, Koki Takeuchi, Motonao Iwaki, Kentaro Miyazaki, Kohsuke Honda, Takashi Hayashi
Summary: Affinity purification of recombinant proteins is an essential technique in biotechnology. However, current methods are costly, limiting their versatile use. To address this issue, we developed the CSAP system, using commercially available chitin powder as a chromatography matrix for low-cost purification of Strep-tag II fusion proteins. We demonstrated the system's effectiveness in protein screening using 96-well format, identifying potential candidates for an abiotic carbene transfer reaction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Morito Sakuma, Shingo Honda, Hiroshi Ueno, Kazuhito V. Tabata, Kentaro Miyazaki, Nobuhiko Tokuriki, Hiroyuki Noji
Summary: Enzymes have inherent heterogeneity in their conformational and functional states, which is key to the evolution of new functions. Single-molecule enzyme assays allow direct observation of these multiple functional substates. We analyzed functional substates in wild-type and mutant Escherichia coli alkaline phosphatase and found that mutant enzymes exhibited significantly heterogeneous functional substates, while the wild-type enzyme showed a highly homogeneous substate. Our study provides comprehensive evidence that functional substates can be easily altered by mutations and that the evolution towards new catalytic activities may involve modulation of these substates.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Microbiology
Kentaro Miyazaki, Toshiyuki Moriya, Natsuko Tokito, Tairo Oshima, Kei Yura, Yoshitaka Bessho
Summary: The Thermus thermophilus strains isolated from the same spot in Mine Hot Spring, Japan, showed a higher level of genetic similarity compared to strains from geographically different places in Japan.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki, Toshiyuki Moriya, Naoki Nemoto, Tairo Oshima, Kei Yura, Yoshitaka Bessho
Summary: The Thermus thermophilus strain HB5018 isolated from Mine Hot Spring in Japan has a 99.1% average nucleotide identity with the type strain HB8, indicating strict species conservation in the habitat over the past 50 years.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki, Hikaru Suenaga, Mamoru Oshiki, Shuichi Kawano, Toshikazu Fukushima
Summary: Thiohalobacter sp. strain COW1, a bacterium capable of degrading thiocyanate, was isolated from activated sludge treating coke oven wastewater, and its complete genome sequence was determined to contain a single circular chromosome with 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Microbiology
Kentaro Miyazaki, Apirak Wiseschart, Kusol Pootanakit, Kei Kitahara
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Microbiology
Kentaro Miyazaki, Erina Hase, Natsuko Tokito
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Microbiology
Kentaro Miyazaki, Erina Hase, Tomomasa Maruya
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Microbiology
Kentaro Miyazaki, Erina Hase, Tomomasa Maruya
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Microbiology
Natsuki Tomariguchi, Kentaro Miyazaki
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)