We study the ecological distribution of a unique syntrophic bacterium, Symbiobacterium thermophilum, and related bacteria. In this study, we found that they were frequently obtained from seashells and several marine samples. Symbiobacterium also grew from sterilized oyster shells incubated undersea for 2 or 3 months on the coast of Shimoda, Shizuoka, Japan. 16S rRNA gene-based phylogeny of the clones obtained from the Symbiobacterium-positive cultures demonstrated the potential diversity of this bacterial group, which constitutes a distinct clade between Actinobacteria and Firmicutes. We successfully isolated two new Symbiobacterium strains from oyster shells. 16S rRNA gene-based phylogeny indicated that one belongs to S. thermophilum, and that the other is affiliated with a different species. We also isolated Ureibacillius spp., which showed activity supporting the growth of S. thermophilum.
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http://dx.doi.org/10.1271/bbb.70619 | DOI Listing |
Microbiol Spectr
October 2024
Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, New York, USA.
Unlabelled: The Gram staining method differentiates bacteria based on their cell envelope structure, with the monoderm and diderm cell envelope types traditionally being synonymous with Gram-positive and Gram-negative stain results, respectively. Monoderms have a single phospholipid membrane surrounded by a thick layer of peptidoglycan, while diderms have a lipopolysaccharide outer membrane exterior to a thin peptidoglycan layer. The (formerly ) phylum has members with both cell wall types, and recent phylogenetic analyses have shown that monoderm evolved from diderm ancestors on multiple occasions.
View Article and Find Full Text PDFJ Biotechnol
September 2024
School of Life Science and Medicine, Shandong University of Technology, Zibo 255000, China. Electronic address:
During the deamination and amination processes of meso-diaminopimelate dehydrogenase (meso-DAPDH) from Symbiobacterium thermophilum (StDAPDH), residue R71 was observed to display distinct functions. H154 has been proposed as a basic residue that facilitates water molecules to attack the D-chiral carbon of meso-DAP during deamination. Inspired by the phenomenon of R71, the effects of H154 during deamination and amination were investigated in this study with the goal of enhancing the amination activities of StDAPDH.
View Article and Find Full Text PDFCommun Chem
May 2024
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
Fluorinated amino acids serve as an entry point for establishing new-to-Nature chemistries in biological systems, and novel methods are needed for the selective synthesis of these building blocks. In this study, we focused on the enzymatic synthesis of fluorinated alanine enantiomers to expand fluorine biocatalysis. The alanine dehydrogenase from Vibrio proteolyticus and the diaminopimelate dehydrogenase from Symbiobacterium thermophilum were selected for in vitro production of (R)-3-fluoroalanine and (S)-3-fluoroalanine, respectively, using 3-fluoropyruvate as the substrate.
View Article and Find Full Text PDFToxins (Basel)
February 2024
Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan.
Toxin-antitoxin systems are preserved by nearly every prokaryote. The type II toxin MazF acts as a sequence-specific endoribonuclease, cleaving ribonucleotides at specific sequences that vary from three to seven bases, as has been reported in different host organisms to date. The present study characterized the MazEF module (MazEF-sth) conserved in the IAM14863 strain, a Gram-negative syntrophic bacterium that can be supported by co-culture with multiple bacteria, including .
View Article and Find Full Text PDFChembiochem
December 2023
National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
Most natural formate dehydrogenases (FDHs) exhibit NAD specificity, making it imperative to explore the engineering of FDH cofactor specificity for NADPH regeneration systems. The endogenous FDH of Komagataella phaffii (K. phaffii), termed KphFDH, is a typical NAD -specific FDH.
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