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Streptomyces: A Potential Source of Natural Antimicrobial Drug Leads
Published in Mahendra Rai, Chistiane M. Feitosa, Eco-Friendly Biobased Products Used in Microbial Diseases, 2022
Mahmoud A. Elfaky, Hanaa Nasr, Ilham Touiss, Mohamed L. Ashour
Aminoglycosides bind to the 30S subunit of bacterial ribosomes in the cytosol and interact with the translation of messenger RNAs into proteins, leaving the ribosome inaccessible for translation and resulting in cell death. Many aminoglycosides bind to 16S ribosomal RNA at the decoding site (site A). While this binding does not impede the forming of the peptide synthesis initiation complex, it does disrupt the elongation of the nascent chain by interfering with the proofreading mechanism that controls translational precision. The erroneous proteins may be injected into the cell membrane, altering permeability and stimulating aminoglycoside transport even further (Krause et al. 2016). Aminoglycosides may function on bacterial cells by more than one process, inducing misreading of the RNA code and/or inhibiting amino acid polymerization.
Infection-driven periodontal disease
Published in Phillip D. Smith, Richard S. Blumberg, Thomas T. MacDonald, Principles of Mucosal Immunology, 2020
Thomas E. Van Dyke, Mike Curtis
Until very recently, only 50% or less of the oral microbiota was cultivable in the laboratory. To further characterize the oral microflora, genetic techniques for bacterial detection are now routinely used. In particular, high-throughput sequence analysis of variable regions of 16S ribosomal RNA facilitates identification of virtually all the bacterial cells in a given sample, including those of very low abundance. The findings reveal that the oral flora in health and disease is extraordinarily diverse and that the level of variability appears to be the individual, not the disease, although there are marked differences in the composition of the flora in health and disease in the same individual. Comparison of the microbial composition in health versus disease using these more recent tools reveals whole scale shifts in the microbial community composition. The change from health to disease is therefore viewed as a disturbance to the normally well-tolerated microbial plaque composition in symbiosis with the host tissues to a dysbiotic community structure where potentially pathogenic organisms or complexes of organisms normally present at low abundance become predominant. These include those bacterial species identified in earlier cultural investigations as well as a significant number of previously unrecognized organisms including Filifactor alocis, Peptostreptococcus stomatis, and species drawn from the Desulfolobus, Dialister, and Synergistetes genera.
Genetics and Mutants
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
The amB2 RNA, together with the wild-type R17 RNA, was used by the sequencing of oligonucleotide coding for the first six amino acid residues of the R17 coat protein (Robinson et al. 1969a). A series of the R17 amber mutants was tested for the inhibition of the synthesis of bacterial proteins and ribosomal RNA, where the latter was found inhibited with phage mutants retaining the ability to produce replicase (Spangler and Iglewski 1972). It was found that the inhibition of 16S ribosomal RNA synthesis occurred solely at the transcriptional level. Following the approaches to the maturation mutants of other phages, the changes in the capsid structure and stability of defective particles of the R17 amA31 mutant were investigated thoroughly by serological and chemical methods (Iglewski 1977).
Combination of the gut microbiota and clinical indicators as a potential index for differentiating idiopathic membranous nephropathy and minimal change disease
Published in Renal Failure, 2023
Yumin Jiang, Ting Wang, Wei Yu, Feng Wu, Ruixue Guo, Huangmin Li, Yiding Zhang, Ge Yan, Li Wang, Zhanzheng Zhao
Microbial genomic DNA of stool samples was extracted as described previously [10]. Samples were chemically lysed using buffer [0.1 M phosphate buffer, 4 M guanidine thiocyanate, 5% N-lauroyl sarcosine and 10% N-lauroyl sarcosine (pH 8.0)]. Physical lysis was then performed by incubation at 70° C for 1 h, followed by mechanical lysis by bead beating. DNA was extracted using the EZNA Stool DNA Kit (Omega Biotek, Inc., GA, USA) and stored at −20 °C until further analysis. After DNA quality inspection, the DNA fragments encoding the 16S ribosomal RNA (rRNA) V3–V4 region were amplified by polymerase chain reaction (PCR). PCRs were run in an EasyCycler 96 PCR system (Analytik Jena Corp., AG) based on the following procedure: 3 min at 95 °C followed by 21 cycles of 0.5 min at 94 °C (denaturation), 0.5 min at 58 °C for annealing, and 0.5 min at 72 °C (elongation), with a final extension at 72 °C for 5 min. Sequencing was performed by Shanghai Mobio Company using the MiSeq platform (Illumina Inc., CA, USA).
Identification of gut microbiome and transcriptome changes in ulcerative colitis and pouchitis
Published in Scandinavian Journal of Gastroenterology, 2022
Xin Gao, Di Huang, Li-Sheng Yang, An-Qi He, Kai-Yu Li, Tong Liu, Gang Liu
According to the OMEGA Stool DNA Kit instructions (D4015, Omega, Inc., Norwalk, CT), genomic DNA extraction from Stool samples was performed. The concentration and purity of DNA samples were determined by NanoDrop2000 spectrophotometer and unqualified DNA samples will be discarded. Primers for the 16S ribosomal DNA V3–V4 regions of the bacterial genome were designed in the experiment. The primer sequence of 336F was 5′-GTACTCCTACGGGAGGCAGCA-3′, and the primer sequence of 806R was 5′-GTGGACTACHVGGGTWTCTAAT-3′. A PCR system was established to specifically amplify the V3–V4 region of the 16S ribosomal DNA of the sample genome. Qualified agarose gels were sent to LC-Bio Technology (Hangzhou, China) for Miseq library construction then performed sequencing on Illumina Miseq PE300 platform.
B. adolescentis ameliorates chronic colitis by regulating Treg/Th2 response and gut microbiota remodeling
Published in Gut Microbes, 2021
Lina Fan, Yadong Qi, Siwen Qu, Xueqin Chen, Aiqing Li, Maher Hendi, Chaochao Xu, Lan Wang, Tongyao Hou, Jianmin Si, Shujie Chen
B. adolescentis ATCC15703 was purchased from American type culture collection (ATCC, USA). V4 of 16S ribosomal RNA sequencing was performed to confirm bacterial strain at the species level. The bacteria were cultured in anaerobic modified Reinforced Clostridium Medium (BD Difco, Sparks, MD, USA) under an atmosphere of 10% H2, 10% CO2, and 80% N2 (AW500SG anaerobic workstations; ELECTROTEK, England) for 24 h. The cultures were centrifuged at 3000 rpm for 5 min at 4°C and then washed twice with sterile anaerobic PBS, then resuspended at a final concentration of 1 × 109 CFU/300 µl under strictly anaerobic conditions. For analysis of the viability of B. adolescentis, the suspension was inoculated on RCM containing 1% agarose and then incubated for at least 2 days at 37°C in the anaerobic incubator.