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Acinetobacter — Microbiology
Published in E. Bergogne-Bénézin, M.L. Joly-Guillou, K.J. Towner, Acinetobacter, 2020
New molecular identification methods are currently being validated against DNA-DNA hybridisation. One method (Jayarao et al., 1992) is based on restriction analysis of 16S rRNA genes amplified by the polymerase chain reaction. Investigation of Acinetobacter strains of different genomic species by this method has indicated that a combination of patterns generated by five restriction enzymes can be used for identification of most genomic species, including genomic species 1,2, 3 and 13TU (Vaneechoutte et al., 1995).
Beneficial Lactic Acid Bacteria
Published in K. Balamurugan, U. Prithika, Pocket Guide to Bacterial Infections, 2019
Molecular-genetic techniques exhibit various levels of discriminatory power, from species level to differentiation of individual strains (typing). Many methods are based on PCR, conducting the selective amplification of targeted DNA fragments using specific oligonucleotide primers. DNA-DNA hybridization (DDH) is one of the first genomic methods used for the comparison of bacteria. A DDH similarity of approximately 70% serves as the recommended demarcation value for bacterial species. Nevertheless, the method is tedious and complicated for wide application (Moore et al. 2010). DDH should be performed in cases where the new taxon contains more than a single strain or when strains share more than 97% of 16S rRNA gene sequence similarity (Mattarelli et al. 2014).
Rotavirus
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
Lijuan Yuan, Tammy Bui, Ashwin Ramesh
Real-time reverse-transcription quantitative polymerase chain reaction is even more sensitive, capable of broad detection of various genotypes of RVA and discrimination of mixed RV infections.168–171 Oligonucleotide microarray hybridization technology combines the high sensitivity of RT-PCR with the selectivity of DNA-DNA hybridization.172 It is useful for RVA genotyping and also capable of discriminating mixed rotavirus infections from nonspecific cross-reactivity, which is the inherent shortcoming of traditional multiplex RT-PCR genotyping.173 Whole genome sequencing, especially with the next-generation sequencing technology, is able to further characterize the genome segment combinations in mixed rotavirus infections.174,175
Prevotella species as oral residents and infectious agents with potential impact on systemic conditions
Published in Journal of Oral Microbiology, 2022
Eija Könönen, Dareen Fteita, Ulvi K. Gursoy, Mervi Gursoy
The P. intermedia group is composed of four phylogenetically close species, i.e. P. intermedia, P. nigrescens, P. pallens, and P. aurantiaca. Their shared biochemical characteristics are the ability to decompose tryptophane into indole, moderate saccharolytic activities, and production of pigment [43–45]. All four species are residents of the oral cavity, which represents their predominant site of isolation. When Shah and Gharbia [43] used DNA–DNA hybridization to propose the separation of the phenotypically identical P. intermedia and P. nigrescens into two genetically distinct species, the division was not only based on their different homology groups but also on their dissimilar virulence properties. While P. intermedia was associated with periodontal infections, P. nigrescens was found at both healthy and diseased periodontal sites and as a core species mediating fluctuations in the subgingival microbiota [22,43,46]. P. pallens recoveries come mainly from healthy children and periodontitis-free women [19] and, in addition, it seems to be a resident species on healthy esophageal mucosae [47]. The newest member of the P. intermedia group, P. aurantiaca, was isolated from the periodontal pocket of a patient with periodontitis [45]. However, the literature is scarce regarding its involvement in oral or systemic infections.
Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children
Published in Journal of Oral Microbiology, 2019
Nezar Noor Al-Hebshi, Divyashri Baraniya, Tsute Chen, Jennifer Hill, Sumant Puri, Marisol Tellez, Nur A. Hasan, Rita R. Colwell, Amid Ismail
Two general microbiological findings, irrespective of dental health status, are worth elaboration. One is that Actinomyces spp. and strains, hence phylum Actinobacteria, were the most abundant taxa in the children’s supragingival plaque samples. This finding is inconsistent with results from previous studies that used universal 16S rRNA amplification (sequencing or reverse-capture DNA-DNA hybridization), and in which Streptococcus and Veillonella spp. and, subsequently phylum Firmicutes, were found to dominate [2,5,6,9,55]. On the other hand, studies based on PCR-independent technologies, namely checkboard DNA-DNA hybridization, reported relative abundance of Actinomyces to be as high as 63% [10,56]. This is also consistent with early culture studies showing a high abundance of Actinomyces, especially in mature plaque [57]. In fact, direct comparison of culture and clonal analysis of 16S rRNA showed Actinobacteria to be underrepresented when the latter method was employed [8]. This observation strongly indicates that estimates of relative abundances using WMS are more reliable than those obtained using 16S rRNA sequencing. Choice of method for DNA extraction also must be considered in accounting for differences between studies, as it has been shown to significantly influence microbial profiling [58] . In the current study, an enzymatic mixture (metapolyzyme) and bead beating were used to achieve lysis for maximum recovery of DNA from the different bacterial species in the samples; the average DNA yield was 113 ng/μl.
Genomic identification of microbial species adhering to maxillofacial prostheses and susceptibility to different hygiene protocols
Published in Biofouling, 2018
Juliana Barchelli Pinheiro, Marina Peris Vomero, Cássio do Nascimento, Evandro Watanabe, Helena de Freitas Oliveira Paranhos, Neide Pena Coto, Reinaldo Brito Dias, Viviane Cássia de Oliveira, Cláudia Helena Silva-Lovato
To compare the efficacy of the hygiene protocols (immersion in 0.12% chlorhexidine, immersion in 10% R. communis and brushing with neutral soap), six microorganisms (including Gram-positive and Gram-negative bacteria and representative yeast species), both commensal and pathogens were selected. The antibacterial efficacy of the solutions was tested against S. aureus (Gram-positive bacterium), which is associated with reduced function of the immune system and can lead to opportunistic infections (Tada et al. 2006). S. aureus has been found as a colonizer on the surfaces of skin and prostheses (Ariani et al. 2012). Furthermore, it is a pathogenic bacterium that has been used as an indicator of antimicrobial effectiveness (NCCLS 2003). Although C. albicans is the species most commonly isolated from fungal biofilms (Zaremba et al. 2006), this study used C. glabrata since it was the most prevalent of the Candida spp. identified by the Checkerboard DNA–DNA hybridization method. According to Hawser and Douglas (1994), Candida spp. are able to form biofilms to different extents. An in vitro study showed that C. parapsilosis, C. glabrata and C. pseudotropicalis produced less biofilm than C. albicans when measured by dry weight and colorimetric assay radioisotope as well as by microscopy (Kuhn et al. 2002). Moreover, studies have shown little variability in the production of biofilm by C. albicans and other species when assessed by biochemical assays (Kuhn et al. 2002).