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Infection Feb 2014Turicella otitidis and Corynebacterium auris, described as new species 20 years ago, have been isolated mainly from the external ear canal and middle ear fluid. While... (Review)
Review
Turicella otitidis and Corynebacterium auris, described as new species 20 years ago, have been isolated mainly from the external ear canal and middle ear fluid. While their taxonomic position has been clearly established, their diagnosis in the routine laboratory is difficult. The question of their pathogenic potential in otitis is still open but might be elucidated better if corynebacteria are speciated more often.
Topics: Actinomycetales; Actinomycetales Infections; Bacteriological Techniques; Ear Canal; Humans; Otitis; Otitis Media with Effusion
PubMed: 23775360
DOI: 10.1007/s15010-013-0488-x -
Journal of Microbiology (Seoul, Korea) May 2021Three rod-shaped, Gram-stain-positive, and catalase-positive, phenotypically closely related isolates (HY052, HY050, and HY045) were obtained from fecal samples...
Three rod-shaped, Gram-stain-positive, and catalase-positive, phenotypically closely related isolates (HY052, HY050, and HY045) were obtained from fecal samples collected from bats in Guangxi province and Chongqing city of China. Circular, smooth, light-yellow colonies appeared on brain heart infusion plate after 24-48 h incubation at 28°C. The optimal pH for growth was between 6.0 and 7.5. Based on 16S rRNA, the three isolates were phylogenetically related to Agromyces terreus DS-10, Agromyces aureus AR33, Agromyces salentinus 20-5, Agromyces allii UMS-62, Agromyces lapidis CD55, and Agromyces italicus CD1. Moreover, based on 296 core genes, the phylogenomic tree indicated that the three isolates clustered together, closest to Agromyces cerinus VKM Ac-1340 and Agromyces fucosus VKM Ac-1345 but separated distantly from other Agromyces species. The average nucleotide identity values between strain HY052 and other Agromyces species ranged from 79.3% to 87.9%, lower than the 95-96% threshold. Furthermore, the genome of strain HY052 contains a circular chromosome of 3,437,203 bp with G + C content of 69.0 mol%. Main fatty acids were anteiso-C and anteiso-C. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Rhamnose, ribose, and glucose were the primary cell wall sugars. The major peptidoglycan amino acids included alanine, glutamic acid, glycine, and 2,4-diaminobutyric acid. An additional remarkable difference from other Agromyces species is that MK-12 was the sole menaquinone in strain HY052. Based on results from the polyphasic characterizations performed in this study, our isolates are proposed to be members of a novel species in genus Agromyces, named Agromyces laixinhei. The type strain is HY052 (= CGMCC 1.17175 = JCM 33695).
Topics: Actinobacteria; Actinomycetales; Animals; Base Composition; China; Chiroptera; DNA, Bacterial; Fatty Acids; Feces; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Whole Genome Sequencing
PubMed: 33779960
DOI: 10.1007/s12275-021-0546-5 -
Proceedings of the National Academy of... Jun 2018Phosphopantetheinyl transferases (PPTases) are a superfamily of essential enzymes required for the synthetic processes of many compounds including fatty acid,...
Phosphopantetheinyl transferases (PPTases) are a superfamily of essential enzymes required for the synthetic processes of many compounds including fatty acid, polyketide, and nonribosomal peptide metabolites. These enzymes activate carrier proteins in specific biosynthetic pathways via the transfer of a phosphopantetheinyl moiety to a serine residue in the conserved motif of carrier proteins. Since many microorganisms produce a number of polyketide and nonribosomal peptide metabolites, the distribution of PPTase genes was investigated in these microorganisms. PPTases were found in bacterial protein databases using a hidden Markov model search with the PF01648 (4'-phosphopantetheinyl transferase superfamily) model. microorganisms harbor several genes encoding AcpS-type and Sfp-type PPTases in individual genomes, many of which were associated with the biosynthetic gene cluster for polyketide or nonribosomal peptide metabolites. The properties of these PPTases were evaluated in the heterologous expression system using the biosynthetic gene clusters and genes encoding PPTases found in the present study. Sfp-type PPTases were classified into two subgroups, and although the substrate specificities of the enzymes in one subgroup were wide, the catalytic activities of enzymes in the other subgroup were low. SAV_1784 of possessed the most characteristic broad-range activity against several type I polyketide synthases and nonribosomal peptide synthetases.
Topics: Actinomycetales; Amino Acid Motifs; Bacterial Proteins; Databases, Protein; Multigene Family; Transferases (Other Substituted Phosphate Groups)
PubMed: 29903901
DOI: 10.1073/pnas.1800715115 -
Emerging Infectious Diseases Jan 2005
Topics: Actinomycetales; Actinomycetales Infections; Aged; Aortic Valve; DNA, Ribosomal; Endocarditis, Bacterial; Heart Valve Prosthesis; Humans; Male; Molecular Sequence Data; Prosthesis-Related Infections; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 15714667
DOI: 10.3201/eid1101.040761 -
Clinical Microbiology Reviews Jul 1990Coryneform isolates from clinical specimens frequently cannot be identified by either reference laboratories or research laboratories. Many of these organisms are skin... (Review)
Review
Coryneform isolates from clinical specimens frequently cannot be identified by either reference laboratories or research laboratories. Many of these organisms are skin flora that belong to a large number of taxonomic groups, only 40% of which are in the genus Corynebacterium. This review provides an update on clinical presentations, microbiological features, and pathogenic mechanisms of infections with nondiphtheria Corynebacterium species and other pleomorphic gram-positive rods. The early literature is also reviewed for a few coryneforms, especially those whose roles as pathogens are controversial. Recognition of newly emerging opportunistic coryneforms is dependent on sound identification schemes which cannot be developed until cell wall analyses and nucleic acid studies have defined the taxonomic groups and all of the reference strains within each taxon have been shown by molecular methods to be authentic members. Only then can reliable batteries of biochemical tests be selected for distinguishing each taxon.
Topics: Actinomycetales; Bacterial Infections; Humans
PubMed: 2116939
DOI: 10.1128/CMR.3.3.227 -
FEMS Microbiology Reviews May 2001Data on the structures of cell wall teichoic acids, the anionic carbohydrate-containing polymers, found in many Gram-positive bacteria have been summarized and the... (Review)
Review
Data on the structures of cell wall teichoic acids, the anionic carbohydrate-containing polymers, found in many Gram-positive bacteria have been summarized and the polymers of the actinomycete genus Nocardiopsis have been considered from the taxonomic standpoint. The structures of these polymers or their combinations have been demonstrated to be indicative of each of seven Nocardiopsis species and two subspecies, verified by the DNA-DNA relatedness data, and to correlate well with the grouping of the organisms based on 16S rDNA sequences. As each of the intrageneric taxa discussed is definable by the composition of teichoic acids, the polymers are considered to be valuable taxonomic markers for the Nocardiopsis species and subspecies. The (13)C NMR spectra of the polymers, data on the products of their chemical degradation, and distinguishing constituents of whole cell walls derived from teichoic acids are discussed, which are useful for identification of certain polymers and members of the genus Nocardiopsis at the species and subspecies level in microbiological practice.
Topics: Actinomycetales; Cell Wall; DNA, Ribosomal; Magnetic Resonance Spectroscopy; Species Specificity; Teichoic Acids
PubMed: 11348685
DOI: 10.1111/j.1574-6976.2001.tb00578.x -
Applied and Environmental Microbiology Mar 2017Among the bacteria, members of the order are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide...
Among the bacteria, members of the order are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by (other than spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the , , , and families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the ). When incubated in a hydrated mixture of blended and grass biomass over a 5-week period, and (a member of the ) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 genomes in the CAZy database and 5 genomes from our isolates, we posit that spp. and select members of the and likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils. Shifts in the relative abundance of taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of phylogeny with lignocellulolytic functional potential.
Topics: Actinomycetales; Carboxymethylcellulose Sodium; Chitin; Climate Change; Colorado; Grassland; Lignin; Pectins; Phylogeny; Polysaccharides; RNA, Ribosomal, 16S; Soil; Soil Microbiology; Xylans
PubMed: 28087533
DOI: 10.1128/AEM.03020-16 -
FEMS Immunology and Medical Microbiology Apr 2009The genus Dietzia has only been established fairly recently. The Gram morphology and colony appearance of the species of this genus is remarkably similar to Rhodococcus... (Review)
Review
The genus Dietzia has only been established fairly recently. The Gram morphology and colony appearance of the species of this genus is remarkably similar to Rhodococcus equi. In the absence of simple, accurate methods for their identification, Dietzia spp. might have been misidentified as a Rhodococcus spp. and/or considered to be contaminants only. This MiniReview is designed to summarize current evidence on the clinical significance of Dietzia species, to consider their potential role as human pathogens, and to outline approaches that can be used to accurately classify and identify members of the genus, with the overall aim of alerting the medical microbiological community to a little known genus that contains clinically significant organisms.
Topics: Actinomycetales; Actinomycetales Infections; Bacterial Typing Techniques; Humans; Phylogeny
PubMed: 19159434
DOI: 10.1111/j.1574-695X.2008.00513.x -
Microbiological Reviews Jun 1993Frankia strains are N2-fixing actinomycetes whose isolation and cultivation were first reported in 1978. They induce N2-fixing root nodules on diverse nonleguminous... (Review)
Review
Frankia strains are N2-fixing actinomycetes whose isolation and cultivation were first reported in 1978. They induce N2-fixing root nodules on diverse nonleguminous (actinorhizal) plants that are important in ecological successions and in land reclamation and remediation. The genus Frankia encompasses a diverse group of soil actinomycetes that have in common the formation of multilocular sporangia, filamentous growth, and nitrogenase-containing vesicles enveloped in multilaminated lipid envelopes. The relatively constant morphology of vesicles in culture is modified by plant interactions in symbiosis to give a diverse array of vesicles shapes. Recent studies of the genetics and molecular genetics of these organisms have begun to provide new insights into higher-plant-bacterium interactions that lead to productive N2-fixing symbioses. Sufficient information about the relationship of Frankia strains to other bacteria, and to each other, is now available to warrant the creation of some species based on phenotypic and genetic criteria.
Topics: Actinomycetales; Base Sequence; Molecular Sequence Data; Plants; Symbiosis; Terminology as Topic
PubMed: 8336669
DOI: 10.1128/mr.57.2.293-319.1993 -
Antonie Van Leeuwenhoek Aug 2010We reconstruct the phylogenetic relationships within the bacterial genus Pseudonocardia to evaluate two models explaining how and why Pseudonocardia bacteria colonize... (Review)
Review
We reconstruct the phylogenetic relationships within the bacterial genus Pseudonocardia to evaluate two models explaining how and why Pseudonocardia bacteria colonize the microbial communities on the integument of fungus-gardening ant species (Attini, Formicidae). The traditional Coevolution-Codivergence model views the integument-colonizing Pseudonocardia as mutualistic microbes that are largely vertically transmitted between ant generations and that supply antibiotics that specifically suppress the garden pathogen Escovopsis. The more recent Acquisition model views Pseudonocardia as part of a larger integumental microbe community that frequently colonizes the ant integument from environmental sources (e.g., soil, plant material). Under this latter model, ant-associated Pseudonocardia may have diverse ecological roles on the ant integument (possibly ranging from pathogenic, to commensal, to mutualistic) and are not necessarily related to Escovopsis suppression. We test distinct predictions of these two models regarding the phylogenetic proximity of ant-associated and environmental Pseudonocardia. We amassed 16S-rRNA gene sequence information for 87 attine-associated and 238 environmental Pseudonocardia, aligned the sequences with the help of RNA secondary structure modeling, and reconstructed phylogenetic relationships using a maximum-likelihood approach. We present 16S-rRNA secondary structure models of representative Pseudonocardia species to improve sequence alignments and identify sequencing errors. Our phylogenetic analyses reveal close affinities and even identical sequence matches between environmental Pseudonocardia and ant-associated Pseudonocardia, as well as nesting of environmental Pseudonocardia in subgroups that were previously thought to be specialized to associate only with attine ants. The great majority of ant-associated Pseudonocardia are closely related to autotrophic Pseudonocardia and are placed in a large subgroup of Pseudonocardia that is known essentially only from cultured isolates (rather than cloned 16S sequences). The preponderance of the known ant-associated Pseudonocardia in this latter clade of culturable lineages may not necessarily reflect abundance of these Pseudonocardia types on the ants, but isolation biases when screening for Pseudonocardia (e.g., preferential isolation of autotrophic Pseudonocardia with minimum-nutrient media). The accumulated phylogenetic patterns and the possibility of isolation biases in previous work further erode support for the traditional Coevolution-Codivergence model and calls for continued revision of our understanding how and why Pseudonocardia colonize the microbial communities on the integument of fungus-gardening ant species.
Topics: Actinomycetales; Animals; Ants; Models, Biological; Molecular Sequence Data; Phylogeny; Symbiosis
PubMed: 20333466
DOI: 10.1007/s10482-010-9427-3