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1.
Braz J Microbiol ; 54(2): 779-790, 2023 Jun.
Article in English | MEDLINE | ID: mdl-36869213

ABSTRACT

Non-diphtheria Corynebacterium species (NDC) belonging to the human skin and mucosa microbiota are frequently neglected as contaminants. However, reports of human infections by Corynebacterium spp. have increased considerably in recent years. In this study, a group of six NDC isolates of urine (n = 5) and sebaceous cyst (n = 1) from two South American countries were identified at genus level or misidentified based on API® Coryne and genetic/molecular analyses. The 16S rRNA (99.09-99.56%) and rpoB (96.18-97.14%) gene sequence similarities of the isolates were higher when compared with Corynebacterium aurimucosum DSM 44532 T. Multilocus sequence analysis (MLSA) indicated that these six NDC isolates compose a distinctive phylogenetic clade. Genome-based taxonomic analysis with the whole-genome sequences was able to separate these six isolates from other known Corynebacterium type strains. Average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between closely related type strains and the six isolates were considerably lower than the currently recommended threshold values for species circumscription. Phylogenetic and genomic taxonomy analyses indicated these microorganisms as a novel Corynebacterium species, for which we formally propose the name Corynebacterium guaraldiae sp. nov. with isolate 13T (= CBAS 827T = CCBH 35012T) as type strain.


Subject(s)
Corynebacterium , DNA , Humans , Sequence Analysis, DNA , Phylogeny , RNA, Ribosomal, 16S/genetics , Corynebacterium/genetics , DNA, Bacterial/genetics , Bacterial Typing Techniques , Fatty Acids/chemistry , Nucleic Acid Hybridization
2.
Syst Appl Microbiol ; 44(4): 126223, 2021 Jul.
Article in English | MEDLINE | ID: mdl-34157595

ABSTRACT

Streptomyces thermoautotrophicus UBT1T has been suggested to merit generic status due to its phylogenetic placement and distinctive phenotypes among Actinomycetia. To evaluate whether 'S. thermoautotrophicus' represents a higher taxonomic rank, 'S. thermoautotrophicus' strains UBT1T and H1 were compared to Actinomycetia using 16S rRNA gene sequences and comparative genome analyses. The UBT1T and H1 genomes each contain at least two different 16S rRNA sequences, which are closely related to those of Acidothermus cellulolyticus (order Acidothermales). In multigene-based phylogenomic trees, UBT1T and H1 typically formed a sister group to the Streptosporangiales-Acidothermales clade. The Average Amino Acid Identity, Percentage of Conserved Proteins, and whole-genome Average Nucleotide Identity (Alignment Fraction) values were ≤58.5%, ≤48%, ≤75.5% (0.3) between 'S. thermoautotrophicus' and Streptosporangiales members, all below the respective thresholds for delineating genera. The values for genomics comparisons between strains UBT1T and H1 with Acidothermales, as well as members of the genus Streptomyces, were even lower. A review of the 'S. thermoautotrophicus' proteomic profiles and KEGG orthology demonstrated that UBT1T and H1 present pronounced differences, both tested and predicted, in phenotypic and chemotaxonomic characteristics compared to its sister clades and Streptomyces. The distinct phylogenetic position and the combination of genotypic and phenotypic characteristics justify the proposal of Carbonactinospora gen. nov., with the type species Carbonactinospora thermoautotrophica comb. nov. (type strain UBT1T, = DSM 100163T = KCTC 49540T) belonging to Carbonactinosporaceae fam. nov. within Actinomycetia.


Subject(s)
Phylogeny , Streptomyces , Actinobacteria , Bacterial Typing Techniques , DNA, Bacterial/genetics , Proteomics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Streptomyces/classification
3.
Int J Syst Evol Microbiol ; 68(9): 2883-2914, 2018 Sep.
Article in English | MEDLINE | ID: mdl-30010524

ABSTRACT

A red pigmented actinobacterium designated G2T, forming extremely branched vegetative hyphae, vesicles and mutilocular sporangia, was isolated from Casuarina equisetifolia nodules. The strain failed to nodulate its original host plant but effectively nodulated members of actinorhizal Rhamnales. The taxonomic position of G2T was determined using a polyphasic approach. The peptidoglycan of the strain contained meso-diaminopimelic acid as diagnostic diamino acid, galactose, glucose, mannose, rhamnose, ribose and xylose. The polar lipid pattern consisted of phosphatidylinositol (PI), diphosphatidylglycerol (DPG), glycophospholipids (GPL1-2), phosphatidylglycerol (PG), aminophospholipid (APL) and unknown lipids (L). The predominant menaquinones were MK-9 (H4) and MK-9 (H6) while the major fatty acids were iso-C16 : 0, C17 : 1ω8c and C15 : 0. The size of the genome of G2T was 9.5 Mb and digital DNA G+C content was 70.9 %. The 16S rRNA gene showed 97.4-99.5 % sequence identity with the type strains of species of the genus Frankia. Digital DNA -DNA hybridisation (dDDH) values between G2T and its nearest phylogenetic neighbours Frankia elaeagniand Frankia discariaewere below the threshold of 70 %. On the basis of these results, strain G2T (=DSM 45899T=CECT 9038T) is proposed to represent the type strain of a novel species Frankia irregularis sp. nov.


Subject(s)
Frankia/classification , Magnoliopsida/microbiology , Phylogeny , Plant Root Nodulation , Bacterial Typing Techniques , Base Composition , Cell Wall/chemistry , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Frankia/genetics , Frankia/isolation & purification , Guadeloupe , Nucleic Acid Hybridization , Peptidoglycan/chemistry , Phospholipids/chemistry , Pigmentation , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Symbiosis , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
4.
Int J Syst Evol Microbiol ; 68(9): 2712-2721, 2018 Sep.
Article in English | MEDLINE | ID: mdl-29969090

ABSTRACT

A polyphasic study was undertaken to establish the taxonomic status of a Blastococcus strain isolated from an extreme hyper-arid Atacama Desert soil. The isolate, strain P6T, was found to have chemotaxonomic and morphological properties consistent with its classification in the genus Blastococcus. It was shown to form a well-supported branch in the Blastococcus 16S rRNA gene tree together with the type strains of Blastococcus capsensis and Blastococcus saxobsidens and was distinguished from the latter, its close phylogenetic neighbour, by a broad range of phenotypic properties. The draft genome sequence of isolate P6T showed 84.6 % average nucleotide identity, 83.0 % average amino acid identity and a digital DNA-DNA hybridisation value of 27.8 % in comparison with the genome sequence of B. saxobsidens DSM 44509T, values consistent with its assignment to a separate species. Based on these data it is proposed that isolate P6T (NCIMB 15090T=NRRL B-65468T) be assigned to the genus Blastococcus as Blastococcus atacamensis sp. nov. Analysis of the whole genome sequence of B. atacamensis P6T, with 3778 open reading frames and a genome size of 3.9 Mb showed the presence of genes and gene clusters that encode for properties that reflect its adaptation to the extreme environmental conditions that prevail in Atacama Desert soils.


Subject(s)
Actinomycetales/classification , Desert Climate , Phylogeny , Soil Microbiology , Actinomycetales/genetics , Actinomycetales/isolation & purification , Bacterial Typing Techniques , Base Composition , Chile , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
5.
Syst Appl Microbiol ; 41(5): 427-436, 2018 Sep.
Article in English | MEDLINE | ID: mdl-29789182

ABSTRACT

A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12T, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus. They were distinguished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic properties. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the whole genome sequences of isolate B12T and G. obscurus DSM 43160T were 89.28%, 87.27% and 37.4%, respectively, metrics consistent with its classification as a separate species. On the basis of these data, it is proposed that the isolates be assigned to the genus Geodermatophilus as Geodermatophilus chilensis sp. nov. with isolate B12T (CECT 9483T=NCIMB 15089T) as the type strain. Analysis of the whole genome sequence of G. chilensis B12T with 5341 open reading frames and a genome size of 5.5Mb highlighted genes and gene clusters that encode for properties relevant to its adaptation to extreme environmental conditions prevalent in extreme hyper-arid Atacama Desert soils.


Subject(s)
Actinobacteria/classification , Actinobacteria/genetics , Desert Climate , Phylogeny , Soil Microbiology , Actinobacteria/chemistry , Actinobacteria/physiology , Chile , DNA, Bacterial/genetics , Genes, Bacterial , Genome, Bacterial/genetics , Multigene Family , Phenotype , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Species Specificity
6.
Int J Infect Dis ; 38: 125-8, 2015 Sep.
Article in English | MEDLINE | ID: mdl-25975652

ABSTRACT

OBJECTIVE: spa-typing of methicillin-resistant Staphylococcus aureus (MRSA) has been used widely in clinical diagnostics and epidemiological studies. The aim of this study was to evaluate high-resolution melting (HRM) as a rapid and cost-effective method, to replace DNA-sequencing, for spa-typing in a global collection of 50 MRSA isolates. METHODS: The polymorphic X region of the spa gene was amplified by colony PCR using the SensiMix HRM kit, and the melting temperature (Tm) and melting curves of the amplicons were analyzed in close tubes using a Rotor-Gene 6000 instrument. RESULTS: Fifteen out of 19 spa-types each had a distinct Tm, which was sufficient to unambiguously type each of these spa-types. The remaining four spa-types could not be separated by Tm alone: t008 and t2770 shared a Tm (80.3°C) and t021 and t311 shared a Tm (80.0°C). However, they could be separated based on the shapes of their melting curves. There are discrepancies between the findings of the present study and those of previous studies, suggesting that standardization remains a challenge for cross-referencing. CONCLUSION: HRM-based spa-typing is reproducible, simple, rapid, and cost-effective. t037 is prevalent in Brazil and Sudan, while diverse spa-types are found in Scotland and Saudi Arabia. Standardization is required for cross-referencing between laboratories globally.


Subject(s)
Methicillin-Resistant Staphylococcus aureus/classification , Molecular Typing , Staphylococcal Protein A/genetics , Brazil , Humans , Methicillin-Resistant Staphylococcus aureus/genetics , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Nucleic Acid Denaturation , Polymerase Chain Reaction , Saudi Arabia , Scotland , Sequence Analysis, DNA , Sudan
7.
J Bacteriol ; 194(11): 3023, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22582380

ABSTRACT

Avian-pathogenic Escherichia coli (APEC) strains cause extraintestinal diseases in avian species. Here, we present the draft genome of an APEC strain (SCI-07) from Brazil that was isolated from skin lesions (gelatinous edema) on the head and periorbital tissues of a laying hen with swollen head syndrome.


Subject(s)
Escherichia coli Infections/veterinary , Escherichia coli Proteins/genetics , Escherichia coli/genetics , Genome, Bacterial , Poultry Diseases/microbiology , Animals , Base Sequence , Brazil , Chickens , Escherichia coli/isolation & purification , Escherichia coli/pathogenicity , Escherichia coli Infections/microbiology , Molecular Sequence Data , Virulence
8.
J Clin Microbiol ; 41(4): 1712-6, 2003 Apr.
Article in English | MEDLINE | ID: mdl-12682166

ABSTRACT

Genotypic analysis of Mycobacterium tuberculosis isolates obtained from human immunodeficiency virus type 1 (HIV-1)-seropositive (n = 80) and -seronegative (n = 25) patients from Lima, Peru, revealed two distinct genotypes correlating with the host immune status. While the level of intrastrain diversity of DNA fingerprints of HIV-seropositive isolates was less pronounced, these isolates showed many clonal groupings.


Subject(s)
HIV Seronegativity , HIV Seropositivity/complications , Mycobacterium tuberculosis/classification , Mycobacterium tuberculosis/genetics , Tuberculosis, Pulmonary/microbiology , AIDS-Related Opportunistic Infections/microbiology , DNA Fingerprinting/methods , Genotype , Humans , Mycobacterium tuberculosis/isolation & purification , Peru , Phylogeny , Polymorphism, Restriction Fragment Length , Tuberculosis, Pulmonary/complications
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