Culturable psychrophilic prokaryotes were obtained of samples of glacier sediment, seaside mud, glacier melted ice, and Deschampsia antarctica rhizosphere from Collins glacier, Antarctica. The taxonomic classification was done by a culture-dependent molecular approach involving the Amplified Ribosomal DNA Restriction Analysis. Two hundred sixty colonies were successfully isolated and sub-cultivated under laboratory conditions. The analysis showed a bacterial profile dominated by Beta-proteobacteria (35.2%) followed by Gamma-proteobacteria (18.5%), Alpha-proteobacteria (16.6%), Gram-positive with high GC content (13%), Cytophaga-Flavobacterium-Bacteroides (13%) and Gram-positive with low GC content (3.7%). Eleven of the isolates have been reported previously and the others microorganisms remain uncharacterized. The isolated microorganisms here could be a potential source for biotechnological products, such as cold-active enzymes and secondary metabolites.

• MeSH
• Bacteroides genetika   izolace a purifikace   MeSH
• biologické přípravky izolace a purifikace   MeSH
• DNA bakterií analýza   genetika   MeSH
• fylogeneze * MeSH
• geologické sedimenty mikrobiologie   MeSH
• ledový příkrov mikrobiologie   MeSH
• molekulární sekvence - údaje MeSH
• Proteobacteria genetika   izolace a purifikace   MeSH
• ribozomální DNA analýza   genetika   MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Antarktida MeSH
• Názvy látek
• biologické přípravky MeSH
• DNA bakterií MeSH
• ribozomální DNA MeSH
• RNA ribozomální 16S MeSH

Species of Acanthamoeba Volkonsky, 1931 are the commonest among free-living amoebae that are widespread in different water resources but with lacking phylogenetic data. This study aims at detecting molecular prevalence and genetic diversity of Acanthamoeba isolates in Kafrelsheikh Governorate, Egypt. Forty-eight water samples were collected from 12 swimming pools; four samples during each season over one year. Samples were filtered, cultivated on non-nutrient agar plates and examined microscopically. Polymerase chain reaction (PCR) and sequence analysis of positive samples targeting diagnostic fragment 3 (DF3) of the small subunit rRNA gene were done. Cultivation succeeded to detect 14 (29%) positive samples while PCR missed three positive samples. The obtained sequences were phylogenetically analysed. The phylogenetic tree was constructed for them with sequences of reference species from the NCBI database. The identified species were Acanthamoeba castellanii Douglas, 1930 (T4), A. astronyxis (Ray et Hayes, 1954) (T9) and A. hatchetti Sawyer, Visvesvara et Harke, 1977 (T11). The prevalence of species of Acanthamoeba was higher during summer and fall. Therefore, the control of the presence of Acanthmoeba spp. in swimming pools needs immediate, effective and practical measures to prevent and control infection with species of Acanthamoeba.

• Klíčová slova
• Acanthamoebidae, phylogenetic analysis, seasonal variation, sequence analysis,
• MeSH
• Acanthamoeba * genetika   MeSH
• fylogeneze MeSH
• genotyp MeSH
• plavecké bazény * MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Egypt MeSH

This study aimed to detect virulence factors, pathovars, and phylogenetic groups of Escherichia coli strains obtained from feces of calves with and without diarrhea up to 70 days old and to determine the association between occurrence of diarrhea, phylogenetic groups, and pathovars. Phylo-typing analysis of the 336 E. coli strains isolated from calves with Clermont method showed that 21 (6.25 %) belong to phylogroup A, 228 (67.85 %) to phylogroup B1, 2 (0.6 %) to phylogroup B2, 5 (1.49 %) to phylogroup C, 57 (16.96 %) to phylogroup E, and 3 (0.9 %) to phylogroup F. Phylogroup D was not identified and 20 strains (5.95 %) were assigned as "unknown." The distribution of phylogenetic groups among pathovars showed that NTEC belong to phylogroups B1 (17) and C (4); EPEC to phylogroups B1 (6) and E (8); STEC to phylogroups A (5), B1 (56), B2 (2), C (1), and E (15); EHEC to phylogroups B1 (95) and E (5); and ETEC to phylogroups A (3), B1 (7), and E (10). The EAST-1 strains were phylogroups A (13), B1 (47), E (19), and F (3); E. coli strains of "unknown" phylogroups belonged to pathovars EPEC (1), EHEC (2), STEC (7), and EAST-1 strains (6). ETEC was associated with diarrhea (P = 0.002). Our study did not find association between the phylogenetic background and occurrence of diarrhea (P = 0.164) but did find some relationship in phylogenetic group and pathovar. The study showed that EHEC and STEC are classified as phylogroup B1, EAST-1 phylogroup A, ETEC, and EPEC phylogroup E.

• Klíčová slova
• Calves, Escherichia coli, Pathovars, Phylogenetic group,
• MeSH
• DNA bakterií genetika   MeSH
• enteropatogenní Escherichia coli klasifikace   genetika   růst a vývoj   patogenita   MeSH
• enterotoxigenní Escherichia coli klasifikace   genetika   růst a vývoj   patogenita   MeSH
• exprese genu MeSH
• faktory virulence genetika   metabolismus   MeSH
• feces mikrobiologie   MeSH
• fylogeneze MeSH
• genotyp MeSH
• infekce vyvolané Escherichia coli diagnóza   mikrobiologie   patologie   veterinární   MeSH
• nemoci skotu diagnóza   mikrobiologie   patologie   MeSH
• polymerázová řetězová reakce MeSH
• průjem diagnóza   mikrobiologie   patologie   veterinární   MeSH
• shiga-toxigenní Escherichia coli klasifikace   genetika   růst a vývoj   patogenita   MeSH
• skot MeSH
• techniky typizace bakterií MeSH
• virulence MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• skot MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Brazílie MeSH
• Názvy látek
• DNA bakterií MeSH
• faktory virulence MeSH

Turnip ringspot virus (TuRSV) has been proposed to be a member of a new species in the genus Comovirus. Its remarkable host-range similarity to radish mosaic virus (RaMV) may have led to its misrecognition in the past. Findings from both sequence analysis and serological tests support the assignment of TuRSV to a new comovirus species. In addition, phylogenetic analysis suggests that the two genome segments of some TuRSV isolates have a heterogeneous origin.

• MeSH
• Brassica napus MeSH
• Comovirus klasifikace   genetika   imunologie   izolace a purifikace   MeSH
• fylogeneze * MeSH
• molekulární sekvence - údaje MeSH
• nemoci rostlin virologie   MeSH
• Raphanus MeSH
• RNA virová genetika   MeSH
• sekvenční analýza DNA MeSH
• sérotypizace MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• RNA virová MeSH

Soil environments are inhabited by microorganisms adapted to its diversified microhabitats. The metabolic activity of individual strains/populations reflects resources available at a particular spot, quality of which may not comply with broad soil characteristics. To explore the potential of individual strains to adapt to particular micro-niches of carbon sources, a set of 331 Actinomycetia strains were collected at ten sites differing in vegetation, soil pH, organic matter content and quality. The strains were isolated on the same complex medium with neutral pH and their metabolites analyzed by UHPLC and LC-MS/MS in spent cultivation medium (metabolic profiles). For all strains, their metabolic profiles correlated with soil pH and organic matter content of the original sites. In comparison, strains phylogeny based on either 16S rRNA or the beta-subunit of DNA-dependent RNA polymerase (rpoB) genes was partially correlated with soil organic matter content but not soil pH at the sites. Antimicrobial activities of strains against Kocuria rhizophila, Escherichia coli, and Saccharomyces cerevisiae were both site- and phylogeny-dependent. The precise adaptation of metabolic profiles to overall sites characteristics was further supported by the production of locally specific bioactive metabolites and suggested that carbon resources represent a significant selection pressure connected to specific antibiotic activities.

• Klíčová slova
• Streptomyces, antibiotic, metabolic differentiation, micro-niche, organic matter, phylogenetic differentiation, soil pH,
• MeSH
• Actinobacteria * MeSH
• Actinomyces MeSH
• chromatografie kapalinová MeSH
• fylogeneze MeSH
• půda chemie   MeSH
• půdní mikrobiologie MeSH
• RNA ribozomální 16S genetika   MeSH
• tandemová hmotnostní spektrometrie MeSH
• uhlík metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• půda MeSH
• RNA ribozomální 16S MeSH
• uhlík MeSH

The survival of isolated small populations is threatened by both demographic and genetic factors. Large carnivores declined for centuries in most of Europe due to habitat changes, overhunting of their natural prey and direct persecution. However, the current rewilding trends are driving many carnivore populations to expand again, possibly reverting the erosion of their genetic diversity. In this study we reassessed the extent and origin of the genetic variation of the Italian wolf population, which is expanding after centuries of decline and isolation. We genotyped wolves from Italy and other nine populations at four mtDNA regions (control-region, ATP6, COIII and ND4) and 39 autosomal microsatellites. Results of phylogenetic analyses and assignment procedures confirmed in the Italian wolves a second private mtDNA haplotype, which belongs to a haplogroup distributed mostly in southern Europe. Coalescent analyses showed that the unique mtDNA haplotypes in the Italian wolves likely originated during the late Pleistocene. ABC simulations concordantly showed that the extant wolf populations in Italy and in south-western Europe started to be isolated and declined right after the last glacial maximum. Thus, the standing genetic variation in the Italian wolves principally results from the historical isolation south of the Alps.

• MeSH
• fylogeneze MeSH
• genetická variace * MeSH
• genotyp * MeSH
• haplotypy MeSH
• mitochondriální DNA genetika   MeSH
• populační genetika MeSH
• vlci genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Itálie MeSH
• Názvy látek
• mitochondriální DNA MeSH

A fructose-6-phosphate phosphoketolase-positive strain (GSD1FST) was isolated from a faecal sample of a 3 weeks old German Shepherd dog. The closest related taxa to isolate GSD1FST based on results from the EZBioCloud database were Bifidobacterium animalis subsp. animalis ATCC 25527T, Bifidobacterium animalis subsp. lactis DSM 10140T and Bifidobacterium anseris LMG 30189T, belonging to the Bifidobacterium pseudolongum phylogenetic group. The resulting 16S rRNA gene identities (compared length of 1454 nucleotides) towards these taxa were 97.30, 97.23 and 97.09 %, respectively. The pairwise similarities of strain GSD1FST using argS, atpA, fusA, hsp60, pyrG, rpsC, thrS and xfp gene fragments to all valid representatives of the B. pseudolongum phylogenetic group were in the concatenated range of 83.08-88.34 %. Phylogenomic analysis based on whole-genome methods such as average nucleotide identity revealed that bifidobacterial strain GSD1FST exhibits close phylogenetic relatedness (88.17 %) to Bifidobacetrium cuniculi LMG 10738T. Genotypic characteristics and phylogenetic analyses based on nine molecular markers, as well as genomic and comparative phenotypic analyses, clearly proved that the evaluated strain should be considered as representing a novel species within the B. pseudolongum phylogenetic group named as Bifidobacterium canis sp. nov. (GSD1FST=DSM 105923T=LMG 30345T=CCM 8806T).

• Klíčová slova
• Bifidobacterium, Bifidobacterium pseudolongum phylogenetic group, MALDI-TOF MS, dogs,
• MeSH
• aldehydlyasy MeSH
• bakteriální geny MeSH
• Bifidobacterium klasifikace   MeSH
• DNA bakterií genetika   MeSH
• feces mikrobiologie   MeSH
• fylogeneze * MeSH
• psi mikrobiologie   MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• techniky typizace bakterií MeSH
• zastoupení bazí MeSH
• zvířata MeSH
• Check Tag
• psi mikrobiologie   MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• aldehydlyasy MeSH
• DNA bakterií MeSH
• fructose-6-phosphate phosphoketolase MeSH Prohlížeč
• RNA ribozomální 16S MeSH

Results of molecular determination of a dog isolate of Neospora caninum in the Czech Republic are presented. Colorless bisporocystic oocysts measuring 10-13 micro m x 10-11 micro m were recovered from feces and used for DNA isolation. A diagnostic PCR procedure using previously described molecular methods was performed to determine the species. The N. caninum species-specific primers based on the Nc 5 region produced a positive result, while primers specific for Hammondia heydorni rDNA internal transcribed spacer 1 (ITS1) was negative. Sequencing and phylogenetic comparison of ITS1 rDNA and the D2 domain of the large subunit rDNA (D2 LSU) determined our isolate to be N. caninum. Phylogenetic analysis of closely related genera Toxoplasma, Neospora and Hammondia based on ITS1 and D2 LSU robustly distinguished three clades: (i). Toxoplasma gondii + Hammondia hammondi, (ii). N. caninum + Neospora hughesi, and (iii). H. heydorni. Based on phylogenetic relationships we propose three acceptable suggestions to solve the problem of taxonomy of these genera.

• MeSH
• Coccidia klasifikace   genetika   MeSH
• druhová specificita MeSH
• feces parazitologie   MeSH
• fylogeneze * MeSH
• kokcidióza diagnóza   parazitologie   MeSH
• nemoci psů diagnóza   parazitologie   MeSH
• Neospora klasifikace   genetika   izolace a purifikace   MeSH
• oocysty klasifikace   genetika   izolace a purifikace   MeSH
• polymerázová řetězová reakce * MeSH
• psi parazitologie   MeSH
• ribozomální DNA analýza   genetika   MeSH
• Toxoplasma klasifikace   genetika   MeSH
• zvířata MeSH
• Check Tag
• psi parazitologie   MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ribozomální DNA MeSH

Microsporidia are a group of obligate intracellular unicellular eukaryotes that can parasitize a wide variety of other eukaryotes ranging from protists to invertebrates and vertebrates. In this study, we examined the microsporidium Nosema sp. isolated from the mulberry pest, Hemerophila atrilineata Butler, 1881, named herein "Nosema sp. HA". The fresh spores were long oval in shape, 3.8 +/- 0.4 microm in length and 1.9 +/- 0.3 microm in width. Analysis of tissue infection of silkworm, Bombyx mori Linnaeus, 1758, indicated that the midgut, Malpighian tubules, muscle, fat body, silk glands, hemocytes, nerve tissue and gonads of silkworm were infected with Nosema sp. HA. The complete rRNA gene sequence of this microsporidium contained 4 305 base pairs (GenBank Accession JN882299), including the large subunit rRNA (2492 bp), the internal transcribed spacer (187 bp), the small subunit rRNA (1232 bp), the intergenic spacer (279 bp) and the 5S region (115 bp). The organization of the rRNA gene is 5'-LSU-ITS-SSU-IGS-5S-3'. Phylogenetic analysis, comparison of sequence identities and the arrangement in the rRNA gene subunits suggested that this isolate is separate from other Nosema species.

• MeSH
• fungální RNA genetika   MeSH
• fylogeneze * MeSH
• interakce hostitele a parazita MeSH
• Microsporidia genetika   fyziologie   ultrastruktura   MeSH
• můry parazitologie   MeSH
• RNA ribozomální genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fungální RNA MeSH
• RNA ribozomální MeSH

The present study was aimed at investigating the relationship between the new Clermont's phylogenetic groups, virulence factors, and pathogenicity island markers (PAIs) among uropathogenic Escherichia coli (UPEC) in Iran. This cross-sectional study was carried out on 140 UPEC isolates collected from patients with urinary tract infections in Bushehr, Iran. All isolates were subjected to phylogenetic typing using a new quadruplex-PCR method. The presence of PAI markers and virulence factors in UPEC strains was evaluated by multiplex PCR. The most predominant virulence gene was fimH (85%), followed by iucC (61.4%), papC (38.6%), hlyA (22.1%), cnf-1 (18.6%), afa (10.7%), papG and neuC (each 9.3%), ibeA (3.6%), and sfa/foc (0.7%). The most common phylogenetic group was related to B2 (39.3%), and the least common to A (0.7%). The most prevalent PAI marker was PAI IV536 (77.14%), while markers for PAI III536 (13.57%), PAI IIJ96 (12.86%), and PAI II536 (12.14%) were the least frequent among the UPEC strains. Meanwhile, the PAI IJ96 marker was not detected. There was a significant association between the phylogenetic group B2 and all the studied virulence genes and PAI markers. To our knowledge, this is the first study to compare the relationship between new phylogenetic groups, virulence genes and PAI markers in UPEC strains in Iran. The phylogenetic group B2 was predominantly represented among the studied virulence genes and PAI markers, indicating the preference of particular strains to carry virulence genes.

• MeSH
• DNA bakterií genetika   MeSH
• faktory virulence genetika   MeSH
• fylogeneze * MeSH
• genom bakteriální MeSH
• genomové ostrovy genetika   MeSH
• infekce močového ústrojí mikrobiologie   MeSH
• lidé MeSH
• průřezové studie MeSH
• uropatogenní Escherichia coli genetika   patogenita   MeSH
• virulence genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Írán MeSH
• Názvy látek
• DNA bakterií MeSH
• faktory virulence MeSH