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Revista Chilena de Infectologia :... Aug 2012
Topics: Achromobacter denitrificans; Drug Resistance, Bacterial
PubMed: 23096549
DOI: 10.4067/S0716-10182012000400016 -
International Journal of Systematic and... Jan 2005A polyphasic taxonomic study of 14 isolates recovered from various human and veterinary clinical samples was performed. Phenotypically these isolates shared several...
A polyphasic taxonomic study of 14 isolates recovered from various human and veterinary clinical samples was performed. Phenotypically these isolates shared several characteristics with members of the Alcaligenaceae and related genera. Random amplified polymorphic DNA fingerprinting and whole-cell protein analysis suggested the presence of multiple genomic groups, which was confirmed by DNA-DNA hybridization experiments. 16S rRNA gene sequence analysis indicated that these isolates were related to the genera Pelistega, Taylorella, Oligella, Pigmentiphaga, Alcaligenes, Kerstersia, Achromobacter and Bordetella and belonged to the family Alcaligenaceae. Based on the results of the present study the organisms were classified in a novel genus, Advenella gen. nov. This genus comprises one named species, Advenella incenata sp. nov. (type strain LMG 22250T=CCUG 45225T) and five currently unnamed genomic species. The DNA G+C content of members of the novel genus Advenella is between 54.0 and 57.7 mol%.
Topics: Adolescent; Adult; Alcaligenaceae; Animals; Bacterial Proteins; Cystic Fibrosis; DNA, Bacterial; Female; Gram-Negative Bacterial Infections; Humans; Male; Middle Aged; Molecular Sequence Data; Nucleic Acid Hybridization; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Random Amplified Polymorphic DNA Technique; Sequence Analysis, DNA
PubMed: 15653883
DOI: 10.1099/ijs.0.63267-0 -
PloS One 2013This study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family Alcaligenaceae of Betaproteobacteria. Towards...
This study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family Alcaligenaceae of Betaproteobacteria. Towards that end, the complete genome sequence of the sulfur-chemolithoautotroph Tetrathiobacter kashmirensis WT001(T) was determined and compared with the soil isolate Achromobacter xylosoxidans A8 and the two pathogens Bordetella bronchiseptica RB50 and Taylorella equigenitalis MCE9. All analyses comprehensively indicated that the RB50 and MCE9 genomes were almost the subsets of A8 and WT001(T), respectively. In the immediate evolutionary past Achromobacter and Bordetella shared a common ancestor, which was distinct from the other contemporary stock that gave rise to Tetrathiobacter and Taylorella. The Achromobacter-Bordetella precursor, after diverging from the family ancestor, evolved through extensive genome inflation, subsequent to which the two genera separated via differential gene losses and acquisitions. Tetrathiobacter, meanwhile, retained the core characteristics of the family ancestor, and Taylorella underwent massive genome degeneration to reach an evolutionary dead-end. Interestingly, the WT001(T) genome, despite its conserved architecture, had only 85% coding density, besides which 578 out of its 4452 protein-coding sequences were found to be pseudogenized. Translational impairment of several DNA repair-recombination genes in the first place seemed to have ushered the rampant and indiscriminate frame-shift mutations across the WT001(T) genome. Presumably, this strain has just come out of a recent evolutionary bottleneck, representing a unique transition state where genome self-degeneration has started comprehensively but selective host-confinement has not yet set in. In the light of this evolutionary link, host-adaptation of Taylorella clearly appears to be the aftereffect of genome implosion in another member of the same bottleneck. Remarkably again, potent virulence factors were found widespread in Alcaligenaceae, corroborating which hemolytic and mammalian cell-adhering abilities were discovered in WT001(T). So, while WT001(T) relatives/derivatives in nature could be going the Taylorella way, the lineage as such was well-prepared for imminent host-confinement.
Topics: Alcaligenaceae; Bacterial Adhesion; Base Composition; Betaproteobacteria; Biological Evolution; Cell Line; Gene Transfer, Horizontal; Genes, Bacterial; Genome, Bacterial; Genomics; Hemolysis; Host-Pathogen Interactions; Humans; Molecular Sequence Annotation; Open Reading Frames; Recombination, Genetic; Virulence Factors
PubMed: 23741407
DOI: 10.1371/journal.pone.0064856 -
Nature May 1958
Topics: Alcaligenes
PubMed: 13566061
DOI: 10.1038/1811540a0 -
International Journal of Systematic and... Jul 2010A beige-pigmented bacterium (strain CCUG 53761A(T)) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene...
A beige-pigmented bacterium (strain CCUG 53761A(T)) was isolated from human blood from an 85-year-old man in Göteborg, Sweden. Comparative analysis of 16S rRNA gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family Alcaligenaceae. It grouped within the radiation of the genus Alcaligenes, but showed only 93.0-94.8 % similarity to type strains of members of this genus (Alcaligenes faecalis subsp. parafaecalis, 94.8 %; Alcaligenes faecalis subsp. faecalis, 94.2 %; Alcaligenes faecalis subsp. phenolicus, 93.4 %). This discrimination was supported by chemotaxonomic differences. The polyamine pattern consisted of the predominant compound putrescine, moderate amounts of spermidine and minor to trace amounts of spermine and cadaverine; 2-hydroxyputrescine was not detectable. The quinone system was ubiquinone Q-8 with minor amounts of Q-7. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylethanolamine and moderate amounts of phosphatidylglycerol and an unknown phospholipid; minor lipids were also detected. The fatty acid profile, with large amounts of C(16 : 0) and C(17 : 0) cyclo and the absence of C(12 : 0) 2-OH as hydroxylated fatty acid, also differed significantly from those reported for Alcaligenes species. On the basis of these data, it is proposed that strain CCUG 53761A(T) represents a novel genus and species, for which the name Paenalcaligenes hominis gen. nov., sp. nov. is proposed. The type strain of Paenalcaligenes hominis is CCUG 53761A(T) =CCM 7698(T).
Topics: Aged; Aged, 80 and over; Alcaligenaceae; Base Sequence; Fatty Acids; Humans; Male; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S
PubMed: 19684310
DOI: 10.1099/ijs.0.016576-0 -
BMC Genomics Mar 2014A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in...
BACKGROUND
A novel Gram-negative, non-haemolytic, non-motile, rod-shaped bacterium was discovered in the lungs of a dead parakeet (Melopsittacus undulatus) that was kept in captivity in a petshop in Basel, Switzerland. The organism is described with a chemotaxonomic profile and the nearly complete genome sequence obtained through the assembly of short sequence reads.
RESULTS
Genome sequence analysis and characterization of respiratory quinones, fatty acids, polar lipids, and biochemical phenotype is presented here. Comparison of gene sequences revealed that the most similar species is Pelistega europaea, with BLAST identities of only 93% to the 16S rDNA gene, 76% identity to the rpoB gene, and a similar GC content (~43%) as the organism isolated from the parakeet, DSM 24701 (40%). The closest full genome sequences are those of Bordetella spp. and Taylorella spp. High-throughput sequencing reads from the Illumina-Solexa platform were assembled with the Edena de novo assembler to form 195 contigs comprising the ~2 Mb genome. Genome annotation with RAST, construction of phylogenetic trees with the 16S rDNA (rrs) gene sequence and the rpoB gene, and phylogenetic placement using other highly conserved marker genes with ML Tree all suggest that the bacterial species belongs to the Alcaligenaceae family. Analysis of samples from cages with healthy parakeets suggested that the newly discovered bacterial species is not widespread in parakeet living quarters.
CONCLUSIONS
Classification of this organism in the current taxonomy system requires the formation of a new genus and species. We designate the new genus Basilea and the new species psittacipulmonis. The type strain of Basilea psittacipulmonis is DSM 24701 (= CIP 110308 T, 16S rDNA gene sequence Genbank accession number JX412111 and GI 406042063).
Topics: Alcaligenaceae; Amino Acid Sequence; Bacterial Proteins; Contig Mapping; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Molecular Sequence Data; Phenotype; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 24581117
DOI: 10.1186/1471-2164-15-169 -
Current Opinion in Infectious Diseases Jun 2019To relate genomic changes to phenotypic adaptation and evolution from environmental bacteria to obligate human pathogens, focusing on the examples within Bordetella... (Review)
Review
PURPOSE OF REVIEW
To relate genomic changes to phenotypic adaptation and evolution from environmental bacteria to obligate human pathogens, focusing on the examples within Bordetella species.
RECENT FINDINGS
Recent studies showed that animal-pathogenic and human-pathogenic Bordetella species evolved from environmental ancestors in soil. The animal-pathogenic Bordetella bronchiseptica can hijack the life cycle of the soil-living amoeba Dictyostelium discoideum, surviving inside single-celled trophozoites, translocating to the fruiting bodies and disseminating along with amoeba spores. The association with amoeba may have been a 'training ground' for bacteria during the evolution to pathogens. Adaptation to an animal-associated life style was characterized by decreasing metabolic versatility and genome size and by acquisition of 'virulence factors' mediating the interaction with the new animal hosts. Subsequent emergence of human-specific pathogens, such as Bordetella pertussis from zoonoses of broader host range progenitors, was accompanied by a dramatic reduction in genome size, marked by the loss of hundreds of genes.
SUMMARY
The evolution of Bordetella from environmental microbes to animal-adapted and obligate human pathogens was accompanied by significant genome reduction with large-scale gene loss during divergence.
Topics: Adaptation, Biological; Adaptation, Physiological; Animals; Biological Evolution; Bordetella bronchiseptica; Bordetella pertussis; Host-Pathogen Interactions; Humans; Soil Microbiology
PubMed: 30921085
DOI: 10.1097/QCO.0000000000000549 -
Applied and Environmental Microbiology Jul 2009Tetrathiobacter spp. and other members of the Alcaligenaceae are metabolically versatile and environmentally significant. A novel, approximately 60-kb conjugative...
Tetrathiobacter spp. and other members of the Alcaligenaceae are metabolically versatile and environmentally significant. A novel, approximately 60-kb conjugative plasmid, pBTK445, from the sulfur chemolithoautotroph Tetrathiobacter kashmirensis, was identified and characterized. This plasmid exists at a low copy number of 2 to 3 per host chromosome. The portion of pBTK445 sequenced so far ( approximately 25 kb) harbors genes putatively involved in replication, transfer functions, partition, and UV damage repair. A 1,373-bp region was identified as the minimal replicon. This region contains a repA gene encoding a protein belonging to the RPA (replication protein A) superfamily and an upstream, iteron-based oriV. A contiguous 11-gene cluster homologous to various type 4 secretion systems (T4SSs) was identified. Insertional inactivation demonstrated that this cluster is involved in the conjugative transfer functions of pBTK445, and thus, it was named the tagB (transfer-associated gene homologous to virB) locus. The core and peripheral TagB components show different phylogenetic affinities, suggesting that this system has evolved by assembling components from evolutionarily divergent T4SSs. A virD4 homolog, putatively involved in nucleoprotein transfer, is also present downstream of the tagB locus. Although pBTK445 resembles IncP plasmids in terms of its genomic organization and the presence of an IncP-specific trbM homolog, it also shows several unique features. Unlike that of IncP, the oriT of pBTK445 is located in close proximity to the oriV, and a traL homolog, which is generally present in the TraI locus of IncP, is present in pBTK445 in isolation, upstream of the tagB locus. A significant outcome of this study is the construction of conjugative shuttle vectors for Tetrathiobacter and related members of the Alkaligenaceae.
Topics: Alcaligenaceae; Base Sequence; Conjugation, Genetic; DNA Repair Enzymes; DNA, Bacterial; Evolution, Molecular; Gene Order; Gene Transfer, Horizontal; Genes, Bacterial; Genetic Vectors; Molecular Sequence Data; Mutagenesis, Insertional; Phylogeny; Plasmids; Replication Origin; Replication Protein A; Replicon; Sequence Analysis, DNA; Sequence Homology
PubMed: 19411426
DOI: 10.1128/AEM.02521-08 -
International Journal of Systematic and... Jul 2009A novel, strictly anaerobic, non-spore-forming, Gram-negative coccobacillus (strain YIT 11859(T)) was isolated from human faeces. Biochemically, this strain was largely...
A novel, strictly anaerobic, non-spore-forming, Gram-negative coccobacillus (strain YIT 11859(T)) was isolated from human faeces. Biochemically, this strain was largely unreactive and was asaccharolytic. Growth of strain YIT 11859(T) in peptone-yeast extract broth produced no visible turbidity, and a trace amount of propionate was detected as an end product of metabolism. 16S rRNA gene sequence analysis showed that strain YIT 11859(T) was related most closely to the type strains of Sutterella species, with 90.8-88.0 % sequence similarity. Phylogenetic analysis of these and other related sequences confirmed that strain YIT 11859(T) was phylogenetically most closely associated with Sutterella species, but formed a separate cluster, indicating that strain YIT 11859(T) represents a novel member of the family Alcaligenaceae. Fatty acid analysis demonstrated the presence of a high concentration of C(18 : 1)omega9c (75 % of the total). The main respiratory quinones were menaquinone (MK-6) and methylated menaquinone (MMK-6). The G+C content of the DNA was 49.8 mol%. These results suggest that strain YIT 11859(T) represents a novel species of a new genus, for which the name Parasutterella excrementihominis gen. nov., sp. nov. is proposed. The type strain of Parasutterella excrementihominis is YIT 11859(T) (=DSM 21040(T) =JCM 15078(T)).
Topics: Alcaligenaceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Feces; Genes, rRNA; Genotype; Humans; Japan; Molecular Sequence Data; Phenotype; Phylogeny; Quinones; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Species Specificity
PubMed: 19542131
DOI: 10.1099/ijs.0.002519-0 -
International Journal of Systematic and... May 2024A Gram-stain-negative bacterium, designated LG-2, was isolated from sludge collected at a pesticide-manufacturing factory in Jiangsu Province, PR China. Cells of strain...
A Gram-stain-negative bacterium, designated LG-2, was isolated from sludge collected at a pesticide-manufacturing factory in Jiangsu Province, PR China. Cells of strain LG-2 were strictly aerobic, non-motile and spherical. Growth was observed at 15-42 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.0) and 0-3.0 % (w/v) NaCl (optimum, 1.0 %). LG-2 showed 95.5-96.9 % 16S rRNA sequence similarity to type strains in the genera , , , and of the family . The phylogenomic tree indicated that strain LG-2 was clustered in the family and formed a clade with IMT-305, while the phylogenetic trees based on 16S rRNA gene sequences indicated that strain LG-2 formed a distinct clade within the family . The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between LG-2 and its closely related type strains in the genera , , , and were 70.8-75.3, 18.9-23.7 and 59.6 %-69.3 %, respectively. The major cellular fatty acids were C, C cyclo, summed feature 3 (C ω7 and/or C ω6), summed feature 8 (C ω7 and/or C ω6) and summed feature 2 (C aldehyde and/or unknown 10.928). The predominant menaquinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, three aminolipids and nine unknown polar lipids. The genome size of strain LG-2 was 3.2 Mb and the DNA G+C content was 63.4 mol%. On the basis of the phenotypic, phylogenetic and genomic results from this study, strain LG-2 represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed, with strain LG-2 (=KCTC 8084= CCTCC AB 2023123) as the type strain.
Topics: Phylogeny; RNA, Ribosomal, 16S; Fatty Acids; DNA, Bacterial; Base Composition; Bacterial Typing Techniques; China; Nucleic Acid Hybridization; Sequence Analysis, DNA; Sewage; Alcaligenaceae; Pesticides; Vitamin K 2
PubMed: 38767617
DOI: 10.1099/ijsem.0.006394