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Microbiological Research Jan 2022The growth of sequenced bacterial genomes has revolutionized the assessment of microbial diversity. Pseudomonas is a widely diverse genus, containing more than 254...
The growth of sequenced bacterial genomes has revolutionized the assessment of microbial diversity. Pseudomonas is a widely diverse genus, containing more than 254 species. Although type strains have been employed to estimate Pseudomonas diversity, they represent a small fraction of the genomic diversity at a genus level. We used 10,035 available Pseudomonas genomes, including 210 type strains, to build a genomic distance network to estimate the number of species through community identification. We identified taxonomic inconsistencies with several type strains and found that 25.65 % of the Pseudomonas genomes deposited on Genbank are misclassified. The phylogenetic tree using single-copy genes from representative genomes in each species cluster in the distance network revealed at least 14 Pseudomonas groups, including the P. alcaligenes group proposed here. We show that Pseudomonas is likely an admixture of different genera and should be further divided. This study provides an overview of Pseudomonas diversity from a network and phylogenomic perspective that may help reduce the propagation of mislabeled Pseudomonas genomes.
Topics: Genetic Variation; Genome, Bacterial; Genomics; Phylogeny; Pseudomonas
PubMed: 34808515
DOI: 10.1016/j.micres.2021.126919 -
Brazilian Dental Journal 2017The aim of this study was to isolate Enterobacteria and Pseudomonas from the oral cavity of hospitalized newborns (NB) and determine their prevalence and the sensitivity...
The aim of this study was to isolate Enterobacteria and Pseudomonas from the oral cavity of hospitalized newborns (NB) and determine their prevalence and the sensitivity profile to most commonly used antibiotics for this age group. Samples from the oral cavity of NB from 24 to 48 h age were collected using swabs. The samples were inoculated on MacConkey agar, incubated and the colonies counted and identified. For each strain, the minimum inhibitory concentration (MIC) was determined using agar dilution test. Tests for enterobacteria producing extended spectrumβ-lactamases (ESBL) were performed using agar diffusion. Descriptive statistics was used for data analysis. Two of the isolated strains were submitted to the susceptibility test in biofilm. Of the collected samples, 8% presented Enterobacteria (mean of 6,141 CFU/mL) and no Pseudomona species was isolated. Positive samples were from NB in accommodation set or in the NB nursery. Enterobacter was the most prevalent genus and some strains were resistant to ampicillin, gentamicin and cephalothin. No ESBL strain was detected. Microorganisms in biofilms were resistant to all antibiotics, with concentrations four times higher than MIC. The presence of enterobacteria in the oral cavity of newborns, especially some strains resistant to normally used antibiotics, warns to the need for care to avoid the early colonization of this niche and the occurrence of a possible hospital infection in this age group.
Topics: Anti-Bacterial Agents; Biofilms; Colony Count, Microbial; Drug Resistance, Bacterial; Enterobacteriaceae; Humans; Infant, Newborn; Microbial Sensitivity Tests; Mouth; Pseudomonas
PubMed: 29160392
DOI: 10.1590/0103-6440201601205 -
International Journal of Molecular... Nov 2021is characterized by its great capacity to colonize different ecological niches, but also by its antimicrobial resistance and pathogenicity, causing human, animal, or...
is characterized by its great capacity to colonize different ecological niches, but also by its antimicrobial resistance and pathogenicity, causing human, animal, or plant diseases. Raw and undercooked food is a potential carrier of foodborne disease. The aim of this study was to determine the occurrence of spp. among raw vegetables, analysing their antimicrobial resistance, virulence, and molecular typing. A total of 163 spp. isolates (12 different species) were recovered from 77 of the 145 analysed samples (53.1%) and were classified into 139 different pulsed-field gel electrophoresis patterns. Low antimicrobial resistance levels, but one multidrug-resistant isolate, were found. Among the 37 recovered strains, 28 sequence-types and nine serotypes were detected. Eleven OprD patterns and an insertion sequence (IS) truncating the gene of one imipenem-resistant strain were found. Ten virulotypes were observed, including four -positive and thirty-one -positive strains. The gene was absent in three ST155 strains and was truncated by different insertion sequences (IS, IS, and IS) in other three strains. High biofilm, motility, pigment, elastase, and rhamnolipid production were detected. Our study demonstrated a low occurrence of (18%) and low antimicrobial resistance, but a high number of virulence-related traits in these strains, highlighting their pathological importance.
Topics: Anti-Bacterial Agents; Biofilms; Drug Resistance, Multiple, Bacterial; Food Microbiology; Microbial Sensitivity Tests; Molecular Typing; Phenotype; Phylogeny; Pseudomonas; Vegetables; Virulence Factors
PubMed: 34884433
DOI: 10.3390/ijms222312626 -
Infection, Genetics and Evolution :... Jan 2022Pseudomonas spp. exhibit considerable differences in host specificity and virulence. Most Pseudomonas species were isolated exclusively from environmental sources,...
Revisiting the intrageneric structure of the genus Pseudomonas with complete whole genome sequence information: Insights into diversity and pathogen-related genetic determinants.
Pseudomonas spp. exhibit considerable differences in host specificity and virulence. Most Pseudomonas species were isolated exclusively from environmental sources, ranging from soil to plants, but some Pseudomonas species have been detected from versatile sources, including both human host and environmental sources. Understanding genome variations that generate the tremendous diversity in Pseudomonas biology is important in controlling the incidence of infections. With a data set of 704 Pseudomonas complete whole genome sequences representing 186 species, Pseudomonas intrageneric structure was investigated by hierarchical clustering based on average nucleotide identity, and by phylogeny analysis based on concatenated core-gene alignment. Further comparative functional analyses indicated that Pseudomonas species only living in natural habitats lack multiple functions that are important in the regulation of bacterial pathogenesis, indicating the possession of these functions might be characteristic of Pseudomonas human pathogens. Moreover, we have performed pan-genome based homogeneity analyses, and detected genes with conserved structures but diversified functions across the Pseudomonas genomes, suggesting these genes play a role in driving diversity. In summary, this study provided insights into the dynamics of genome diversity and pathogen-related genetic determinants in Pseudomonas, which might help the development of more targeted antibiotics for the treatment of Pseudomonas infections.
Topics: Genetic Variation; Genome, Bacterial; Host Specificity; Phylogeny; Plant Diseases; Plants; Pseudomonas; Species Specificity; Virulence; Whole Genome Sequencing
PubMed: 34920102
DOI: 10.1016/j.meegid.2021.105183 -
Genes Oct 2019spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of spp. have been...
spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic spp. are unique, as they are highly dissimilar to the other known plasmids of spp.
Topics: Antarctic Regions; Biofilms; DNA Transposable Elements; Gene Transfer, Horizontal; Genes, Bacterial; Microbiota; Phylogeny; Plasmids; Pseudomonas
PubMed: 31661808
DOI: 10.3390/genes10110850 -
Applied and Environmental Microbiology Oct 1988Over 100 strains that utilized naphthalene as the only carbon and energy source were isolated from samples of marine sediments taken from a heavily polluted area. The...
Over 100 strains that utilized naphthalene as the only carbon and energy source were isolated from samples of marine sediments taken from a heavily polluted area. The isolates were characterized taxonomically and physiologically. Most of these strains belonged to the genus Pseudomonas, and seven of them did not fit any previous taxonomic description. They differed from type strains in a few biochemical characteristics and in the utilization of aromatic compounds. None had catechol 1,2-dioxygenase activity, and catechol 2,3-dioxygenase was responsible for the aromatic ring cleavage. DNA hybridization demonstrated a close relationship between two isolates and the Pseudomonas stutzeri type strain, and between five isolates and the Pseudomonas testosteroni type strain. On the basis of nutritional and enzymatic characteristics, it was assumed that the seven isolates represent new biovars belonging to the species P. testosteroni and P. stutzeri that are able to degrade aromatic hydrocarbons.
Topics: Biodegradation, Environmental; DNA, Bacterial; Flagella; Naphthalenes; Pseudomonas; Seawater; Water Microbiology
PubMed: 3202629
DOI: 10.1128/aem.54.10.2478-2485.1988 -
Journal of Applied Microbiology Jun 2015To screen and identify biosurfactant-producing Pseudomonas strains isolated from floral nectar; to characterize the produced biosurfactants; and to investigate the...
AIMS
To screen and identify biosurfactant-producing Pseudomonas strains isolated from floral nectar; to characterize the produced biosurfactants; and to investigate the effect of different carbon sources on biosurfactant production.
METHODS AND RESULTS
Four of eight nectar Pseudomonas isolates were found to produce biosurfactants. Phylogenetic analysis based on three housekeeping genes (16S rRNA gene, rpoB and gyrB) classified the isolates into two groups, including one group closely related to Pseudomonas fluorescens and another group closely related to Pseudomonas fragi and Pseudomonas jessenii. Although our nectar pseudomonads were able to grow on a variety of water-soluble and water-immiscible carbon sources, surface active agents were only produced when using vegetable oil as sole carbon source, including olive oil, sunflower oil or waste frying sunflower oil. Structural characterization based on thin layer chromatography (TLC) and ultra high performance liquid chromatography-accurate mass mass spectrometry (UHPLC-amMS) revealed that biosurfactant activity was most probably due to the production of fatty acids (C16:0; C18:0; C18:1 and C18:2), and mono- and diglycerides thereof.
CONCLUSIONS
Four biosurfactant-producing nectar pseudomonads were identified. The active compounds were identified as fatty acids (C16:0; C18:0; C18:1 and C18:2), and mono- and diglycerides thereof, produced by hydrolysis of triglycerides of the feedstock.
SIGNIFICANCE AND IMPACT OF THE STUDY
Studies on biosurfactant-producing micro-organisms have mainly focused on microbes isolated from soils and aquatic environments. Here, for the first time, nectar environments were screened as a novel source for biosurfactant producers. As nectars represent harsh environments with high osmotic pressure and varying pH levels, further screening of nectar habitats for biosurfactant-producing microbes may lead to the discovery of novel biosurfactants with broad tolerance towards different environmental conditions.
Topics: DNA, Bacterial; Flowers; Molecular Sequence Data; Phylogeny; Plant Nectar; Pseudomonas; RNA, Ribosomal, 16S; Surface-Active Agents
PubMed: 25801599
DOI: 10.1111/jam.12799 -
The New Phytologist Dec 2012Comparative genomics and functional analysis of Pseudomonas syringae and related pathogens have mainly focused on diseases of herbaceous plants; however, there is a...
Comparative genomics and functional analysis of Pseudomonas syringae and related pathogens have mainly focused on diseases of herbaceous plants; however, there is a general lack of knowledge about the virulence and pathogenicity determinants required for infection of woody plants. Here, we applied signature-tagged mutagenesis (STM) to Pseudomonas savastanoi pv. savastanoi during colonization of olive (Olea europaea) knots, with the goal of identifying the range of genes linked to growth and symptom production in its plant host. A total of 58 different genes were identified, and most mutations resulted in hypovirulence in woody olive plants. Sequence analysis of STM mutations allowed us to identify metabolic pathways required for full fitness of P. savastanoi in olive and revealed novel mechanisms involved in the virulence of this pathogen, some of which are essential for full colonization of olive knots by the pathogen and for the lysis of host cells. This first application of STM to a P. syringae-like pathogen provides confirmation of functional capabilities long believed to play a role in the survival and virulence of this group of pathogens but not adequately tested before, and unravels novel factors not correlated previously with the virulence of other plant or animal bacterial pathogens.
Topics: Computer Simulation; Host-Pathogen Interactions; Metabolic Networks and Pathways; Mutagenesis; Mutation; Olea; Plant Diseases; Pseudomonas; Virulence
PubMed: 23088618
DOI: 10.1111/j.1469-8137.2012.04357.x -
Journal of Bacteriology Jun 2020Phage tail-like bacteriocins (tailocins) are bacterially produced protein toxins that mediate competitive interactions between cocolonizing bacteria. Both theoretical...
Phage tail-like bacteriocins (tailocins) are bacterially produced protein toxins that mediate competitive interactions between cocolonizing bacteria. Both theoretical and experimental research has shown there are intransitive interactions between bacteriocin-producing, bacteriocin-sensitive, and bacteriocin-resistant populations, whereby producers outcompete sensitive cells, sensitive cells outcompete resistant cells, and resistant cells outcompete producers. These so-called rock-paper-scissors dynamics explain how all three populations occupy the same environment, without one driving the others extinct. Using as a model, we demonstrate that otherwise sensitive cells survive bacteriocin exposure through a physiological mechanism. This mechanism allows cells to survive bacteriocin killing without acquiring resistance. We show that a significant fraction of the target cells that survive a lethal dose of tailocin did not exhibit any detectable increase in survival during a subsequent exposure. Tailocin persister cells were more prevalent in stationary- rather than log-phase cultures. Of the fraction of cells that gained detectable resistance, there was a range from complete (insensitive) to incomplete (partially sensitive) resistance. By using genomic sequencing and genetic engineering, we showed that a mutation in a hypothetical gene containing 8 to 10 transmembrane domains causes tailocin high persistence and that genes of various glycosyltransferases cause incomplete and complete tailocin resistance. Importantly, of the several classes of mutations, only those causing complete tailocin resistance compromised host fitness. This result indicates that bacteria likely utilize persistence to survive bacteriocin-mediated killing without suffering the costs associated with resistance. This research provides important insight into how bacteria can escape the trap of fitness trade-offs associated with gaining tailocin resistance. Bacteriocins are bacterially produced protein toxins that are proposed as antibiotic alternatives. However, a deeper understanding of the responses of target bacteria to bacteriocin exposure is lacking. Here, we show that target cells of survive lethal bacteriocin exposure through both physiological persistence and genetic resistance mechanisms. Cells that are not growing rapidly rely primarily on persistence, whereas those growing rapidly are more likely to survive via resistance. We identified various mutations in lipopolysaccharide biogenesis-related regions involved in tailocin persistence and resistance. By assessing host fitness of various classes of mutants, we showed that persistence and subtle resistance are mechanisms uses to survive competition and preserve host fitness. These results have important implications for developing bacteriocins as alternative therapeutic agents.
Topics: Bacterial Proteins; Bacteriocins; Drug Resistance, Bacterial; Microbial Viability; Pseudomonas
PubMed: 32312747
DOI: 10.1128/JB.00142-20 -
Nature Communications Sep 2017All social organisms experience dilemmas between cooperators performing group-beneficial actions and cheats selfishly exploiting these actions. Although bacteria have...
All social organisms experience dilemmas between cooperators performing group-beneficial actions and cheats selfishly exploiting these actions. Although bacteria have become model organisms to study social dilemmas in laboratory systems, we know little about their relevance in natural communities. Here, we show that social interactions mediated by a single shareable compound necessary for growth (the iron-scavenging pyoverdine) have important consequences for competitive dynamics in soil and pond communities of Pseudomonas bacteria. We find that pyoverdine non- and low-producers co-occur in many natural communities. While non-producers have genes coding for multiple pyoverdine receptors and are able to exploit compatible heterologous pyoverdines from other community members, producers differ in the pyoverdine types they secrete, offering protection against exploitation from non-producers with incompatible receptors. Our findings indicate that there is both selection for cheating and cheating resistance, which could drive antagonistic co-evolution and diversification in natural bacterial communities.Lab strains of Pseudomonas are model systems for the evolution of cooperation over public goods (iron-scavenging siderophores). Here, Butaitė et al. add ecological and evolutionary insight into this system by showing that cheating and resistance to cheating both shape competition for iron in natural Pseudomonas communities.
Topics: Fresh Water; Iron; Oligopeptides; Phylogeny; Pseudomonas; Siderophores; Soil; Soil Microbiology
PubMed: 28871205
DOI: 10.1038/s41467-017-00509-4