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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 -
Microbiology Spectrum Oct 2022Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a pathogen of global concern due to the fact that therapeutic drugs are limited. Metallo-β-lactamase...
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a pathogen of global concern due to the fact that therapeutic drugs are limited. Metallo-β-lactamase (MBL)-producing P. aeruginosa has become a critical part of CRPA. Alcaligenes faecalis metallo-β-lactamase (AFM) is a newly identified subclass B1b MBL. In this study, 487 P. aeruginosa strains isolated from patients and the environment in an intensive care unit were screened for AFM alleles. Five AFM-producing strains were identified, including four AFM-2-producing strains (ST262) and one AFM-4-producing strain (ST671). AFM-2-producing strains were isolated from rectal and throat swabs, and AFM-4-producing strains were isolated from the water sink. The carrying plasmids belonged to the IncP-2 type, while the carrying plasmid pAR19438 was a pSTY-like megaplasmid. Plasmid pAR19438 was acquired by the integration of the Tn-like transposon. All genes were embedded in an IS- unit core module flanked by class 1 integrons. The core module of was IS-Δ---Δ-ΔIS, while the core module of was IS-Δ---Δ-IS-----ΔIS. The flanking sequences of IS- units also differed. The expression of AFM-2 and AFM-4 in DH5α and PAO1 illustrated the same effect for the evaluation of the MICs of β-lactams, except for aztreonam. Identification of AFM-4 underscores that the quick spread and emerging development of mutants of MBLs require continuous surveillance in P. aeruginosa. Acquiring metallo-β-lactamase genes is one of the important carbapenem resistance mechanisms of P. aeruginosa. Alcaligenes faecalis metallo-β-lactamase is a newly identified metallo-β-lactamase, the prevalence and genetic context of which need to be explored. In this study, we identified AFM-producing P. aeruginosa strains among clinical isolates and found a new mutant of AFM, AFM-4. The carrying plasmid pAR19438 was a pSTY-like megaplasmid, unlike the plasmids encoding other alleles. The genetic context of was also different. However, AFM-2 and AFM-4 had the same impacts on antibiotic susceptibility. The presence and transmission of AFM alleles in P. aeruginosa pose a challenge to clinical practice.
Topics: Humans; Alleles; Anti-Bacterial Agents; Aztreonam; beta-Lactam Resistance; beta-Lactamases; Carbapenems; Microbial Sensitivity Tests; Plasmids; Pseudomonas aeruginosa; Pseudomonas Infections
PubMed: 36000902
DOI: 10.1128/spectrum.02035-22 -
Frontiers in Cellular and Infection... 2022To evaluate antibacterial activity of MRX-8 against gram-negative bacteria recently isolated from China, 765 clinical isolates were collected randomly from 2017 to...
To evaluate antibacterial activity of MRX-8 against gram-negative bacteria recently isolated from China, 765 clinical isolates were collected randomly from 2017 to 2020, including and and , and spp. isolates. All strains were performed with antimicrobial susceptibility testing by broth microdilution method according to the CLSI 2021. Antimicrobial agents included MRX-8, polymyxin B, colistin, amikacin, ceftriaxone, ceftazidime, cefepime, ceftazidime-avibactam, cefoperazone-sulbactam, meropenem, ciprofloxacin, ampicillin, ampicillin-sulbactam and levofloxacin. For carbapenem-susceptible and carbapenem-resistant isolates, the MIC of MRX-8 was 0.125/0.25 mg/L and 0.06/0.125 mg/L, respectively. For carbapenem-susceptible and carbapenem-resistant isolates, the MIC of MRX-8 was 0.25/0.5 mg/L and 0.125/0.5 mg/L, respectively. For polymyxins (polymyxin B and colistin)-resistant and , MIC of MRX-8 was 4-16 mg/L and MIC was >32 mg/L. The MIC and MIC of MRX-8 for other spp. except , spp., and spp. isolates ranged 0.06-0.125 mg/L and 0.06-0.25mg/L, respectively. For spp. spp. spp. spp., and , all MIC of MRX-8 was >32mg/L. For carbapenem susceptible and resistant , the MIC and MIC of MRX-8 was both 1mg/L, and that for was 0.5mg/L and 0.5-1mg/L. For spp. and spp., MIC was 1/4 mg/L and 0.25/0.5 mg/L. MRX-8 was more effective against most clinically isolated gram-negative isolates, including carbapenem-resistant , , and , highlighting its potential as valuable therapeutics.
Topics: Carbapenems; Colistin; Escherichia coli; Gram-Negative Bacteria; Klebsiella pneumoniae; Microbial Sensitivity Tests; Polymyxin B; Pseudomonas aeruginosa
PubMed: 35646734
DOI: 10.3389/fcimb.2022.829592 -
Microbiome Feb 2020The holistic view of bacterial symbiosis, incorporating both host and microbial environment, constitutes a major conceptual shift in studies deciphering host-microbe...
BACKGROUND
The holistic view of bacterial symbiosis, incorporating both host and microbial environment, constitutes a major conceptual shift in studies deciphering host-microbe interactions. Interactions between Steinernema entomopathogenic nematodes and their bacterial symbionts, Xenorhabdus, have long been considered monoxenic two partner associations responsible for the killing of the insects and therefore widely used in insect pest biocontrol. We investigated this "monoxenic paradigm" by profiling the microbiota of infective juveniles (IJs), the soil-dwelling form responsible for transmitting Steinernema-Xenorhabdus between insect hosts in the parasitic lifecycle.
RESULTS
Multigenic metabarcoding (16S and rpoB markers) showed that the bacterial community associated with laboratory-reared IJs from Steinernema carpocapsae, S. feltiae, S. glaseri and S. weiseri species consisted of several Proteobacteria. The association with Xenorhabdus was never monoxenic. We showed that the laboratory-reared IJs of S. carpocapsae bore a bacterial community composed of the core symbiont (Xenorhabdus nematophila) together with a frequently associated microbiota (FAM) consisting of about a dozen of Proteobacteria (Pseudomonas, Stenotrophomonas, Alcaligenes, Achromobacter, Pseudochrobactrum, Ochrobactrum, Brevundimonas, Deftia, etc.). We validated this set of bacteria by metabarcoding analysis on freshly sampled IJs from natural conditions. We isolated diverse bacterial taxa, validating the profile of the Steinernema FAM. We explored the functions of the FAM members potentially involved in the parasitic lifecycle of Steinernema. Two species, Pseudomonas protegens and P. chlororaphis, displayed entomopathogenic properties suggestive of a role in Steinernema virulence and membership of the Steinernema pathobiome.
CONCLUSIONS
Our study validates a shift from monoxenic paradigm to pathobiome view in the case of the Steinernema ecology. The microbial communities of low complexity associated with EPNs will permit future microbiota manipulation experiments to decipher overall microbiota functioning in the infectious process triggered by EPN in insects and, more generally, in EPN ecology.
Topics: Animals; Biological Control Agents; DNA Barcoding, Taxonomic; Host Microbial Interactions; Larva; Life Cycle Stages; Microbiota; Moths; Proteobacteria; Rhabditida; Rhabditida Infections; Symbiosis; Virulence
PubMed: 32093774
DOI: 10.1186/s40168-020-00800-5 -
Applied and Environmental Microbiology Mar 2008Preliminary observations in a large-scale fermentation process suggested that the lipase expression of Pseudomonas alcaligenes can be switched on by the addition of... (Comparative Study)
Comparative Study
Preliminary observations in a large-scale fermentation process suggested that the lipase expression of Pseudomonas alcaligenes can be switched on by the addition of certain medium components, such as soybean oil. In an attempt to elucidate the mechanism of induction of lipase expression, we have set up a search method for genes controlling lipase expression by use of a cosmid library containing fragments of P. alcaligenes genomic DNA. A screen for lipase hyperproduction resulted in the selection of multiple transformants, of which the best-producing strains comprised cosmids that shared an overlapping genomic fragment. Within this fragment, two previously unidentified genes were found and named lipQ and lipR. Their encoded proteins belong to the NtrBC family of regulators that regulate gene expression via binding to a specific upstream activator sequence (UAS). Such an NtrC-like UAS was identified in a previous study in the P. alcaligenes lipase promoter, strongly suggesting that LipR acts as a positive regulator of lipase expression. The regulating role could be confirmed by down-regulated lipase expression in a strain with an inactivated lipR gene and a threefold increase in lipase yield in a large-scale fermentation when expressing the lipQR operon from the multicopy plasmid pLAFR3. Finally, cell extracts of a LipR-overexpressing strain caused a retardation of the lipase promoter fragment in a band shift assay. Our results indicate that lipase expression in Pseudomonas alcaligenes is under the control of the LipQR two-component system.
Topics: Base Sequence; DNA Primers; Electrophoretic Mobility Shift Assay; Fermentation; Gene Expression Regulation, Enzymologic; Gene Library; Lipase; Molecular Sequence Data; Plasmids; Promoter Regions, Genetic; Pseudomonas alcaligenes; Reverse Transcriptase Polymerase Chain Reaction; Sequence Analysis, DNA; Trans-Activators
PubMed: 18192420
DOI: 10.1128/AEM.01632-07 -
Applied and Environmental Microbiology Apr 1984Twelve denitrifying bacteria representing six genera were tested for an ability to nitrify pyruvic oxime heterotrophically. Six of these bacteria exhibited appreciable... (Comparative Study)
Comparative Study
Twelve denitrifying bacteria representing six genera were tested for an ability to nitrify pyruvic oxime heterotrophically. Six of these bacteria exhibited appreciable nitrification activity, yielding as much as 5.8 mM nitrite and little or no nitrate when grown in a mineral salts medium containing 7 mM pyruvic oxime and 0.05% yeast extract. Of the six active bacteria, four (Pseudomonas denitrificans, Pseudomonas aeruginosa, and two strains of Pseudomonas fluorescens) could grow on yeast extract but not pyruvic oxime, one (Pseudomonas aureofaciens) could grow slowly on pyruvic oxime, and one (Alcaligenes faecalis) could apparently grow on pyruvic oxime in the presence of yeast extract but not in its absence. Eight of the twelve bacteria in the resting state could oxidize hydroxylamine to nitrite, and P. aureofaciens was remarkably active in this regard. In general, those denitrifiers active in the nitrification of pyruvic oxime or hydroxylamine or both are abundant in soils. A possible advantage of having nitrification and denitrification capabilities in the same organism is discussed.
Topics: Alcaligenes; Bacteria; Chromobacterium; Flavobacterium; Kinetics; Nitrates; Nitrites; Paracoccus denitrificans; Pseudomonas; Species Specificity
PubMed: 6721486
DOI: 10.1128/aem.47.4.620-623.1984 -
Environmental Health Perspectives Sep 1994Bacterial plasmids contain specific genes for resistances to toxic heavy metal ions including Ag+, AsO2-, AsO4(3-), Cd2+, Co2+, CrO4(2-), Cu2+, Hg2+, Ni2+, Pb2+, Sb3+,... (Comparative Study)
Comparative Study Review
Bacterial plasmids contain specific genes for resistances to toxic heavy metal ions including Ag+, AsO2-, AsO4(3-), Cd2+, Co2+, CrO4(2-), Cu2+, Hg2+, Ni2+, Pb2+, Sb3+, and Zn2+. Recent progress with plasmid copper-resistance systems in Escherichia coli and Pseudomonas syringae show a system of four gene products, an inner membrane protein (PcoD), an outer membrane protein (PcoB), and two periplasmic Cu(2+)-binding proteins (PcoA and PcoC). Synthesis of this system is governed by two regulatory proteins (the membrane sensor PcoS and the soluble responder PcoR, probably a DNA-binding protein), homologous to other bacterial two-component regulatory systems. Chromosomally encoded Cu2+ P-type ATPases have recently been recognized in Enterococcus hirae and these are closely homologous to the bacterial cadmium efflux ATPase and the human copper-deficiency disease Menkes gene product. The Cd(2+)-efflux ATPase of gram-positive bacteria is a large P-type ATPase, homologous to the muscle Ca2+ ATPase and the Na+/K+ ATPases of animals. The arsenic-resistance system of gram-negative bacteria functions as an oxyanion efflux ATPase for arsenite and presumably antimonite. However, the structure of the arsenic ATPase is fundamentally different from that of P-type ATPases. The absence of the arsA gene (for the ATPase subunit) in gram-positive bacteria raises questions of energy-coupling for arsenite efflux. The ArsC protein product of the arsenic-resistance operons of both gram-positive and gram-negative bacteria is an intracellular enzyme that reduces arsenate [As(V)] to arsenite [As(III)], the substrate for the transport pump. Newly studied cation efflux systems for Cd2+, Zn2+, and Co2+ (Czc) or Co2+ and Ni2+ resistance (Cnr) lack ATPase motifs in their predicted polypeptide sequences. Therefore, not all plasmid-resistance systems that function through toxic ion efflux are ATPases. The first well-defined bacterial metallothionein was found in the cyanobacterium Synechococcus. Bacterial metallothionein is encoded by the smtA gene and contains 56 amino acids, including nine cysteine residues (fewer than animal metallothioneins). The synthesis of Synechococcus metallothionein is regulated by a repressor protein, the product of the adjacent but separately transcribed smtB gene. Regulation of metallothionein synthesis occurs at different levels; quickly by derepression of repressor activity, or over a longer time by deletion of the repressor gene at fixed positions and by amplification of the metallothionein DNA region leading to multiple copies of the gene.
Topics: Alcaligenes; Bacteria; Base Sequence; Copper; Drug Resistance, Microbial; Metallothionein; Metals; Molecular Sequence Data; Plasmids
PubMed: 7843081
DOI: 10.1289/ehp.94102s3107 -
Biotechnology For Biofuels 2017Recently, issues concerning the sustainable and harmless disposal of organic solid waste have generated interest in microbial biotechnologies aimed at converting waste... (Review)
Review
Recently, issues concerning the sustainable and harmless disposal of organic solid waste have generated interest in microbial biotechnologies aimed at converting waste materials into bioenergy and biomaterials, thus contributing to a reduction in economic dependence on fossil fuels. To valorize biomass, waste materials derived from agriculture, food processing factories, and municipal organic waste can be used to produce biopolymers, such as biohydrogen and biogas, through different microbial processes. In fact, different bacterial strains can synthesize biopolymers to convert waste materials into valuable intracellular (e.g., polyhydroxyalkanoates) and extracellular (e.g., exopolysaccharides) bioproducts, which are useful for biochemical production. In particular, large numbers of bacteria, including , , , , , methylotrophs, spp., spp., spp., spp., and recombinant , have been successfully used to produce polyhydroxyalkanoates on an industrial scale from different types of organic by-products. Therefore, the development of high-performance microbial strains and the use of by-products and waste as substrates could reasonably make the production costs of biodegradable polymers comparable to those required by petrochemical-derived plastics and promote their use. Many studies have reported use of the same organic substrates as alternative energy sources to produce biogas and biohydrogen through anaerobic digestion as well as dark and photofermentation processes under anaerobic conditions. Therefore, concurrently obtaining bioenergy and biopolymers at a reasonable cost through an integrated system is becoming feasible using by-products and waste as organic carbon sources. An overview of the suitable substrates and microbial strains used in low-cost polyhydroxyalkanoates for biohydrogen and biogas production is given. The possibility of creating a unique integrated system is discussed because it represents a new approach for simultaneously producing energy and biopolymers for the plastic industry using by-products and waste as organic carbon sources.
PubMed: 28469708
DOI: 10.1186/s13068-017-0802-4 -
Journal of Dairy Science Dec 2011Pseudomonas spp. are aerobic, gram-negative bacteria that are recognized as major food spoilage microorganisms. A total of 32 (22.9%) Pseudomonas spp. from 140 homemade...
Pseudomonas spp. are aerobic, gram-negative bacteria that are recognized as major food spoilage microorganisms. A total of 32 (22.9%) Pseudomonas spp. from 140 homemade white cheese samples collected from the open-air public bazaar were isolated and characterized. The aim of the present study was to investigate the biochemical characteristics, the production of extracellular enzymes, slime and β-lactamase, and antimicrobial susceptibility of Pseudomonas spp. isolated from cheeses. The identified isolates including Pseudomonas pseudoalcaligenes, Pseudomonas alcaligenes, Pseudomonas aeruginosa, Pseudomonas fluorescens biovar V, and P. pseudoalcaligenes ssp. citrulli were found to produce extracellular enzymes, respectively: protease and lecithinase production (100%), and lipase activity (85.7, 42.9, 100, and 100%, and nonlipolytic, respectively). The isolates did not produce slime and had no detectable β-lactamase activity. The antimicrobial susceptibility of the isolates was tested using the disk diffusion method. Pseudomonas spp. had the highest resistance to penicillin G (100%), then sulphamethoxazole/trimethoprim (28.1%). However, all Pseudomonas spp. isolates were 100% susceptible to ceftazidime, ciprofloxacin, amikacin, gentamicin, and imipenem. Multidrug-resistance patterns were not observed among these isolates. In this study, Pseudomonas spp., exhibiting spoilage features, were isolated mainly from cheeses. Isolation of this organism from processed milk highlights the need to improve the hygienic practices. All of the stages in the milk processing chain during manufacturing have to be under control to achieve the quality and safety of dairy products.
Topics: Anti-Bacterial Agents; Cheese; Food Microbiology; Food Preservation; Microbial Sensitivity Tests; Pseudomonas; Pseudomonas aeruginosa; Pseudomonas alcaligenes; Pseudomonas fluorescens; Pseudomonas pseudoalcaligenes; beta-Lactamases
PubMed: 22118075
DOI: 10.3168/jds.2011-4676 -
Applied and Environmental Microbiology Apr 2015Inorganic arsenic (As) is highly toxic and ubiquitous in the environment. Inorganic As can be transformed by microbial methylation, which constitutes an important part...
Inorganic arsenic (As) is highly toxic and ubiquitous in the environment. Inorganic As can be transformed by microbial methylation, which constitutes an important part of the As biogeochemical cycle. In this study, we investigated As biotransformation by Pseudomonas alcaligenes NBRC14159. P. alcaligenes was able to methylate arsenite [As(III)] rapidly to dimethylarsenate and small amounts of trimethylarsenic oxide. An arsenite S-adenosylmethionine methyltransferase, PaArsM, was identified and functionally characterized. PaArsM shares low similarities with other reported ArsM enzymes (<55%). When P. alcaligenes arsM gene (PaarsM) was disrupted, the mutant lost As methylation ability and became more sensitive to As(III). PaarsM was expressed in the absence of As(III) and the expression was further enhanced by As(III) exposure. Heterologous expression of PaarsM in an As-hypersensitive strain of Escherichia coli conferred As(III) resistance. Purified PaArsM protein methylated As(III) to dimethylarsenate as the main product in the medium and also produced dimethylarsine and trimethylarsine gases. We propose that PaArsM plays a role in As methylation and detoxification of As(III) and could be exploited in bioremediation of As-contaminated environments.
Topics: Amino Acid Sequence; Arsenites; Bacterial Proteins; Biotransformation; Methyltransferases; Molecular Sequence Data; Pseudomonas alcaligenes; Sequence Alignment
PubMed: 25681184
DOI: 10.1128/AEM.03804-14