Isolation and Whole-Genome Sequencing of Four Antibiotic-Producing Pseudomonas Strains.
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ABSTRACT:
SUBMITTER: Armstrong ALE
PROVIDER: S-EPMC9302146 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Antimicrobial resistance (AMR) is a global threat to human health since infections caused by antimicrobial-resistant bacteria are life-threatening conditions with minimal treatment options. Bacteria become resistant when they develop the ability to overcome the compounds that are meant to kill them, i.e., antibiotics. The increasing number of resistant pathogens worldwide is contrasted by the slow progress in the discovery and production of new antibiotics. About 700,000 global deaths per year are estimated as a result of drug-resistant infections, which could escalate to nearly 10 million by 2050 if we fail to address the AMR challenge. In this study, we collected and isolated bacteria from the environment to screen for antibiotic resistance. We identified several bacteria that showed resistance to multiple clinically relevant antibiotics when tested in antibiotic susceptibility disk assays. We also found that two strains, identified as Pantoea rodasii RIT 836 and Pseudomonas endophytica RIT 838 via whole genome sequencing and annotation, produce bactericidal compounds against both Gram-positive and Gram-negative bacteria in disc-diffusion inhibitory assays. We mined the two strains' whole-genome sequences to gain more information and insights into the antibiotic resistance and production by these bacteria. Subsequently, we aim to isolate, identify, and further characterize the novel antibiotic compounds detected in our assays and bioinformatics analysis.
| S-EPMC10898753 | biostudies-literature
Project description:ObjectiveThere is an urgent need for the discovery and/or development of novel antibiotics. We report an exploration of "slow"-growing bacteria, which can be difficult to isolate using rich media as they are usually outcompeted by "fast"-growing bacteria, as potential sources of novel antimicrobials.ResultsPseudomonas sp. RIT 623 was isolated using pond water agar from a pond located on the campus of the Rochester Institute of Technology (RIT). The genome was sequenced and analyzed for potential secondary metabolite gene clusters. Bioinformatics analysis revealed 14 putative gene clusters predicted to encode pathways for the anabolism of secondary metabolites. Ethyl acetate extracts from spent growth medium of Pseudomonas sp. RIT 623 were tested against two Gram-negative (E. coli ATCC 25922 and P. aeruginosa ATCC 27853) and two Gram-positive (B. subtilis BGSC 168 and S. aureus ATCC 25923) type strains to assess antibiotic activity. The antibiotic assays demonstrated that extracts of Pseudomonas sp. RIT 623 were able to inhibit the growth of the four strains. The active compound was separated using diethyl ether in a multi-solvent extraction and reverse phase chromatography. The bioactive compound/s were subsequently eluted in two consecutive fractions corresponding to approximately 16-22% acetonitrile, indicative of polar compound/s.
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Project description:BackgroundNematodes are parasitic animals that cause over 100 billion US dollars loss in agricultural business. The whole-genomes of two Streptomyces strains, Streptomyces spectabilis KCTC9218T and Streptomyces sp. AN091965, were sequenced. Both strains produce spectinabilin, an antinematode drug. Its secondary metabolism was examined to aid the development of an efficient nematicidal drug-producing host strain.ResultsThe whole-genome sequences of S. spectabilis KCTC9218T and Streptomyces sp. AN091965 were analyzed using PacBio and Illumina sequencing platforms, and assembled using hybrid methodology. The total contig lengths for KCTC9218T and AN091965 were 9.97 Mb and 9.84 Mb, respectively. A total of 8,374 and 8,054 protein-coding genes, as well as 39 and 45 secondary metabolite biosynthetic gene clusters were identified in KCTC9218T and AN091965, respectively. 18.4 ± 6.45 mg/L and 213.89 ± 21.30 mg/L of spectinabilin were produced by S. spectabilis KCTC9218T and Streptomyces sp. AN091965, respectively. Pine wilt disease caused by nematode was successfully prevented by lower concentration of spectinabilin injection than that of abamectin recommended by its manufacturer. Production of multiple antinematode drugs, including spectinabilin, streptorubin B, and undecylprodigiosin was observed in both strains using high-resolution liquid chromatography mass spectrometry (LC-MS) analysis.ConclusionsWhole-genome sequencing of spectinabilin-producing strains, coupled with bioinformatics and mass spectrometry analyses, revealed the production of multiple nematicidal drugs in the KCTC9218T and AN091965 strains. Especially, Streptomyces sp. AN091965 showed high production level of spectinabilin, and this study provides crucial information for the development of potential nematicidal drug producers.
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Project description:We report the isolation, whole-genome sequencing, and annotation of Enterobacter sp. strain RIT 637, Pseudomonas sp. strain RIT 778, and Deinococcus sp. strain RIT 780. Disk diffusion assays using spent medium demonstrated that all bacteria produced bactericidal compounds against Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, and Staphylococcus aureus ATCC 25923.
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Project description:BackgroundMarine cold-temperature environments are an invaluable source of psychrophilic microbial life for new biodiscoveries. An Arctic marine bacterial strain collection was established consisting of 1448 individual isolates originating from biota, water and sediment samples taken at a various depth in the Barents Sea, North of mainland Norway, with an all year round seawater temperature of 4 °C. The entire collection was subjected to high-throughput screening for detection of extracellular laccase activity with guaiacol as a substrate.ResultsIn total, 13 laccase-positive isolates were identified, all belonging to the Psychrobacter genus. From the most diverse four strains, based on 16S rRNA gene sequence analysis, all originating from the same Botryllus sp. colonial ascidian tunicate sample, genomic DNA was isolated and genome sequenced using a combined approach of whole genome shotgun and 8 kb mate-pair library sequencing on an Illumina MiSeq platform. The genomes were assembled and revealed genome sizes between 3.29 and 3.52 Mbp with an average G + C content of around 42%, with one to seven plasmids present in the four strains. Bioinformatics based genome mining was performed to describe the metabolic potential of these four strains and to identify gene candidates potentially responsible for the observed laccase-positive phenotype. Up to two different laccase-like multicopper oxidase (LMCO) encoding gene candidates were identified in each of the four strains. Heterologous expression of P11F6-LMCO and P11G5-LMCO2 in Escherichia coli BL21 (DE3) resulted in recombinant proteins exhibiting 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid (ABTS) and guaiacol oxidizing activity.ConclusionsThirteen Psychrobacter species with laccase-positive phenotype were isolated from a collection of Arctic marine bacteria. Four of the isolates were genome sequenced. The overall genome features were similar to other publicly available Psychrobacter genome sequences except for P11G5 harboring seven plasmids. However, there were differences at the pathway level as genes associated with degradation of phenolic compounds, nicotine, phenylalanine, styrene, ethylbenzene, and ethanolamine were detected only in the Psychrobacter strains reported in this study while they were absent among the other publicly available Psychrobacter genomes. In addition, six gene candidates were identified by genome mining and shown to possess T1, T2 and T3 copper binding sites as the main signature of the three-domain laccases. P11F6-LMCO and P11G5-LMCO2 were recombinantly expressed and shown to be active when ABTS and guaiacol were used as substrates.
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Project description:BackgroundMultidrug-resistant Pseudomonas aeruginosa has become a hazard to public health, making medical treatment challenging and ineffective. Whole-genome sequencing for antibiotic susceptibility testing offers a powerful replacement for conventional microbiological methods.ObjectiveThe present study evaluated the presence of antibiotic resistance genes in selected clinical strains of P. aeruginosa using whole-genome sequencing for antibiotic susceptibility testing.ResultsWhole-genome sequencing of P. aeruginosa susceptible to common antibiotics showed the presence of 4 antibiotic resistance gene types, fosA, catB7, blaPAO, and blaOXA-50. Whole genome sequencing of resistant or multidrug-resistant P. aeruginosa showed the presence of multiple ARGs, such as sul1, aac(3)-Ic, blaPAO, blaGES-1, blaGES-5 aph (3')-XV, blaOXA-50, aacA4, catB7, aph(3')-IIb, aadA6, fosA, tet(G), cmlA1, aac(6')Ib-cr, and rmtF.ConclusionThe acquisition of antibiotic resistance genes was found to depend on the resistance of Pseudomonas to antibiotics. The strain with the highest resistance to antibiotics had the highest acquisition of antibiotic resistance genes. MDR-P. aeruginosa produces antibiotic resistance genes against aminoglycoside, β-lactam, fluoroquinolones, sulfonamides, phenicol, and fosfomycin antibiotics.
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Project description:Non-O157 Shiga toxin-producing Escherichia coli (STEC) strains are emerging food-borne pathogens causing life-threatening diseases and food-borne outbreaks. A better understanding of their evolution provides a framework for developing tools to control food safety. We obtained 15 genomes of non-O157 STEC strains, including O26, O111, and O103 strains. Phylogenetic trees revealed a close relationship between O26:H11 and O111:H11 and a scattered distribution of O111. We hypothesize that STEC serotypes with the same H antigens might share common ancestors.
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Project description:Dataset aims to uncover beneficial mutations on yeast strains (CEN.PK 113-11D based) engineered for polyamine over-production. We observed substantial heterogeneity between colony sizes and polyamine titers obtained between parent and final strains. Further physiological characterization of re-streaked colonies confirmed this phenotype, meaning that the sudden heterogeneity is heritable. Sequencing data presented here is used for identification differences between these mutated and parental strains.
2021-03-31 | E-MTAB-9898 | biostudies-arrayexpress
Project description:Four enterovirus D68 (EV-D68) strains from four children with influenza-like illness were identified in Shenzhen, southern China, in late 2015. Here, we announce the availability of these viral genomes in GenBank. The genomic sequences of these EV-D68 strains showed the closest phylogenetic relationship to strains from northern China.
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