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MSphere Jun 2021Laura-Isobel McCall studies the relationship between location and disease pathogenesis, with a focus on infectious diseases and neglected diseases of poverty. In this...
Laura-Isobel McCall studies the relationship between location and disease pathogenesis, with a focus on infectious diseases and neglected diseases of poverty. In this mSphere of Influence article, she reflects on how three papers, "Opposing effects of fasting metabolism on tissue tolerance in bacterial and viral inflammation" (A. Wang, S. C. Huen, H. H. Luan, S. Yu, et al., Cell 166:1512-1525.e12, 2016, https://doi.org/10.1016/j.cell.2016.07.026), "Three-dimensional microbiome and metabolome cartography of a diseased human lung" (N. Garg, M. Wang, E. Hyde, R. R. da Silva, et al., Cell Host Microbe 22:705-716.e4, 2017, https://doi.org/10.1016/j.chom.2017.10.001), and "'It's like a phantom disease': patient perspectives on access to treatment for Chagas disease in the United States" (C. J. Forsyth, S. Hernandez, C. A. Flores, M. F. Roman, et al., Am J Trop Med Hyg 98:735-741, 2018, https://doi.org/10.4269/ajtmh.17-0691), shaped her spatial approach to infectious disease pathogenesis and helped her broaden her perspective from a pathogen-centric focus to a holistic view that include diseases tolerance mechanisms and barriers to health care access.
Topics: Host-Pathogen Interactions; Humans; Listeria monocytogenes; Listeriosis; Lung; Pseudomonas; Viral Tropism
PubMed: 34160240
DOI: 10.1128/mSphere.00520-21 -
International Journal of Systematic and... Feb 2020Two yellow-pigmented, Gram-stain-negative and rod-shaped bacterial strains, designated as RY24 and ZYY160, were isolated from rice. Results of phylogenetic analysis...
Two yellow-pigmented, Gram-stain-negative and rod-shaped bacterial strains, designated as RY24 and ZYY160, were isolated from rice. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strains RY24 and ZYY160 belonged to the genus , and the 16S rRNA gene sequence similarity was 100 % The DNA homology between the two strains was 99.7 %. The 16S rRNA and gene sequences of the two strains showed highest similarity values to CGMCC 1.3392 and DSM 15758 (sharing 99.31 and 94.34 %, respectively). The major fatty acids of two strains were identified as summed feature 8 (Cω7 and/or Cω6), C and summed feature 3 (Cω7 and/or Cω6), and the major respiratory quinone was identified as ubiquinone Q-9, which are typical chemotaxonomic features of members of the genus . The genomic DNA G+C contents of strains RY24 and ZYY160 were determined to be 64.25 and 64.21 mol%, respectively. The DNA-DNA relatedness and average nucleotide identity values between the two strains and their closely related type strains were below 36 and 90 %, which supported that RY24 and ZYY160 represent a novel species in the genus . Phylogenetic and chemotaxonomic evidence, together with phenotypic characteristics, showed that the two isolates constitute a novel species of the genus . The type strain is RY24 (JCM 33201=ACCC 61555), for which the name sp. nov. is proposed.
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Nucleic Acid Hybridization; Oryza; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone
PubMed: 31751195
DOI: 10.1099/ijsem.0.003852 -
Molecules (Basel, Switzerland) Dec 2021Microbial genome sequencing has uncovered a myriad of natural products (NPs) that have yet to be explored. Bacteria in the genus serve as pathogens, plant growth...
Microbial genome sequencing has uncovered a myriad of natural products (NPs) that have yet to be explored. Bacteria in the genus serve as pathogens, plant growth promoters, and therapeutically, industrially, and environmentally important microorganisms. Though most species of have a large number of NP biosynthetic gene clusters (BGCs) in their genomes, it is difficult to link many of these BGCs with products under current laboratory conditions. In order to gain new insights into the diversity, distribution, and evolution of these BGCs in for the discovery of unexplored NPs, we applied several bioinformatic programming approaches to characterize BGCs from reference genome sequences available in public databases along with phylogenetic and genomic comparison. Our research revealed that most BGCs in the genomes of species have a high diversity for NPs at the species and subspecies levels and built the correlation of species with BGC taxonomic ranges. These data will pave the way for the algorithmic detection of species- and subspecies-specific pathways for NP development.
Topics: Algorithms; Biological Products; Computational Biology; Databases, Genetic; Phylogeny; Pseudomonas
PubMed: 34946606
DOI: 10.3390/molecules26247524 -
Archives of Microbiology Mar 2021A novel Gram-stain-negative, aerobic strain, designated Y22, was isolated from peanut field soil in Laoshan Mountain in China. Cells of strain Y22 were rod-shaped and...
A novel Gram-stain-negative, aerobic strain, designated Y22, was isolated from peanut field soil in Laoshan Mountain in China. Cells of strain Y22 were rod-shaped and motile by a single flagellum. The strain was found to be oxidase- and catalase-positive. 16S rRNA gene sequence based on phylogenetic analysis indicated that strain Y22 belonged to the genus Pseudomonas, and showed the highest 16S rRNA gene sequence similarity of 99.0% to Pseudomonas pelagia JCM 15562, followed by Pseudomonas salina JCM 19469 (98.4%), Pseudomonas sabulinigri JCM 14963 (97.9%), Pseudomonas bauzanensis CGMCC 1.9095 (97.6%) and Pseudomonas litoralis KCTC23093 (97.5%). The phylogenetic analysis based on multilocus sequence analyses with concatenated 16S rRNA, gyrB, rpoD and rpoB genes indicated that strain Y22 belonged to Pseudomonas pertucinogena lineage. The average nucleotide identity scores between strain Y22 and closely related species were 74.6-82.8%, and the Genome-to-Genome Distance Calculator scores were 16.4-44.9%. The predominant cellular fatty acids of strain Y22 were Cω7c (29.6%), C cyclo (17.5%) and summed feature 3 (Cω7c and/or Cω6c) (17.4%). The genomic DNA G+C content was 57.9 mol%. On the basis of phenotypic characteristics, phylogenetic analyses and in silico DNA-DNA relatedness, a novel species, Pseudomonas laoshanensis sp. nov. is proposed. The type strain is Y22 (= JCM 32580 = KCTC 62385 = CGMCC 1.16552).
Topics: Arachis; China; Genes, Bacterial; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Soil Microbiology; Species Specificity
PubMed: 33070233
DOI: 10.1007/s00203-020-02067-8 -
Microbial Biotechnology Jan 2020The use of renewable waste feedstocks is an environment-friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of... (Review)
Review
The use of renewable waste feedstocks is an environment-friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by-products. Glycerol (1,2,3-propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by-product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole-cell biocatalysts with both wild-type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value-added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost-effective substrate. The unique genetic and metabolic features of glycerol-grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate - and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.
Topics: Biofuels; Biotechnology; Fermentation; Glycerol; Pseudomonas
PubMed: 30883020
DOI: 10.1111/1751-7915.13400 -
Current Microbiology Dec 2020Due to its ubiquity, ability to form biofilms, and acquire resistance mechanisms, Pseudomonas spp. become one of the major challenge for healthcare settings and food...
Due to its ubiquity, ability to form biofilms, and acquire resistance mechanisms, Pseudomonas spp. become one of the major challenge for healthcare settings and food industry. The aims of this study were to assess the biofilm production of Pseudomonas spp. recovered from clinical and food specimens and to evaluate their antimicrobial resistance. A total of 108 isolates of Pseudomonas spp. were included in the study, 48 being clinical isolates recovered from patients admitted to four tertiary care hospitals throughout Serbia and 60 were isolated from the bulk tank milk samples and meat carcasses. Biofilm production was analyzed by microtiter plate assay. Antimicrobial susceptibility was evaluated by disk diffusion method according to the CLSI guidelines, while class A and B β-lactamases encoding genes were screened by PCR. A total of 98 (90.7%) strains were biofilm producers (moderate producer: 68, 69.4%; strong producer: 8, 8.2%). Although a slightly higher percentage of clinical isolates were biofilm producers (91.7%) compared to food isolates (90%), statistical significance was not observed (P > 0.05). The proportion of carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates was significantly higher among clinical (42%) isolates compared to food (1.7%) Pseudomonads (P < 0.05). The bla and bla genes were found in ESBL (seven isolates) and MBL (two isolates) production, respectively. In the present study, we confirmed that biofilm formation was highly present in both clinical and food Pseudomonas spp. irrespective of the prior existence of resistance genes. Additionally, clinical settings pose a major reservoir of MDR Pseudomonas spp. and especially CRPA isolates.
Topics: Anti-Bacterial Agents; Biofilms; Drug Resistance, Bacterial; Food Microbiology; Humans; Microbial Sensitivity Tests; Pseudomonas; Pseudomonas Infections; Pseudomonas aeruginosa; beta-Lactamases
PubMed: 33057751
DOI: 10.1007/s00284-020-02236-4 -
Genomics Nov 2021The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the...
The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7 to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and its potential for biotechnological applications.
Topics: Gene Transfer, Horizontal; Humans; Phylogeny; Plasmids; Pseudomonas
PubMed: 34530104
DOI: 10.1016/j.ygeno.2021.09.008 -
Environmental Microbiology Oct 2021Productive plant-bacteria interactions, either beneficial or pathogenic, require that bacteria successfully sense, integrate and respond to continuously changing... (Review)
Review
Productive plant-bacteria interactions, either beneficial or pathogenic, require that bacteria successfully sense, integrate and respond to continuously changing environmental and plant stimuli. They use complex signal transduction systems that control a vast array of genes and functions. The Gac-Rsm global regulatory pathway plays a key role in controlling fundamental aspects of the apparently different lifestyles of plant beneficial and phytopathogenic Pseudomonas as it coordinates adaptation and survival while either promoting plant health (biocontrol strains) or causing disease (pathogenic strains). Plant-interacting Pseudomonas stand out for possessing multiple Rsm proteins and Rsm RNAs, but the physiological significance of this redundancy is not yet clear. Strikingly, the components of the Gac-Rsm pathway and the controlled genes/pathways are similar, but the outcome of its regulation may be opposite. Therefore, identifying the target mRNAs bound by the Rsm proteins and their mode of action (repression or activation) is essential to explain the resulting phenotype. Some technical considerations to approach the study of this system are also given. Overall, several important features of the Gac-Rsm cascade are now understood in molecular detail, particularly in Pseudomonas protegens CHA0, but further questions remain to be solved in other plant-interacting Pseudomonas.
Topics: Bacterial Proteins; Gene Expression Regulation, Bacterial; Pseudomonas; RNA, Messenger; Signal Transduction
PubMed: 33939255
DOI: 10.1111/1462-2920.15558 -
Microbial Biotechnology Jan 2021Rhamnolipids are biosurfactants with a wide range of industrial applications that entered into the market a decade ago. They are naturally produced by Pseudomonas... (Review)
Review
Rhamnolipids are biosurfactants with a wide range of industrial applications that entered into the market a decade ago. They are naturally produced by Pseudomonas aeruginosa and some Burkholderia species. Occasionally, some strains of different bacterial species, like Pseudomonas chlororaphis NRRL B-30761, which have acquired RL-producing ability by horizontal gene transfer, have been described. P. aeruginosa, the ubiquitous opportunistic pathogenic bacterium, is the best rhamnolipids producer, but Pseudomonas putida has been used as heterologous host for the production of this biosurfactant with relatively good yields. The molecular genetics of rhamnolipids production by P. aeruginosa has been widely studied not only due to the interest in developing overproducing strains, but because it is coordinately regulated with the expression of different virulence-related traits by the quorum-sensing response. Here, we highlight how the research of the molecular mechanisms involved in rhamnolipid production have impacted the development of strains that are suitable for industrial production of this biosurfactant, as well as some perspectives to improve these industrial useful strains.
Topics: Glycolipids; Molecular Biology; Pseudomonas; Pseudomonas aeruginosa; Pseudomonas putida; Surface-Active Agents
PubMed: 33151628
DOI: 10.1111/1751-7915.13700 -
International Journal of Systematic and... Jan 2022A novel canavanine-degrading bacterium, strain HB002, was isolated from rhizosphere soil of a catch crop field collected from the island of Reichenau in Konstanz,...
A novel canavanine-degrading bacterium, strain HB002, was isolated from rhizosphere soil of a catch crop field collected from the island of Reichenau in Konstanz, Germany, and characterized by using polyphasic taxonomy. The facultative aerobe, rod-shaped, Gram-stain-negative bacterium was oxidase- and catalase-positive. The isolate was able to grow on canavanine as a sole carbon and nitrogen source. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed highest similarities to (L22-9, 99.93 %), subsp. (ATCC 49054, 99.76 %), subsp. (DBK 11, 99.63 %), (DSM 13194, 99.51 %), (DSM 13647, 99.39 %) and (ATCC29736, 99.39 %). Marker gene analysis placed the strain in the intrageneric group of , subgroup . DNA-DNA hybridization and average nucleotide identity values were both under the recommended thresholds for species delineation. The predominant fatty acids of strain HB002 were C, C cyclo ω7 and C ω7. The major respiratory quinone was Q9, followed by Q8 and minor components of Q7 and Q10. Results from the phenotypic characterization showd the strain's inability to hydrolyse gelatin and to assimilate -acetyl glucosamide and a positive enzymatic activity of acid phosphatase and naphthol-AS-BI phosphohydrolase that distinguish this strain from closely related type strains. Taken together, these results show that strain HB002 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is HB002 (=DSM 112525=LMG 32336).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Germany; Phospholipids; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Rhizosphere; Sequence Analysis, DNA; Soil Microbiology
PubMed: 35072599
DOI: 10.1099/ijsem.0.005203