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The ISME Journal Mar 2022Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by...
Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.
Topics: Bacillus; Microbiota; Plant Roots; Pseudomonas stutzeri; Rhizosphere; Soil Microbiology
PubMed: 34593997
DOI: 10.1038/s41396-021-01125-3 -
Pediatrics Jul 2017The pathogens that cause bacterial meningitis in infants and their antimicrobial susceptibilities may have changed in this era of increasing antimicrobial resistance,...
OBJECTIVES
The pathogens that cause bacterial meningitis in infants and their antimicrobial susceptibilities may have changed in this era of increasing antimicrobial resistance, use of conjugated vaccines, and maternal antibiotic prophylaxis for group B (GBS). The objective was to determine the optimal empirical antibiotics for bacterial meningitis in early infancy.
METHODS
This was a cohort study of infants <90 days of age with bacterial meningitis at 7 pediatric tertiary care hospitals across Canada in 2013 and 2014.
RESULTS
There were 113 patients diagnosed with proven meningitis ( = 63) or suspected meningitis ( = 50) presented at median 19 days of age, with 63 patients (56%) presenting a diagnosis from home. Predominant pathogens were ( = 37; 33%) and GBS ( = 35; 31%). Two of 15 patients presenting meningitis on day 0 to 6 had isolates resistant to both ampicillin and gentamicin ( and type B). Six of 60 infants presenting a diagnosis of meningitis from home from day 7 to 90 had isolates, for which cefotaxime would be a poor choice ( [ = 3], , , and ). Sequelae were documented in 84 infants (74%), including 8 deaths (7%).
CONCLUSIONS
and GBS remain the most common causes of bacterial meningitis in the first 90 days of life. For empirical therapy of suspected bacterial meningitis, one should consider a third-generation cephalosporin (plus ampicillin for at least the first month), potentially substituting a carbapenem for the cephalosporin if there is evidence for Gram-negative meningitis.
Topics: Anti-Bacterial Agents; Cohort Studies; Community-Acquired Infections; Female; Humans; Infant; Infant, Newborn; Male; Meningitis, Bacterial; Retrospective Studies; Treatment Outcome
PubMed: 28600447
DOI: 10.1542/peds.2017-0476 -
MBio May 2015Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require...
UNLABELLED
Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn5 and mariner transposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with any transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq with Escherichia coli, Phaeobacter inhibens, Pseudomonas stutzeri, Shewanella amazonensis, and Shewanella oneidensis. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. In P. inhibens, we used our mutant fitness data to identify genes important for the utilization of diverse carbon substrates, including a putative d-mannose isomerase that is required for mannitol catabolism. RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling.
IMPORTANCE
A large challenge in microbiology is the functional assessment of the millions of uncharacterized genes identified by genome sequencing. Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach to assign phenotypes and functions to genes. However, the current strategies for TnSeq are too laborious to be applied to hundreds of experimental conditions across multiple bacteria. Here, we describe an approach, random bar code transposon-site sequencing (RB-TnSeq), which greatly simplifies the measurement of gene fitness by using bar code sequencing (BarSeq) to monitor the abundance of mutants. We performed 387 genome-wide fitness assays across five bacteria and identified phenotypes for over 5,000 genes. RB-TnSeq can be applied to diverse bacteria and is a powerful tool to annotate uncharacterized genes using phenotype data.
Topics: Base Sequence; Chromosome Mapping; DNA Barcoding, Taxonomic; DNA Transposable Elements; Escherichia coli; Gene Library; Genetic Fitness; High-Throughput Nucleotide Sequencing; Mutagenesis, Insertional; Mutation; Phenotype; Pseudomonas; Reproducibility of Results; Rhodobacteraceae; Shewanella
PubMed: 25968644
DOI: 10.1128/mBio.00306-15 -
Revista Chilena de Infectologia :... Aug 2020
Topics: Pseudomonas stutzeri
PubMed: 33399664
DOI: 10.4067/S0716-10182020000400443 -
Methods in Molecular Biology (Clifton,... 2022Functional and structural studies on membrane proteins are often hampered by insufficient yields, misfolding and aggregation during the production and purification...
Functional and structural studies on membrane proteins are often hampered by insufficient yields, misfolding and aggregation during the production and purification process. Escherichia coli is the most commonly used expression host for the production of recombinant prokaryotic integral membrane proteins. However, in many cases expression hosts other than E. coli are more appropriate for certain target proteins. Here, we report a convenient, systematically developed expression system using the γ-proteobacterium Pseudomonas stutzeri as an alternative production host for over-expression of integral membrane proteins. P. stutzeri can be easily and inexpensively cultured in large quantities. The Pseudomonas expression vectors are designed for inducible expression of affinity-tagged fusion proteins controlled by the P promoter. This chapter provides detailed protocols of the different steps required to successfully produce and isolate recombinant membrane proteins with high yields in P. stutzeri.
Topics: Escherichia coli; Membrane Proteins; Promoter Regions, Genetic; Pseudomonas stutzeri; Recombinant Proteins
PubMed: 35773579
DOI: 10.1007/978-1-0716-2368-8_6 -
Infectious Disease Reports Dec 2020bacteria are widespread pathogens that account for considerable infections with significant morbidity and mortality, especially in hospitalized patients. The genus... (Review)
Review
bacteria are widespread pathogens that account for considerable infections with significant morbidity and mortality, especially in hospitalized patients. The genus contains a large number of species; however, the majority of infections are caused by , infections by other species are less reported. is a ubiquitous Gram-negative bacterium that has been reported as a causative agent of some infections, particularly in immunocompromised patients but has rarely been reported as a cause of infective endocarditis. Here, we report a case of a 55-year-old female with no significant medical history who presented with exertional dyspnea, productive cough, and fever. She was diagnosed as a case of acute anterior ST myocardial infarction, underwent double valve replacement surgery, and was found to have infective endocarditis caused by .
PubMed: 33276629
DOI: 10.3390/idr12030020 -
Current Microbiology Feb 2020Mobile genetic elements (MGE) play a large role in the plasticity of genomes, participating in several phenomena which involve genes acquisition. Pseudomonas stutzeri is...
Mobile genetic elements (MGE) play a large role in the plasticity of genomes, participating in several phenomena which involve genes acquisition. Pseudomonas stutzeri is an environmental widely distributed bacteria. This bacteria has a very large genomic plasticity, which would explain its occurrence in several different environments. NCBI data bank and online programs were used to build an inventory to investigate diversity and structure of MGE in Pseudomonas stutzeri, searching for insertion sequences (IS), integrases/transposases, plasmids and prophages. Five hundred and forty-eight ISs, 62 integrases, 166 transposases, five plasmids and eight complete prophages were found. MGE location and adjacent genes were investigated. Possible implications of the presence of these mobile elements explaining phenotypic diversity of Pseudomonas stutzeri were discussed. The study showed that MGEs might be good clues to understand the dynamics of genomes and their phenotypic plasticity, although they are not the only elements responsible for these characteristics.
Topics: Conjugation, Genetic; DNA Transposable Elements; Genetic Variation; Genome, Bacterial; Genomics; Phenotype; Plasmids; Prophages; Pseudomonas stutzeri
PubMed: 31754823
DOI: 10.1007/s00284-019-01812-7 -
Frontiers in Microbiology 2021is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic...
is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic scale. To address these issues, we systematically and comprehensively defined the taxonomy and nomenclature for this species complex and explored its genetic diversity using hundreds of sequenced genomes. By combining average nucleotide identity (ANI) evaluation and phylogenetic inference approaches, we identified 123 complex genomes covering at least six well-defined species among all sequenced genomes; of these, 25 genomes represented novel members of this species complex. ANI values of ≥∼95% and digital DNA-DNA hybridization (dDDH) values of ≥∼60% in combination with phylogenomic analysis consistently and robustly supported the division of these strains into 27 genomovars (most likely species to some extent), comprising 16 known and 11 unknown genomovars. We revealed that 12 strains had mistaken taxonomic assignments, while 16 strains without species names can be assigned to the species level within the species complex. We observed an open pan-genome of the complex comprising 13,261 gene families, among which approximately 45% gene families do not match any sequence present in the COG database, and a large proportion of accessory genes. The genome contents experienced extensive genetic gain and loss events, which may be one of the major mechanisms driving diversification within this species complex. Surprisingly, we found that the ectoine biosynthesis gene cluster () was present in all genomes of species complex strains but distributed at very low frequency (43 out of 9548) in other genomes, suggesting a possible origin of the ancestors of species complex in high-osmolarity environments. Collectively, our study highlights the potential of using whole-genome sequences to re-evaluate the current definition of the complex, shedding new light on its genomic diversity and evolutionary history.
PubMed: 35095786
DOI: 10.3389/fmicb.2021.755874 -
Frontiers in Microbiology 2022Soil salinity is one of the most important abiotic factors limiting plant productivity. The aim of this study was to determine the effect of selected halotolerant plant...
Soil salinity is one of the most important abiotic factors limiting plant productivity. The aim of this study was to determine the effect of selected halotolerant plant growth-promoting endophytes (PGPEs, ISE12 and CSE9) on the growth parameters of barley (), lettuce (), and sunflower () cultivated under salt stress conditions. A negative effect of two higher tested salinities (150 and 300 mM NaCl) was observed on the growth parameters of all investigated plants, including germination percentage and index (decreasing compared to the non-saline control variant in the ranges 5.3-91.7 and 13.6-90.9%, respectively), number of leaves (2.2-39.2%), fresh weight (24.2-81.6%); however, differences in salt stress tolerance among the investigated crops were observed ( > > ). Our data showed that the most crucial traits affected by endophyte inoculation under salt stress were chlorophyll concentration, leaf development, water storage, root development, and biomass accumulation. Thus, the influence of endophytes was species specific. CSE9 promoted the growth of all tested plant species and could be considered a universal PGPEs for many plant genotypes cultivated under saline conditions (e.g., increasing of fresh weight compared to the non-inoculated control variant of barley, lettuce, and sunflower in the ranges 11.4-246.8, 118.9-201.2, and 16.4-77.7%, respectively). ISE12 stimulated growth and mitigated salinity stress only in the case of barley. Bioaugmentation of crops with halotolerant bacterial strains can alleviate salt stress and promote plant growth; however, the selection of compatible strains and the verification of universal plant stress indicators are the key factors.
PubMed: 35350624
DOI: 10.3389/fmicb.2022.788893 -
Microorganisms Jan 2023Illite is a widely distributed clay mineral with huge reserves in Earth's crust, but its effect on heavy oil biodegradation is rarely reported. This study made an...
Illite is a widely distributed clay mineral with huge reserves in Earth's crust, but its effect on heavy oil biodegradation is rarely reported. This study made an investigation of the interactions between illite and a -heavy oil complex (HO). Results showed that, although illite exerted a negative effect on degrading heavy oil by inhibiting the biodegradation of 64 saturated hydrocarbons (SHs) and 50 aromatic hydrocarbons (AHs), it selectively stimulated the biodegradation of 45 AHs with a specific structure, and its biogenic kaolinization at room temperature (35 °C) and pressure (1 atm) was observed in HO for the first time. The finding points out for the first time that, in HO, illite may change the quasi-sequential of AHs biodegradation of heavy oil, as well as its kaolinization without clay intermediate.
PubMed: 36838295
DOI: 10.3390/microorganisms11020330