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Pseudomonas

Q: What are the different types or variations of Pseudomonas?

Pseudomonas is a diverse genus that includes several species, each with unique characteristics and applications. Some of the most well-known Pseudomonas species include P. aeruginosa, P. fluorescens, P. putida, and P. syringae. These species can be found in a variety of environments, from soil and water to clinical settings, and exhibit diverse metabolic capabilities, making them useful in various biotechnological and industrial processes.

Q: What are the common usage challenges associated with Pseudomonas?

Pseudomonas can be a challenging microorganism to work with due to its adaptability and resistance to many antimicrobial agents. For example, P. aeruginosa is a common opportunistic pathogen that can cause serious infections, particularly in immunocompromised individuals. Researchers and clinicians must be mindful of Pseudomonas' ability to rapidly develop resistance to antibiotics, making treatment and management of Pseudomonas-related infections difficult. Additionally, the metabolic versatility of Pseudomonas can complicate its cultivation and control in various applications, requiring careful optimization of growth conditions and protocols.

Q: How can PubCompare.ai assist in the optimal use and comparison of Pseudomonas protocols?

PubCompare.ai is a powerful tool that can help researchers working with Pseudomonas by streamlining the process of identifying the most effective protocols from the literature. The platform's AI-driven analysis allows you to quickly screen a large number of protocols, pinpointing the critical insights that can help you choose the best option for your specific research goals. For example, the platform's comparative analysis can highlight key differences in protocol effectiveness, enabling you to select the most reproducible and accurate approach for your Pseudomonas studies. This can be particularly useful when dealing with the adaptive nature and resistance challenges associated with this versatile genus of bacteria.

Q: What are some of the specific applications of Pseudomonas?

Pseudomonas has a wide range of applications, ranging from medical and environmental to industrial and biotechnological. In the medical field, Pseudomonas species are important pathogens that can cause severe infections, but they also have potential use in phage therapy and the production of various enzymes and biopharmaceuticals. In the environmental sector, Pseudomonas is known for its ability to degrade a variety of pollutants, making it useful in bioremediation and wastewater treatment. Additionally, Pseudomonas has been explored for its potential in biofuel production and as a plant growth-promoting agent in agriculture.

Pseudomonas is a genus of Gram-negative bacteria that are widely distributed in nature and play a significant role in various fields, including medicine, biotechnology, and environmental sciences.
These versatile microorganisms are known for their metabolic diversity, ability to adapt to diverse environmental conditions, and potential in bioremediation and biofuel production.
Pseudomonas species are also important pathogens, causing a range of infections in humans, animals, and plants, particularly in immunocompromised individuals.
Researching and understanding Pseudomonas is crucial for adavncing our knowledge of these fascinating bacteria and developing effective strategies for their management and control.

Most cited protocols related to «Pseudomonas»

Virus Genome Fragmentation and Host Identification

We collected 1562 virus RefSeq genomes infecting prokaryotes and 31,986 prokaryotic host RefSeq genomes from NCBI in May 2015. The NCBI accession numbers of the RefSeq sequences are provided in the Additional file 2: Table S2. To mimic fragmented metagenomic sequences, for a given length L = 500, 1000, 3000, 5000, and 10000 bp, viruses were split into non-overlapping fragments of length L and the same number of non-overlapping fragments of length L were randomly subsampled from the prokaryotic genomes. Fragments were generated for virus genomes discovered before 1 January 2014 and after 1 January 2014 and were separately used as training and testing sets, respectively (Table 1). To generate evaluation datasets containing 10, 50, and 90% viral contigs, the number of viral contigs was set as in Table 1 and was combined with 9 times more, equal numbers, or 9-fold less randomly sampled host contigs, respectively.
Highly represented host phyla (Actinobacteria, Cyanobacteria, Firmicutes, Proteobacteria) and genera (Mycobacterium, Escherichia, Pseudomonas, Staphylococcus, Bacillus, Vibrio, and Streptococcus) were selected for the analyses where viruses infecting these taxa were excluded from the training of VirFinder. For evaluation of the different trained VirFinder models, equal numbers of contigs of the excluded viruses and all other viruses were selected and then combined with randomly selected host contigs such that total virus and host contigs were equal in number.
For the analysis of VirFinder trained with 14,722 prokaryotic genomes with or without proviruses removed, these genomes were downloaded from the database cited in [6 (link)]. Likewise, the positions of proviruses predicted by VirSorter in these 14,722 genomes were obtained from the published data of [6 (link)] and were used to remove theses sequence from their corresponding host genomes.

Ren J., Ahlgren N.A., Lu Y.Y., Fuhrman J.A, & Sun F. (2017). VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome, 5, 69.

Publication 2017

Actinomycetes Bacillus Cyanobacteria Escherichia Firmicutes Genome Metagenome Mycobacterium Prokaryotic Cells Proteobacteria Proviruses Pseudomonas Staphylococcus Streptococcus Vibrio Viral Genome Virus

Expanding the Reference Gene Catalog for Stress and Virulence Genes

We have expanded the Reference Gene Catalog^{8 (link)} to include genetic elements related to stress response and virulence genes; these expansions can be visualized in the Reference Gene Catalog Browser (https://www.ncbi.nlm.nih.gov/pathogens/refgene/). One reason we expanded AMRFinderPlus is to understand the linkages between AMR genes and stress response and virulence genes in food-borne pathogens; thus, the stress response and virulence genes included in the Reference Gene Catalog are composed primarily of E. coli-related genes derived primarily from González-Escalona et al.^{23 (link)} as well as BacMet^{24 (link)}, but also have been supplemented by manual curation efforts for other taxa. Stx gene nomenclature adopts the system of Scheutz et al.^{25 (link)} and the intimin (eae) gene nomenclature uses existing designations in the literature^{26 (link),27 (link)}. Genes are incorporated only if there is literature supporting the function of that protein or closely related sequences that meet the identification criteria. As a major focus of our work is to improve NCBI’s Pathogen Detection system^{16 (link)}, we excluded genes that belonged to organisms not deemed clinically relevant. To remove ‘housekeeping’ proteins that were universally found in one or more taxa in the Pathogen Detection system, sequences were not included if they were found at a frequency of greater than 95% in a survey of 58,531 RefSeq bacterial assemblies belonging to any of the following species: Acinetobacter, Campylobacter, Citrobacter, Enterococcus, Enterobacter, Escherichia/Shigella, Klebsiella, Listeria, Salmonella, Staphylococcus, Pseudomonas, and Vibrio. If genes of particular interest in foodborne pathogens exceeded this threshold, they were excluded in the taxa where they appear to be nearly universal (see “Identifying genomic elements” below). In addition, genes with misidentified functions, such as copper-binding proteins that use copper as a co-factor yet do not confer resistance to copper, also were excluded. As we continue to expand the database, we use similar criteria when adding genes.

Feldgarden M., Brover V., Gonzalez-Escalona N., Frye J.G., Haendiges J., Haft D.H., Hoffmann M., Pettengill J.B., Prasad A.B., Tillman G.E., Tyson G.H, & Klimke W. (2021). AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific Reports, 11, 12728.

Publication 2021

Acinetobacter Bacteria Bears Campylobacter Citrobacter Copper copper-binding protein Enterobacter Enterococcus Escherichia Escherichia coli factor A Food Gene Components Genome Components Klebsiella Linkage, Genetic Listeria Operator, Genetic Pathogenicity Proteins Pseudomonas Salmonella Shigella Staphylococcus Vibrio Virulence

Identifying Orthologous Genes for Phylogenetic Analysis

We applied a stringent criterion for eliminating nonhomologous sequences and paralogous sequences, since both are likely to lead to false conclusions regarding the organismal phylogeny and frequency of LGT. In particular, the criterion of “best reciprocal hits” between sequences for a genome pair can lead to false conclusions of orthology because the resulting gene pairs are not always closest relatives phylogenetically (Koski and Golding 2001 (link)). Instead, we used a cutoff for the degree of similarity as reflected in the BLASTP bit scores (Altschul et al. 1997 (link)). The bit score is dependent upon the scoring system (substitution matrix and gap costs) employed and takes into account both the degree of similarity and the length of the alignment between the query and the match sequences. We used it to detect homologous genes, described as follows. A bank of all annotated protein sequences of all included species was created. A BLASTP (Altschul et al. 1997 (link)) search was performed for all the proteins in each genome against the protein bank. This implies that all proteins were searched against both their resident genome and those from the 12 other species. The match of a given protein against itself gives a maximal bit score. To determine a threshold to group genes into a family, we examined the distribution of the ratio of the bit score to the maximal (self) bit score based on the proteins of E. coli compared against proteins of the 12 genomes (Figure 6). In each case, the distribution showed a clear bimodal pattern with a first peak of low similarity values, which is constant among comparisons and therefore probably represents random matches, and a second peak of higher similarity values, representing true homologous genes. For comparisons of E. coli proteins with those of the most distant species in our set, such as Vibrio, Xanthomonas, Xylella, and Pseudomonas, the separation of the two portions of the distribution occurs at about 30% of the maximal bit score. Thus, in order to apply a stringent criterion for homology, we inferred as homologous genes those presenting a bit score value higher or equal to 30% of the maximal bit score. A protein was included in a family if this criterion was satisfied for at least one member. Our cutoff was chosen to minimize inclusion of nonhomologous sequences within a family; consequently, it may exclude some homologs, especially fast-evolving ones.
After establishing homolog families, we selected the set that contained a single sequence in each represented genome and regarded these as likely orthologs that could give information about the organismal phylogeny and the frequency of LGT affecting orthologs in this bacterial group.

Lerat E., Daubin V, & Moran N.A. (2003). From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria. PLoS Biology, 1(1), e19.

Publication 2003

Bacteria Escherichia coli Proteins Genes Genes, vif Genome Proteins Pseudomonas Staphylococcal Protein A Vibrio Xanthomonas Xylella

Validation of Carbapenemase Identification Method

For validation of the CIM, a selection of 30 Gram-negative isolates was used. This selection included isolates obtained from different institutes across the world carrying known carbapenemase encoding genes and carbapenem susceptible isolates, according to the submitter (Table 1). In addition, 694 isolates submitted to the National Institute for Public Health and the Environment for the national surveillance of carbapenemase-producing Enterobacteriaceae (CPE) by Dutch medical microbiology laboratories (MMLs) during the first six months of 2012 and the first six months of 2013 were used. For the national surveillance of CPE in the Netherlands, Dutch MMLs are requested to submit Enterobacteriaceae isolates with an MIC for meropenem > 0.25 μg/ml. However, more than half of the isolates (411/694, 59%) sent in for CPE surveillance were non-fermenting Gram-negatives belonging to the genera Pseudomonas and Acinetobacter. Furthermore, 35% of the isolates had MICs below 0.25 μg/ml. Nevertheless, all isolates were included in this study.
The species identification, as performed by the MMLs, was confirmed using MALDI-TOF (Bruker Daltonics GmbH, Bremen, Germany) and the MIC for all isolates was confirmed by E-test (BioMerieux Inc., Marcy L’Etoile, France). Culturing of isolates was done on Columbia Sheep Blood (bioTRADING Benelux BV, Mijdrecht, The Netherlands) and Mueller-Hinton agarplates (Oxoid Ltd, Hampshire, United Kingdom). An overview of all CPE surveillance isolates and their characteristics is displayed in Tables 2 and 3.

van der Zwaluw K., de Haan A., Pluister G.N., Bootsma H.J., de Neeling A.J, & Schouls L.M. (2015). The Carbapenem Inactivation Method (CIM), a Simple and Low-Cost Alternative for the Carba NP Test to Assess Phenotypic Carbapenemase Activity in Gram-Negative Rods. PLoS ONE, 10(3), e0123690.

Publication 2015

Acinetobacter Blood Carbapenem-Resistant Enterobacteriaceae carbapenemase Carbapenems Domestic Sheep Enterobacteriaceae Genes Meropenem Pseudomonas Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

Construction and Curing of Pseudomonas Mutants

Pseudomonas and E. coli strains were grown in Luria Bertani medium (LB) at 37°C with aeration and when necessary pseudomonas cultures were supplemented with kanamycin (400 μg/ml), gentamycin (15 μg/ml) or carbenicillin (300 μg/ml). Pseudomonas strains used in this study include ΔpqsA [16 (link)], ΔpqsE [17 (link)], ΔmvfR [18 (link)], PA14_42880::MAR2xT7 and PA14_43100::MAR2xT7 [11 (link)]. The trpE-phnAB- double mutant was constructed in this study: 1293 bp of phnA and 300 bp of phnB were deleted by allelic exchange in the auxotroph trpE::Mar2xT7 mutant background. The vector pKOBEG-sacB [4 (link)] contains the Red operon expressed under the control of the arabinose inducible pBAD promoter and the sacB gene that is necessary to cure the plasmid [2 (link),4 (link)]. Since pKOBEG-sacB was not capable of replication in P. aeruginosa, the Red operon-araC fragment obtained after digestion with KpnI and HindIII was cloned into the multi clonal site of the E. coli – P. aeruginosa shuttle vector pUCP18 (Genbank U07164) [19 (link)] to create the plasmid pUCP18-Red. In addition, the NdeI sacB fragment from pKOBEG-sacB was cloned into pUCP18-Red, previously digested with NdeI, to create pUCP18-RedS (Genbank EU073163) (Additional file 1). P. aeruginosa recombinants were easily cured from pUCP18-RedS by streaking the mutant strains on NaCl-free LB agar plates supplemented with 10% sucrose.

Lesic B, & Rahme L.G. (2008). Use of the lambda Red recombinase system to rapidly generate mutants in Pseudomonas aeruginosa. BMC Molecular Biology, 9, 20.

Publication 2008

Agar Alleles Ara-C Arabinose Carbenicillin Cloning Vectors Digestion DNA Replication Escherichia coli Genes Gentamicin Kanamycin Operon Plasmids PRO 140 Pseudomonas Pseudomonas aeruginosa Shuttle Vectors Sodium Chloride Strains Sucrose

Most recents protocols related to «Pseudomonas»

Microbial Seed Treatments for Enhanced Crop Performance

Not available on PMC !

Example 2

A. Seed Treatment with Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as a seed coating to seeds of corn (Zea mays). Upon applying the isolated microbe as a seed coating, the corn will be planted and cultivated in the standard manner.

A control plot of corn seeds, which did not have the isolated microbe applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiably higher biomass than the control corn plants.

The biomass from the treated plants may be about 1-10% higher, 10-20% higher, 20-30% higher, 30-40% higher, 40-50% higher, 50-60% higher, 60-70% higher, 70-80% higher, 80-90% higher, or more.

The biomass from the treated plants may equate to about a 1 bushel per acre increase over the controls, or a 2 bushel per acre increase, or a 3 bushel per acre increase, or a 4 bushel per acre increase, or a 5 bushel per acre increase, or more.

In some aspects, the biomass increase is statistically significant. In other aspects, the biomass increase is not statistically significant, but is still quantifiable.

B. Seed Treatment with Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as a seed coating to seeds of corn (Zea mays). Upon applying the microbial consortium as a seed coating, the corn will be planted and cultivated in the standard manner.

A control plot of corn seeds, which did not have the microbial consortium applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiably higher biomass than the control corn plants.

The biomass from the treated plants may be about 1-10% higher, 10-20% higher, 20-30% higher, 30-40% higher, 40-50% higher, 50-60% higher, 60-70% higher, 70-80% higher, 80-90% higher, or more.

In some aspects, the biomass increase is statistically significant. In other aspects, the biomass increase is not statistically significant, but is still quantifiable.

C. Treatment with Agricultural Composition Comprising Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

For example, it is anticipated that a farmer will apply the agricultural composition to the corn seeds simultaneously upon planting the seeds into the field. This can be accomplished, for example, by applying the agricultural composition to a hopper/bulk tank on a standard 16 row planter, which contains the corn seeds and which is configured to plant the same into rows. Alternatively, the agricultural composition can be contained in a separate bulk tank on the planter and sprayed into the rows upon planting the corn seed.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the agricultural composition will exhibit a quantifiably higher biomass than the control corn plants.

The biomass from the treated plants may be about 1-10% higher, 10-20% higher, 20-30% higher, 30-40% higher, 40-50% higher, 50-60% higher, 60-70% higher, 70-80% higher, 80-90% higher, or more.

In some aspects, the biomass increase is statistically significant. In other aspects, the biomass increase is not statistically significant, but is still quantifiable.

D. Treatment with Agricultural Composition Comprising Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the agricultural composition will exhibit a quantifiably higher biomass than the control corn plants.

The biomass from the treated plants may be about 1-10% higher, 10-20% higher, 20-30% higher, 30-40% higher, 40-50% higher, 50-60% higher, 60-70% higher, 70-80% higher, 80-90% higher, or more.

In some aspects, the biomass increase is statistically significant. In other aspects, the biomass increase is not statistically significant, but is still quantifiable.

A. Seed Treatment with Isolated Microbe

A control plot of corn seeds, which did not have the isolated microbe applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiable and superior ability to tolerate drought conditions and/or exhibit superior water use efficiency, as compared to the control corn plants.

The drought tolerance and/or water use efficiency can be based on any number of standard tests from the art, e.g leaf water retention, turgor loss point, rate of photosynthesis, leaf color and other phenotypic indications of drought stress, yield performance, and various root morphological and growth patterns.

B. Seed Treatment with Microbial Consortia

A control plot of corn seeds, which did not have the microbial consortium applied as a seed coating, will also be planted.

C. Treatment with Agricultural Composition Comprising Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the with the agricultural composition will exhibit a quantifiable and superior ability to tolerate drought conditions and/or exhibit superior water use efficiency, as compared to the control corn plants.

D. Treatment with Agricultural Composition Comprising Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

A. Seed Treatment with Isolated Microbe

A control plot of corn seeds, which did not have the isolated microbe applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiable and superior ability to utilize nitrogen, as compared to the control corn plants.

The nitrogen use efficiency can be quantified by recording a measurable change in any of the main nitrogen metabolic pool sizes in the assimilation pathways (e.g., a measurable change in one or more of the following: nitrate, nitrite, ammonia, glutamic acid, aspartic acid, glutamine, asparagine, lysine, leucine, threonine, methionine, glycine, tryptophan, tyrosine, total protein content of a plant part, total nitrogen content of a plant part, and/or chlorophyll content), or where the treated plant is shown to provide the same or elevated biomass or harvestable yield at lower nitrogen fertilization levels compared to the control plant, or where the treated plant is shown to provide elevated biomass or harvestable yields at the same nitrogen fertilization levels compared to a control plant.

B. Seed Treatment with Microbial Consortia

A control plot of corn seeds, which did not have the microbial consortium applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiable and superior ability to utilize nitrogen, as compared to the control corn plants.

C. Treatment with Agricultural Composition Comprising Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the agricultural composition will exhibit a quantifiable and superior ability to utilize nitrogen, as compared to the control corn plants.

D. Treatment with Agricultural Composition Comprising Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

The inoculants were prepared from isolates grown as spread plates on R2A incubated at 25° C. for 48 to 72 hours. Colonies were harvested by blending with sterile distilled water (SDW) which was then transferred into sterile containers. Serial dilutions of the harvested cells were plated and incubated at 25° C. for 24 hours to estimate the number of colony forming units (CFU) in each suspension. Dilutions were prepared using individual isolates or blends of isolates (consortia) to deliver 1×10⁵cfu/microbe/seed and seeds inoculated by either imbibition in the liquid suspension or by overtreatment with 5% vegetable gum and oil.

Seeds corresponding to the plants of table 15 were planted within 24 to 48 hours of treatment in agricultural soil, potting media or inert growing media. Plants were grown in small pots (28 mL to 200 mL) in either a controlled environment or in a greenhouse. Chamber photoperiod was set to 16 hours for all experiments on all species. Air temperature was typically maintained between 22-24° C.

Unless otherwise stated, all plants were watered with tap water 2 to 3 times weekly. Growth conditions were varied according to the trait of interest and included manipulation of applied fertilizer, watering regime and salt stress as follows:

- Low N—seeds planted in soil potting media or inert growing media with no applied N fertilizer
- Moderate N—seeds planted in soil or growing media supplemented with commercial N fertilizer to equivalent of 135 kg/ha applied N
- Insol P—seeds planted in potting media or inert growth substrate and watered with quarter strength Pikovskaya's liquid medium containing tri-calcium phosphate as the only form phosphate fertilizer.
- Cold Stress—seeds planted in soil, potting media or inert growing media and incubated at 10° C. for one week before being transferred to the plant growth room.
- Salt stress—seeds planted in soil, potting media or inert growing media and watered with a solution containing between 100 to 200 mg/L NaCl.

Untreated (no applied microbe) controls were prepared for each experiment. Plants were randomized on trays throughout the growth environment. Between 10 and 30 replicate plants were prepared for each treatment in each experiment. Phenotypes were measured during early vegetative growth, typically before the V3 developmental stage and between 3 and 6 weeks after sowing. Foliage was cut and weighed. Roots were washed, blotted dry and weighed. Results indicate performance of treatments against the untreated control.

TABLE 15

StrainShootRoot

Microbe sp.IDCropAssayIOC (%)IOC (%)

Bosea thiooxidans123EfficacyEfficacy

overall100%100%

Bosea thiooxidans54522WheatEarly vigor - insol P30-40 —

Bosea thiooxidans54522RyegrassEarly vigor50-60 50-60

Bosea thiooxidans54522RyegrassEarly vigor - moderate P0-100-10

Duganella violaceinigra111EfficacyEfficacy

overall100%100%

Duganella violaceinigra66361TomatoEarly vigor0-100-10

Duganella violaceinigra66361TomatoEarly vigor30-40 40-50

Duganella violaceinigra66361TomatoEarly vigor20-30 20-30

Herbaspirillum huttiense222Efficacy—

overall100%

Herbaspirillum huttiense54487WheatEarly vigor - insol P30-40 —

Herbaspirillum huttiense60507MaizeEarly vigor - salt stress0-100-10

Janthinobacterium sp.222Efficacy—

Overall100%

Janthinobacterium sp.54456WheatEarly vigor - insol P30-40 —

Janthinobacterium sp.54456WheatEarly vigor - insol P0-10—

Janthinobacterium sp.63491RyegrassEarly vigor - drought0-100-10

stress

Massilia niastensis112EfficacyEfficacy

overall80%80%

Massilia niastensis55184WheatEarly vigor - salt stress0-1020-30

Massilia niastensis55184WinterEarly vigor - cold stress0-1010-20

wheat

Massilia niastensis55184WinterEarly vigor - cold stress20-30 20-30

wheat

Massilia niastensis55184WinterEarly vigor - cold stress10-20 10-20

wheat

Massilia niastensis55184WinterEarly vigor - cold stress<0<0

wheat

Novosphingobium rosa211EfficacyEfficacy

overall100%100%

Novosphingobium rosa65589MaizeEarly vigor - cold stress0-100-10

Novosphingobium rosa65619MaizeEarly vigor - cold stress0-100-10

Paenibacillus amylolyticus111EfficacyEfficacy

overall100%100%

Paenibacillus amylolyticus66316TomatoEarly vigor0-100-10

Paenibacillus amylolyticus66316TomatoEarly vigor10-20 10-20

Paenibacillus amylolyticus66316TomatoEarly vigor0-100-10

Pantoea agglomerans323EfficacyEfficacy

33%50%

Pantoea agglomerans54499WheatEarly vigor - insol P40-50 —

Pantoea agglomerans57547MaizeEarly vigor - low N<00-10

Pantoea vagans55529MaizeEarly vigor<0<0

(formerly P. agglomerans)

Polaromonas ginsengisoli111EfficacyEfficacy

66%100%

Polaromonas ginsengisoli66373TomatoEarly vigor0-100-10

Polaromonas ginsengisoli66373TomatoEarly vigor20-30 30-40

Polaromonas ginsengisoli66373TomatoEarly vigor<010-20

Pseudomonas fluorescens122Efficacy—

100%

Pseudomonas fluorescens54480WheatEarly vigor - insol P>100 —

Pseudomonas fluorescens56530MaizeEarly vigor - moderate N0-10—

Rahnella aquatilis334EfficacyEfficacy

80%63%

Rahnella aquatilis56532MaizeEarly vigor - moderate N10-20 —

Rahnella aquatilis56532MaizeEarly vigor - moderate N0-100-10

Rahnella aquatilis56532WheatEarly vigor - cold stress0-1010-20

Rahnella aquatilis56532WheatEarly vigor - cold stress<00-10

Rahnella aquatilis56532WheatEarly vigor - cold stress10-20 <0

Rahnella aquatilis57157RyegrassEarly vigor<0—

Rahnella aquatilis57157MaizeEarly vigor - low N0-100-10

Rahnella aquatilis57157MaizeEarly vigor - low N0-10<0

Rahnella aquatilis58013MaizeEarly vigor0-1010-20

Rahnella aquatilis58013MaizeEarly vigor - low N0-10<0

Rhodococcus erythropolis313Efficacy—

66%

Rhodococcus erythropolis54093MaizeEarly vigor - low N40-50 —

Rhodococcus erythropolis54299MaizeEarly vigor - insol P>100 —

Rhodococcus erythropolis54299MaizeEarly vigor<0<0

Stenotrophomonas chelatiphaga611EfficacyEfficacy

60%60%

Stenotrophomonas chelatiphaga54952MaizeEarly vigor0-100-10

Stenotrophomonas chelatiphaga47207MaizeEarly vigor<0 0

Stenotrophomonas chelatiphaga64212MaizeEarly vigor0-1010-20

Stenotrophomonas chelatiphaga64208MaizeEarly vigor0-100-10

Stenotrophomonas chelatiphaga58264MaizeEarly vigor<0<0

Stenotrophomonas maltophilia612EfficacyEfficacy

43%66%

Stenotrophomonas maltophilia54073MaizeEarly vigor - low N50-60 —

Stenotrophomonas maltophilia54073MaizeEarly vigor<00-10

Stenotrophomonas maltophilia56181MaizeEarly vigor0-10<0

Stenotrophomonas maltophilia54999MaizeEarly vigor0-100-10

Stenotrophomonas maltophilia54850MaizeEarly vigor 00-10

Stenotrophomonas maltophilia54841MaizeEarly vigor<00-10

Stenotrophomonas maltophilia46856MaizeEarly vigor<0<0

Stenotrophomonas rhizophila811EfficacyEfficacy

12.5%37.5%

Stenotrophomonas rhizophila50839MaizeEarly vigor<0<0

Stenotrophomonas rhizophila48183MaizeEarly vigor<0<0

Stenotrophomonas rhizophila45125MaizeEarly vigor<0<0

Stenotrophomonas rhizophila46120MaizeEarly vigor<00-10

Stenotrophomonas rhizophila46012MaizeEarly vigor<0<0

Stenotrophomonas rhizophila51718MaizeEarly vigor0-100-10

Stenotrophomonas rhizophila66478MaizeEarly vigor<0<0

Stenotrophomonas rhizophila65303MaizeEarly vigor<00-10

Stenotrophomonas terrae221EfficacyEfficacy

50%50%

Stenotrophomonas terrae68741MaizeEarly vigor<0<0

Stenotrophomonas terrae68599MaizeEarly vigor<00-10

Stenotrophomonas terrae68599Capsicum *Early vigor20-30 20-30

Stenotrophomonas terrae68741Capsicum *Early vigor10-20 20-30

The data presented in table 15 describes the efficacy with which a microbial species or strain can change a phenotype of interest relative to a control run in the same experiment. Phenotypes measured were shoot fresh weight and root fresh weight for plants growing either in the absence of presence of a stress (assay). For each microbe species, an overall efficacy score indicates the percentage of times a strain of that species increased a both shoot and root fresh weight in independent evaluations. For each species, the specifics of each independent assay is given, providing a strain ID (strain) and the crop species the assay was performed on (crop). For each independent assay the percentage increase in shoot and root fresh weight over the controls is given.

US11871752B2. Agriculturally beneficial microbes, microbial compositions, and consortia (2024-01-16). BIOCONSORTIA, INC. [US]. Inventors: Peter Wigley [NZ], Susan Turner [US], Caroline George [NZ], Thomas Williams [US], Kelly Roberts [US], Graham Hymus [US], Kelvin Lau [NZ].

Patent 2024

Ammonia Asparagine Aspartic Acid Biological Assay Bosea thiooxidans Calcium Phosphates Capsicum Cells Chlorophyll Cold Shock Stress Cold Temperature Crop, Avian Dietary Fiber DNA Replication Droughts Drought Tolerance Embryophyta Environment, Controlled Farmers Fertilization Glutamic Acid Glutamine Glycine Growth Disorders Herbaspirillum Herbaspirillum huttiense Leucine Lolium Lycopersicon esculentum Lysine Maize Massilia niastensis Methionine Microbial Consortia Nitrates Nitrites Nitrogen Novosphingobium rosa Paenibacillus Paenibacillus amylolyticus Pantoea agglomerans Pantoea vagans Phenotype Phosphates Photosynthesis Plant Development Plant Embryos Plant Leaves Plant Proteins Plant Roots Plants Polaromonas ginsengisoli Pseudoduganella violaceinigra Pseudomonas Pseudomonas fluorescens Rahnella Rahnella aquatilis Retention (Psychology) Rhodococcus erythropolis Rosa Salt Stress Sodium Chloride Sodium Chloride, Dietary Stenotrophomonas chelatiphaga Stenotrophomonas maltophilia Stenotrophomonas rhizophila Stenotrophomonas terrae Sterility, Reproductive Strains Technique, Dilution Threonine Triticum aestivum Tryptophan Tyrosine Vegetables Zea mays

Combination Therapy for LVAD Driveline Infection

Not available on PMC !

Example 4

The patient received an artificial heart (LVAD) in 2013. From fall 2015, he was initially in outpatient treatment for driveline infection. The first documented driveline treatment with ActiMaris took Place®. A few months later, inpatient admission was required for operative remediation of the infection. The finding was so pronounced that odor of the Pseudomonas infestation could be detected before the patient entered through the door. The degree of infection is shown in FIGS. 1A and 1B. Operative revision was carried out immediately. After the bleeding tendency subsided, the patient was treated with the combination method according to the invention. The infection parameters normalized within only three weeks (CRP<0.5) (see FIG. 1C) and the patient was discharged with the wound into outpatient care at his own request.

It should be noted that treatment with ActiMaris Alone® was unsuccessful for more than six months, so that the infection progressed significantly with an increase in the infection parameters. After three weeks of combination therapy, the improvement in findings shown above could be achieved with normalization of the infection values.

US11872247B2. Combination of a wound-rinsing solution and cold plasma for the treatment of wounds (2024-01-16). Westfaelische Wilhelms-Universitaet Muenster [DE]. Inventors: Heinrich Rotering [DE].

Patent 2024

Blood Coagulation Disorders Care, Ambulatory Cold Plasma Combined Modality Therapy Heart, Artificial Infection Inpatient Odors Parasitic Diseases Patients Pseudomonas Wounds

Isolation and Characterization of Denitrifier Strains

Denitrifier strains were isolated from patches in the presence/absence of AMF at the second harvest in pot expt 2 to examine the enriched denitrifier community in the hyphosphere. Fresh soil was vortexed and suspended in ddH₂O. Then, 10⁵-fold dilutions of the soil suspension were spread on bromothymol blue (BTB) agar plates to isolate the denitrifiers [31 (link)]. Each sample was prepared in triplicate. The plates were incubated at 30 °C for 1–3 days. Separate blue colonies were isolated and purified by repeated streaking on BTB plates. The total bacterial DNA of each isolate was extracted from 1 mL culture suspension with a genomic DNA extraction kit (Tiangen Biotech, Beijing, China). The bacterial primers 27F/1492R were used for 16S rDNA amplification, and sequencing was performed by Tsingke Biotech, Beijing, China. The PCR thermal conditions are shown in Table S2. Following dereplication with a cut off value of 99% sequence similarity, the sequences were aligned with reference sequences in the National Center for Biotechnology Information (NCBI) GenBank database. A phylogenetic tree was then constructed by the neighbor-joining method [32 (link)] with bootstrap analysis of 1000 replicates using MEGA version 5 [33 (link)].
The bacterial primers nosZ1527F/nosZ1773R were used for nosZ gene amplification to examine whether the Pseudomonas isolates possessed the nosZ gene (Table S2). The target band was detected, sequenced and then identified using a BLAST search in GenBank in NCBI. Three Pseudomonas fluorescens isolates (JL1, JL2, and JL3) possessing the nosZ gene were screened. The draft genomes of the three strains were sequenced. Details are shown in the Supplementary Information.

Li X., Zhao R., Li D., Wang G., Bei S., Ju X., An R., Li L., Kuyper T.W., Christie P., Bender F.S., Veen C., van der Heijden M.G., van der Putten W.H., Zhang F., Butterbach-Bahl K, & Zhang J. (2023). Mycorrhiza-mediated recruitment of complete denitrifying Pseudomonas reduces N2O emissions from soil. Microbiome, 11, 45.

Publication 2023

Agar Bacteria Bromthymol Blue DNA, Bacterial DNA, Ribosomal Gene Amplification Genes Genome Oligonucleotide Primers Pseudomonas Pseudomonas fluorescens Strains Technique, Dilution

Microbial PHA Production Optimization

Cells from starter cultures were spun down in sterile 50 mL tubes at 11000 g for 10 minutes at 25°C and re-suspended in 50 mL MM_PHA1 (Halomonas sp. R5-57) or MM_PHA2 (Pseudomonas sp. MR4-99) medium in 250 mL baffled flasks incubated at 25°C, 200 rpm for 120 hours (Halomonas sp. R5-57) or 72 hours (Pseudomonas sp. MR4-99). Samples for measuring OD_600nm (100 μL) and for FTIR analysis (900 μL) were taken at 24 hours interval.
At the end of the experiment, 40 mL of culture was centrifuged in pre-weighed 50 mL plastic tubes at 18000 g, 20 minutes at 4°C and washed one time with 15 g/L (Pseudomonas sp. MR4-99) or 35 g/L (Halomonas sp. R5-57) sodium chloride solution. The bacterial pellets were frozen at—80°C before lyophilization, analytical weighing, and GC-FID analysis for identification and quantification of PHA production.

Christensen M., Chiciudean I., Jablonski P., Tanase A.M., Shapaval V, & Hansen H. (2023). Towards high-throughput screening (HTS) of polyhydroxyalkanoate (PHA) production via Fourier transform infrared (FTIR) spectroscopy of Halomonas sp. R5-57 and Pseudomonas sp. MR4-99. PLOS ONE, 18(3), e0282623.

Publication 2023

Bacteria Cell Culture Techniques Freeze Drying Freezing Halomonas Pellets, Drug Pseudomonas Saline Solution Spectroscopy, Fourier Transform Infrared Sterility, Reproductive

Isolation and Cultivation of Marine Bacteria

Halomonas sp. R5-57 and Pseudomonas sp. MR4-99 were isolated from the Barents sea and obtained from Marbank—The National Marine Biobank of Norway (Tromsø, Norway) [28 (link)]. Both strains were streaked on MA plates from cryo-stocks (- 80°C, 20% glycerol) and incubated for 1 day at room temperature (~ 25°C). Individual colonies were picked and, unless otherwise stated, inoculated into 3 mL of LB1-5 (Pseudomonas sp. MR4-99) or LB3-5 (Halomonas sp. R5-57) medium for preparing starter cultures in biological triplicates and incubated with 1270 shakes per minute on a Heidolph Multi Reax multi-vortexer at room temperature. Overnight cultures were re-suspended into fresh medium to an optical density at 600 nm (OD_600nm) of ~ 0.15 and incubated until early- to middle exponential phase (OD_600nm of 0.6–1.5). Similarly, overnight starter cultures were used to inoculate 50 mL LB1-5 or LB3-5 medium and incubated until OD ~ 1 for use in shake flask PHA production experiments.

Publication 2023

Biopharmaceuticals Glycerin Halomonas Marines Pseudomonas Strains Tremor Vision

Top products related to «Pseudomonas»

Pseudomonas isolation agar by BD

Sourced in United States, Germany

Pseudomonas isolation agar is a selective and differential culture medium used for the isolation and identification of Pseudomonas species from clinical and environmental samples. It contains various components that inhibit the growth of non-Pseudomonas bacteria, while allowing Pseudomonas species to grow and form distinctive colonies.

Pseudomonas agar base by Thermo Fisher Scientific

Sourced in United Kingdom, Italy

Pseudomonas Agar Base is a culture medium used for the selective isolation and identification of Pseudomonas species from clinical and non-clinical samples. It contains specific nutrients and selective agents that support the growth of Pseudomonas while inhibiting the growth of other bacteria.

Pseudomonas cetrimide agar by Thermo Fisher Scientific

Sourced in United Kingdom

Pseudomonas cetrimide agar is a selective and differential culture medium used for the isolation and identification of Pseudomonas aeruginosa in clinical and environmental samples. The medium contains cetrimide, which inhibits the growth of many gram-positive and gram-negative bacteria, allowing Pseudomonas aeruginosa to grow selectively. The medium also contains substances that promote the production of pyocyanin, a characteristic pigment produced by Pseudomonas aeruginosa, which aids in the identification of the organism.

Pseudomonas isolation agar by Merck Group

Sourced in United States, United Kingdom

Pseudomonas isolation agar is a microbiological growth medium used for the selective isolation and identification of Pseudomonas species from clinical and environmental samples. It contains ingredients that support the growth of Pseudomonas while inhibiting the growth of other bacteria.

Wizard genomic dna purification kit by Promega

Sourced in United States, France, Germany, China, United Kingdom, Japan, Switzerland, Australia, Italy, Spain, Ireland, Canada, Brazil

The Wizard Genomic DNA Purification Kit is a product designed to isolate and purify genomic DNA from a variety of sample types. It utilizes a simple, rapid, and efficient protocol to extract high-quality DNA that can be used in various downstream applications.

Macconkey agar by Thermo Fisher Scientific

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MacConkey agar is a selective and differential culture medium used for the isolation and identification of Gram-negative enteric bacteria, particularly members of the Enterobacteriaceae family. It inhibits the growth of Gram-positive bacteria while allowing the growth of Gram-negative bacteria.

Glycerol by Merck Group

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Glycerol is a colorless, odorless, and viscous liquid used in various laboratory applications. It is a basic chemical compound with the molecular formula C₃H₈O₃. Glycerol is commonly used as a solvent, humectant, and stabilizer in many laboratory procedures.

Pseudomonas isolation agar pia by BD

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Pseudomonas Isolation Agar (PIA) is a selective and differential culture medium used for the isolation and identification of Pseudomonas species. It contains ingredients that inhibit the growth of most other bacterial species, allowing Pseudomonas to grow selectively.

Vitek 2 by bioMérieux

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The Vitek 2 is a compact automated microbiology system designed for the identification and antimicrobial susceptibility testing of clinically significant bacteria and yeasts. The system utilizes advanced colorimetric technology to enable rapid and accurate results for clinical decision-making.

Pseudomonas aeruginosa by American Type Culture Collection

Sourced in United States, Brazil, China, Germany, Australia, United Kingdom, Italy, Malaysia

Pseudomonas aeruginosa is a bacterial strain available from the American Type Culture Collection (ATCC). It is a Gram-negative, aerobic bacterium commonly found in soil and water environments. This strain can be used for various research and testing purposes.

What are the different types or variations of Pseudomonas?

Pseudomonas is a diverse genus that includes several species, each with unique characteristics and applications. Some of the most well-known Pseudomonas species include P. aeruginosa, P. fluorescens, P. putida, and P. syringae. These species can be found in a variety of environments, from soil and water to clinical settings, and exhibit diverse metabolic capabilities, making them useful in various biotechnological and industrial processes.

What are the common usage challenges associated with Pseudomonas?

Pseudomonas can be a challenging microorganism to work with due to its adaptability and resistance to many antimicrobial agents. For example, P. aeruginosa is a common opportunistic pathogen that can cause serious infections, particularly in immunocompromised individuals. Researchers and clinicians must be mindful of Pseudomonas' ability to rapidly develop resistance to antibiotics, making treatment and management of Pseudomonas-related infections difficult. Additionally, the metabolic versatility of Pseudomonas can complicate its cultivation and control in various applications, requiring careful optimization of growth conditions and protocols.

How can PubCompare.ai assist in the optimal use and comparison of Pseudomonas protocols?

PubCompare.ai is a powerful tool that can help researchers working with Pseudomonas by streamlining the process of identifying the most effective protocols from the literature. The platform's AI-driven analysis allows you to quickly screen a large number of protocols, pinpointing the critical insights that can help you choose the best option for your specific research goals. For example, the platform's comparative analysis can highlight key differences in protocol effectiveness, enabling you to select the most reproducible and accurate approach for your Pseudomonas studies. This can be particularly useful when dealing with the adaptive nature and resistance challenges associated with this versatile genus of bacteria.

What are some of the specific applications of Pseudomonas?

Pseudomonas has a wide range of applications, ranging from medical and environmental to industrial and biotechnological. In the medical field, Pseudomonas species are important pathogens that can cause severe infections, but they also have potential use in phage therapy and the production of various enzymes and biopharmaceuticals. In the environmental sector, Pseudomonas is known for its ability to degrade a variety of pollutants, making it useful in bioremediation and wastewater treatment. Additionally, Pseudomonas has been explored for its potential in biofuel production and as a plant growth-promoting agent in agriculture.

More about "Pseudomonas"

Pseudomonas, a versatile genus of Gram-negative bacteria, has garnered significant attention in various fields, including medicine, biotechnology, and environmental sciences.
These resilient microorganisms are renowned for their metabolic diversity, adaptability to diverse environmental conditions, and potential applications in bioremediation and biofuel production.
Pseudomonas species are not only beneficial but also important pathogens, causing a range of infections in humans, animals, and plants, particularly in immunocompromised individuals.
Researchers utilize specialized media, such as Pseudomonas Agar Base and Pseudomonas cetrimide agar, to isolate and identify these bacteria.
The Wizard Genomic DNA Purification Kit is a valuable tool for extracting high-quality DNA from Pseudomonas samples.
Beyond diagnostics, Pseudomonas research also involves the use of MacConkey agar and Glycerol, which can provide insights into the growth and metabolism of these microbes.
Advances in automated identification systems, like Vitek 2, have further enhanced the ability to detect and characterize Pseudomonas aeruginosa, a clinically significant species within the genus.
Optimizing Pseudomonas research is crucial for expanding our understanding of these fascinating bacteria and developing effective strategies for their management and control.
PubCompare.ai, an AI-driven platform, empowers researchers to easily locate protocols from literature, pre-prints, and patents, while leveraging AI-driven comparisons to identify the best protocols and products.
This tool enhances reproducibility and accuracy in Pseudomonas studies, ensuring researchers can confidently explore the full potential of these versatile microorganisms.