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Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Reprints and Permissions. Kumar, H. Pseudomonas fluorescens : a potential food spoiler and challenges and advances in its detection. Ann Microbiol 69, — They also are used in certain food products, mainly, the production of yogurt. They cause the degradation of certain proteins leading to the appearance of the trademark sour taste.
All around these bacteria are considered a very mild hazard. They have only been known to infect immuno-compromised patients, such as cancer patients and those with immunodeficient diseases like lupus. There only danger is to the small percentage of humans in the categories above and in food spoilage.
The properties of P. Although they grow best in degree Celsius environments, they are known to be sustained at temperatures as low as 4 degrees Celsius such as those in a refrigerator. GM33, P. GM55, P. GM49, P. GM74, P. GM78 and P. GM48, and P. This marker is also present in all the strains from P. Primer set was designed to amplify a bp fragment from nucleotide 28 to nucleotide pb of this gene Table 2.
Finally, for the P. As expected, given the genetic heterogeneity of the P. However, the combination of two different markers allows their correct affiliation. On the other hand, P. Primer sequences were aligned against all the genomes from their group. When mismatches where detected, degenerated bases were introduced to ensure optimal primer hybridization.
Primer sequences and their marker target regions for PCR amplification are listed in Table 2. After in silico PCR see below , primer sequences were checked again and degenerated bases were introduced to maximize theoretical hybridization in the additional P.
Primer sets and annealing temperatures were empirically tested in gradient temperature PCRs in nine model P. The optimal annealing temperatures are specified in Table 2. Additionally, three other Pseudomonas model strains, outside the P.
All the PCRs for the P. Table 3. Seventeen putative P. PCR results unequivocally assigned each isolate to a single phylogroup. Six No isolate from P.
Additionally, whole-genome sequence of four of these isolates EMC3, 3. Table 4. Pseudomonas isolates and environmental samples affiliation to the different P. An environmental soil sample was also tested. These primer combination suggest the presence of DNA from P. On the other hand, the absence of certain markers in these samples strongly suggests lack of certain phylogroups.
However, in rhizosphere samples, where most of strains from the P. This finding makes the system not only suited for testing isolates, but also for testing environmental samples in order to assess the diversity of P. This dataset also included the 71 genomes used for generating the markers set. Thirty-two of these genomes These genomes were further analyzed by phylogenomics in order to corroborate their classification. Another genomes randomly sampled from the remaining 2, Pseudomonas genomes available at the NCBI ftp server ftp.
As shown in Figure 1 , from the genomes identified as belonging to the P. The remaining seven genomes 3. Two of these genomes P. ML96, and P. LFMO46, P. On the other hand, from the randomly sampled genomes, none of them were shown to be false negatives. In consequence, the is PCR has shown that the system has a Interestingly, the phylogenomic analysis has also shown the presence of two more phylogroups within the same branch that leads to the P.
The most distal one includes P. However, this phylogroup has only been identified based on MLSA, as no sequenced genome was available at the time of these analysis. For the same reason, this group was not included for the markers identification. The other group, identified as P. However, none of the previous studies of the Pseudomonas genus place it inside of the P.
These discrepancies with previous studies could be due to the larger number of genomes included here. The three species within the P. In any case, none of the genomes from these groups resulted in positive amplification for any of the markers. More worrying is the finding that several strains have been wrongly classified at the species level.
This is the case of P. All these strains clearly do not belong to the species they have been assigned to, highlighting that more efforts should be done to avoid inaccurate and misleading species naming and the need for databases curing.
The results presented here provide an accurate, easy to perform and cheap method for the initial profiling of strains belonging to the P. Considering the phylogenetic distribution of biotechnology relevant traits, the method could be included as one of the first steps in protocols that require the screening of a large number of pseudomonads isolates in the search for inoculants for agriculture or environmental technologies.
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