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Frontiers in Plant Science 2022
PubMed: 35317016
DOI: 10.3389/fpls.2022.855262 -
Microorganisms Aug 2021The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera and often involves bacterial viruses (bacteriophages).... (Review)
Review
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera and often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting and that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
PubMed: 34576713
DOI: 10.3390/microorganisms9091819 -
Microorganisms Jan 2021is a type of chemical communication by which bacterial populations control expression of their genes in a coordinated manner. This regulatory mechanism is commonly used... (Review)
Review
is a type of chemical communication by which bacterial populations control expression of their genes in a coordinated manner. This regulatory mechanism is commonly used by pathogens to control the expression of genes encoding virulence factors and that of genes involved in the bacterial adaptation to variations in environmental conditions. In phytopathogenic bacteria, several mechanisms of have been characterized. In this review, we describe the different systems present in phytopathogenic bacteria, such as those using the signal molecules named -acyl-homoserine lactone (AHL), diffusible signal factor (DSF), and the unknown signal molecule of the virulence factor modulating (VFM) system. We focus on studies performed on phytopathogenic bacteria of major importance, including , , , , and spp. For each system, we present the mechanism of regulation, the functions targeted by the system, and the mechanisms by which is regulated.
PubMed: 33498890
DOI: 10.3390/microorganisms9020239 -
Frontiers in Plant Science 2022Soft rot Pectobacteriaceae (SRP), typical of and , are a class of Gram-negative bacterial pathogens that cause devastating diseases on a wide range of crops and... (Review)
Review
Soft rot Pectobacteriaceae (SRP), typical of and , are a class of Gram-negative bacterial pathogens that cause devastating diseases on a wide range of crops and ornamental plants worldwide. Quorum sensing (QS) is a cell-cell communication mechanism regulating the expression of specific genes by releasing QS signal molecules associated with cell density, in most cases, involving in the vital process of virulence and infection. In recent years, several types of QS systems have been uncovered in pathogens to control diverse biological behaviors, especially bacterial pathogenicity and transkingdom interactions. This review depicts an integral QS regulation network of , elaborates in detail the regulation of specific QS system on different biological functions of the pathogens and hosts, aiming at providing a systematic overview of pathogenicity and interactions with hosts, and, finally, expects the future prospective of effectively controlling the bacterial soft rot disease caused by by quenching the key QS signal.
PubMed: 35211146
DOI: 10.3389/fpls.2022.838125 -
PloS One 2021The pectinolytic genus Dickeya (formerly Erwinia chrysanthemi) comprises numerous pathogenic species which cause diseases in various crops and ornamental plants across...
The pectinolytic genus Dickeya (formerly Erwinia chrysanthemi) comprises numerous pathogenic species which cause diseases in various crops and ornamental plants across the globe. Their pathogenicity is governed by complex multi-factorial processes of adaptive virulence gene regulation. Extracellular polysaccharides and lipopolysaccharides present on bacterial envelope surface play a significant role in the virulence of phytopathogenic bacteria. However, very little is known about the genomic location, diversity, and organization of the polysaccharide and lipopolysaccharide biosynthetic gene clusters in Dickeya. In the present study, we report the diversity and structural organization of the group 4 capsule (G4C)/O-antigen capsule, putative O-antigen lipopolysaccharide, enterobacterial common antigen, and core lipopolysaccharide biosynthesis clusters from 54 Dickeya strains. The presence of these clusters suggests that Dickeya has both capsule and lipopolysaccharide carrying O-antigen to their external surface. These gene clusters are key regulatory components in the composition and structure of the outer surface of Dickeya. The O-antigen capsule/group 4 capsule (G4C) coding region shows a variation in gene content and organization. Based on nucleotide sequence homology in these Dickeya strains, two distinct groups, G4C group I and G4C group II, exist. However, comparatively less variation is observed in the putative O-antigen lipopolysaccharide cluster in Dickeya spp. except for in Dickeya zeae. Also, enterobacterial common antigen and core lipopolysaccharide biosynthesis clusters are present mostly as conserved genomic regions. The variation in the O-antigen capsule and putative O-antigen lipopolysaccharide coding region in relation to their phylogeny suggests a role of multiple horizontal gene transfer (HGT) events. These multiple HGT processes might have been manifested into the current heterogeneity of O-antigen capsules and O-antigen lipopolysaccharides in Dickeya strains during its evolution.
Topics: Base Sequence; Dickeya; Gene Transfer, Horizontal; Genetic Variation; Genome, Bacterial; Multigene Family; O Antigens; Open Reading Frames; Phylogeny; Plant Diseases; Sequence Homology
PubMed: 33571209
DOI: 10.1371/journal.pone.0245727 -
Microorganisms Oct 2021and species are the causal agents of blackleg and soft rot diseases in potatoes. The main pathogenic species identified so far on potatoes are , , , , , and . Ten...
and species are the causal agents of blackleg and soft rot diseases in potatoes. The main pathogenic species identified so far on potatoes are , , , , , and . Ten years ago, the most prevalent Soft Rot Pectobacteriaceae in Europe were the species, and , with some variations among countries. Since then, a drastic increase in the abundance of has been observed in most European countries. This shift is difficult to explain without comparing the pathogenicity of all and species. The pathogenicity of all the above-mentioned bacterial species was assessed in field trials and in vitro tuber slice trials in Switzerland. Two isolates of each species were inoculated by soaking tubers of cv. Desiree in a suspension of 10 CFU/mL, before planting in the field. For all trials, the species were the most virulent ones, but long-term strain surveys performed in Switzerland indicate that is currently the most frequent species detected. Our results show that the pathogenicity of the species is not the main factor explaining the high prevalence of and in the Swiss potato fields.
PubMed: 34835395
DOI: 10.3390/microorganisms9112270 -
Microbiology Spectrum Aug 2023Genome evolution, and more specifically gene duplication, is a key process shaping host-microorganism interaction. The conserved paralogs usually provide an advantage to...
Genome evolution, and more specifically gene duplication, is a key process shaping host-microorganism interaction. The conserved paralogs usually provide an advantage to the bacterium to thrive. If not, these genes become pseudogenes and disappear. Here, we show that during the emergence of the genus , the gene encoding the porin OmpF was duplicated. Our results show that the expression is deleterious to the virulence of , the agent causing soft rot disease. Interestingly, 2 is regulated while is constitutive but activated by the EnvZ-OmpR two-component system. , acidic pH triggers the system. The pH measured in four eudicotyledons increased from an initial pH of 5.5 to 7 within 8 h post-infection. Then, the pH decreased to 5.5 at 10 h post-infection and until full maceration of the plant tissue. Yet, the production of phenolic acids by the plant's defenses prevents the activation of the EnvZ-OmpR system to avoid the expression even though environmental conditions should trigger this system. We highlight that gene duplication in a pathogen is not automatically an advantage for the infectious process and that, there was a need for our model organism to adapt its genetic regulatory networks to conserve these duplicated genes. IMPORTANCE species cause various diseases in a wide range of crops and ornamental plants. Understanding the molecular program that allows the bacterium to colonize the plant is key to developing new pest control methods. Unlike other enterobacterial pathogens, , the causal agent of soft rot disease, does not require the EnvZ-OmpR system for virulence. Here, we showed that during the emergence of the genus , the gene encoding the porin OmpF was duplicated and that the expression of was deleterious for virulence. We revealed that while the EnvZ-OmpR system was activated by acidic pH and even though the pH was acidic when the plant is colonized, this system was repressed by phenolic acid (generated by the plant's defenses). These results provide a unique- biologically relevant-perspective on the consequence of gene duplication and the adaptive nature of regulatory networks to retain the duplicated gene.
PubMed: 37642428
DOI: 10.1128/spectrum.00833-23 -
Microorganisms Feb 2021Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they... (Review)
Review
Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot biosensors, often inoculated in potato , are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, and -tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence , in the near future.
PubMed: 33535657
DOI: 10.3390/microorganisms9020295 -
PloS One 2023The prognostic and pathophysiologic significance of the biliary microbiota in pancreaticobiliary malignancies is little understood. Our goal was to find...
BACKGROUND
The prognostic and pathophysiologic significance of the biliary microbiota in pancreaticobiliary malignancies is little understood. Our goal was to find malignancy-related microbiomic fingerprints in bile samples taken from patients with benign and malignant pancreaticobiliary diseases.
METHODS
Bile specimens were collected from consenting patients during routine endoscopic retrograde cholangiopancreatography. We used PowerViral RNA/DNA Isolation kit to extract DNA from bile specimens. The Illumina 16S Metagenomic Sequencing Library Preparation guide was used to amplify the bacterial 16S rRNA gene and create libraries. QIIME (Quantitative Insights Into Microbial Ecology), Bioconductor phyloseq, microbiomeSeq, and mixMC packages were used for post-sequencing analysis.
RESULTS
Of 46 enrolled patients, 32 patients had pancreatic cancers, 6 had cholangiocarcinoma and 1 had gallbladder cancer. Rest of the patients had benign diseases including gallstones, and acute and chronic pancreatitis. We used multivariate approach in mixMC to classify Operational Taxonomic Units (OTUs). Doing this, we found a predominance of genera Dickeya (p = 0.00008), [Eubacterium] hallii group (p = 0.0004), Bacteroides (p = 0.0006), Faecalibacterium (p = 0.006), Escherichia-Shigella (p = 0.008), and Ruminococcus 1 (p = 0.008) in bile samples from pancreaticobiliary cancers as compared to benign diseases. Additionally, bile samples from patients with pancreatic cancer exhibited a predominance of genus Rothia (p = 0.008) as compared to those with cholangiocarcinoma, whereas bile samples from patients with cholangiocarcinoma exhibited a predominance of genera Akkermansia (p = 0.031) and Achromobacter (p = 0.031) as compared to those with pancreatic cancers.
CONCLUSIONS
Both benign and malignant pancreaticobiliary diseases have distinct microbiomic fingerprints. The relative abundance of OTUs in bile samples varies between patients with benign and malignant pancreaticobiliary diseases, as well as between cholangiocarcinoma and pancreatic cancer. Our data suggest that either these OTUs play a role in carcinogenesis or that benign disease-specific microenvironmental changes differ from cancer-specific microenvironmental changes, resulting to a clear separation of OTU clusters. We need more research to confirm and expand on our findings.
Topics: Humans; Bile; RNA, Ribosomal, 16S; Cholangiopancreatography, Endoscopic Retrograde; Pancreatic Neoplasms; Cholangiocarcinoma; Bile Duct Neoplasms; Bile Ducts, Intrahepatic; Pancreatic Ducts
PubMed: 37071646
DOI: 10.1371/journal.pone.0283021 -
Frontiers in Plant Science 2023The genus includes plant pathogenic bacteria attacking a wide range of crops and ornamentals as well as a few environmental isolates from water. Defined on the basis of...
The genus includes plant pathogenic bacteria attacking a wide range of crops and ornamentals as well as a few environmental isolates from water. Defined on the basis of six species in 2005, this genus now includes 12 recognized species. Despite the description of several new species in recent years, the diversity of the genus is not yet fully explored. Many strains have been analyzed for species causing diseases on economically important crops, such as for the potato pathogens and . In contrast, only a few strains have been characterized for species of environmental origin or isolated from plants in understudied countries. To gain insights in the diversity, recent extensive analyzes were performed on environmental isolates and poorly characterized strains from old collections. Phylogenetic and phenotypic analyzes led to the reclassification of (containing strains from tropical or subtropical regions) in the new genus, , the identification of three water species , and , the description of a new species including Australian strains isolated from grasses, and the characterization of the new species and , resulting from the subdivision of the species . Traits distinguishing each new species were identified from genomic and phenotypic comparisons. The high heterogeneity observed in some species, notably for , indicates that additional species still need to be defined. The objective of this study was to clarify the present taxonomy of the genus and to reassign the correct species to several strains isolated before the current classification.
PubMed: 37409305
DOI: 10.3389/fpls.2023.1168480