2024

The genus Dickeya consists of Gram-negative bacteria capable of causing soft rot symptoms in plants, which involves tissue breakdown, particularly in storage organs such as tubers, rhizomes, and bulbs. These bacteria are ranked among the top ten most relevant phytopathogens and seriously threaten economically valuable crops and ornamental plants. This study employs a genomic analysis approach to taxonomically classify and characterize the resistome and virulome of two new strains, CCRMP144 and CCRMP250, identified as Dickeya dadantii. These strains were found to be the causative agents of soft rot symptoms in chili pepper (Capsicum spp.) and lettuce (Lactuca sativa), respectively, in the northeastern region of Brazil. The methodology employed in silico techniques, including tetra correlation search (TCS) and Average Nucleotide Identity (ANI) analysis, in association with a phylogenomic tree inference. TCS and ANI analysis showed that the studied strains belong to the Dickeya dadantii species. The phylogenomic analysis grouped the studied strains in the D. dadantii clade. The genomic characterization demonstrates 68 virulence genes, 54 resistances of biocide and heavy metal genes, and 23 antibiotic resistance genes. As far as we know, this is the first genomic study with Brazilian D. dadantii strains. This study demonstrates the efficacy to taxonomic classification and provides insights into the pathogenesis, host range, and adaptability of these strains which are crucial for the development of more effective management and control strategies for soft rot diseases.

Gizzard erosion and ulceration (GEU) is characterized by defects and necrosis in the koilin layer, particularly in broilers. This condition has been associated with growth retardation, runting, and economic implications for poultry producers; nevertheless, its influence on gut microbiota remains unknown. This study investigated the compositional changes in the bacterial community of the ileum of seven-day-old broiler chicks with GEU using next-generation sequencing (NGS) technology. Twenty-two samples were obtained from the ileal mucosa and contents of sixteen chicks with GEU and six without GEU raised in a conventional system located on a farm in southeast Brazil. The results revealed that bacterial phyla in both groups exhibited a similar composition, with Firmicutes representing the most abundant. Porphyromonas, Candidatus Arthromitus, and Limosilactobacillus were statistically more abundant in the group without GEU. The most prevalent genera in the group with GEU were Lactobacillus and Enterococcus, and the relative abundance of Enterococcus in the ilea of some chicks with GEU was considerable. Based on the results of the current study, necrosis in the koilin layer can change the composition of ileal microbiota. Therefore, further studies should be carried out to clarify whether GEU and consequently poor digestibility of the feed cause significant changes in the intestinal microbiota.

Proliferative enteropathy is an enteric disease caused by the bacterium Lawsonia intracellularis, which affects several species of domestic and wild animals. The mechanisms underlying the mechanisms employed by L. intracellularis to cause host cell proliferation are poorly understood, mostly because this bacterium is extremely difficult to isolate and propagate in vitro. Comparative genomics methods for searching for genes orthologous to genes known to be associated with pathogenesis allow identification of genes potentially involved in pathogenesis by the pathogen of interest. The goal of this study was to carry out in silico research on L. intracellularis genes orthologous to genes required for intracellular invasion and survival present in other pathogenic bacteria, particularly Brucella abortus, B. melitensis, B. suis, Listeria monocytogenes, Mycobacterium tuberculosis, Mycobacterium avium subspecies paratuberculosis, Salmonella enterica, Yersinia pestis, Y. enterocolitica, and Y. pseudotuberculosis. A total of 127 genes associated with invasion and intracellular survival from five known intracellular bacteria were mapped against the predicted proteomes of all L. intracellularis strains publicly available on GenBank, using the OrthoFinder program. A total of 45 L. intracellularis genes were orthologous to genes associated with pathogenesis of other intracellular bacteria. Genes putatively associated with signal the transduction of chemotaxis and cell motility were identified. Genes related to DNA binding and repair were also identified, with some of them supporting a possible association of bacteria with macrophages or inducing pro-inflammatory responses. The homology-based identification of these genes suggests their potential involvement in the virulence and pathogenicity of L. intracellularis, opening avenues for future research and insights into the molecular mechanisms of Lawsonia-elicited proliferative enteropathy.

Lactobacillus delbrueckii is a bacterium used in the dairy industry, improving dairy products' organoleptic characteristics and nutritional value. Preclinical studies have demonstrated the probiotic effects of these microorganisms. However, unlike other lactic acid bacteria species, few studies have explored L. delbrueckii strains, using a probiogenomics approach, about their benefits and safety for host health. This comprehensive review describes the main health effects and safety features of L. delbrueckii strains. Furthermore, it also identifies potential genetic factors and molecular mechanisms obtained through the probiogenomics approach, which can offer insights into this species' effects on host health and its safety level for biotechnological and therapeutic applications. L. delbrueckii can tolerate industrial and gastrointestinal stressors, and this property could be enhanced by incorporating these microorganisms into dairy matrices. The biotherapeutic activity of L. delbrueckii has been extensively demonstrated in intestinal inflammation, enteric infections, and metabolic and psychological disorders. Many beneficial effects are elicited by components of the bacteria cell membrane or secreted molecules, such as cell surface proteins, exopolysaccharides, bioactive metabolites, and peptides. Furthermore, few plasmids were identified in L. delbrueckii, reducing the spread of antibiotic-resistance genes. Additionally, this species has a lower capacity to act as a pathogen. However, studies show a discrepancy between the phenotype and genotype data, which may be related to the gene expression level or regulation in specific environmental conditions. Therefore, further studies should be conducted to characterize the possible biological role of this species and identify the genetic markers linked to these processes.

Histoplasmosis is a widespread systemic disease caused by Histoplasma capsulatum, prevalent in the Americas. Despite its significant morbidity and mortality rates, no vaccines are currently available. Previously, five vaccine targets and specific epitopes for H. capsulatum were identified. Immunoinformatics has emerged as a novel approach for determining the main immunogenic components of antigens through in silico methods. Therefore, we predicted the main helper and cytotoxic T lymphocytes and B-cell epitopes for these targets to create a potential multi-epitope vaccine known as HistoVAC-TSFM. A total of 38 epitopes were found: 23 common to CTL and B-cell responses, 11 linked to HTL and B cells, and 4 previously validated epitopes associated with the B subunit of cholera toxin, a potent adjuvant. In silico evaluations confirmed the stability, non-toxicity, non-allergenicity, and non-homology of these vaccines with the host. Notably, the vaccine exhibited the potential to trigger both innate and adaptive immune responses, likely involving the TLR4 pathway, as supported by 3D modeling and molecular docking. The designed HistoVAC-TSFM appears promising against Histoplasma, with the ability to induce important cytokines, such as IFN-γ, TNF-α, IL17, and IL6. Future studies could be carried out to test the vaccine’s efficacy in in vivo models.

Currently, reports of the presence of emerging pathogens in cheeses are low and new outbreaks have occurred at an alarming rate, with the Vibrio and Aeromonas genera being the main causes of gastroenteritis in the world. Therefore, Multi-Omics integration has been a strategy to identify and develop detection methods for these pathogens in food. We investigated the presence of emerging pathogens in artisanal cheeses and predicted proteins with immunogenic potential, in silico, for food diagnostics. For this, multiomics integration was used: (a) metagenomics; (b) subtractive genomics; and (c) pan-genomics. Eight species of the genera Vibrio and Aeromonas were identified, the latter being the most abundant (89.7%) and identified in eight regions, with emphasis on the species A. caviae and A. veronii. Pan-genomic analyses revealed intra- and inter-species differences in both genera. Essential, non-cytoplasmic proteins were identified, without homology and with immunological potential for the species researched. Functional annotation of genes present in pan-genomic subsets reveals functionality between the core genome (transcription; amino acid transport and metabolism; and inorganic ion transport and metabolism) and the shared genome (signal transduction and carbohydrate transport and metabolism). A reinterpretation of the genomic plasticity of V. furnissii reveals the presence of mobile genetic elements critical for virulence in human isolates and the RTX toxin, also identified in this species, is present in the pathogenicity islands of V. alginolyticus and V. fluvialis. Collectively, the results provide important information for the development of a diagnostic strategy for emerging pathogens in food using immunoassays.