Article
Microbiology
Wanyu Meng, Shanyu Chen, Lin Huang, Jinpeng Yang, Wenqing Zhang, Zhijun Zhong, Ziyao Zhou, Haifeng Liu, Hualin Fu, Tingmei He, Guangneng Peng
Summary: This study isolated C. pseudotuberculosis biovar equi strains from three alpacas, conducted antibiotic susceptibility tests and pathogenicity tests, and sequenced one strain. The strains showed resistance to aztreonam, fosfomycin, and nitrofurantoin. Genome analysis revealed the presence of virulence genes and antibiotic resistance genes.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Roselane Goncalves dos Santos, Nubia Seyffert, Elaine M. S. Dorneles, Eric R. G. R. Aguiar, Carolina P. Ramos, Dionei J. Haas, Thiago L. P. . Castro, Gabriella B. N. Assis, Ricardo Dias Portela, Aristoteles Goes-Neto, Luis G. C. Pacheco, Henrique C. P. . Figueiredo, Thiago de Jesus Sousa, Sandeep Tiwari, Arun Kumar Jaiswal, Andrey L. P. Lage, Vasco Azevedo
Summary: This study evaluated the use of MALDI Biotyper and OGRI analysis for optimizing the identification and differentiation of biovars of C. pseudotuberculosis. The results showed that these two analysis techniques can accurately identify C. pseudotuberculosis at the species and biovar levels.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Genetics & Heredity
Hendor N. R. Jesus, Juliana N. N. Ramos, Danilo J. P. G. Rocha, Daniele A. A. Alves, Carolina S. S. Silva, Joao V. O. Cruz, Veronica V. Vieira, Cassius Souza, Louisy S. S. Santos, Jesus Navas, Rommel T. J. Ramos, Vasco Azevedo, Eric R. G. R. Aguiar, Ana L. L. Mattos-Guaraldi, Luis G. C. Pacheco
Summary: This study analyzed the genomes of C. striatum isolates and identified genomic characteristics that contribute to its pathogenicity and multidrug resistance. The research sheds light on the transition of C. striatum from a normal skin microbiome constituent to a multidrug-resistant and invasive pathogen.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Microbiology
Hendor N. R. Jesus, Danilo J. P. G. Rocha, Rommel T. J. Ramos, Artur Silva, Bertram Brenig, Aristoteles Goes-Neto, Mateus M. Costa, Siomar C. Soares, Vasco Azevedo, Eric R. G. R. Aguiar, Luiz Martinez-Martinez, Alain Ocampo, Sana Alibi, Alexis Dorta, Luis G. C. Pacheco, Jesus Navas
Summary: This study conducted a pan-genomic analysis of C. amycolatum, a nonlipophilic coryneform that is increasingly recognized as a relevant pathogen with multidrug resistance. The analysis revealed an open pan-genome and the acquisition of antimicrobial resistance genes through genomic islands. Despite the absence of classic corynebacterial virulence factors, genes associated with immune evasion, toxin, and antiphagocytosis were identified.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Juliana S. Bernardes, Raphael J. Eberle, Fabio R. J. Vieira, Monika A. Coronado
Summary: Analysis of the pan-genome of Corynebacterium pseudotuberculosis revealed that the equi biovar is more variable, with a higher number of biovar-specific domains associated with virulence mechanisms. Functional differences were identified between strains of the ovis and equi biovars, potentially related to niche-adaptation and virulence mechanisms. This may impact bacterial physiology and lifestyle, and could lead to the development of new diagnostics, vaccines, and treatments for C. pseudotuberculosis diseases.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Multidisciplinary Sciences
Wanderson Marques da Silva, Nubia Seyffert, Artur Silva, Vasco Azevedo
Summary: This article highlights the importance of using proteomics and bioinformatics tools in genomic functional studies of Corynebacterium pseudotuberculosis, revealing different patterns of protein modulation and identifying potential drug and vaccine targets. The combination of these studies expands our knowledge of the pathophysiology of this pathogen.
Article
Biochemical Research Methods
Hao Wu, Dan Wang, Feng Gao
Summary: Pan-genome analysis is widely used to study species evolution and genetic diversity, particularly in bacteria. However, the influence of strain selection on the accuracy and reliability of pan-genome results is not well understood. This study found that including confounding strains in pan-genome analyses of Bacillus subtilis can significantly affect the quality and accuracy of the results, emphasizing the importance of removing biases from such strains in the data processing stage to achieve a closer representation of the true pan-genome landscape.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Hyun-Hee Lee, Jungwook Park, Hyejung Jung, Young-Su Seo
Summary: Burkholderia gladioli demonstrates high adaptability and versatility in various ecological niches, with niche-associated genomes playing important roles in competition with hosts, degradation of compounds, and DNA repair. The conservation of rhizomide biosynthetic gene cluster is observed in all strains, with a higher concentration in human isolates. Additionally, absence of CRISPR/Cas system in plant and human pathogenic strains, but presence in those living in nature, suggests a potential inverse relationship with virulence.
Article
Microbiology
Ellen Ruth A. Morris, Jing Wu, Angela Bordin, Sara D. Lawhon, Noah D. Cohen
Summary: This study characterized the genomic and methylomic differences of multiple SEE and SEZ isolates from Texas. The results showed that genetic mobile elements in SEE and differential methylation of shared genes between SEE and SEZ might contribute to the host specificity of SEE.
MICROBIOLOGY SPECTRUM
(2022)
Article
Veterinary Sciences
Jessica Schlicher, Sarah Schmitt, Marc J. A. Stevens, Roger Stephan, Giovanni Ghielmetti
Summary: This study provides further insights into the genetic diversity of Corynebacterium pseudotuberculosis isolates in Switzerland and Liechtenstein, demonstrating the presence of multiple MLSA sequence types over a 15-year period. No specific MLSA sequence types unique to sheep and goats were found.
VETERINARY SCIENCES
(2021)
Article
Infectious Diseases
Fathiah Zakham, Tarja Sironen, Olli Vapalahti, Ravi Kant
Summary: This study aimed to conduct a comparative genome analysis of human adapted Mycobacterium tuberculosis complex species, including BCG vaccine strains, to identify and pinpoint conserved genes related to virulence across all species. The core genome consists of 1166 conserved genes among these species, representing a small portion of the 7036 genes in the pan-genome, suggesting potential for vaccine candidate development.
Article
Microbiology
Antoine Zboralski, Adrien Biessy, Marie Ciotola, Melanie Cadieux, Daphne Albert, Jochen Blom, Martin Filion
Summary: Lettuce, a major vegetable crop worldwide, is affected by various bacterial pathogens. In a study to develop new methods to control these pathogens, researchers screened over 1,200 plant-associated Pseudomonas strains and identified 35 strains that showed significant antagonistic capabilities against the three bacterial pathogens under study.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Infectious Diseases
Genglin Guo, Dechao Du, Yanfei Yu, Yuhang Zhang, Yunyun Qian, Wei Zhang
Summary: Streptococcus suis is an emerging zoonotic pathogen that causes severe infections in swine and humans, with serotype 2 being most frequently associated with infections. Understanding the genomic features of different virulent strains is important, with core genes involved in basic physiological functions and accessory genes related to evolution. Comparative analysis revealed significant differences in pilus clusters between virulent and avirulent strains, with avirulent strains having larger genomes and more prophage sequences.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Microbiology
Na Liu, Danping Liu, Kexin Li, Songnian Hu, Zilong He
Summary: This study utilized Staphylococcus aureus as a model organism to investigate the driving factors influencing bacterial pan-genome composition. The research found that the sequence type plays a significant role in the dynamic distribution of bacterial genes. A new classification method and marker gene combination were proposed, providing insights for the classification of Staphylococcus aureus.
MICROBIOLOGY SPECTRUM
(2022)
Article
Infectious Diseases
Willian Klassen Oliveira, Hugo Leonardo Avila, Michelle Zibeti Tadra, Rodrigo Luiz Cardoso, Cyntia Maria Teles Fadel-Pichet, Emanuel Maltempi de Souza, Fabio de Oliveira Pedrosa, Helisson Faoro
Summary: The genus Herbaspirillum is known for its ability to associate with grasses and participate in biological nitrogen fixation, but can also be isolated from clinical samples. The genome analysis of H. frisingense AU14559 revealed unique metabolic characteristics that allow it to infect and colonize human hosts, along with shared antibiotic resistance genes with other strains. These findings suggest potential for monitoring emerging pathogens and predicting outbreaks.
Article
Biochemistry & Molecular Biology
Daniel Ferreira de Lima Neto, Vagner Fonseca, Ronaldo Jesus, Leonardo Hermes Dutra, Layssa Miranda de Oliveria Portela, Carla Freitas, Eduardo Fillizola, Breno Soares, Andre Luiz de Abreu, Sandeep Twiari, Vasco Azevedo, Aristoteles Goes-Neto, Arnaldo Correia de Medeiros, Norberto Peporine Lopes, Paolo Marinho de Andrade Zanotto, Rodrigo Bentes Kato
Summary: This study used the structure of SARS-CoV-2 spike protein to examine the impact of mutations on the protein's stability and interaction with ACE-2 receptor. Molecular dynamics simulations and protein-protein docking experiments revealed that the mutations affected the stability of the protein and improved its interaction with ACE-2 receptor, particularly in the Gamma variant.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Immunology
Carine Rodrigues Pereira, Thiago de Jesus Sousa, Alessandra Lima da Silva, Roselane Goncalves dos Santos, Silvia Minharro, Dirceia Aparecida Costa Custodio, Derek J. Pickard, David O'Callaghan, Jeffrey T. Foster, Siomar de Castro Soares, Rommel Thiago Juca Ramos, Aristoteles Goes-Neto, Mateus Matiuzzi da Costa, Andrey Pereira Lage, Vasco Azevedo, Elaine Maria Seles Dorneles
Summary: This study reports the first isolation, identification, and characterization of Pseudochrobactrum saccharolyticum (strain 115) from Latin America. The strain was classified as P. saccharolyticum based on the analysis of its whole-genome sequence and 16S rRNA and recA gene sequences. This provides important insights into the diagnosis of bovine brucellosis and highlights the value of including the sequencing of these genes in routine diagnostics.
MICROBES AND INFECTION
(2023)
Article
Microbiology
Thais Almeida de Menezes, Flavia Figueira Aburjaile, Gabriel Quintanilha-Peixoto, Luiz Marcelo Ribeiro Tome, Paula Luize Camargos Fonseca, Thairine Mendes-Pereira, Daniel Silva Araujo, Tarcisio Silva Melo, Rodrigo Bentes Kato, Jacques Hubert Charles Delabie, Servio Pontes Ribeiro, Bertram Brenig, Vasco Azevedo, Elisandro Ricardo Drechsler-Santos, Bruno Silva Andrade, Aristoteles Goes-Neto
Summary: Ophiocordyceps australis is a fungal species that parasitizes ants and also has genes for degrading plant cell walls, allowing it to both parasitize insects and live inside plant tissue. The genome of O. australis strain CCMB661 was sequenced and characterized, revealing a total length of 30.31 Mb, 8,043 protein-coding genes, and 175 genes coding for plant cell wall degrading enzymes.
Article
Biology
Amanda de Oliveira Matos, Thais Cristina Vilela Rodrigues, Sandeep Tiwari, Pedro Henrique dos Santos Dantas, Geraldo Rodrigues Sartori, Vasco Ariston de Carvalho Azevedo, Joao Herminio Martins Da Silva, Siomar de Castro Soares, Marcelle Silva-Sales, Helioswilton Sales-Campos
Summary: Researchers developed a multi-epitope vaccine using immunoinformatics tools to prevent severe acute gastroenteritis caused by RV and NV. The vaccine contains multiple epitopes that are immunogenic and can induce a Th1 immune response, while being safe without allergenic or toxic regions.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemical Research Methods
Carine R. Pereira, Raquel C. Neia, Saulo B. Silva, Charles H. D. Williamson, John D. Gillece, David O'Callaghan, Jeffrey T. Foster, Izabela R. C. Oliveira, Julio S. S. Bueno Filho, Andrey P. Lage, Vasco A. C. Azevedo, Elaine M. S. Dorneles
Summary: Numerous genotyping techniques are available for understanding the transmission dynamics of brucellosis, with varying costs and resolution levels. In this study, the genotypes of 53 Brazilian B. abortus isolates were compared using different genotyping methods, with MLVA showing higher resolution and cost-effectiveness, and SNP techniques and cgMLST showing the highest resolution and being recommended for outbreak investigations.
JOURNAL OF MICROBIOLOGICAL METHODS
(2023)
Article
Ecology
Priscyla dos Santos Ribeiro, Natalia Barbosa Carvalho, Flavia Aburjaile, Thiago Sousa, Graciete Verissimo, Talita Gomes, Fabio Neves, Luiza Blanco, Joao Antonio Lima, Daiana de Oliveira, Arun Kumar Jaiswal, Bertram Brenig, Siomar Soares, Rommel Ramos, Mateus Matiuzzi, Aristoteles Goes-Neto, Claudio Pereira Figueira, Federico Costa, Paula Ristow, Vasco Azevedo
Summary: This study identified a new non-pathogenic species of spirochetes in biofilms in a polluted urban environment, suggesting that biofilms may serve as natural reservoirs for leptospires.
Article
Multidisciplinary Sciences
Marcus Vinicius Canario Viana, Jose Henrique Galdino, Rodrigo Profeta, Manuela Oliveira, Luis Tavares, Siomar de Castro Soares, Paulo Carneiro, Alice Rebecca Wattam, Vasco Azevedo
Summary: Several Corynebacterium silvaticum strains from Portugal show unique genetic diversity and may be able to produce diphtheria toxin, causing caseous lymphadenitis in wild boars, domestic pigs, and roe deer. These findings contribute to the identification and epidemiology of the species.
Article
Immunology
Muhammad Usman, Aaima Ayub, Sabahat Habib, Muhammad Suleman Rana, Zaira Rehman, Ali Zohaib, Syed Babar Jamal, Arun Kumar Jaiswal, Bruno Silva Andrade, Vasco de Carvalho Azevedo, Muhammad Faheem, Aneela Javed
Summary: In this study, a multivalent vaccine was designed using VP4 and VP7 proteins of Rotavirus A. Epitopes with antigenicity, non-allergenicity, homology with humans, and anti-inflammatory properties were screened to construct the vaccine. Immune simulation showed promising results in both Asia and worldwide. However, in-vitro/in-vivo screening is necessary for a definitive conclusion.
Article
Microbiology
Joyce Dutra, Glen Garcia, Rosimeire Gomes, Mariana Cardoso, Arley Cortes, Tales Silva, Luis de Jesus, Luciano Rodrigues, Andria Freitas, Vinicius Waldow, Juliana Laguna, Gabriela Campos, Monique Americo, Rubens Akamine, Maira de Sousa, Claudia Groposo, Henrique Figueiredo, Vasco Azevedo, Aristoteles Goes-Neto
Summary: The study aimed to analyze the physicochemical features of microbial communities occurring in produced water and enrichment cultures in oil pipelines. It was found that produced water samples have higher phylogenetic diversity of bacteria and archaea, while enrichment cultures have higher dominance of bacterial genera associated with microbial influenced corrosion (MIC). All samples had a core community composed of 19 distinct genera, with Desulfovibrio as the dominant genus. Metabarcoding of uncultured produced water samples, along with physicochemical characterization, was suggested as a more efficient method for monitoring MIC in oil industry facilities.
Article
Genetics & Heredity
Carine Rodrigues Pereira, Rodrigo Bentes Kato, Fabricio Almeida Araujo, Alessandra Lima da Silva, Roselane Goncalves dos Santos, Thiago de Jesus Sousa, Raquel Costa Neia, Saulo Britto da Silva, Charles H. D. Williamson, John Gillece, Andrey Pereira Lage, David O'Callaghan, Derek Pickard, Rommel Thiago Juca Ramos, Vasco Ariston de Carvalho Azevedo, Jeffrey T. Foster, Elaine Maria Seles Dorneles
Summary: This study investigated the genetic determinants responsible for antimicrobial resistance in 53 genomes of B. abortus strains isolated from cattle in Brazil. Eight genes associated with antimicrobial resistance were identified, but no association was found between the genetic polymorphisms in these genes and the observed resistance phenotypes in the Brazilian strains.
Article
Immunology
Maisa Santos Fonseca, Kathleen Ramos Deegan, Luiz Marcelo Tome, Marcos Antonio Mendonca, Ana Rita Sokolonski, Leane Queiroz Gondim, Vasco Azevedo, Roberto Meyer, Ljubica Tasic, Aristoteles Goes-Neto, Ricardo Wagner Portela
Summary: This study examines a novel pathogen, Candida haemulonii, causing cutaneous infection in a Boa constrictor snake. The fungus was identified and its drug sensitivity was tested, revealing strong inhibition for all drugs except fluconazole and itraconazole. A biogenic silver nanoparticle-based ointment successfully treated the clinical symptoms in the snake. The presence of these infections in snakes near human habitats highlights the importance of wildlife health monitoring for emerging and opportunistic diseases in peri-urban environments.
MICROBIAL PATHOGENESIS
(2023)
Review
Multidisciplinary Sciences
Lucas Gabriel R. Gomes, Joyce C. F. Dutra, Rodrigo Profeta, Mariana V. Dias, Glen J. Y. GarcIa, Diego Lucas N. Rodrigues, Aristoteles Goes Neto, Flavia F. Aburjaile, Sandeep Tiwari, Siomar C. Soares, Vasco Azevedo, Arun K. Jaiswal
Summary: Sexually Transmitted Infections (STIs) are a global public health burden, and the development of vaccines is crucial for controlling their spread. Immunoinformatics has emerged as a powerful tool for vaccine development, but there are gaps in its application in non-viral STI research.
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS
(2023)
Article
Infectious Diseases
Juliana Nunes Ramos, Max Roberto Batista Araujo, Lincoln Oliveira Sant'Anna, Sergio Bokermann, Carlos Henrique Camargo, Fernanda Diniz Prates, Claudio Tavares Sacchi, Veronica Viana Vieira, Karoline Rodrigues Campos, Marlon Benedito Nascimento Santos, Marcus Vinicius Canario Viana, Vasco Azevedo, Flavia Figueira Aburjaile, Ana Luiza de Mattos-Guaraldi, Louisy Sanches dos Santos
Summary: This study presents a case of skin lesion caused by nontoxigenic Corynebacterium diphtheriae and provides genomic taxonomy analysis and drug susceptibility testing. The research found that the strain carried a gene conferring resistance to sulfonamide antibiotics and predicted the presence of virulence factors and the CRISPR-Cas system. Additionally, MLST analysis identified a previously reported sequence type in French Guiana (a European territory).
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2023)
Article
Food Science & Technology
Rodrigo Dias de Oliveira Carvalho, Houem Rabah, Juan Carlos Ariute, Flavia Figueira Aburjaile, Bertram Brenig, Eric Guedon, Yves Le Loir, Gwenael Jan, Vasco Azevedo
Summary: This study investigated the effects of two types of cheese fermented by probiotic bacteria on gut microbiota and metabolic pathways. The results showed that these cheeses did not disturb the microbial community ecology, but Emmental cheese increased the abundance of some beneficial bacteria. Furthermore, Emmental cheese may produce bioactive metabolites and cooperate with other commensal species to produce beneficial substances. Mice with colitis showed restored metabolic functions of the impaired microbiome when treated with a specific cheese.