• CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species 

      Hongo, Jorge Augusto; de Castro, Giovanni Marques; Albuquerque Menezes, Alison Pelri; Rios Picorelli, Agnello César; Martins da Silva, Thieres Tayroni; Imada, Eddie Luidy; Marchionni, Luigi; Del-Bem, Luiz-Eduardo; Vieira Chaves, Anderson; de Freitas Almeida, Gabriel Magno; Campelo, Felipe; Lobo, Francisco Pereira (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-06-09)
      Living species vary significantly in phenotype and genomic content. Sophisticated statistical methods linking genes with phenotypes within a species have led to breakthroughs in complex genetic diseases and genetic breeding. Despite the abundance of genomic and phenotypic data available for thousands of species, finding genotype-phenotype associations across species is challenging due to the ...
    • Mucin induces CRISPR-Cas defense in an opportunistic pathogen 

      de Freitas Almeida, Gabriel Magno; Hoikkala, Ville; Ravantti, Janne; Rantanen, Noora; Sundberg, Lotta-Riina (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-06-25)
      Mucin induces CRISPR-Cas defense in an opportunistic pathogen
    • Mucosal Environment Induces Phage Susceptibility in Streptococcus mutans 

      Sundberg, Lotta-Riina; Rantanen, Noora; de Freitas Almeida, Gabriel Magno (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-09-19)
      Pathogenic bacteria are attracted toward mucosa, as it is their way of entry into the body. However, we know surprisingly little about the phage-bacterium interactions in the mucosal environment. Here, we explored the effect of the mucosal environment on growth characteristics and phage-bacterium interactions in Streptococcus mutans, a causative agent of dental caries. We found that although mucin ...
    • Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control 

      Runtuvuori-Salmela, Anniina; Kunttu, Heidi M. T.; Laanto, Elina; de Freitas Almeida, Gabriel Magno; Mäkelä, Kati; Middelboe, Mathias; Sundberg, Lotta-Riina (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-01-20)
      Intensive aquaculture conditions expose fish to bacterial infections, leading to significant financial losses, extensive antibiotic use and risk of antibiotic resistance in target bacteria. Flavobacterium columnare causes columnaris disease in aquaculture worldwide. To develop a bacteriophage-based control of columnaris disease, we isolated and characterized 126 F. columnare strains and 63 ...