Browsing by Author "Setubal, Joao Carlos"
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- Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent MechanismFachi, Jose Luis; Felipe, Jaqueline de Souza; Pral, Lais Passariello; da Silva, Bruna Karadi; Correa, Renan Oliveira; Pereira de Andrade, Mirella Cristiny; da Fonseca, Denise Morais; Basso, Paulo Jose; Saraiva Camara, Niels Olsen; de Sales e Souza, Ericka Lorenna; Martins, Flaviano dos Santos; Sato Guima, Suzana Eiko; Thomas, Andrew M.; Setubal, Joao Carlos; Magalhaes, Yuli Thamires; Forti, Fabio Luis; Candreva, Thamiris; Rodrigues, Hosana Gomes; de Jesus, Marcelo Bispo; Consonni, Silvio Roberto; Farias, Alessandro dos Santos; Varga-Weisz, Patrick; Ramirez Vinolo, Marco Aurelio (Cell Press, 2019-04-16)Antibiotic-induced dysbiosis is a key factor predisposing intestinal infection by Clostridium difficile. Here, we show that interventions that restore butyrate intestinal levels mitigate clinical and pathological features of C. difficile-induced colitis. Butyrate has no effect on C. difficile colonization or toxin production. However, it attenuates intestinal inflammation and improves intestinal barrier function in infected mice, as shown by reduced intestinal epithelial permeability and bacterial translocation, effects associated with the increased expression of components of intestinal epithelial cell tight junctions. Activation of the transcription factor HIF-1 in intestinal epithelial cells exerts a protective effect in C. difficile-induced colitis, and it is required for butyrate effects. We conclude that butyrate protects intestinal epithelial cells from damage caused by C. difficile toxins via the stabilization of HIF-1, mitigating local inflammatory response and systemic consequences of the infection.
- Global Distribution and Evolution of Mycobacterium bovis LineagesZimpel, Cristina Kraemer; Patane, Jose Salvatore L.; Proenga Guedes, Aureliano Coelho; de Souza, Robson F.; Silva-Pereira, Taiana T.; Soler Camargo, Naila C.; de Souza Filho, Antonio F.; Ikuta, Cassia Y.; Ferreira Neto, Jose Soares; Setubal, Joao Carlos; Heinemann, Marcos Bryan; Sa Guimaraes, Ana Marcia (2020-05-07)Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. Previous studies suggested the existence of genetic groups of M. bovis strains based on limited DNA markers (a.k.a. clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains, gathering 1,969 genomes from 23 countries and at least 24 host species, including humans, to complete a phylogenomic analyses. We propose the existence of four distinct global lineages of M. bovis (Lb1, Lb2, Lb3, and Lb4) underlying the current disease distribution. These lineages are not fully represented by clonal complexes and are dispersed based on geographic location rather than host species. Our data divergence analysis agreed with previous studies reporting independent archeological data of ancient M. bovis (South Siberian infected skeletons at similar to 2,000 years before present) and indicates that extant M. bovis originated between 715 and 3,556 years BP, with later emergence in the New World and Oceania, likely influenced by trades among countries.
- Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes RemissionAl Assal, Karina; Prifti, Edi; Belda, Eugeni; Sala, Priscila; Clement, Karine; Dao, Maria-Carlota; Dore, Joel; Levenez, Florence; Taddei, Carla R.; Fonseca, Danielle Cristina; Rocha, Ilanna Marques; Balmant, Bianca Depieri; Thomas, Andrew M.; Santo, Marco A.; Dias-Neto, Emmanuel; Setubal, Joao Carlos; Zucker, Jean-Daniel; Belarmino, Giliane; Torrinhas, Raquel Susana; Waitzberg, Dan L. (2020-02)Gut microbiota composition is influenced by environmental factors and has been shown to impact body metabolism. Objective: To assess the gut microbiota profile before and after Roux-en-Y gastric bypass (RYGB) and the correlation with food intake and postoperative type 2 diabetes remission (T2Dr). Design: Gut microbiota profile from obese diabetic women was evaluated before (n = 25) and 3 (n = 20) and 12 months (n = 14) after RYGB, using MiSeq Illumina-based V4 bacterial 16S rRNA gene profiling. Data on food intake (7-day record) and T2Dr (American Diabetes Association (ADA) criteria) were recorded. Results: Preoperatively, the abundance of five bacteria genera differed between patients with (57%) and without T2Dr (p < 0.050). Preoperative gut bacteria genus signature was able to predict the T2Dr status with 0.94 accuracy ROC curve (receiver operating characteristic curve). Postoperatively (vs. preoperative), the relative abundance of some gut bacteria genera changed, the gut microbial richness increased, and the Firmicutes to Bacteroidetes ratio (rFB) decreased (p < 0.05) regardless of T2Dr. Richness levels was correlated with dietary profile pre and postoperatively, mainly displaying positive and inverse correlations with fiber and lipid intakes, respectively (p < 0.05). Conclusions: Gut microbiota profile was influenced by RYGB and correlated with diet and T2Dr preoperatively, suggesting the possibility to assess its composition to predict postoperative T2Dr.
- Metagenomic Analysis of a Tropical Composting Operation at the Sao Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and OrganismsMartins, Layla Farage; Antunes, Luciana Principal; Pascon, Renata C.; Franco de Oliveira, Julio Cezar; Digiampietri, Luciano A.; Barbosa, Deibs; Peixoto, Bruno Malveira; Vallim, Marcelo A.; Viana-Niero, Cristina; Ostroski, Eric H.; Telles, Guilherme P.; Dias, Zanoni; da Cruz, Joao Batista; Juliano, Luiz; Verjovski-Almeida, Sergio; da Silva, Aline M.; Setubal, Joao Carlos (PLOS, 2013-04-24)Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.
- Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environmentsCaneschi, Washington Luiz; Sanchez, Angelica Bianchini; Felestrino, Erica Barbosa; de Carvalho Lemes, Camila Gracyelle; Cordeiro, Isabella Ferreira; Fonseca, Natasha Peixoto; Villa, Morghana Marina; Vieira, Izadora Tabuso; Goncalves Moraes, Lauro Angelo; Barbosa Assis, Renata de Almeida; do Carmo, Flavio Fonseca; Yoshino Kamino, Luciana Hiromi; Silva, Robson Soares; Ferro, Jesus Aparecido; Tiraboschi Ferro, Maria Ines; Ferreira, Rafael Marini; Santos, Vera Lucia; Mourao Silva, Ubiana de Cassia; Almeida, Nalvo F.; Varani, Alessandro de Mello; Machado Garcia, Camila Carriao; Setubal, Joao Carlos; Moreira, Leandro Marcio (2019-11-29)Serratia liquefaciens strain FG3 (SlFG3), isolated from the flower of Stachytarpheta glabra in the Brazilian ferruginous fields, has distinctive genomic, adaptive, and biotechnological potential. Herein, using a combination of genomics and molecular approaches, we unlocked the evolution of the adaptive traits acquired by S1FG3, which exhibits the second largest chromosome containing the largest conjugative plasmids described for Serratia. Comparative analysis revealed the presence of 18 genomic islands and 311 unique protein families involved in distinct adaptive features. S1FG3 has a diversified repertoire of genes associated with Nonribosomal peptides (NRPs/PKS), a complete and functional cluster related to cellulose synthesis, and an extensive and functional repertoire of oxidative metabolism genes. In addition, S1FG3 possesses a complete pathway related to protocatecuate and chloroaromatic degradation, and a complete repertoire of genes related to DNA repair and protection that includes mechanisms related to UV light tolerance, redox process resistance, and a laterally acquired capacity to protect DNA using phosphorothioation. These findings summarize that SlFG3 is well-adapted to different biotic and abiotic stress situations imposed by extreme conditions associated with ferruginous fields, unlocking the impact of the lateral gene transfer to adjust the genome for extreme environments, and providing insight into the evolution of prokaryotes.