Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism

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

Composição microbiana de inóculo e do composto maduro no processo de compostagem do Zoológico de São Paulo avaliada por meio de metagenômica

Composting piles consist in a thermophilic environment that can contain bacteria and enzymes potentially related to lignocellulosic deconstruction. Inoculum is the composting material in advanced stage added to the organic matter to be decomposed, while mature compost is the final product of composting product ready to be used as fertilizer. Here, we present results of 16S rRNA profile and metagenome-assembled genomes (MAGs) analysis from inoculum and mature compost samples collected from a composting facility at the São Paulo Zoo Park. We were able to recover 17 MAGs from inoculum samples and 16 MAGs from mature compost samples. Variation in abundance over time shows that these MAGs are likely present during the whole composting process, even if they are present in low abundance. Groups of MAGs can contribute to the lignocellulosic deconstruction in different stages of composting. Genes encoding cellulases, endohemicellulases, and oligosaccharide-degrading enzymes were distributed in MAGs from both inoculum and mature compost samples. Auxiliary activity enzymes were found especially in MAGs recovered from mature compost samples. Mature compost material can contain bacteria that play an important role to the lignin degradation, and as such they can be potential candidates for lignocellulose degradation biotechnological processes.As pilhas de compostagem consistem em um ambiente termofílico que pode conter bactérias e enzimas potencialmente relacionadas à desconstrução lignocelulósica. O inóculo é o material de compostagem em estágio avançado adicionado à matéria orgânica a ser decomposta, enquanto o composto maduro é o produto final da compostagem pronto para ser utilizado como fertilizante. Aqui, apresentamos os resultados da análise do perfil de rRNA 16S e dos genomas montados a partir do metagenoma (MAGs) de amostras de inóculo e composto maduro coletadas de uma instalação de compostagem no Parque Zoológico de São Paulo. Recuperamos 17 MAGs das amostras de inóculo e 16 MAGs das amostras de composto maduro. A variação na abundância ao longo do tempo mostra que esses MAGs provavelmente estão presentes durante todo o processo de compostagem, mesmo que estejam presentes em baixa abundância. Grupos de MAGs podem contribuir para a desconstrução lignocelulósica em diferentes estágios da compostagem. Os genes que codificam celuloses, endohemicelulases e enzimas de degradação de oligossacarídeos estavam distribuídos nos MAGs das amostras de inóculo e de composto maduro. Enzimas da classe de atividades auxiliares foram encontradas especialmente em MAGs recuperados de amostras de composto maduro. O composto maduro pode conter bactérias que desempenham um papel importante na degradação da lignina e, assim, podem ser candidatos potenciais para processos biotecnológicos de degradação da lignocelulose

New Insights into the Effect of Fipronil on the Soil Bacterial Community

Fipronil is a broad-spectrum insecticide with remarkable efficacy that is widely used to control insect pests around the world. However, its extensive use has led to increasing soil and water contamination. This fact is of concern and makes it necessary to evaluate the risk of undesirable effects on non-target microorganisms, such as the microbial community in water and/or soil. Studies using the metagenomic approach to assess the effects of fipronil on soil microbial communities are scarce. In this context, the present study was conducted to identify microorganisms that can biodegrade fipronil and that could be of great environmental interest. For this purpose, the targeted metabarcoding approach was performed in soil microcosms under two environmental conditions: fipronil exposure and control (without fipronil). After a 35-day soil microcosm period, the 16S ribosomal RNA (rRNA) gene of all samples was sequenced using the ion torrent personal genome machine (PGM) platform. Our study showed the presence of Proteobacteria, Actinobacteria, and Firmicutes in all of the samples; however, the presence of fipronil in the soil samples resulted in a significant increase in the concentration of bacteria from these phyla. The statistical results indicate that some bacterial genera benefited from soil exposure to fipronil, as in the case of bacteria from the genus Thalassobacillus, while others were affected, as in the case of bacteria from the genus Streptomyces. Overall, the results of this study provide a potential contribution of fipronil-degrading bacteria

The beginning and the end of a microbial community and their carbohydrate-active enzymes at a thermophilic composting

<p>Composting harbors a rich microbial diversity and is a source of potential microbial candidates and enzymes for lignocellulosic degradation that can be of interest for industrial, clinical, environmental, and biotechnological applications. Our goal is to analyze this microbial diversity focusing on metagenome-assembled genomes (MAGs) recovered from the beginning (inoculum) and the end (mature compost) of the composting process and genes annotated for carbohydrate-active enzymes (CAZymes). We collected five samples from inoculum (ZCI) and two from mature compost (ZMC) in the composting facility at the São Paulo Zoo Park. Inoculum consists of a compost pile in a later phase of the composting process that is extracted and added to alternate layers of plant and animal waste to start a new composting pile. Mature compost is the product of the composting process ready to be used as fertilizer. Total DNA was sequenced with Illumina technology. ZCI reads were co-assembled using metaSPAdes. We used the metaWRAP pipeline for MAG recovery with three binners: MetaBAT2, MaxBin2, and Concoct. All the bins were consolidated using the bin_refinement module from the metaWRAP pipeline with minimum completeness of 50% and maximum contamination of 10%. We used the same method to recover MAGs from ZMC. MAGs were taxonomically classified using GTDB-tk and annotated for CAZymes using dbcan2. We also used dbcan2 for contigs not included in MAGs. From the total of ~7,4 million reads for ZCI and ~6,8 million reads for ZMC, we obtained respectively 500,267 (N50=1349) and 399,726 (N50=1584) contigs for ZCI and ZMC. We retrieved 22 and 20 MAGs respectively for ZCI and ZMC. For ZCI MAGs, we found 891 hits for CAZymes distributed in 138 CAZy families, while for ZMC MAGs, 1141 hits were distributed in 176 families. For ZCI contigs not included in MAGs, 2437 hits for CAZymes were distributed in 218 CAZy families while for ZMC, 2206 hits were distributed in 220 families. Therefore, we were able to obtain a catalog of CAZymes for MAGs and contigs not included in MAGs from the inoculum and the mature compost of the Sao Paulo Zoo composting, comprising cellulases, hemicellulases, xilanases, and manases. These results reinfor ce the composting as a source of potential microbial candidates for lignocellulose degradation and other analysis is ongoing for further understanding of the composting microbiology.</p&gt

Tributyrin Attenuates Metabolic and Inflammatory Changes Associated with Obesity through a GPR109A-Dependent Mechanism

Obesity is linked with altered microbial short-chain fatty acids (SCFAs), which are a signature of gut dysbiosis and inflammation. In the present study, we investigated whether tributyrin, a prodrug of the SCFA butyrate, could improve metabolic and inflammatory profiles in diet-induced obese mice. Mice fed a high-fat diet for eight weeks were treated with tributyrin or placebo for another six weeks. We show that obese mice treated with tributyrin had lower body weight gain and an improved insulin responsiveness and glucose metabolism, partly via reduced hepatic triglycerides content. Additionally, tributyrin induced an anti-inflammatory state in the adipose tissue by reduction of Il-1β and Tnf-a and increased Il-10, Tregs cells and M2-macrophages. Moreover, improvement in glucose metabolism and reduction of fat inflammatory states associated with tributyrin treatment were dependent on GPR109A activation. Our results indicate that exogenous targeting of SCFA butyrate attenuates metabolic and inflammatory dysfunction, highlighting a potentially novel approach to tackle obesity