Project description:This study evaluated the ammonium oxidizing communities (COA) associated with a potato crop (Solanum phureja) rhizosphere soil in the savannah of Bogotá (Colombia) by examining the presence and abundance of amoA enzyme genes and transcripts by qPCR and next-generation sequence analysis. amoA gene abundance could not be quantified by qPCR due to problems inherent in the primers; however, the melting curve analysis detected increased fluorescence for Bacterial communities but not for Archaeal communities. Transcriptome analysis by next-generation sequencing revealed that the majority of reads mapped to ammonium-oxidizing Archaea, suggesting that this activity is primarily governed by the microbial group of the Crenarchaeota phylum. In contrast,a lower number of reads mapped to ammonia-oxidizing bacteria.
Project description:Effects of Enterococcus faecalis administration on the community structure of airborne bacteria in weanling piglet and layer hen houses
Project description:Human breast milk contains a diverse community of bacteria but factors that produce variation in the breast milk microbiome are largely unknown. We evaluated if 1) maternal factors including breastfeeding practices modified the diversity and abundance of bacterial communities in breast milk and 2) if subclinical mastitis (SCM), an asymptomatic inflammatory condition occurring during lactation, induced a distinctive microbiota signature.
Project description:The objective of the present study was to identify the nutrient utilization and the SCFA production potential of gut microbes during the first year of life. The 16S sequencing data represents 100 mother-child pairs, longitudinally for the infants (0, 3mo, 6mo and 12mo) and mothers 18 weeks pregnancy. We wanted to identify the SCFA composition in pregnant woman and their infants through the first year of life, and their correlation to gut bacteria and other influencal factors. Metaproteomics on selected infants were analyzed to look for nutrient sources used by potential SCFA producers.
Project description:Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genome amplification and metagenomics to retrieve draft genomes of three marine Candidatus Electrothrix and one freshwater Ca. Electronema species. These genomes contain >50% of unknown genes but still largely share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few genes lost and 212 unique genes conserved among cable bacteria. Last common ancestor analysis indicated gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomic data of Ca. Electronema, the genomes suggest that cable bacteria oxidize sulfide by inversing the canonical sulfate reduction pathway and fix CO2 using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, type IV pili as integral components of conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, while cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.
