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Buffalo rumen microbiome experiences a variety of diet stress and represents reservoir of Dormancy and Sporulation genes. However, the information on genomic responses to such conditions is very limited. The Ion Torrent PGM next generation sequencing technology was used to characterize general microbial diversity and the repertoire of microbial genes present, including genes associated with Dormancy and Sporulation in Mehsani buffalo rumen metagenome. The research findings revealed the abundance of bacteria at the domain level and presence of Dormancy and Sporulation genes which were predominantly associated with the Clostridia and Bacilli taxa belonging to the phyla Firmicutes. Genes associated with Sporulation cluster and Sporulation orphans were increased from 50% to 100% roughage treatment, thereby promoting sporulation all along the treatments. The spore germination is observed to be the highest in the 75% roughage treatment both in the liquid and solid rumen fraction samples with respect to the decrease in the values of the genes associated with spore core dehydration, thereby facilitating spore core hydration which is necessary for spore germination.
Pubmed ID: 25606408
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The SEED is a framework to support comparative analysis and annotation of genomes. The cooperative effort focuses on the development of the comparative genomics environment and, more importantly, on the development of curated genomic data. Curation of genomic data (annotation) is done via the curation of subsystems by an expert annotator across many genomes, not on a gene by gene basis. From the curated subsystems we extract a set of freely available protein families (FIGfams). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available. We also provide a SEED-Viewer that allows read-only access to the latest curated data sets. We currently have 58 Archaea, 902 Bacteria, 562 Eukaryota, 1254 Plasmids and 1713 Viruses in our database. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org
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