Facts and ideas presented in this short review are addressed to those computer scientists and mathematicians that want to learn about some open questions on the bioinformatics of microbial organisms. We present some recent results of our group on the statistical analysis of microbial genomes involving the formalization of microbial spaces, metabolic network comparison, minimal gene sets, host-p...

BACKGROUND Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packa...

Background & Aim:The main aim of this study was stabilizing D. Sophia beverage and reduce its sedimentation rate. Experimental: Xanthan and Carboxy methyl cellulose gums have been used in three levels (0.05, .01 and .02 gr/lit) and mixture of Guar-xanthan and carboxymethyl cellulose (each .1 g/l) and extracted dried gum from D. Sophia in (1, 2 an...

traditional microbiology concepts are being renewed since the development of new microbiological technologies, such as, sequencing and large-scale genome analysis. since the entry into the new millennium, a lot of new information has emerged regarding the oral microbiome. this revision presents an overview of this renewed knowledge on oral microbial community acquisition in the newborn and on t...

Forest management often results in changes in soil microbial communities. To understand how forest management can change microbial communities, we studied soil microbial abundance and community structure in a natural Chamaecyparis (NCP) forest, a disturbed Chamaecyparis (DCP) forest, a secondary (regenerated) Chamaecyparis (SCP) forest and a secondary (reforested) Cryptomeria (SCD) forest. We a...

GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial ...

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of...