Various microbial species construct functional eco-system in our intestine. The field of human gut microbiome study is rapidly expanding due to metagenomics based on the development of next generation sequencers. Metagenomics provides huge amount of sequence data, therefore, functional reference database, such as KEGG or COG, is essential to interpret the functionality of the derived sequences.

Database is one of the most important factor in the modern life science. The high accuracy and coverage of the contents in the database improves and facilitates the biological big data analysis.

In this review, I introduce the basic of life sciecnce database for functional annotation. In addition, our own metabolic pathway database is also illustrated here. We are developing the database to understand

metabolic functionality for human gut microbiome. This database contains basic metabolic pathways and modules for microbiome living in human large intestine. This database complements current reference database, such as KEGG or COG.

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Fate of so-called functional food components varies from those that are readily absorbed into the human body to exert their health maintaining or promoting property to those that become functional, non-functional or even hazardous after being exposed to gastric acid, digestive enzymes, bile acids, or intestinal microbiota of the host. Practical functionality and safety of a given food component should be therefore evaluated based on its pharmacokinetics within the host alimentary tract. However, the conventional tissue culture or laboratory animal based tests are usually, if not always, difficult to yield such a comprehensive result, while conventional human intervention trails would be again difficult to perform due to the heavier economic load as well as higher ethical clearance. In order to bypass the dilemma, we have recently developed what we call “Kobe University Human Intestinal Models”, by which we are currently evaluating practical functionality and safety of both conventional and novel food components before being evaluated in genuine human intervention trails, which are described in this review paper.

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Long-read sequencing represented by Pacific Biosciences’ single-molecule real-time (SMRT) technology has been widely used for microbial genomes. We overview an analysis procedure of Lactobacillus hokkaidonensis LOOC260^T genome using the so-called “PacBio“ data. We describe (i) the characteristics of PacBio data, (ii) genome assembly using the HGAP program provided in the web-based NGS analysis tool called “DDBJ Pipeline”, (iii) the survey of assembled contigs such as quality scores and circularization. We also describe a typical strategy of finishing the circular contig (plasmid).

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