The Ministry of the Environment, Government of Japan, defines a Satoumi as a coastal area where biological productivity and biodiversity has increased through human interaction. In other words, Satoumi areas are fishing villages, towns, or cities where humans coexist with nature. Moreover, traditions, social systems, and organizations have originated in these coastal areas. Now, to get the useful microorganisms, many researchers try to isolate from the traditional fermented foods not well known and extreme environments in all over the world. On the other hand, we try to isolate lactic acid bacteria (LAB) and yeasts that can be expected to be useful from the familiar coast environments and name that “Satoumi LAB and yeasts”. In this review, fermentative abilities and characteristics as functional foods of several Satoumi LAB and yeast strains isolated from traditional fermented fish products, fish intestines and beach cast algae are shown.

The metabolism of the food occurs not only in human intestines but also in intestinal bacteria living in host intestines.

Therefore, it is important to understand the food metabolism by intestinal bacteria and its physiological effects on human health. In this article, we introduce recent knowledge about the lipid metabolism by intestinal bacteria, focusing on the unsaturated fatty acid metabolism.

We revealed novel unsaturated fatty acid metabolisms in lactic acid bacteria, which is one of the representative intestinal bacteria. Lactic acid bacteria can convert linoleic acid included in edible oils into hydroxy, oxo, conjugated, and partially saturated fatty acids as intermediates. Some intermediates have physiological effects, such as stimulation of adipogenesis, enhancement of energy metabolism, suppression of macrophage-mediated inflammation, reduction of triacylglycerol levels, cytoprotection against oxidative stress, and amelioration of intestinal epithelial barrier impairment. These results show the possibility that these intermediates formed specifically by intestinal bacteria have some influence on the human health.

Furthermore, by utilizing the unique function of lactic acid bacteria metabolism to produce various functional fatty acid, additional functional fatty acid development is expected in the future.

Metabolome, a total profile of whole metabolites, is placed on downstream of proteome. Metabolome is thought to be results of implementation of genomic information. In other words, metabolome can be called as high

resolution phenotype. The easiest operation of metabolomics is the integration to the upstream ome information including transcriptome and / or proteome. Those trials have been reported at a certain scientific level. In addition, metabolomics can be operated in stand-alone mode without any other ome information. Among metabolomics tactics, the author’s group is particularly focusing on metabolic fingerprinting, in which metabolome information is employed as explanatory variant to evaluate response variant. Metabolic fingerprinting technique is expected not only for analyzing slight difference depending on genotype difference but also for expressing dynamic variation of living organisms. The author introduces several good examples which he performed. Those are useful for easy understanding of the power of metabolomics.

Immediately after the birth, a number of bacteria start to colonize in the gut of newborn and a complex microbiota consisting of a several hundred species was eventually established through dynamic changes under lactation and

weaning. To understand a complex ecosystem of gut microbiota in human, a vast number of studies, including birth cohort studies and world cohort studies, are being performed extensively. Notably, recently developed next generation sequencer used to profile gut microbial community structure has gained deep insight in the diversity of gut microbiota in human beings. The authors are also collecting gut microbiota profiles of a large number of Japanese infants and Asians from newborns to elderly. In this review, these microbiome data are shown with discussion on the dynamism and diversity of gut microbiota in human beings.

Many fermented foods are produced in Japan, and the preparation conditions are set very carefully so that strict microbial control can be carried out. Even the manufacturing methods of them have been developed empirically,

specific microorganism is established to be reproduced well in the fermentation medium of each food from ancient times. Although the history of bacterial flora research of fermented foods is old, it has become possible to obtain more detailed information by development of high-throughput 16S rRNA gene analysis using next-generation sequencing. Analysis of the bacterial flora of the fermented food of Ishikawa prefecture, Japan, showed that various bacterial species are intermingled among the fermented products, and that sometimes different kinds of bacteria became dominant even for the same type of food. Lactobacillus sakei, which is known as the predominant lactic acid bacterium in Japanese sake starter, prominently proliferated in “kaburazushi” that contains rice koji, which is a shared ingredient among the both foods. Six “narezushi” products obtained from Noto peninsula were found to be dominated by various Lactobacillus and Pediococcus species. In “yamahai-moto”, nitrate-reducing bacteria normally found in the early stage of fermentation was hardly detected, while Lactobacillus acidipiscis was present at the stage. This review illustrates, through introducing several case studies, how the bacterial flora of fermented foods are robustly and/or variably controlled to achieve the final dominance of lactic acid bacteria.

The International Nucleotide Sequence Database Collaboration (INSDC) has maintained a primary sequence database that collects experimentally-determined nucleotide sequence data directly from researchers. Now data deposition to the INSDC is mandatory for research publication at most of the scientific journals. However, the procedure to deposit data to the INSDC is a big burden, especially for those who are not familiar with computer skills. Recently, we have developed a genome annotation pipeline DFAST, which also assists data deposition to the INSDC. In this article, we show the instruction to deposit annotated genome sequence data using the DFAST web service. Supplementary materials are available at our web site, http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html#about_book_JSLAB.