Genome research on lactic acid bacteria

In late June 2000, President Clinton of the U.S. and Prime Minister Blair of the U.K. together appeared on TV and announced the completion of the international project to decode the human genome, surprising people around the world. The decoding of genomes such as seen in this project, which is expected to contribute greatly to the wellbeing of humankind, has been attempted not only on humans but also various other organisms, including lactic acid bacteria. Indeed, genome research on a number of different genera and strains of lactic acid bacteria has been conducted since the late 1990s, and some of these projects have already achieved the full decoding of the targeted genomes. As a result, significant amounts of genome data on lactic acid bacteria have been accumulated rapidly in recent years.

Both a lactic acid bacterium that only consists of a single cell and a human being made up of some 60 trillion cells must receive nutrients from external sources to generate energy and replace aged parts of their bodies with new ones constantly in order to stay alive. Genomes are collections of genetic information on all functions that are necessary for the maintenance of such biological activities, and are sometimes referred to as the blueprint of life.
The genes in a genome consist of DNA in a thin chain-like structure, which is formed by a series of four different types of bases, called A, T, G, and C, all lined up like characters. In other words, an organism’s genetic information is determined by the sequence of these four letters. In the case of lactic acid bacteria, their genetic information consists of about 2 million base pairings per bacterium, while that of a human has as many as 3 billion base pairings.
In addition, those base sequences include a number of genes that dictate how proteins are created to sustain each organism’s biological activities. In the case of bacteria, a single gene typically exists for every 1000 bases or so in a genome, and each bacterium is known to have roughly 2000 genes.
What does sequencing a genome actually mean? It means the act of reading and determining all base sequences that exist in the DNA of an organism. Once you definitively know the base sequences of an organism, it is possible to estimate the number of genes it might have and also the function of each gene constituting the organism.

Why is it so important to sequence the genomes of lactic acid bacteria? During the fermentation process of lactic acid bacteria, lactose and other sugars become lactic acid. While much research has already been done on this particular process, lactic acid bacteria perform various other functions besides producing lactic acid, including determining the flavor of the fermented foods they are used in, and creating chemical substances that are health-enhancing for humans. As lactic acid bacteria have various functions and potentials, there are still many unknown aspects that require additional exploration. One of the reasons why genome sequencing is so important is that it helps us better understand the various characteristics and potentially useful functions of lactic acid bacteria, by shedding light on the significance and mechanisms of their existence and behavior that are not yet well understood. For example, assume you are looking for a lactic acid bacterium that is optimal in terms of a certain characteristic. If you know which genes are involved in determining that characteristic, you can accomplish your goal by simply finding the lactic acid bacterium in which those genes are manifested most strongly. In other words, genome information can provide valuable clues for efficiently identifying specific lactic acid bacteria that meet a desired profile.
Another important point regarding genome sequencing is that even if you fully clarify the base sequences of lactic acid bacteria, the precise functions of many of their genes are still not fully understood by science. When those genes are studied and understood thoroughly, it may be possible to discover new characteristics and functions that were previously overlooked. When that is achieved, their genome information will become fundamental data sets that we can leverage to unlock the full potential of lactic acid bacteria that still remain a mystery.

At the moment, efforts to sequence the genomes of lactic acid bacteria are mainly led by Europe, the U.S., and Japan. In particular, Europe has constantly been the driving force behind the progress of those endeavors. As dairy farming has long existed in Europe, yogurt, cheese, and other fermented dairy products are essential components of people’s diets. Economically, dairy farming has been an important source of income, and so the importance of research on lactic acid bacteria has been recognized in the region from an early stage. With this background, research on lactic acid bacteria has been increasingly conducted as large-scale EU-wide projects in recent years, instead of by individual member states. As a result, more and more researchers from various EU nations are communicating and collaborating with each other across national borders to work on joint research projects and exchange ideas and information. Thanks to such favorable research environment, the Europeans were the first to start genome sequencing, and it was a national research institute of France that published the first complete genome sequence in 2001.
Meanwhile, the U.S. lagged slightly behind Europe in the sequencing of the lactic acid bacteria genome; they started a national project several years ago to focus on the genome sequencing of 10 particular strains of lactic acid bacteria and one strain of Bifidobacterium that would prove to be useful in industrial applications. While the project is not yet completed, they have already published on the Internet related sequence data that have been decoded. Where does Japan stand? While genome sequencing started several years ago, only a limited number of universities and companies that produce fermented dairy products are conducting sequencing projects, and these organizations are much smaller in scale and number compared to their counterparts in Europe and the U.S. So, unfortunately Japan lags behind instead of leading this global genome research movement.

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