What is already known
The gut microbiota, the largest microbial community of the human body, has been implicated in both health and disease. But although many studies focused on the bacterial and viral communities found in the guts of people of European descent, little is known about the Japanese gut virome.
What this research adds
Researchers reconstructed more than 19,000 bacterial and about 31,000 viral genomes from the gut metagenomes of 787 Japanese people. The found that the levels of specific bacteria may derive from the consumption of traditional Japanese food, whereas other bacteria are associated with dairy consumption. Most of the viral genomes identified were new, and the abundance of a class of crAss-like phages, a group of related viruses that includes some of the most abundant viruses of the human gut, were higher in populations with non-westernized dietary habits compared to those with westernized dietary habits. Several types of crAss-like phages were found at decreased levels in people with rheumatoid arthritis, systemic lupus erythematosus, ulcerative colitis and Crohn disease, and at increased levels in people with colon cancer.
Conclusions
The findings suggest that several viruses are linked to specific populations and diseases.
The gut microbiota, the largest microbial community of the human body, has been implicated in both health and disease. A new study reconstructed the genome sequence of bacteria and viruses found in the guts of hundreds of Japanese people, revealing that several viruses are linked to specific populations and diseases.
The reconstructed microbial genomes and related information are publicly available, and the database will be a useful resource for future studies, the researchers say. Their results were detailed in Cell Genomics.
Many previous studies have focused on the bacterial and viral communities found in the guts of people of European descent. However, little is known about the Japanese gut virome.
To better characterize the bacteria and viruses found in the gut of Japanese people, researchers led by Yoshihiko Tomofuji at Osaka University analyzed metagenome sequences from 787 individuals.
Dietary habits
The researchers reconstructed 19,084 bacterial and 31,395 viral genomes from sequencing data. Firmicutes and Bacteroidota were common in the gut of Japanese people, and Actinobacteriota and Bacillus subtilis were more frequent in those individuals than in individuals from other populations. Bacillus subtilis is a key component of a Japanese traditional fermented food called natto.
Other bacteria such as Enterococcus lactis and Streptococcus thermophilus were associated with dairy consumption. These microbes have been linked with a genetic variant that causes alcohol intolerance and has ties to diseases such as colorectal cancer.
An analysis of the proteins present in the Japanese gut metagenomes revealed that beta-porphyranase, an enzyme that breaks down seaweed-derived carbohydrates, was detectable in the Japanese gut but not in the European gut — likely because Japanese people eat nori, a dried seaweed made from red algae.
Disease link
Most of the viral genomes identified were new, and the abundance of a class of crAss-like phages, a group of related viruses that includes some of the most abundant viruses of the human gut, were higher in populations with non-westernized dietary habits compared to those with westernized dietary habits. In line with previous reports, Bacteroidota were the major host of crAss-like phages.
The researchers also found that several types of crAss-like phages were present at decreased levels in people with rheumatoid arthritis, systemic lupus erythematosus, ulcerative colitis and Crohn disease, and at increased levels in people with colon cancer.
The reconstructed microbial genomes and related information are available at Japan’s National Bioscience Database Center.
