Japanese adult gut microbiome, cross-sectional study

The human gut microbiome has profound influences on the host’s health largely through its inter-ference with various intestinal functions. As recent studies have suggested diversity in the humangut microbiome among human populations, it will be interesting to analyse how gut microbiomeis correlated with geographical, cultural, and traditional differences. The Japanese people areknown to have several characteristic features such as eating a variety of traditional foods and exhibit-ing a low BMI and long life span. In this study, we analysed gut microbiomes of the Japanese by com-paring the metagenomic data obtained from 106 Japanese individuals with those from 11 othernations. We found that the composition of the Japanese gut microbiome showed more abundantin the phylum Actinobacteria, in particular in the genus Bifidobacterium, than other nations. Regard-ing the microbial functions, those of carbohydrate metabolism were overrepresented with a concur-rent decrease in those for replication and repair, and cell motility. The remarkable low prevalence ofgenes for methanogenesis with a significant depletion of the archaeon Methanobrevibacter smithii and en-richment of acetogenesis genes in the Japanese gut microbiome compared with others suggested adifference in the hydrogen metabolism pathway in the gut between them. It thus seems that the gutmicrobiome of the Japanese is considerably different from those of other populations, which cannotbe simply explained by diet alone. We postulate possible existence of hitherto unknown factorscontributing to the population-level diversity in human gut microbiomes.

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.68. Assay shotgun_dna.

• host run.host_tax_id · “9606”
• body site study.title · “Metagenomics of Japanese gut microbiomes”
• life stage study.description · “low BMI and long life span”

400 runs over 255 samples · mean 0.76 Gbp per run (median 0.50 Gbp, total 305.06 Gbp; 400 runs with a base count) · layout SINGLE 336, PAIRED 64 · platform ION_TORRENT 177, LS454 159, ILLUMINA 64 · models 454 GS FLX Titanium (97), Ion Torrent PGM (89), Ion Torrent Proton (88), Illumina MiSeq (64), 454 GS FLX+ (62) · 14% of runs with a Sandpiper profile · first public 2016-03-10

Nishijima S first · Suda W · Oshima K · Kim SW · Hirose Y · Morita H · Hattori M last · Yoshida K first · Hirano R · Sakai Y · Choi M · Sakanaka M · Kurihara S · Iino H · Xiao JZ · Katayama T · Odamaki T last · Qin F first · Li J · Mao T · Feng S · Lai M last · Golisch B first · Cordeiro RL · Fraser ASC · Briggs J · Stewart WA · Van Petegem F · Brumer H last · Zhao Y first · Chen H · Huang J · Chistoserdova L · Yu Z last

PRJDB3601.csv.gz (7.6 KB) · parquet (81.0 KB) — all 255 samples, every field with route and confidence · PRJDB3601_determinations.csv.gz (16.9 KB) — 2,314 evidence rows