Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

BMC Microbiol. 2016 May 25;16:90. doi: 10.1186/s12866-016-0708-5.


Background: It has been reported that the composition of human gut microbiota changes with age; however, few studies have used molecular techniques to investigate the long-term, sequential changes in gut microbiota composition. In this study, we investigated the sequential changes in gut microbiota composition in newborn to centenarian Japanese subjects.

Results: Fecal samples from 367 healthy Japanese subjects between the ages of 0 and 104 years were analyzed by high-throughput sequencing of amplicons derived from the V3-V4 region of the 16S rRNA gene. Analysis based on bacterial co-abundance groups (CAGs) defined by Kendall correlations between genera revealed that certain transition types of microbiota were enriched in infants, adults, elderly individuals and both infant and elderly subjects. More positive correlations between the relative abundances of genera were observed in the elderly-associated CAGs compared with the infant- and adult-associated CAGs. Hierarchical Ward's linkage clustering based on the abundance of genera indicated five clusters, with median (interquartile range) ages of 3 (0-35), 33 (24-45), 42 (32-62), 77 (36-84) and 94 (86-98) years. Subjects were predominantly clustered with their matched age; however, some of them fell into mismatched age clusters. Furthermore, clustering based on the proportion of transporters predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) showed that subjects were divided into two age-related groups, the adult-enriched and infant/elderly-enriched clusters. Notably, all the drug transporters based on Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology groups were found in the infant/elderly-enriched cluster.

Conclusion: Our results indicate some patterns and transition points in the compositional changes in gut microbiota with age. In addition, the transporter property prediction results suggest that nutrients in the gut might play an important role in changing the gut microbiota composition with age.

Keywords: Aging; Commensal bacteria; Gut microbiota; Japanese population.

MeSH terms

  • Adolescent
  • Adult
  • Age Factors
  • Aged
  • Aged, 80 and over
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Child
  • Child, Preschool
  • Cluster Analysis
  • Cross-Sectional Studies
  • Feces / microbiology
  • Female
  • Gastrointestinal Microbiome*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Infant
  • Infant, Newborn
  • Male
  • Middle Aged
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA / methods*
  • Young Adult


  • RNA, Ribosomal, 16S