Edited by Jeffrey I. Gordon, Washington University School of Medicine, St. Louis, MO, and approved June 1, 2010 (received for review February 5, 2010)
Alterations in the human intestinal microbiota are linked to conditions including inflammatory bowel disease, irritable bowel syndrome, and obesity. The microbiota also undergoes substantial changes at the extremes of life, in infants and older people, the ramifications of which are still being explored. We applied pyrosequencing of over 40,000 16S rRNA gene V4 region amplicons per subject to characterize the fecal microbiota in 161 subjects aged 65 y and older and 9 younger control subjects. The microbiota of each individual subject constituted a unique profile that was separable from all others. In 68% of the individuals, the microbiota was dominated by phylum Bacteroides, with an average proportion of 57% across all 161 baseline samples. Phylum Firmicutes had an average proportion of 40%. The proportions of some phyla and genera associated with disease or health also varied dramatically, including Proteobacteria, Actinobacteria, and Faecalibacteria. The core microbiota of elderly subjects was distinct from that previously established for younger adults, with a greater proportion of Bacteroides spp. and distinct abundance patterns of Clostridium groups. Analyses of 26 fecal microbiota datasets from 3-month follow-up samples indicated that in 85% of the subjects, the microbiota composition was more like the corresponding time-0 sample than any other dataset. We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.
Author contributions: J.R.M., T.D., G.F., C.S., D.v.S., D.O., A.P.F., F.S., C. Hill, R.P.R., and P.W.O. designed research; M.J.C., S.C., O.O., R.G.-D., E.F., M.O., N.H., K.O., C. Henry, D.O., A.P.F., and C.T. performed research; H.d.W., M.O., N.H., K.O., C. Henry, D.O., and C.T. contributed new reagents/analytic tools; M.J.C., S.C., O.O., R.G.-D., H.d.W., J.R.M., D.F., T.D., A.P.F., F.S., C.T., C. Hill, R.P.R., and P.W.O. analyzed data; and M.J.C., S.C., J.R.M., G.F., C.S., D.v.S., F.S., C. Hill, R.P.R., and P.W.O. wrote the paper.
The authors declare no conflict of interest.
This paper results from the Arthur M. Sackler Colloquium of the National Academy of Sciences, “Microbes and Health” held November 2–3, 2009, at the Arnold and Mabel Beckman Center of the National Academies of Sciences and Engineering in Irvine, CA. The complete program and audio files of most presentations are available on the NAS Web site at http://www.nasonline.org/SACKLER_Microbes_and_Health.
This article is a PNAS Direct Submission.
Data deposition: The sequence data reported in this paper have been deposited in the National Center for Biotechnology Information Short Read Archive (accession no. SRA021022).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1000097107/-/DCSupplemental.
