Developmental trajectory of the healthy human gut microbiota during the first 5 years of life

Josefine Roswall, Lisa M. Olsson, Petia Kovatcheva-Datchary, Staffan Nilsson, Valentina Tremaroli, Marie Christine Simon, Pia Kiilerich, Rozita Akrami, Manuela Krämer, Mathias Uhlén, Anders Gummesson, Karsten Kristiansen, Jovanna Dahlgren, Fredrik Bäckhed*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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The gut is inhabited by a densely populated ecosystem, the gut microbiota, that is established at birth. However, the succession by which different bacteria are incorporated into the gut microbiota is still relatively unknown. Here, we analyze the microbiota from 471 Swedish children followed from birth to 5 years of age, collecting samples after 4 and 12 months and at 3 and 5 years of age as well as from their mothers at birth using 16S rRNA gene profiling. We also compare their microbiota to an adult Swedish population. Genera follow 4 different colonization patterns during establishment where Methanobrevibacter and Christensenellaceae colonize late and do not reached adult levels at 5 years. These late colonizers correlate with increased alpha diversity in both children and adults. By following the children through age-specific community types, we observe that children have individual dynamics in the gut microbiota development trajectory.

Original languageEnglish
JournalCell Host and Microbe
Issue number5
Pages (from-to)765-776.e3
Publication statusPublished - 12 May 2021

Bibliographical note

Funding Information:
This study was supported by Knut and Alice Wallenberg Foundation , the Swedish Research Council ( 2019-01599, 2016-01040 ), the ALF -agreement ( ALFGBG-71810 , ALFGBG-427731 and ALFGBG-719711 ), and a grant from a Transatlantic Networks of Excellence Award from the Leducq Foundation ( 17CVD01 ). F.B. is Torsten Söderberg Professor in Medicine and Wallenberg scholar. The computations and data handling for 16S rRNA gene analyses were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at UPPMAX partially funded by the Swedish Research Council through grant agreement no. 2016-07213.

Publisher Copyright:
© 2021 The Authors


  • 16S rRNA
  • C-section
  • Developing microbiota
  • Infant microbiota
  • Longitudinal cohort
  • Microbiota


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