Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Moran Yassour; Tommi Vatanen; Heli Siljander; Anu-Maaria Hämäläinen; Taina Härkönen; Samppa J. Ryhänen; Eric A. Franzosa; Hera Vlamakis; Curtis Huttenhower; Dirk Gevers; Eric S. Lander; Mikael Knip; on behalf of the DIABIMMUNE Study Group; Ramnik J. Xavier

doi:10.1126/scitranslmed.aad0917

Research ArticlesMicrobiome

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Moran Yassour¹,²,
Tommi Vatanen¹,³,
Heli Siljander⁴,⁵,⁶,
Anu-Maaria Hämäläinen⁷,
Taina Härkönen⁴,⁵,
Samppa J. Ryhänen⁴,⁵,
Eric A. Franzosa⁸,
Hera Vlamakis¹,
Curtis Huttenhower¹,⁸,
Dirk Gevers¹,*,
Eric S. Lander¹,⁹,¹⁰,†,
Mikael Knip⁴,⁵,⁶,¹¹,†,
on behalf of the DIABIMMUNE Study Group‡ and
Ramnik J. Xavier¹,²,¹²,¹³,†,§

¹Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA.
²Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
³Department of Computer Science, Aalto University School of Science, 02150 Espoo, Finland.
⁴Children’s Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.
⁵Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland.
⁶Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland.
⁷Department of Pediatrics, Jorvi Hospital, Helsinki University Hospital, 02740 Espoo, Finland.
⁸Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
⁹Department of Biology, MIT, Cambridge, MA 02139, USA.
¹⁰Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA.
¹¹Folkhälsan Research Center, 00290 Helsinki, Finland.
¹²Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
¹³Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA.

↵§Corresponding author. Email: xavier{at}molbio.mgh.harvard.edu

↵† Co-senior authors.
↵* Present address: Janssen Human Microbiome Institute, Janssen Research and Development, Cambridge, MA 02142, USA.
↵‡ The investigators in the DIABIMMUNE Study Group are listed in the Supplementary Materials.

See allHide authors and affiliations

Science Translational Medicine 15 Jun 2016:
Vol. 8, Issue 343, pp. 343ra81
DOI: 10.1126/scitranslmed.aad0917

Moran Yassour

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Tommi Vatanen

Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA.Department of Computer Science, Aalto University School of Science, 02150 Espoo, Finland.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Heli Siljander

Children’s Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland.Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Anu-Maaria Hämäläinen

Department of Pediatrics, Jorvi Hospital, Helsinki University Hospital, 02740 Espoo, Finland.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Taina Härkönen

Children’s Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Samppa J. Ryhänen

Children’s Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Eric A. Franzosa

Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Hera Vlamakis

Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Curtis Huttenhower

Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA.Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Dirk Gevers

Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Eric S. Lander

Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA.Department of Biology, MIT, Cambridge, MA 02139, USA.Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Mikael Knip

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Ramnik J. Xavier

Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA.Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site
For correspondence: xavier@molbio.mgh.harvard.edu

Article
Figures & Data
Info & Metrics
eLetters
PDF

eLetters is an online forum for ongoing peer review. Submission of eLetters are open to all. Please read our Terms of Service before submitting your own eLetter.

Submit a Response to This Article

Compose eLetter

Title

Contents

More information about text formats

Plain text

Plain text
No HTML tags allowed.
Web page addresses and e-mail addresses turn into links automatically.
Lines and paragraphs break automatically.

Author Information

Contributors
First name and middle name First or given name, e.g. 'Peter'. Last Name Your last, or family, name, e.g. 'MacMoody'. Email Your email address, e.g. higgs-boson@gmail.com Role / Occupation Your role and/or occupation, e.g. 'Orthopedic Surgeon'. Affiliation Your organization or institution (if applicable), e.g. 'Royal Free Hospital'.

Statement of Competing Interests

Competing interests?

Yes

Please describe the competing interests

Publication Date - String

First Publication Date - String

Electronic Publication Date - String

Print Publication Date - String

CAPTCHA

This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.

What code is in the image? Enter the characters shown in the image.

Vertical Tabs

No eLetters have been published for this article.

View Full Text

A longitudinal strain-level analysis of the infant gut microbiome after repeated antibiotic treatments reveals decreased diversity and stability, as well as transient increases in antibiotic resistance genes.

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Plain text

Vertical Tabs

Science Translational Medicine

Article Tools