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 ArticleMicrobiome

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.

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

Moran Yassour

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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.

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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.

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Anu-Maaria Hämäläinen

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

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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.

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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.

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Eric A. Franzosa

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

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Hera Vlamakis

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

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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.

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Dirk Gevers

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

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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.

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Mikael Knip

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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.

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For correspondence: xavier@molbio.mgh.harvard.edu

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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

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