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Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 5.

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Author information

1
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
2
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
3
Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland; Research Program Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland.
4
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Information and Computer Science, Aalto University School of Science, 02150 Espoo, Finland.
5
Steno Diabetes Center, 2820 Gentofte, Denmark; VTT Technical Research Centre of Finland, 02044 Espoo, Finland.
6
Department of Pediatrics, Jorvi Hospital, 02740 Espoo, Finland.
7
Department of Pediatrics, University of Tartu, Estonia and Tartu University Hospital, 51014 Tartu, Estonia.
8
Faculty of Pharmacy, University of Helsinki, 00290 Helsinki, Finland; VTT Technical Research Centre of Finland, 02044 Espoo, Finland.
9
Department of Information and Computer Science, Aalto University School of Science, 02150 Espoo, Finland.
10
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
11
Research Program Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland.
12
Department of Medical Microbiology, University Medical Center Groningen and University of Groningen, 9713 GZ Groningen, the Netherlands.
13
Immunogenetics Laboratory, University of Turku, 20520 Turku, Finland; Department of Clinical Microbiology, University of Eastern Finland, 70211 Kuopio, Finland.
14
Department of Lifestyle and Participation, National Institute for Health and Welfare, 00271 Helsinki, Finland; School of Health Sciences, University of Tampere, 33014 Tampere, Finland; Science Centre, Pirkanmaa Hospital District, 33521 Tampere, Finland.
15
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
16
Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland; Research Program Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland; Folkhälsan Research Center, 00290 Helsinki, Finland; Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland.
17
Broad Institute of MIT and Harvard, 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, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: xavier@molbio.mgh.harvard.edu.

Abstract

Colonization of the fetal and infant gut microbiome results in dynamic changes in diversity, which can impact disease susceptibility. To examine the relationship between human gut microbiome dynamics throughout infancy and type 1 diabetes (T1D), we examined a cohort of 33 infants genetically predisposed to T1D. Modeling trajectories of microbial abundances through infancy revealed a subset of microbial relationships shared across most subjects. Although strain composition of a given species was highly variable between individuals, it was stable within individuals throughout infancy. Metabolic composition and metabolic pathway abundance remained constant across time. A marked drop in alpha-diversity was observed in T1D progressors in the time window between seroconversion and T1D diagnosis, accompanied by spikes in inflammation-favoring organisms, gene functions, and serum and stool metabolites. This work identifies trends in the development of the human infant gut microbiome along with specific alterations that precede T1D onset and distinguish T1D progressors from nonprogressors.

Comment in

PMID:
25662751
PMCID:
PMC4689191
DOI:
10.1016/j.chom.2015.01.001
[Indexed for MEDLINE]
Free PMC Article

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