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

Aleksandar D. Kostic; Dirk Gevers; Heli Siljander; Tommi Vatanen; Tuulia Hyötyläinen; Anu-Maaria Hämäläinen; Aleksandr Peet; Vallo Tillmann; Päivi Pöhö; Ismo Mattila; Harri Lähdesmäki; Eric A. Franzosa; Outi Vaarala; Marcus de Goffau; Hermie Harmsen; Jorma Ilonen; Suvi M. Virtanen; Clary B. Clish; Matej Orešič; Curtis Huttenhower; Mikael  Knip; Ramnik J. Xavier; DIABIMMUNE Study Group

doi:10.1016/j.chom.2015.01.001

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

Aleksandar D. Kostic, Dirk Gevers, Heli Siljander, Tommi Vatanen, Tuulia Hyötyläinen, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Päivi Pöhö, Ismo Mattila, Harri Lähdesmäki, Eric A. Franzosa, Outi Vaarala, Marcus de Goffau, Hermie Harmsen, Jorma Ilonen, Suvi M. Virtanen, Clary B. Clish, Matej Orešič, Curtis HuttenhowerMikael Knip, Ramnik J. Xavier (Corresponding Author), DIABIMMUNE Study Group

VTT Technical Research Centre of Finland

Research output: Contribution to journal › Article › Scientific › peer-review

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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.

Original language	English
Pages (from-to)	260-273
Journal	Cell Host and Microbe
Volume	17
Issue number	2
DOIs	https://doi.org/10.1016/j.chom.2015.01.001
Publication status	Published - 2015
MoE publication type	A1 Journal article-refereed

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Kostic, A. D., Gevers, D., Siljander, H., Vatanen, T., Hyötyläinen, T., Hämäläinen, A.-M., Peet, A., Tillmann, V., Pöhö, P., Mattila, I., Lähdesmäki, H., Franzosa, E. A., Vaarala, O., de Goffau, M., Harmsen, H., Ilonen, J., Virtanen, S. M., Clish, C. B., Orešič, M., ... DIABIMMUNE Study Group (2015). The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host and Microbe, 17(2), 260-273. https://doi.org/10.1016/j.chom.2015.01.001

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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.",

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doi = "10.1016/j.chom.2015.01.001",

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Kostic, AD, Gevers, D, Siljander, H, Vatanen, T, Hyötyläinen, T, Hämäläinen, A-M, Peet, A, Tillmann, V, Pöhö, P, Mattila, I, Lähdesmäki, H, Franzosa, EA, Vaarala, O, de Goffau, M, Harmsen, H, Ilonen, J, Virtanen, SM, Clish, CB, Orešič, M, Huttenhower, C, Knip, M, Xavier, RJ & DIABIMMUNE Study Group 2015, 'The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes', Cell Host and Microbe, vol. 17, no. 2, pp. 260-273. https://doi.org/10.1016/j.chom.2015.01.001

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T1 - The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes

AU - Kostic, Aleksandar D.

AU - Gevers, Dirk

AU - Siljander, Heli

AU - Vatanen, Tommi

AU - Hyötyläinen, Tuulia

AU - Hämäläinen, Anu-Maaria

AU - Peet, Aleksandr

AU - Tillmann, Vallo

AU - Pöhö, Päivi

AU - Mattila, Ismo

AU - Lähdesmäki, Harri

AU - Franzosa, Eric A.

AU - Vaarala, Outi

AU - de Goffau, Marcus

AU - Harmsen, Hermie

AU - Ilonen, Jorma

AU - Virtanen, Suvi M.

AU - Clish, Clary B.

AU - Orešič, Matej

AU - Huttenhower, Curtis

AU - Knip, Mikael

AU - Xavier, Ramnik J.

AU - DIABIMMUNE Study Group

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

U2 - 10.1016/j.chom.2015.01.001

DO - 10.1016/j.chom.2015.01.001

M3 - Article

SN - 1931-3128

VL - 17

SP - 260

EP - 273

JO - Cell Host and Microbe

JF - Cell Host and Microbe

IS - 2

ER -

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

Abstract

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