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 Oresic, Curtis HuttenhowerMikael Knip, Ramnik J. Xavier

Research output: Contribution to journalArticleScientificpeer-review

355 Citations (Scopus)

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 languageEnglish
Pages (from-to)260-273
JournalCell Host and Microbe
Volume17
Issue number2
DOIs
Publication statusPublished - 2015
MoE publication typeA1 Journal article-refereed

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Type 1 Diabetes Mellitus
Microbiota
Disease Susceptibility
Human Development
Child Development
Metabolic Networks and Pathways
Gastrointestinal Microbiome
Inflammation
Serum
Genes

Cite this

Kostic, A. D., Gevers, D., Siljander, H., Vatanen, T., Hyötyläinen, T., Hämäläinen, A-M., ... Xavier, R. J. (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
Kostic, Aleksandar D. ; Gevers, Dirk ; Siljander, Heli ; Vatanen, Tommi ; Hyötyläinen, Tuulia ; Hämäläinen, Anu-Maaria ; Peet, Aleksandr ; Tillmann, Vallo ; Pöhö, Päivi ; Mattila, Ismo ; Lähdesmäki, Harri ; Franzosa, Eric A. ; Vaarala, Outi ; de Goffau, Marcus ; Harmsen, Hermie ; Ilonen, Jorma ; Virtanen, Suvi M. ; Clish, Clary B. ; Oresic, Matej ; Huttenhower, Curtis ; Knip, Mikael ; Xavier, Ramnik J. / The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. In: Cell Host and Microbe. 2015 ; Vol. 17, No. 2. pp. 260-273.
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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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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, Oresic, M, Huttenhower, C, Knip, M & Xavier, RJ 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

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. / Kostic, Aleksandar D.; Gevers, Dirk; Siljander, Heli; Vatanen, Tommi; Hyötyläinen, Tuulia; Hämäläinen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Pöhö, Päivi; Mattila, Ismo; Lähdesmäki, Harri; Franzosa, Eric A.; Vaarala, Outi; de Goffau, Marcus; Harmsen, Hermie; Ilonen, Jorma; Virtanen, Suvi M.; Clish, Clary B.; Oresic, Matej; Huttenhower, Curtis; Knip, Mikael ; Xavier, Ramnik J.

In: Cell Host and Microbe, Vol. 17, No. 2, 2015, p. 260-273.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

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 - Oresic, Matej

AU - Huttenhower, Curtis

AU - Knip, Mikael

AU - Xavier, Ramnik J.

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

VL - 17

SP - 260

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JO - Cell Host and Microbe

JF - Cell Host and Microbe

SN - 1931-3128

IS - 2

ER -