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The dynamics of a family's gut microbiota reveal variations on a theme.

Schloss PD, Iverson KD, Petrosino JF, Schloss SJ - Microbiome (2014)

Bottom Line: A combination of genetics, diet, environment, and life history are all thought to impact the development of the gut microbiome.Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member.This transition was associated with increased diversity, decreased stability, and the colonization of significant abundances of Bacteroidetes and Clostridiales.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Immunology, University of Michigan, 1520A Medical Science Research Building I, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA.

ABSTRACT

Background: It is clear that the structure and function of the human microbiota has significant impact on maintenance of health and yet the factors that give rise to an adult microbiota are poorly understood. A combination of genetics, diet, environment, and life history are all thought to impact the development of the gut microbiome. Here we study a chronosequence of the gut microbiota found in eight individuals from a family consisting of two parents and six children ranging in age from two months to ten years old.

Results: Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member. Interestingly, there was a significant core membership to the family members' microbiota where the abundance of this core accounted for the differences between individuals. It was clear that the introduction of solids represents a significant transition in the development of a mature microbiota. This transition was associated with increased diversity, decreased stability, and the colonization of significant abundances of Bacteroidetes and Clostridiales. Although the children and mother shared essentially the identical diet and environment, the children's microbiotas were not significantly more similar to their mother than they were to their father.

Conclusions: This analysis underscores the complex interactions that give rise to a personalized microbiota and suggests the value of studying families as a surrogate for longitudinal studies.

No MeSH data available.


Diversity and stability of the microbiota found within family members and individuals sampled from the broader community. (A) Each point represents the inverse Simpson alpha diversity index for a sample collected from each individual. (B) The average similarity between samples collected from the same individual with varying number of days between when the samples were collected.
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Figure 1: Diversity and stability of the microbiota found within family members and individuals sampled from the broader community. (A) Each point represents the inverse Simpson alpha diversity index for a sample collected from each individual. (B) The average similarity between samples collected from the same individual with varying number of days between when the samples were collected.

Mentions: We measured the association between age and diversity and age and stability of each family member’s microbiota. Diversity was strongly associated with the degree to which the child was being breastfed (Figure 1A). The infant (exclusively breastfed) had the lowest diversity, the two-year-old (breastfed and eating solid food) had the next to lowest diversity, and the remaining four children (all weaned) had a similarly high level of diversity; the diversities of the three groups of children were significantly different from each other and the weaned children were not significantly different from each other. The mother and father each had diversities that were significantly different from each other and the children. Interestingly, the mother’s diversity was considerably higher than those observed within the family and among the Ann Arbor cohort and the father’s diversity was more similar to that of the Ann Arbor cohort. This is in contrast to previous observations that women who had recently given birth had lower diversity than normal women [39]. To assess whether these differences in diversity resulted in differences in the stability of each microbiota, we calculated the average β-diversity between an individual’s samples as a function of the number of days between their collection (Figure 1B). This analysis indicated that the infant had the most stable community and that the stabilities of the other family members were indistinguishable. Samples collected a day apart were just as similar as samples collected ten days apart. These data suggest that the transition from breast milk to solid foods brings about increased diversity and decreased stability in the gut microbiota.


The dynamics of a family's gut microbiota reveal variations on a theme.

Schloss PD, Iverson KD, Petrosino JF, Schloss SJ - Microbiome (2014)

Diversity and stability of the microbiota found within family members and individuals sampled from the broader community. (A) Each point represents the inverse Simpson alpha diversity index for a sample collected from each individual. (B) The average similarity between samples collected from the same individual with varying number of days between when the samples were collected.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4109379&req=5

Figure 1: Diversity and stability of the microbiota found within family members and individuals sampled from the broader community. (A) Each point represents the inverse Simpson alpha diversity index for a sample collected from each individual. (B) The average similarity between samples collected from the same individual with varying number of days between when the samples were collected.
Mentions: We measured the association between age and diversity and age and stability of each family member’s microbiota. Diversity was strongly associated with the degree to which the child was being breastfed (Figure 1A). The infant (exclusively breastfed) had the lowest diversity, the two-year-old (breastfed and eating solid food) had the next to lowest diversity, and the remaining four children (all weaned) had a similarly high level of diversity; the diversities of the three groups of children were significantly different from each other and the weaned children were not significantly different from each other. The mother and father each had diversities that were significantly different from each other and the children. Interestingly, the mother’s diversity was considerably higher than those observed within the family and among the Ann Arbor cohort and the father’s diversity was more similar to that of the Ann Arbor cohort. This is in contrast to previous observations that women who had recently given birth had lower diversity than normal women [39]. To assess whether these differences in diversity resulted in differences in the stability of each microbiota, we calculated the average β-diversity between an individual’s samples as a function of the number of days between their collection (Figure 1B). This analysis indicated that the infant had the most stable community and that the stabilities of the other family members were indistinguishable. Samples collected a day apart were just as similar as samples collected ten days apart. These data suggest that the transition from breast milk to solid foods brings about increased diversity and decreased stability in the gut microbiota.

Bottom Line: A combination of genetics, diet, environment, and life history are all thought to impact the development of the gut microbiome.Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member.This transition was associated with increased diversity, decreased stability, and the colonization of significant abundances of Bacteroidetes and Clostridiales.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Immunology, University of Michigan, 1520A Medical Science Research Building I, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA.

ABSTRACT

Background: It is clear that the structure and function of the human microbiota has significant impact on maintenance of health and yet the factors that give rise to an adult microbiota are poorly understood. A combination of genetics, diet, environment, and life history are all thought to impact the development of the gut microbiome. Here we study a chronosequence of the gut microbiota found in eight individuals from a family consisting of two parents and six children ranging in age from two months to ten years old.

Results: Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member. Interestingly, there was a significant core membership to the family members' microbiota where the abundance of this core accounted for the differences between individuals. It was clear that the introduction of solids represents a significant transition in the development of a mature microbiota. This transition was associated with increased diversity, decreased stability, and the colonization of significant abundances of Bacteroidetes and Clostridiales. Although the children and mother shared essentially the identical diet and environment, the children's microbiotas were not significantly more similar to their mother than they were to their father.

Conclusions: This analysis underscores the complex interactions that give rise to a personalized microbiota and suggests the value of studying families as a surrogate for longitudinal studies.

No MeSH data available.