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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.


Related in: MedlinePlus

Comparison of microbiota similarity within and between weaned family members and among members of the broader community. Each point represents the average similarity for each individual within that comparison. Stars represent significance using non-parametric Wilcoxon test (*P < 0.05, **P < 0.01, ***P < 0.001). Lines drawn between points for similarity between the children and the mother and father indicate points that correspond to the same child. This comparison was not significant.
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Figure 4: Comparison of microbiota similarity within and between weaned family members and among members of the broader community. Each point represents the average similarity for each individual within that comparison. Stars represent significance using non-parametric Wilcoxon test (*P < 0.05, **P < 0.01, ***P < 0.001). Lines drawn between points for similarity between the children and the mother and father indicate points that correspond to the same child. This comparison was not significant.

Mentions: Given the large family size, it was possible to assess the relative importance of genetics and environment/diet on shaping the gut community structure using the children who had been weaned, their parents, and members of the Ann Arbor cohort (Figure 4). As expected, the community structure of each individual in the family was more similar to themselves than to any other family member (P < 0.001). Even though each of the children share 50% of their DNA with each other and their parents, the median similarity between children (θYC = 0.41) was significantly higher than their median similarity to either of their parents (θYC-Mother = 0.34; θYC-Father = 0.32; both P = 0.010); additionally, the children were more similar to each other than their mother and father were to each other (θYC-Parents = 0.33; P = 0.031). The similarity between each child and their mother was higher than to their father (ΔθYC = 0.02); however, this difference was not statistically significant (P = 0.125) and not likely to be biologically significant. Interestingly, previous family-based studies have excluded the children’s father from the analysis [6,11]. This is notable when one considers that the children in this study were homeschooled by their mother with whom they share nearly all of their meals. These observations suggest that the father and his microbiota may be just as important as the mother in shaping a child’s microbiota. More broadly, it is likely that other caregivers and their environment may participate in shaping a child’s microbiota. Finally, the family members were as similar to each other as individuals from the Ann Arbor cohort were to each other (P = 0.433); however, based on the earlier Random Forest analysis, the family’s microbiota was clearly different from the broader community. The different microbiota represented within the family were clearly unique relative to each other and the broader community. The mechanisms that give rise to this uniqueness are likely a complex mixture of factors. Regardless, the family members appear to represent variations of a shared familial microbiota.


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

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

Comparison of microbiota similarity within and between weaned family members and among members of the broader community. Each point represents the average similarity for each individual within that comparison. Stars represent significance using non-parametric Wilcoxon test (*P < 0.05, **P < 0.01, ***P < 0.001). Lines drawn between points for similarity between the children and the mother and father indicate points that correspond to the same child. This comparison was not significant.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Comparison of microbiota similarity within and between weaned family members and among members of the broader community. Each point represents the average similarity for each individual within that comparison. Stars represent significance using non-parametric Wilcoxon test (*P < 0.05, **P < 0.01, ***P < 0.001). Lines drawn between points for similarity between the children and the mother and father indicate points that correspond to the same child. This comparison was not significant.
Mentions: Given the large family size, it was possible to assess the relative importance of genetics and environment/diet on shaping the gut community structure using the children who had been weaned, their parents, and members of the Ann Arbor cohort (Figure 4). As expected, the community structure of each individual in the family was more similar to themselves than to any other family member (P < 0.001). Even though each of the children share 50% of their DNA with each other and their parents, the median similarity between children (θYC = 0.41) was significantly higher than their median similarity to either of their parents (θYC-Mother = 0.34; θYC-Father = 0.32; both P = 0.010); additionally, the children were more similar to each other than their mother and father were to each other (θYC-Parents = 0.33; P = 0.031). The similarity between each child and their mother was higher than to their father (ΔθYC = 0.02); however, this difference was not statistically significant (P = 0.125) and not likely to be biologically significant. Interestingly, previous family-based studies have excluded the children’s father from the analysis [6,11]. This is notable when one considers that the children in this study were homeschooled by their mother with whom they share nearly all of their meals. These observations suggest that the father and his microbiota may be just as important as the mother in shaping a child’s microbiota. More broadly, it is likely that other caregivers and their environment may participate in shaping a child’s microbiota. Finally, the family members were as similar to each other as individuals from the Ann Arbor cohort were to each other (P = 0.433); however, based on the earlier Random Forest analysis, the family’s microbiota was clearly different from the broader community. The different microbiota represented within the family were clearly unique relative to each other and the broader community. The mechanisms that give rise to this uniqueness are likely a complex mixture of factors. Regardless, the family members appear to represent variations of a shared familial 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.


Related in: MedlinePlus