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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.


Relative abundance of operational taxonomic units (OTUs) detected in all weaned individuals within the family. The colors represent the average relative abundance of each OTU in each individual and as observed in the broader community. The percentages at the bottom of the heatmap indicate the percentage of sequences these OTUs represent in each individual.
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Figure 2: Relative abundance of operational taxonomic units (OTUs) detected in all weaned individuals within the family. The colors represent the average relative abundance of each OTU in each individual and as observed in the broader community. The percentages at the bottom of the heatmap indicate the percentage of sequences these OTUs represent in each individual.

Mentions: It has been repeatedly shown that an individual’s microbiota is more similar to itself over time and more similar to family members than it is to unrelated individuals [6,18,19]. Thus, it was hypothesized that within the family there exists a ‘theme’ or core microbiota that distinguishes it from other families. To identify the core microbiota for each individual we identified those OTUs that had a relative abundance over 0.05% in at least 95% of their samples. This resulted in the identification of between 4 (infant) and 58 (mother) OTUs, which represented the core for each individual (Table 1); these represented between 1.8 and 7.7% of the OTUs that were detected for each individual. When we compared the lists of core OTUs from each individual to identify the family’s core microbiota, there was no overlap; however, when we removed the infant from the analysis, we identified 12 OTUs that were common to each person’s core microbiota (Figure 2). We also analyzed the Ann Arbor cohort and identified four OTUs that were found in 95% of the cohort members. These OTUs affiliated with members of the genus Bacteroides (OTU 3), family Lachnospiraceae (OTUs 4 and 9), and genus Subdoligranulum (OTU 12); OTUs 4, 9, and 12 were shared with the family core microbiota. The 12 OTUs that comprised the family’s core microbiota represented between 32.0 and 57.9% of the sequences in the 7 family members who were eating solids, 3.6% of the sequences in the infant, and 13.4% of the sequences obtained from the Ann Arbor cohort (Figure 2). These data indicate that a considerable fraction of each individual’s microbiota is represented by a core microbiota consisting of anaerobic Gram-positive spore formers.


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

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

Relative abundance of operational taxonomic units (OTUs) detected in all weaned individuals within the family. The colors represent the average relative abundance of each OTU in each individual and as observed in the broader community. The percentages at the bottom of the heatmap indicate the percentage of sequences these OTUs represent in each individual.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Relative abundance of operational taxonomic units (OTUs) detected in all weaned individuals within the family. The colors represent the average relative abundance of each OTU in each individual and as observed in the broader community. The percentages at the bottom of the heatmap indicate the percentage of sequences these OTUs represent in each individual.
Mentions: It has been repeatedly shown that an individual’s microbiota is more similar to itself over time and more similar to family members than it is to unrelated individuals [6,18,19]. Thus, it was hypothesized that within the family there exists a ‘theme’ or core microbiota that distinguishes it from other families. To identify the core microbiota for each individual we identified those OTUs that had a relative abundance over 0.05% in at least 95% of their samples. This resulted in the identification of between 4 (infant) and 58 (mother) OTUs, which represented the core for each individual (Table 1); these represented between 1.8 and 7.7% of the OTUs that were detected for each individual. When we compared the lists of core OTUs from each individual to identify the family’s core microbiota, there was no overlap; however, when we removed the infant from the analysis, we identified 12 OTUs that were common to each person’s core microbiota (Figure 2). We also analyzed the Ann Arbor cohort and identified four OTUs that were found in 95% of the cohort members. These OTUs affiliated with members of the genus Bacteroides (OTU 3), family Lachnospiraceae (OTUs 4 and 9), and genus Subdoligranulum (OTU 12); OTUs 4, 9, and 12 were shared with the family core microbiota. The 12 OTUs that comprised the family’s core microbiota represented between 32.0 and 57.9% of the sequences in the 7 family members who were eating solids, 3.6% of the sequences in the infant, and 13.4% of the sequences obtained from the Ann Arbor cohort (Figure 2). These data indicate that a considerable fraction of each individual’s microbiota is represented by a core microbiota consisting of anaerobic Gram-positive spore formers.

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.