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Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome.

Nayfach S, Pollard KS - Genome Biol. (2015)

Bottom Line: We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples.We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences.In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism.

View Article: PubMed Central - PubMed

ABSTRACT
Average genome size is an important, yet often overlooked, property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples. We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences. In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism. Importantly, we found that average genome size variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes.

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Average genome size varies systematically in human microbiome data. (A) Distribution of estimated AGS for 736 samples from the Human Microbiome Project. (B) Distribution of estimated AGS for 725 stool samples obtained from subjects originating from five different countries. (C) Estimated relative abundance of Bacteroides for the same samples shown in (B). (D) Country-specific correlations between AGS and Bacteroides relative abundance for stool samples.
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Fig5: Average genome size varies systematically in human microbiome data. (A) Distribution of estimated AGS for 736 samples from the Human Microbiome Project. (B) Distribution of estimated AGS for 725 stool samples obtained from subjects originating from five different countries. (C) Estimated relative abundance of Bacteroides for the same samples shown in (B). (D) Country-specific correlations between AGS and Bacteroides relative abundance for stool samples.

Mentions: We found significant differences in AGS between nearly all body sites within the HMP dataset (Figure 5A; Additional file 11). The stool communities had an especially large and broad range of AGS (2.8 to 5.8 Mb, mean = 3.9 Mb), which may reflect adaptation to variability in the human diet and rapid changes in the availability of nutrients. This is also consistent with previous reports that stool communities have the highest ratio of genes per operational taxonomic unit [20], and that several prominent members of the gut have large genomes, including B. thetaiotamicron (6.5 Mb), B. ovatus (6.5 Mb), and B. vulgatus (4.9 Mb). The skin and nares communities had intermediate AGS, but each contained several outliers greater than 6 Mb, while the oral and urogenital communities were characterized by the lowest AGS (mean = 2.23 and 2.11 Mb, respectively). For example, only 3 of the 396 oral samples had an estimated AGS that exceeded any of the 146 stool samples. Furthermore, we found that AGS was remarkably stable within each of the oral sites - the maximum coefficient of variation in any of the oral sites was only 0.08, in contrast to high values in stool (0.16), urogenital tract (0.23), airways (0.36), and skin (0.45) - which may be due to a combination of factors, including lower beta diversity, greater functional convergence, and less environmental variability, although these possibilities need to be investigated in greater detail.Figure 5


Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome.

Nayfach S, Pollard KS - Genome Biol. (2015)

Average genome size varies systematically in human microbiome data. (A) Distribution of estimated AGS for 736 samples from the Human Microbiome Project. (B) Distribution of estimated AGS for 725 stool samples obtained from subjects originating from five different countries. (C) Estimated relative abundance of Bacteroides for the same samples shown in (B). (D) Country-specific correlations between AGS and Bacteroides relative abundance for stool samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4389708&req=5

Fig5: Average genome size varies systematically in human microbiome data. (A) Distribution of estimated AGS for 736 samples from the Human Microbiome Project. (B) Distribution of estimated AGS for 725 stool samples obtained from subjects originating from five different countries. (C) Estimated relative abundance of Bacteroides for the same samples shown in (B). (D) Country-specific correlations between AGS and Bacteroides relative abundance for stool samples.
Mentions: We found significant differences in AGS between nearly all body sites within the HMP dataset (Figure 5A; Additional file 11). The stool communities had an especially large and broad range of AGS (2.8 to 5.8 Mb, mean = 3.9 Mb), which may reflect adaptation to variability in the human diet and rapid changes in the availability of nutrients. This is also consistent with previous reports that stool communities have the highest ratio of genes per operational taxonomic unit [20], and that several prominent members of the gut have large genomes, including B. thetaiotamicron (6.5 Mb), B. ovatus (6.5 Mb), and B. vulgatus (4.9 Mb). The skin and nares communities had intermediate AGS, but each contained several outliers greater than 6 Mb, while the oral and urogenital communities were characterized by the lowest AGS (mean = 2.23 and 2.11 Mb, respectively). For example, only 3 of the 396 oral samples had an estimated AGS that exceeded any of the 146 stool samples. Furthermore, we found that AGS was remarkably stable within each of the oral sites - the maximum coefficient of variation in any of the oral sites was only 0.08, in contrast to high values in stool (0.16), urogenital tract (0.23), airways (0.36), and skin (0.45) - which may be due to a combination of factors, including lower beta diversity, greater functional convergence, and less environmental variability, although these possibilities need to be investigated in greater detail.Figure 5

Bottom Line: We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples.We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences.In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism.

View Article: PubMed Central - PubMed

ABSTRACT
Average genome size is an important, yet often overlooked, property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples. We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences. In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism. Importantly, we found that average genome size variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes.

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