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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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MicrobeCensus enables accurate quantification of gene family abundance. Each plot shows the median abundance of essential single-copy genes across 84 stool samples from the HMP. (A) Gene family abundance was computed using relative abundance, which is scaled so the abundance of all genes sums to 1.0 for each sample. (B) Gene family abundance was computed using RPKG (reads per kilobase per genome equivalent). RPKG leverages estimates of AGS made by MicrobeCensus to normalize gene family abundance values.
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Fig6: MicrobeCensus enables accurate quantification of gene family abundance. Each plot shows the median abundance of essential single-copy genes across 84 stool samples from the HMP. (A) Gene family abundance was computed using relative abundance, which is scaled so the abundance of all genes sums to 1.0 for each sample. (B) Gene family abundance was computed using RPKG (reads per kilobase per genome equivalent). RPKG leverages estimates of AGS made by MicrobeCensus to normalize gene family abundance values.

Mentions: Strikingly, we found that the relative abundance of essential single-copy KOs (Additional file 1) varied significantly across stool samples, ranging from a minimum of 4.0e-4 to a maximum of 1.2e-3 (Figure 6A). In other words, genes that were a priori known to be present at equal copy number per cell appeared to vary in magnitude by threefold across the study. To identify the source of this bias, we first compared the inter-sample variation of essential KOs to inter-sample variation in AGS. As expected, samples with high AGS had an artificially low abundance of essential single-copy KOs. We found that AGS alone was sufficient to explain approximately 40% of the inter-sample variation of essential KOs (P = 7e-11).Figure 6


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)

MicrobeCensus enables accurate quantification of gene family abundance. Each plot shows the median abundance of essential single-copy genes across 84 stool samples from the HMP. (A) Gene family abundance was computed using relative abundance, which is scaled so the abundance of all genes sums to 1.0 for each sample. (B) Gene family abundance was computed using RPKG (reads per kilobase per genome equivalent). RPKG leverages estimates of AGS made by MicrobeCensus to normalize gene family abundance values.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: MicrobeCensus enables accurate quantification of gene family abundance. Each plot shows the median abundance of essential single-copy genes across 84 stool samples from the HMP. (A) Gene family abundance was computed using relative abundance, which is scaled so the abundance of all genes sums to 1.0 for each sample. (B) Gene family abundance was computed using RPKG (reads per kilobase per genome equivalent). RPKG leverages estimates of AGS made by MicrobeCensus to normalize gene family abundance values.
Mentions: Strikingly, we found that the relative abundance of essential single-copy KOs (Additional file 1) varied significantly across stool samples, ranging from a minimum of 4.0e-4 to a maximum of 1.2e-3 (Figure 6A). In other words, genes that were a priori known to be present at equal copy number per cell appeared to vary in magnitude by threefold across the study. To identify the source of this bias, we first compared the inter-sample variation of essential KOs to inter-sample variation in AGS. As expected, samples with high AGS had an artificially low abundance of essential single-copy KOs. We found that AGS alone was sufficient to explain approximately 40% of the inter-sample variation of essential KOs (P = 7e-11).Figure 6

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.

Show MeSH