Estimate of the sequenced proportion of the global prokaryotic genome

Abstract

Background: Sequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases.

Results: Our results showed that the median proportions of the genome-sequenced cells and taxa (at 100% identities in the 16S-V4 region) in different biomes reached 38.1% (16.4-86.3%) and 18.8% (9.1-52.6%), respectively. The sequenced proportions of the prokaryotic genomes in biomes were significantly negatively correlated with the alpha diversity indices, and the proportions sequenced in host-associated biomes were significantly higher than those in free-living biomes. Due to a set of cosmopolitan OTUs that are found in multiple samples and preferentially sequenced, only 2.1% of the global prokaryotic taxa are represented by sequenced genomes. Most of the biomes were occupied by a few predominant taxa with a high relative abundance and much higher genome-sequenced proportions than numerous rare taxa.

Conclusions: These results reveal the current situation of prokaryotic genome sequencing for earth biomes, provide a more reasonable and efficient exploration of prokaryotic genomes, and promote our understanding of microbial ecological functions. Video Abstract.

Keywords: Earth microbiome project; Genome sequencing; Microbiome; Predominant taxa; Prokaryotic biome.

Fig. 1

Genome-sequenced degree of prokaryotic biomes. a Genome-sequenced proportion of cells. b Genome-sequenced proportion of taxa. OTUs share 100% identities with the sequenced genomes. Based on the analysis of 10,000 EMP samples, each gray point represents a single sample. For the box plots, the middle line indicates the median, the box represents the 25th–75th percentiles, and the error bar indicates the 10th–90th percentiles of observations. Environment types were classified by EMPO; red represents host associated and green represents free living

Fig. 2

High genome-sequenced proportion of prokaryotic cosmopolitan taxa. a OTUs that can exist in one or more samples. b OTUs that can exist in one or more environment types. The gray column represents the proportion of OTUs that can exist in one or more samples (environments), and the red column represents the genome-sequenced proportion of OTUs. c Lower P_OTU than B_OTU is caused by a high genome-sequenced proportion of cosmopolitan taxa

Fig. 3

Genome-sequenced proportion of prokaryotic taxa from global or different environment types. a As the number of samples increases, the P_{OTU (100%)} shows an exponential declining trend and finally stabilizes at 2.1%. A random selection of 1000, 2000…, 9000 samples was performed 10 times for each group to calculate the mean value and standard deviation. b Significant difference of P_OTU among environment types. The red point is P_{OTU (100%)}, the blue point is P_{OTU (98.6%)}, and the orange point is P_{OTU (97%)}

Fig. 4

High genome-sequenced proportion of prokaryotic taxa with high abundance. a The top 1% of the prokaryotic taxa account for 72.9% of the global prokaryotic biomes. b The top 1% of the prokaryotic taxa from different environment types accounted for more than 40% with a genome-sequenced proportion greater than 10%. The gray column represents the cellular proportion of the top 1% of the taxa, and the red column represents the P_{OTU (100%)}. c High genome-sequenced proportion of the top 1%. The red line is P_{OTU (100%)}, the blue line is P_{OTU (98.6%)}, and the orange line is P_{OTU (97%)}