Consistent metagenome-derived metrics verify and define bacterial species boundaries

Abstract

Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. We compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity, and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of non-synonymous and synonymous nucleotide differences ( dN / dS ) decrease until ANI values approach 98%, estimates for homologous recombination approached zero at~95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full length 16S rRNA genes were least useful because they were under-recovered from metagenomes, but many ribosomal proteins displayed both high metagenomic recoverability and species-discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination.

Genome of a Novel Bacterium “Candidatus Jettenia ecosi” Reconstructed From the Metagenome of an Anammox Bioreactor

“…Among the members of the genus “ Candidatus Jettenia,” genome sequence is available only for “ Candidatus Jettenia caeni” KSU-1 (GenBank NZ_BAFH00000000); the value of in silico DNA-DNA hybridization of J2 and KSU-1 genomes was about 60%, which does not allow whether these bacteria belong to a single or different species to be defined. The ANI between the genomes of J2 and KSU-1 was 94.91%, a value just below the species boundary cutoff of 95% (Konstantinidis and Tiedje, 2005; Jain et al, 2018), suggesting a recent divergence and speciation of these species (Olm et al, 2019).…”

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

“…To compare microbial community compositions across samples with various depths, vegetations, and bedrock lithologies, assembled sequences of ribosomal protein S3 (rpS3) were used as marker genes for identifying different taxa. RpS3 is a universal single-copy gene, assembles well from metagenomic data, and is recovered more frequently than whole genomes, which allows a more inclusive view of microbial communities (20). Our rpS3 analysis indicates that microbial communities across the Eel River Critical Zone Observatory (CZO) were generally dominated by the same bacterial phyla (Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, Chloroflexi, and Gemmatimonadetes) but that community compositions were distinct between sampling sites and at different depths within the same site ( Fig.…”

Comprehensive mouse gut metagenome catalog reveals major difference to the human counterpart

“…To remove this potential redundancy, we clustered the genomes based on the ANI calculated using bindash (Zhao, 2018). 95% ANI was used as a threshold to delineate genomes from the same species (Jain et al, 2018;Olm et al, 2019). For each species cluster, the genome with the highest quality and lowest fragmentation was selected as representative, but reference genomes were preferred over MAGs.…”