Microbial species delineation using whole genome sequences

Varghese, Neha; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T.; Mavrommatis, Konstantinos; Kyrpides, Nikos C.; Pati, Amrita

doi:10.1093/nar/gkv657

Cited by 621 publications

(616 citation statements)

References 30 publications

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“…Genomes with an AAI of ≥ 99.5% to a seed genome, as calculated over the 120 bacterial or 122 archaeal marker genes used for phylogenetic inference, were clustered with the seed genome and do not appear as separate genomes in the genome trees. This cutoff correlated with the proposed 96.5% ANI threshold for defining bacterial and archaeal species 57 ( Supplementary Fig. 6).…”

Section: Nature Microbiologysupporting

confidence: 67%

“…The 3,438 nearcomplete (≥ 90% complete; ≤ 5% contamination) UBA genomes were compared to complete isolate genomes in RefSeq release 76. Of these, 207 of the UBA genomes were determined to be conspecific strains of complete isolate genomes based on an average nucleotide identity (ANI) and alignment fraction (AF) above 96.5% and 60%, respectively 57 . ANI and AF values were determined using ANI Calculator 57 v.1.…”

Section: Nature Microbiologymentioning

confidence: 99%

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

et al. 2017

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Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from > 1,500 public metagenomes. All genomes are estimated to be ≥ 50% complete and nearly half are ≥ 90% complete with ≤ 5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by > 30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter. Articles NATuRe MiCRobiologyform the UBA data set as they met our filtering criteria of having an estimated quality ≥ 50 (defined as the estimated completeness of a genome minus five times its estimated contamination) and consisting of ≤ 500 scaffolds with an N50 ≥ 10 kb ( Fig. 1 and Supplementary Table 2). Over 93% of the 7,903 UBA genomes have an average coverage of ≥ 10× (5th percentile, 9.2× , 95th percentile, 268× ) and 95.8% have > 5× coverage over 90% of bases, providing assurance of high-quality base-calling across the genomes 3,36 . Among the UBA genomes is a subset of 3,438 near-complete genomes (3,225 bacterial and 213 archaeal) estimated to be ≥ 90% complete with ≤ 5% contamination (Fig. 1a). These genomes consist of ≤ 100 scaffolds in 70.2% of cases (≤ 200 scaffolds in 92.0% genomes) and have an average N50 of 136 kb. Comparison of near-complete UBA genomes that are conspecific strains of complete isolate genomes also suggest that the recovered MAGs have no systematic loss of genomic content, with the exception of extrachromosomal elements such as plasmids (Supplementary Note 1).The UBA data set was also assessed relative to the criteria used by the Human Microbiome Project (HMP) for defining high-quality draft genomes 3,37 . Of the 3,438 UBA genomes we have defined as near complete, 3,201 (93.1%) pass all of the HMP criteria, with the only substantial exception being 4.8% of the genomes having scaffolds with an N50 of < 20 kb (Supplementary Table 3). Nearly half of the remaining 4,465 UBA genomes also pass the HMP criteria for being high quality except that they are estimated to be < 90% complete.The presence of tRNAs for the standard 20 amino acids was examined as a secondary measure of genome quality (Fig. 1c). The 3,438 near-complete UBA genomes have tRNAs that encode for an average of 17.3 ± 2.2 of the 20 amino acids and ≥ 15 amino acids in 90.3% of the genomes. The correlation between estimated genome completeness and identified tRN...

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Section: Nature Microbiologysupporting

confidence: 67%

Section: Nature Microbiologymentioning

confidence: 99%

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

et al. 2017

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“…The Ca. U. copiosus genome shares only 69.3% average nucleotide identity 21 with the genome of its closest sequenced relative C. flavus, further supporting its proposed placement in the distinct genus 'Candidatus Udaeobacter'. Although no 16S rRNA gene was assembled within the Ca.…”

Section: Resultsmentioning

confidence: 85%

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

et al. 2016

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Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name ‘Candidatus Udaeobacter copiosus’. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

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“…The gyrB database is composed of 30,525 sequences retrieved from 30,175 genomic sequences available in the IMG database v4 (Markowitz et al 2012). According to the gANI cliques defined previously by Varghese and collaborators (Varghese et al 2015), the gyrB marker has the best precision (0.964) and sensitivity (0.955) at a genetic distance of 0.02 (Barret et al 2015).…”

Section: Resultsmentioning

confidence: 99%

Assembly of seed-associated microbial communities within and across successive plant generations

et al. 2017

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Background and aims Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.Methods Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model. Results Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota. Conclusions These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.

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Microbial species delineation using whole genome sequences

Cited by 621 publications

References 30 publications

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

Assembly of seed-associated microbial communities within and across successive plant generations

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