Towards estimating the number of strains that make up a natural bacterial population

Viver, Tomeu; Conrad, Roth E.; Rodriguez‐R, Luis M.; Ramírez, Ana S.; Venter, Stephanus; Rocha-Cardenas, Jairo; Llabrés, Mercè; Amann, Rudolf; Konstantinidis, Konstantinos T.; Rosselló‐Móra, Ramon

doi:10.1101/2023.02.20.529252

Cited by 8 publications

(23 citation statements)

References 34 publications

(50 reference statements)

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“…The term genomovar was originally used to name distinct genomic groups within species that cannot be distinguished phenotypically from each other and therefore cannot be classified as distinct species based on the standard taxonomic practices ( 33 ). Hence, genomovar may capture conceptually well the 99.5% ANI groups, as we also proposed recently elsewhere ( 11 ).…”

Section: Resultssupporting

confidence: 79%

“…To circumvent some of these limitations, we have recently proposed a definition threshold for strain at 99.99% ANI based on the high gene-content similarity among genomes related at this level (>99.0% of total genes, typically) and thus, phenotypic relatedness. This study was based on comparisons among 162 coexisting Salinibacter ruber isolate genomes recovered from two saltern sites in Spain ( 11 ). Testing this definition with a larger collection of genomes and how it precisely relates to STs and CCs has not been performed yet.…”

Section: Introductionmentioning

confidence: 99%

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An ANI gap within bacterial species that advances the definitions of intra-species units

Rodriguez-R,

Conrad,

Viver

et al. 2024

mBio

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Large-scale surveys of prokaryotic communities (metagenomes), as well as isolate genomes, have revealed that their diversity is predominantly organized in sequence-discrete units that may be equated to species. Specifically, genomes of the same species commonly show genome-aggregate average nucleotide identity (ANI) >95% among themselves and ANI <90% to members of other species, while genomes showing ANI 90%–95% are comparatively rare. However, it remains unclear if such “discontinuities” or gaps in ANI values can be observed within species and thus used to advance and standardize intra-species units. By analyzing 18,123 complete isolate genomes from 330 bacterial species with at least 10 genome representatives each and available long-read metagenomes, we show that another discontinuity exists between 99.2% and 99.8% (midpoint 99.5%) ANI in most of these species. The 99.5% ANI threshold is largely consistent with how sequence types have been defined in previous epidemiological studies but provides clusters with ~20% higher accuracy in terms of evolutionary and gene-content relatedness of the grouped genomes, while strains should be consequently defined at higher ANI values (>99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity. IMPORTANCE Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.

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Section: Resultssupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

An ANI gap within bacterial species that advances the definitions of intra-species units

Rodriguez-R,

Conrad,

Viver

et al. 2024

mBio

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“…Figure 1A only shows the genomes sharing OBC-types. A somewhat expected observation was that in most cases SAGs sharing the OBCs were also >99 % AAI overall i.e., they belonged to the same clonal frame or genomovar (1). This result was not surprising, since this is the fundament of strain serotyping of Gram-negative bacteria using O-antigens (12, 44).…”

Section: Resultsmentioning

confidence: 95%

“…What is the relevance of arms race processes then? In the Enterobacteriales, the gain or loss of a small number of genes (1–3) has been described within relatively short (epidemiological) timescales (19). Experimental studies have shown that isolated SNPs can make a strain resistant to one phage and also very small variations in the phage receptor-binding protein can revert the resistance (67).…”

Section: Discussionmentioning

confidence: 99%

Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales

Haro-Moreno,

López-Pérez,

Molina-Pardines

et al. 2024

Preprint

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In this study, we have used single-amplified genomes (SAGs) and long-read metagenomics to examine the intrapopulation diversity of the O-chain polysaccharide biosynthesis cluster (OBC) in marine bacteria of the Pelagibacterales order. OBCs are notorious for their diversity and have been used to type strains in pathogens and saprophytes, but their patterns of variation in free-living bacteria are little known. We found that, for these major photoheterotrophic bacteria, the diversity is comparable to that of saprophytes, such as Enterobacteriales i.e. nearly each strain carries a different OBC involved in its synthesis. Therefore, different OBCs had completely different gene complements, as they had few ortholog genes. However, although OBC inheritance was largely vertical, the existence of some shared clusters allowed a comparative analysis that showed that the cluster diverges along with the genome, indicative of old horizontal gene transfer (HGT). Only 14 cases of recent HGT were detected and they happened independently of taxonomy or location. Although the O-chain is a major phage receptor in Gram-negative bacteria, the exchange of the complete cluster seems to play a minor role in arms-race evolution. However, dN/dS was significantly larger for the genes in the OBC than for the whole genome so OBC genes appear to be more variable. By long-read metagenomics, we could detect 380 different OBCs in a single sampling site in the Mediterranean. A single population (single species and sample) of the endemic Ia.3/VII genomospecies had a set of 158 OBCs of which 130 were different.

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“…No other pronounced ANI gap within the 300 evaluated species was consistently observed, and thus we recommend the use of the term strain only for nearly identical genomes. Specifically, we propose to define a strain as a collection of genomes sharing ANI > 99.99% based on the high gene content similarity observed at this level based on the genomes compared; for example, typically, >99.0% gene content is shared (Viver et al 31 and Table 1). It should be mentioned, however, that a 1% gene content difference for a 5 Mbp genome (e.g., E. coli 's average genome size) translates to 50 genes, which represents a substantial (nontrivial) gene content difference and could underlie significant phenotypic differences such as different antibiotic resistance profiles and plasmid DNA content 28 .…”

Section: An Ani Gap Within Species To Define Subspecies Unitsmentioning

confidence: 99%

Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues

Konstantinidis

2023

mLife

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Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence‐discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter “intermediate” organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often—but not always—appears to be around 85%–95% genome‐average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.

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Towards estimating the number of strains that make up a natural bacterial population

Cited by 8 publications

References 34 publications

An ANI gap within bacterial species that advances the definitions of intra-species units

An ANI gap within bacterial species that advances the definitions of intra-species units

Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales

Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues

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