Metagenomic Insights into Bacterial Species

Konstantinidis, Konstantinos T.

doi:10.1002/9781118010518.ch11

Cited by 5 publications

(8 citation statements)

References 67 publications

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“…Similarly, populations of Group I Crenarchaea, an abundant ammonia-oxidizing marine archaeal group, were genetically very similar between the Mediterranean Sea and the Pacific Ocean at similar depths (3000 m and 4000 m respectively) [ Fig. 2 and in Konstantinidis (2011)]. In contrast, populations of Prochlo- (Konstantinidis and DeLong, 2008) by selected crenarchaeal populations from the same site but different depths (Station Aloha, Pacific Ocean) or the Mediterranean Sea (figure key).…”

Section: Biogeography Of Sequence-discrete Populations and Cases Of Imentioning

confidence: 90%

“…Similarly, populations of Group I Crenarchaea , an abundant ammonia‐oxidizing marine archaeal group, were genetically very similar between the Mediterranean Sea and the Pacific Ocean at similar depths (3000 m and 4000 m respectively) [Fig. 2 and in Konstantinidis (2011)]. In contrast, populations of Prochlorococcus (Coleman and Chisholm, 2010) and Crenarchaea (Konstantinidis, 2011) were distinct at different depths within the water column, resulting from genomic adaptations to the unique physicochemical conditions that characterize each depth (e.g.…”

Section: Biogeography Of Sequence‐discrete Populations and Cases Of Imentioning

confidence: 91%

“…2 and in Konstantinidis (2011)]. In contrast, populations of Prochlorococcus (Coleman and Chisholm, 2010) and Crenarchaea (Konstantinidis, 2011) were distinct at different depths within the water column, resulting from genomic adaptations to the unique physicochemical conditions that characterize each depth (e.g. different hydrostatic pressure, light and resource availability).…”

Section: Biogeography Of Sequence‐discrete Populations and Cases Of Imentioning

confidence: 99%

“…they are roughly as divergent from each other as each population is from the 4000 m population, while the 500 m population is more related (∼ 90% ANI) to the population from 200 m (data not shown), which is consistent with the vertical zonation of the water column. The graph is drawn based on the data in Konstantinidis (2011) and Konstantinidis and DeLong (2008).…”

Section: Biogeography Of Sequence‐discrete Populations and Cases Of Imentioning

confidence: 99%

“…In fact, when organisms from different depths were analysed together, a genetic continuum, which included organisms showing the whole range of nucleotide identity relatedness from 70% to 100%, as opposed to sequence-discrete clusters, was observed [ Fig. 2 and in Konstantinidis (2011)]. These results reveal that the sequence-discrete populations are not limited to a specific site or represent an artefact of a few samples analysed; rather, they are distributed worldwide in interconnected habitats that are characterized by similar environmental conditions, which is consistent with the notion that they represent the important units of diversity.…”

Section: Biogeography Of Sequence-discrete Populations and Cases Of Imentioning

confidence: 99%

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Bacterial species may exist, metagenomics reveal

Caro‐Quintero¹,

Konstantinidis

2011

Environmental Microbiology

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SummaryWhether or not bacterial species exist remains an unresolved issue of paramount theoretical as well as practical consequences. Here we review and synthesize the findings emerging from metagenomic surveys of natural microbial populations and argue that microbial communities are predominantly organized in genetically and ecologically discernible populations, which possess the attributes expected for species. These sequence-discrete populations represent a major foundation for beginning highresolution investigations on how populations are organized, interact, and evolve within communities. We also attempt to reconcile these findings with those of previous studies that reported indiscrete species and a genetic continuum within bacterial taxa and discuss the implications for the current bacterial species definition.

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Section: Biogeography Of Sequence-discrete Populations and Cases Of Imentioning

confidence: 90%

Section: Biogeography Of Sequence‐discrete Populations and Cases Of Imentioning

confidence: 91%

Section: Biogeography Of Sequence‐discrete Populations and Cases Of Imentioning

confidence: 99%

Section: Biogeography Of Sequence‐discrete Populations and Cases Of Imentioning

confidence: 99%

Section: Biogeography Of Sequence-discrete Populations and Cases Of Imentioning

confidence: 99%

See 3 more Smart Citations

Bacterial species may exist, metagenomics reveal

Caro‐Quintero¹,

Konstantinidis

2011

Environmental Microbiology

Self Cite

177

136

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Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal

Konstantinidis

Rosselló‐Móra

2015

Systematic and Applied Microbiology

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Microbial taxonomists have generally been reluctant to accept the valid publication of names of uncultured taxa given that only pure cultures allow for a thorough description of the genealogy, genetics and phenotype of the putative taxa to be classified. The classification of conspicuous uncultured organisms has been considered into the Candidatus provisional status, but this is only possible with organisms for which it is possible to retrieve basic data on phylogeny, morphology, ecology and some metabolic traits that unequivocally identify them. The current developments on modern sequencing techniques, and especially metagenomics, allow the recognition of discrete populations of DNA sequences in environmental samples, which can be considered to belong to individual closely related populations that may be identified as members of yet-to-be described species. The recognition of such populations of (meta)genomes allow the retrieval of valuable taxonomic information, i.e. genealogy, genome, phenotypic coherence with other populations, and ecological relevant traits. Such traits may be included in the Candidatus proposals of environmentally occurring, yet uncultured species not exhibiting exceptional morphologies, phenotypes or ecological relevancies.

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Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species”

Rodriguez-R

Jain²,

Conrad

et al. 2021

Nat Commun

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It has recently been reported 1 that when one removes multiple genomes within a named species or species defined at the 95% genome-aggregate average nucleotide identity (ANI) level by sampling one genome per species or only two genomes that maximize the represented diversity within the species 1 , the ANI discontinuity (or "ANI gap") observed between species based on all available genomes is lost. [Discontinuity or gap here refers to the small number of genome pairs showing 85-95% ANI relative to counts of pairs showing >95% and <85% ANI]. In other words, the bimodal distribution of ANI values previously observed by comparing the ~90,000 genomes available in the NCBI database 2 disappears. These results also echo earlier findings by others based on different genome datasets [e.g 3 ,]. Murray and colleagues have interpreted these results as evidence that a natural genetic discontinuity (i.e., an ANI boundary) between species may not exist, and the previously observed ANI boundary could simply be the result of isolation biases that favor redundant (or closely related) organisms. Note that there is no universally accepted species concept for prokaryotes (i.e., what a species is) but there are widely used standards on how to name species (i.e., a working species definition) 4 . The ~10,000 species that have been described to date and have sequenced representative genomes in the public databases in order to be included in our analysis (out of a total 17,000 described species) are largely consistent (>95% of the cases) with the application of the 95% ANI criterion, i.e., genomes showing <95% ANI among themselves have been typically assigned to different species 2 .

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Metagenomic Insights into Bacterial Species

Cited by 5 publications

References 67 publications

Bacterial species may exist, metagenomics reveal

Bacterial species may exist, metagenomics reveal

Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal

Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species”

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