Cited by 5,748Genomics and Phylogenetic StudiesBacterial Identification and Susceptibility TestingMicrobial Community Ecology and Physiology

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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

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Jain, Chirag, Rodriguez-R, Luis M., Phillippy, Adam M., Konstantinidis, Konstantinos T., Aluru, Srinivas·2018·Nature Communications

DOI 10.1038/s41467-018-07641-9PMC PMC6269478

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Abstract

A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average Nucleotide Identity (ANI) help address this question by facilitating high resolution taxonomic analysis of thousands of genomes from diverse phylogenetic lineages. To scale to available genomes and beyond, we present FastANI, a new method to estimate ANI using alignment-free approximate sequence mapping. FastANI is accurate for both finished and draft genomes, and is up to three orders of magnitude faster compared to alignment-based approaches. We leverage FastANI to compute pairwise ANI values among all prokaryotic genomes available in the NCBI database. Our results reveal clear genetic discontinuity, with 99.8% of the total 8 billion genome pairs analyzed conforming to >95% intra-species and <83% inter-species ANI values. This discontinuity is manifested with or without the most frequently sequenced species, and is robust to historic additions in the genome databases.

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Fig. 1 Correlation of FastANI and Mash-based ANI output with ANIb values for datasets D1–D5. Because FastANI assumes a probabilistic identity cutoff that is set to 80% by default, it reports 76, 570, 4271, 464, and 130 genome matches for the individual queries in datasets D1–D5 respectively. To enable a direct quality comparison against FastANI, Mash is executed for only those pairs that are reported by FastANI. Notice that each dataset encompasses a different nucleotide identity range (x-axes). Gray line represents a straight line y = x plot for reference. Pearson correlation coefficients corresponding to these plots are listed separately in Table 2. Last plot shows error of these methods w.r.t. ANIb using all five datasetsCC BY · PubMed Central

Fig. 2 Scaling up FastANI’s performance using multi-core parallel execution. We executed parallel FastANI processes on 40 physical cores, where each process was assigned an equally sized part of the reference D1–D5 databases. Left and right plots evaluate FastANI’s compute and indexing phase, respectively. FastANI achieves reasonable speedups on all datasets except the compute phase in D1 and D5, as their runtime on a single core is too small to begin with (Table 3)CC BY · PubMed Central

Fig. 3 Genetic discontinuity observed using 90 K genomes. a Histogram plot showing the distribution of ANI values among the 90 K genomes. Only ANI values in the 76–100% range are shown. Out of total 8.01 billion pairwise genome comparisons, FastANI reported only 17M ANI values (0.21%) with ANI between 83 and 95% indicating a genetic discontinuum. Multiple colors are used to show how genomes from different genera are contributing to this distribution. Few peaks in the histogram arise from genera that have been extensively sequenced and dominate the database. b Density curves of ANI values in the ANI range 76–100%. Each curve shows the density curve corresponding to the database at a particular time period. Discontinuity in all four curves is observed consistently. c. Distribution of ANI values with each comparison labeled by the nomenclature of genomes being compared. All the comparisons between Escherichia coli and Shigella spp. have been labeled separately. The 95% ANI threshold on x-axis serves as a valid classifier for comparisons belonging to same and different speciesCC BY · PubMed Central

Fig. 4 FastANI algorithm explained using synthetic and real examples. a Illustration of FastANI’s work-flow for computing ANI between a query genome and a reference genome. Five mappings are obtained from three query fragments using Mashmap24. Mforward saves the maximum identity mapping for each query fragment. In this example, Mforward = {m2, m4, m5}. From this set, Mreciprocal picks m4 and m5 as the maximum identity mapping for each reference bin. Mapping identities of orthologous mappings, thus found in Mreciprocal, are finally averaged to compute ANI. b FastANI supports visualization of the orthologous mappings Mreciprocal that are used to estimate the ANI value using genoPlotR39. In this figure, ANI is computed between Bartonella quintana strain (NC_018533.1) as query and Bartonella henselae strain (NC_005956.1) as reference. Red line segments denote the orthologous mappings computed by FastANI for ANI estimationCC BY · PubMed Central

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098
Fast and sensitive protein alignment using DIAMOND
Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,260
Self-citation
Shifting the genomic gold standard for the prokaryotic species definition
Richter, M., & Rossello-Mora, R. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906412106 · Cited by 6,343
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Self-citation
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T. (2004) · Genome Research · doi:10.1101/gr.2289704 · Cited by 4,949
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P. A. R., & Tiedje, J. M. (2007) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.64483-0 · Cited by 4,733 · cited 2×
“Nevertheless, it closely reﬂects the traditional microbiological concept of DNA-DNA hybridization relatedness for deﬁning species (3), as it takes into account the ﬂuid nature of the bacterial gene pool and hence implicitly considers shared function.”
BackgroundMethodSelf-citation
A large-scale evaluation of algorithms to calculate average nucleotide identity
Yoon, S.-H., Ha, S. M., Lim, J., Kwon, S., & Chun, J. (2017) · Antonie van Leeuwenhoek · doi:10.1007/s10482-017-0844-4 · Cited by 3,614

Show all 40 references

Research works printed but not linked: 1

Staley, J. The phylogenomic species concept. Microbiol. Today 36, 80–83 (2009).

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“3 [40] through the Linux command line ‘.”
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Result
Phylonium: fast estimation of evolutionary distances from large samples of similar genomes
Klötzl, F., & Haubold, B. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz903 · Cited by 28
Whole-genome sequencing of dog-specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host-associated genes
Kooyman, F. N. J., Wagenaar, J. A., & Zomer, A. (2019) · Microbial Genomics · doi:10.1099/mgen.0.000302 · Cited by 28
“Average nucleotide identity (ANI) calculations were performed using FastANI [30] using default settings.”
Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation
Han, S., Kim, B., Jang, J., Park, H., & Oh, T. (2021) · BMC Genomics · doi:10.1186/s12864-021-07734-8 · Cited by 28
Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera
Raittz, R. T., Pierri, C. R. D., Maluk, M., Batista, M. B., Carmona, M., Junghare, M., Faoro, H., Cruz, L. M., Battistoni, F., de Souza, E. M., et al. (2021) · Genes · doi:10.3390/genes12010071 · Cited by 29
Emergence of Erythromycin Resistance Methyltransferases in Campylobacter coli Strains in France
Jehanne, Q., Bénéjat, L., Ducournau, A., Martins, C. D., Cousinou, T., Bessède, E., & Lehours, P. (2021) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01124-21 · Cited by 28
Comparative Genomic and Physiological Analysis against Clostridium scindens Reveals Eubacterium sp. c-25 as an Atypical Deoxycholic Acid Producer of the Human Gut Microbiota
Song, I., Gotoh, Y., Ogura, Y., Hayashi, T., Fukiya, S., & Yokota, A. (2021) · Microorganisms · doi:10.3390/microorganisms9112254 · Cited by 27
Identification of ADS024, a newly characterized strain of Bacillus velezensis with direct Clostridiodes difficile killing and toxin degradation bio-activities
Donnell, M. M. O., Hegarty, J. W., Healy, B., Schulz, S., Walsh, C. J., Hill, C., Ross, R. P., Rea, M. C., Farquhar, R., & Chesnel, L. (2022) · Scientific Reports · doi:10.1038/s41598-022-13248-4 · Cited by 28
A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters
Crits‐Christoph, A., Diamond, S., Al-Shayeb, B., Valentin-Alvarado, L. E., & Banfield, J. F. (2022) · ISME Communications · doi:10.1038/s43705-022-00140-5 · Cited by 28
“8% ANI with one of the genomes obtained from Michigan soils, indicating that they could be considered the same species based on a 95% ANI definition of microbial species [29]; all of the other genomes appeared to be separate species.”
Background
Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane
Merino, D. B., Zehnle, H., Teske, A., & Wegener, G. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.988871 · Cited by 28
Genomic and Phenotypic Trait Variation of the Opportunistic Human Pathogen Aspergillus flavus and Its Close Relatives
Hatmaker, E. A., Rangel‐Grimaldo, M., Raja, H. A., Pourhadi, H., Knowles, S. L., Fuller, K. K., Adams, E. M., Lightfoot, J. D., Bastos, R. W., Goldman, G. H., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.03069-22 · Cited by 30
“parasiticus SU-1 to confirm isolate identity using fastANI (119), which compares average nucleotide identity (ANI) between genomes.”
Method
Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host
Rosado, P. M., Cardoso, P., Rosado, J. G., Schultz, J., da Rocha, U. N., Keller‐Costa, T., & Peixoto, R. S. (2023) · mSystems · doi:10.1128/msystems.00921-22 · Cited by 28
“95% are widely used as a cutoff to determine the same-species status of genome sequences (103, 105, 106).”
BackgroundMethod
Metabarcoding using nanopore long‐read sequencing for the unbiased characterization of apicomplexan haemoparasites
Huggins, L. G., Colella, V., Young, N. D., & Traub, R. J. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13878 · Cited by 33
Efficient and robust search of microbial genomes via phylogenetic compression
Břinda, K., Lima, L., Pignotti, S., Quinones‐Olvera, N., Salikhov, K., Chikhi, R., Kucherov, G., Iqbal, Z., & Baym, M. (2025) · Nature Methods · doi:10.1038/s41592-025-02625-2 · Cited by 37
“…input genomes, MiniPhy builds upon the empirical observation that microbial genomes in public repositories tend to form clusters corresponding to individual species 34 , and species for individual genomes can be identified rapidly via metagenomic classification 35 by the Kraken suite 26 (Fig.”
Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis
Hackl, T., Martin, R., Barenhoff, K., Duponchel, S., Heider, D., & Fischer, M. (2020) · Scientific Data · doi:10.1038/s41597-020-0363-4 · Cited by 27
Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria
Uzun, M., Koziaeva, V. V., Dziuba, M. V., Leão, P., Krutkina, M. S., & Grouzdev, D. S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.945734 · Cited by 27
Population genomics of emerging Elizabethkingia anophelis pathogens reveals potential outbreak and rapid global dissemination
Hu, S., Xu, H., Meng, X., Bai, X., Xu, J., Ji, J., Ying, C., Chen, Y., Shen, P., Zhou, Y., et al. (2022) · Emerging Microbes & Infections · doi:10.1080/22221751.2022.2132880 · Cited by 27
De novogenomic analysis ofEnterobacter asburiaeEBRJ12, a plant growth-promoting rhizobacteria isolated from the rhizosphere ofPhaseolus vulgarisL
Saikia, J., Kotoky, R., Debnath, R., Kumar, N., Gogoi, P., Yadav, A., & Saikia, R. (2022) · Journal of Applied Microbiology · doi:10.1093/jambio/lxac090 · Cited by 27
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes
Yorki, S., Shea, T., Cuomo, C. A., Walker, B. J., LaRocque, R. C., Manson, A. L., Earl, A. M., & Worby, C. J. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad050 · Cited by 27
Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations
Li, D., Ren, Z., Zhou, Y., Jiang, L., Zheng, M., & Liu, G. (2023) · Applied and Environmental Microbiology · doi:10.1128/aem.00047-23 · Cited by 27
“2.11 (109) was used to calculate the ANI using the BLAST mode (2m ANIb) between the putative ammonia oxidizer MAGs and their close species in NCBI databases.”
BackgroundInfluential
New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data
Bezdíček, M., Hansliková, J., Nykrýnová, M., Dufková, K., Kocmanová, I., Kubáčková, P., Mayer, J., & Lengerová, M. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.05107-22 · Cited by 27
“To ensure the accuracy of our data set, we used high-throughput average nucleotide identity (ANI) analysis (32) against a reference E.”
Method
Isolation and Characterization of Lactic Acid Bacteria With Probiotic Attributes From Different Parts of the Gastrointestinal Tract of Free-living Wild Boars in Hungary
Keresztény, T., Libisch, B., Orbe, S. C., Nagy, T., Kerényi, Z., Kocsis, R., Posta, K., Papp, P., & Olasz, F. (2023) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-023-10113-2 · Cited by 29
“The used commands were the following for Limosilactobacillus :tree1 <- read.tree(“Limosilactobacillus.tree”); plot(tree1)and for Leuconostoc : tree2 <- read.tree(“Leuconostoc.tree”); plot(tree2) Similarity matrixes were created by using FastANI (version 1.33) [43].”
MethodInfluential
Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions
Chan, C. S., Dykes, G. E., Hoover, R. L., Limmer, M. A., & Seyfferth, A. L. (2023) · Applied and Environmental Microbiology · doi:10.1128/aem.00570-23 · Cited by 30
Genomic revisitation and reclassification of the genus Providencia
Dong, X., Jia, H., Yu, Y., Xiang, Y., & Zhang, Y. (2024) · mSphere · doi:10.1128/msphere.00731-23 · Cited by 27
“33 (51) and genome-to-genome distance calculator (formula 2) (25, 52), respectively.”
The global speciation continuum of the cyanobacterium Microcoleus
Stanojković, A., Skoupý, S., Johannesson, H., & Dvořák, P. (2024) · Nature Communications · doi:10.1038/s41467-024-46459-6 · Cited by 29
Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia
Yu, L., Jia, R., Liu, S., Li, S., Zhong, S., Liu, G., Zeng, R. J., Rensing, C., & Zhou, S. (2024) · ISME Communications · doi:10.1093/ismeco/ycae030 · Cited by 27
“%) demarcating different species [ 53], suggesting that it is possibly a novel Methylocystis sp. Particulate methane monooxygenase and soluble methane monooxygenase,encoded bythe pmoCAB operonand mmoXYBZDC operon, respectively, are two central enzymes for converting methane to methanol [54]. pmoC…”
Background
Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes
Ridley, R. S., Conrad, R. E., Lindner, B. G., Woo, S., & Konstantinidis, K. T. (2024) · Scientific Reports · doi:10.1038/s41598-024-59279-x · Cited by 32
“All vs. all genome comparisons across the study were completed at the ANI and AAI level using fastANI 106 and fastAAI 121 respectively.”
MethodSelf-citation
Genomic characterization and probiotic potential assessment of an exopolysaccharide-producing strain Pediococcus pentosaceus LL-07 isolated from fermented meat
Lu, K., Wang, X., Zhou, Y., & Zhu, Q. (2024) · BMC Microbiology · doi:10.1186/s12866-024-03304-6 · Cited by 27
“ANI values surpass 95% for the same species and fall below 95% for different species [50].”
Background
Inhibition of autotrophic nitrifiers in a nitrogen-rich paddy soil by elevated CO2
Zhang, K., Lei, W., Zhang, H., Xu, C., Xiao, J., Li, S., Liang, M., He, J., Lai, Y., Li, R., et al. (2024) · Nature Geoscience · doi:10.1038/s41561-024-01583-2 · Cited by 28
“The pairwise average nucleotide identities and average amino acid identities were calculated using FastANI (v.1.33) 70 and CompareM (v.0.1.2, https://github.com/dparks1134/CompareM), respectively.”
Influential
Growth promotion on maize and whole-genome sequence analysis of Bacillus velezensis D103
Zhang, Y., Zhang, N., Bi, X., Bi, T., Baloch, F. B., Miao, J., Zeng, N., Li, B., & An, Y. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.01147-24 · Cited by 27
Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina
Tagirdzhanova, G. M., Scharnagl, K., Sahu, N., Xia, Y., Bucknell, A., Bentham, A. R., Jégousse, C., Ament‐Velásquez, S. L., Brännström, I. O., Johannesson, H., et al. (2025) · Current Biology · doi:10.1016/j.cub.2024.12.041 · Cited by 31
Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes
Murovec, B., Deutsch, L., & Stres, B. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz237 · Cited by 27
“Although the tools are widely used, a number of limitations (supplementary table S1, Supplementary Material online) and their dispersed and boutique nature is limiting their integration and presents an obstacle to their reproducible use within community, their further adoption alongside the ubiquitous increases in seq…”
BackgroundMethodResultInfluential
Completed Genomic Sequence of Bacillus thuringiensis HER1410 Reveals a Cry -Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage
Lechuga, A., Lood, C., Salas, M., van Noort, V., Lavigne, R., & Redrejo‐Rodríguez, M. (2020) · G3 Genes Genomes Genetics · doi:10.1534/g3.120.401361 · Cited by 27
Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae
Kehlet-Delgado, H., Häse, C. C., & Mueller, R. (2020) · BMC Genomics · doi:10.1186/s12864-020-06980-6 · Cited by 27
“Average-nucleotide identity (ANI) values between all sequenced genomes and a downloaded set of reference genomes from all Vibrio species available from NCBI Genbank (date accessed: May 1st 2018) were calculated using the tool FastANI [74].”
Method
Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice
Onetto, C. A., Schmidt, S. A., Roach, M. J., & Borneman, A. R. (2020) · FEMS Yeast Research · doi:10.1093/femsyr/foaa052 · Cited by 27
Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment
Mancabelli, L., Mancino, W., Lugli, G. A., Milani, C., Viappiani, A., Anzalone, R., Longhi, G., van Sinderen, D., Ventura, M., & Turroni, F. (2021) · Applied and Environmental Microbiology · doi:10.1128/aem.02899-20 · Cited by 27
“crispatus genomes analyzed was calculated with fastANI software (103).”
Method
Rapid and Accurate Campylobacter jejuni Detection With CRISPR-Cas12b Based on Newly Identified Campylobacter jejuni-Specific and -Conserved Genomic Signatures
Huang, Y. L., Gu, D., Xue, H., Yu, J., Tang, Y., Huang, J., Zhang, Y., & Jiao, X. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.649010 · Cited by 29
“1) or C. colitype strain NCTC 11366 (refseq ID GCF_900446355), calculated using FastANI (Jain et al., 2018), was higher than the species demarcation threshold of 95% (Richter and Rossello-Mora, 2009); and (ii) the genome harbored mapA or ceuE genes and the corresponding genes could be in silico amplified (Stucki et al…”
Method
Genomic Approaches to Plant-Pathogen Epidemiology and Diagnostics
Weisberg, A. J., Grünwald, N. J., Savory, E. A., Putnam, M. L., & Chang, J. H. (2021) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-020620-121736 · Cited by 27
Isolation of AmpC- and extended spectrum β-lactamase-producing Enterobacterales from fresh vegetables in the United States
Moon, S. H., Udaondo, Z., Abram, K. Z., Li, X., Xu, Y., DiCaprio, E. L., Jun, S., & Huang, E. (2021) · Food Control · doi:10.1016/j.foodcont.2021.108559 · Cited by 27
Bartonella machadoae sp. nov. isolated from wild rodents in the Pantanal wetland
do Amaral, R. B., Cardozo, M. V., Varani, A. M., Gonçalves, L. R., Furquim, M. E. C., Dias, C. M., Santana, M. D. S., de Assis, W. O., da Silva, A. R., Herrera, H. M., et al. (2022) · Acta Tropica · doi:10.1016/j.actatropica.2022.106368 · Cited by 27
Genome Sequencing and Analysis of Trichoderma (Hypocreaceae) Isolates Exhibiting Antagonistic Activity against the Papaya Dieback Pathogen, Erwinia mallotivora
Tamizi, A. A., Amin, N. M., Weaver, J. A., Olumakaiye, R., Akbar, M. A., Jin, S., Bunawan, H., & Alberti, F. (2022) · Journal of Fungi · doi:10.3390/jof8030246 · Cited by 27
Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria
Nie, J., Utter, D., Kerns, K. A., Lamont, E., Hendrickson, E., Liu, J., Wu, T., He, X., McLean, J., & Bor, B. (2022) · mSystems · doi:10.1128/msystems.01488-21 · Cited by 29
“These ANI values stand out from typical intraspecific ANI values, which are at or above 95% or 97%, although known exceptions exist (31, 32, 40).”
Background
Strain-level profiling of viable microbial community by selective single-cell genome sequencing
Hosokawa, M., Endoh, T., Kamata, K., Arikawa, K., Nishikawa, Y., Kogawa, M., Saeki, T., Yoda, T., & Takeyama, H. (2022) · Scientific Reports · doi:10.1038/s41598-022-08401-y · Cited by 27
In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region
Belaouni, H. A., Compant, S., Antonielli, L., Nikolić, B., Zitouni, A., & Sessitsch, A. (2022) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-022-11907-0 · Cited by 27
“3 (Jain et al. 2018) and Morpheus (https:// softw are.”
Modular evolution of secretion systems and virulence plasmids in a bacterial species complex
Chou, L., Lin, Y.-C., Haryono, M., Santos, M. N. M., Cho, S., Weisberg, A. J., Wu, C., Chang, J. H., Lai, E., & Kuo, C. (2022) · BMC Biology · doi:10.1186/s12915-021-01221-y · Cited by 27
Providencia manganoxydans sp. nov., a Mn(II)-oxidizing bacterium isolated from heavy metal contaminated soils in Hunan Province, China
Li, Z., Liao, F., Ding, Z., Chen, S., & Li, D. (2022) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.005474 · Cited by 27
Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas
Li, J., Dong, C., Lai, Q., Wang, G., & Shao, Z. (2022) · mSystems · doi:10.1128/msystems.00864-22 · Cited by 27
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera
Tandon, K., Ricci, F., Costa, J. F., Medina, M., Kühl, M., Blackall, L. L., & Verbruggen, H. (2022) · GigaScience · doi:10.1093/gigascience/giac127 · Cited by 27
RND pumps across the genus Acinetobacter: AdeIJK is the universal efflux pump
Darby, E. M., Bavro, V. N., Dunn, S. J., McNally, A., & Blair, J. M. A. (2023) · Microbial Genomics · doi:10.1099/mgen.0.000964 · Cited by 27
“1) was confirmed to be >95 % using fastANI (v.1.31) [39].”
Influential
Public health implications of Yersinia enterocolitica investigation: an ecological modeling and molecular epidemiology study
Yue, Y., Zheng, J., Sheng, M., Liu, X., Hao, Q., Zhang, S.-X., Xu, S., Liu, Z., Hou, X., Jing, H., et al. (2023) · Infectious Diseases of Poverty · doi:10.1186/s40249-023-01063-6 · Cited by 27

Authors: Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S.
Affiliations: National Institutes of Health (US)
Georgia Institute of Technology (US)
Corresponding author: Konstantinidis, Konstantinos T.
Aluru, Srinivas
ORCID: Jain, Chirag
Rodriguez-R, Luis M.
Phillippy, Adam M.
Konstantinidis, Konstantinos T.
Aluru, Srinivas
Venue: Nature Communications
Publisher: Springer Science and Business Media LLC
Published: 2018-11-30
Volume: 9
Issue: 1
Pages: 5114-5114
ISSN: 2041-1723 (ISSN-L)
DOI: 10.1038/s41467-018-07641-9
PMC: PMC6269478
OpenAlex: W2951254987
Cited by: 5,748
References: 40
Citations by year: 2026: 1107 · 2025: 1110 · 2024: 977 · 2023: 789 · 2022: 695 · 2021: 617 · 2020: 305 · 2019: 128 · 2018: 16
FWCI: 96.11
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0 (tdm)
creativecommons.org/licenses/by/4.0 (vor)
Locations: Nature Communications (publishedVersion, cc-by)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, other-oa)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders: National Science Foundation (1416259, 1816027, 1356288)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Health Sciences › Medicine › Microbiology (medical) › Bacterial Identification and Susceptibility Testing
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: average nucleotide identity, prokaryotic genomes, species boundaries, taxonomic classification, draft genome sequence
MeSH terms: Phylogeny, Prokaryotic Cells, Genetic Variation, Databases, Factual, Genome, Bacterial, Sequence Analysis, DNA

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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

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