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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Self-citation
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Osvatic, J., Wilkins, L. G. E., Leibrecht, L., Leray, M., Zauner, S., Polzin, J., Camacho-García, Y. E., Gros, O., van Gils, J. A., Eisen, J. A., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2104378118 · Cited by 37
Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium
Colombi, E., Perry, B. J., Sullivan, J. T., Bekuma, A. A., Terpolilli, J. J., Ronson, C. W., & Ramsay, J. P. (2021) · Microbial Genomics · doi:10.1099/mgen.0.000657 · Cited by 38
Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena
de la Haba, R. R., Minegishi, H., Kamekura, M., Shimane, Y., & Ventosa, A. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.740909 · Cited by 37
“…can also be employed for genus demarcation–, ANIb (Goris et al., 2007), ANIm, TETRA (Richter and Rossello-Mora, 2009), MUMi (Deloger et al., 2009), dDDH (Meier-Kolthoff et al., 2013), gANI, alignment fraction (Varghese et al., 2015), OrthoANI (Lee et al., 2016), and FastANI (Jain et al., 2018).”
Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota
Bhattacharjee, D., Flores, C., Woelfel-Monsivais, C., & Seekatz, A. M. (2022) · mSphere · doi:10.1128/msphere.00569-22 · Cited by 38
“an expected cutoff for a genus (90%)- or species-level (95%) comparison (53, 54) (Fig.”
Background
Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis
Osvatic, J., Yuen, B., Kunert, M., Wilkins, L. G. E., Hausmann, B., Girguis, P. R., Lundin, K., Taylor, J. D., Jospin, G., & Petersen, J. M. (2023) · The ISME Journal · doi:10.1038/s41396-022-01355-z · Cited by 34
Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.
Kiu, R., Darby, E. M., Alcon-Giner, C., Acuna-Gonzalez, A., Camargo, A., Lamberte, L. E., Phillips, S., Sim, K., Shaw, A. G., Clarke, P., et al. (2025) · Nature communications · doi:10.1038/s41467-025-62584-2 · Cited by 36
A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH
Cortez, D., Neira, G., González, C., Vergara, E., & Holmes, D. S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.803241 · Cited by 38
A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans
Li, F., Li, X., Cheng, C. C., Bujdoš, D., Tollenaar, S. L., Simpson, D. J. W., Tasseva, G., Pérez-Muñoz, M. E., Frese, S. A., Gänzle, M. G., et al. (2023) · BMC Biology · doi:10.1186/s12915-023-01541-1 · Cited by 34
Pangenomic Study of Fusobacterium nucleatum Reveals the Distribution of Pathogenic Genes and Functional Clusters at the Subspecies and Strain Levels
Ma, X., Sun, T., Zhou, J., Zhi, M., Shen, S., Wang, Y., Gu, X., Li, Z., Gao, H., Wang, P., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.05184-22 · Cited by 34
“nucleatum, an ANI analysis was performed using the FastANI software (58) with default parameters, and the results were visualized as a heatmap.”
Method
Bacterial and archaeal community distributions and cosmopolitanism across physicochemically diverse hot springs
Sriaporn, C., Campbell, K. A., Kranendonk, M. J. V., & Handley, K. M. (2023) · ISME Communications · doi:10.1038/s43705-023-00291-z · Cited by 35
Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species
Marin, M. G., Quinones‐Olvera, N., Wippel, C., Behruznia, M., Jeffrey, B. M., Harris, M., Mann, B., Rosenthal, A., Jacobson, K. R., Warren, R. M., et al. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf219 · Cited by 36
“3) run with default parameters to estimate Average Nucleotide Identity (ANI) between all pairs of complete genomes (Jain et al. 2018).”
Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat
Nguyen, H. D. T., Sultana, T., Kesanakurti, P. R., & Hambleton, S. (2019) · IMA Fungus · doi:10.1186/s43008-019-0011-9 · Cited by 36
High-Risk International Clones of Carbapenem-Nonsusceptible Pseudomonas aeruginosa Endemic to Indonesian Intensive Care Units: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level
Pelegrin, A. C., Saharman, Y. R., Griffon, A., Palmieri, M., Mirande, C., Karuniawati, A., Sedono, R., Aditianingsih, D., Goessens, W. H. F., van Belkum, A., et al. (2019) · mBio · doi:10.1128/mbio.02384-19 · Cited by 35
New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements
Mageeney, C. M., Lau, B. Y., Wagner, J. M., Hudson, C. M., Schoeniger, J. S., Krishnakumar, R., & Williams, K. P. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa156 · Cited by 36
“Pairwise average nucleotide identity (ANI) values between IGEs were taken using fastANI (52) with arguments ‘-k -t 120 –fragLen 500 –minFrag 2’ to accommodate the minimum size allowed for our IGEs.”
Method
Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics
Zhang, Y., Xu, J. H., Wang, E. T., & Wang, N. (2020) · Microorganisms · doi:10.3390/microorganisms8040583 · Cited by 36
Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System
Merino, N., Kawai, M., Boyd, E. S., Colman, D. R., McGlynn, S. E., Nealson, K. H., Kurokawa, K., & Hongoh, Y. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01031 · Cited by 36
Tenacibaculum piscium sp. nov., isolated from skin ulcers of sea-farmed fish, and description of Tenacibaculum finnmarkense sp. nov. with subdivision into genomovars finnmarkense and ulcerans
Olsen, A. B., Spilsberg, B., Nilsen, H., Lagesen, K., Gulla, S., Avendaño-Herrera, R. E., Irgang, R., Duchaud, É., & Colquhoun, D. J. (2020) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.004501 · Cited by 36
Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains
Volpiano, C. G., Sant’Anna, F. H., Ambrosini, A., José, J. F. B. D. S., Beneduzi, A., Whitman, W. B., de Souza, E. M., Lisboa, B. B., Vargas, L. K., & Passaglia, L. M. P. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.614957 · Cited by 36
“…with OGRI values, new algorithms with optimized search parameters (Lee I. et al., 2016; Rodriguez-R and Konstantinidis, 2016) or to speeding up the search process (Richter and RossellóMóra, 2009; Varghese et al., 2015; Yoon et al., 2017b; Jain et al., 2018) are continuously being developed.”
MethodInfluential
Comparative Genomic Analysis of the Foodborne Pathogen Burkholderia gladioli pv. cocovenenans Harboring a Bongkrekic Acid Biosynthesis Gene Cluster
Peng, Z., Dottorini, T., Hu, Y., Li, M., Yan, S., Fanning, S., Baker, M., Xu, J., & Li, F. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.628538 · Cited by 37
“324 (Jain et al., 2018).”
BackgroundResultInfluential
Recent paradigm shifts in the perception of the role of Bacillus thuringiensis in foodborne disease
Biggel, M., Jeßberger, N., Kovač, J., & Johler, S. (2022) · Food Microbiology · doi:10.1016/j.fm.2022.104025 · Cited by 44
Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence
Seol, D., Lim, J. S., Sung, S., Lee, Y. H., Jeong, M., Cho, S., Kwak, W., & Kim, H. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02017-21 · Cited by 37
Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets
Mohite, O. S., Lloyd, C. J., Monk, J. M., Weber, T., & Palsson, B. Ø. (2022) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2022.04.011 · Cited by 35
Comparative Genomics of Members of the Genus Defluviicoccus With Insights Into Their Ecophysiological Importance
Bessarab, I. N., Maszenan, A. M., Haryono, M., Arumugam, K., Saw, N. M. M. T., Seviour, R. J., & Williams, R. B. H. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.834906 · Cited by 35
Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system
Wang, Y.-L., Zhang, Y.-L., Hu, Y., Liu, L., Liu, S.-J., & Zhang, T. (2023) · Microbiome · doi:10.1186/s40168-023-01494-1 · Cited by 32
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota
Lugli, G. A., Mancabelli, L., Milani, C., Fontana, F., Tarracchini, C., Alessandri, G., van Sinderen, D., Turroni, F., & Ventura, M. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00392-6 · Cited by 36
Rhizobium brockwellii sp. nov., Rhizobium johnstonii sp. nov. and Rhizobium beringeri sp. nov., three genospecies within the Rhizobium leguminosarum species complex
Young, J. P. W., Jorrín, B., Moeskjær, S., & James, E. K. (2023) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.005979 · Cited by 35
Genomic and transcriptomic insights into complex virus–prokaryote interactions in marine biofilms
Zhou, K., Wong, T. Y., Long, L., Anantharaman, K., Zhang, W., Wong, W. C., Zhang, R., & Qian, P. (2023) · The ISME Journal · doi:10.1038/s41396-023-01546-2 · Cited by 35
“FastANI v.1.33 was employed to calculate ANI for viruses with custom parameters (--fragLen 500 -minFraction 0.8) and for prokaryotic hosts with a custom setting (-minFraction 0.5) [44].”
MethodInfluential
Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany
Wahl, A., Fischer, M. A., Klaper, K., Müller, A., Borgmann, S., Friesen, J., Hunfeld, K., Ilmberger, A., Kolbe-Busch, S., Kresken, M., et al. (2024) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2024.151601 · Cited by 36
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes
Sulaiman, J. E., Thompson, J. C., Qian, Y., Vivas, E. I., Diener, C., Gibbons, S. M., Safdar, N., & Venturelli, O. S. (2024) · Nature Communications · doi:10.1038/s41467-024-51062-w · Cited by 36
The functional dominance and metabolic diversity of comammox Nitrospira in recirculating aquaculture systems
Chai, Z., Tian, Z., Zheng, M., Wang, B., Li, Y., Cui, J., Ju, F., Niu, J., & Guo, J. (2024) · Water Research · doi:10.1016/j.watres.2024.122949 · Cited by 35
High-throughput analysis of microbiomes in a meat processing facility: are food processing facilities an establishment niche for persisting bacterial communities?
Xu, Z. S., Pham, V. D., Yang, X., & Gänzle, M. G. (2025) · Microbiome · doi:10.1186/s40168-024-02026-1 · Cited by 37
Interindividual variability in gut microbiome mediates the efficacy of resistant starch on MASLD
Long, X., Wang, H., Lu, Y., Gao, X., Xiao, Y., Zhang, M., Guo, J., Yang, H. J., Zhang, R., Li, Q., et al. (2025) · Cell Metabolism · doi:10.1016/j.cmet.2025.10.017 · Cited by 37
Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters
González, V., Santamaría, R. I., Bustos, P., Pérez-Carrascal, O. M., Vinuesa, P., Juárez, S., Martínez‐Flores, I., Cevallos, M. A., Brom, S., Martínez‐Romero, E., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00910 · Cited by 35
“…et al., 2006; Young et al., 2006; Shamseldin et al., 2016); and, (iii) the fact that large mobile plasmids—known as symbiotic plasmids, or pSym—and symbiotic islands encode most of the essential genes for root nodulation and nitrogen fixation (Johnston et al., 1978; Sullivan and Ronson, 1998).”
Background
Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila
Kosakamoto, H., Yamauchi, T., Akuzawa-Tokita, Y., Nishimura, K., Soga, T., Murakami, T., Mori, H., Yamamoto, K., Miyazaki, R., Koto, A., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107938 · Cited by 35
Microbial Strategies for Survival in the Glass Sponge Vazella pourtalesii
Bayer, K., Busch, K., Kenchington, E., Beazley, L. I., Franzenburg, S., Michels, J., Hentschel, U., & Slaby, B. M. (2020) · mSystems · doi:10.1128/msystems.00473-20 · Cited by 35
“The phylogenomic trees produced by GTDB-Tk (77, 92, 93) were visualized on the Interactive Tree Of Life (iTOL) platform v4.”
Method
‘Species’ without species
Novick, A., & Doolittle, W. F. (2021) · Studies in History and Philosophy of Science Part A · doi:10.1016/j.shpsa.2021.03.006 · Cited by 35
Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster
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“The species affiliations of the genomes encoding the full kleboxymycin BGC were determined using FastANI v1.”
BackgroundMethodInfluential
Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes
Ramírez-Fernández, L., Orellana, L. H., Johnston, E. R., Konstantinidis, K. T., & Orlando, J. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.147693 · Cited by 33
Self-citation
Genomic and Physiological Characterization of Bacilli Isolated From Salt-Pans With Plant Growth Promoting Features
Petrillo, C., Castaldi, S., Lanzilli, M., Selci, M., Cordone, A., Giovannelli, D., & Isticato, R. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.715678 · Cited by 35
Strategy for enhancing Cr(VI)-contaminated soil remediation and safe utilization by microbial-humic acid-vermiculite-alginate immobilized biocomposite
Wu, M., Wang, Q., Wang, C., Zeng, Q., Li, J., Wu, H., Wu, B., Xu, H. Y., & Qiu, Z. (2022) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2022.113956 · Cited by 35
Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes
Bista, P. K., Pillai, D., Roy, C., Scaria, J., & Narayanan, S. K. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00297-22 · Cited by 33
“necrophorum were analyzed using the FastANI algorithm by constructing an ANI heat map (53).”
Method
Linking prokaryotic genome size variation to metabolic potential and environment
Rodríguez-Gijón, A., Buck, M., Andersson, A., Izabel-Shen, D., Nascimento, F. J. A., & Garcia, S. (2023) · bioRxiv · doi:10.1038/s43705-023-00231-x · Cited by 29
Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research
Baker, J. L. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad051 · Cited by 37
Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice
Gellman, R., Olm, M. R., Terrapon, N., Enam, F., Higginbottom, S. K., Sonnenburg, J. L., & Sonnenburg, E. D. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113233 · Cited by 34
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets
Nuhamunada, M., Mohite, O. S., Phaneuf, P. V., Palsson, B. Ø., & Weber, T. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae314 · Cited by 36
Characterization of two virulent Salmonella phages and transient application in egg, meat and lettuce safety
Sun, X., Xue, F., Cong, C., Murtaza, B., Wang, L., Li, X., Li, S., & Xu, Y. (2024) · Food Research International · doi:10.1016/j.foodres.2024.114607 · Cited by 34
Genomes OnLine Database (GOLD) v.10: new features and updates
Mukherjee, S., Stamatis, D., Li, C. T., Ovchinnikova, G., Kandimalla, M., Handke, V., Reddy, A., Ivanova, N., Woyke, T., Eloe‐Fadrosh, E. A., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1000 · Cited by 39
Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up
Wilson, B. C., Zuppi, M., Derraik, J. G. B., Albert, B. B., Tweedie‐Cullen, R. Y., Leong, K. S. W., Beck, K. L., Vatanen, T., O'Sullivan, J. M., Cutfield, W. S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-62752-4 · Cited by 40

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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