Microbial species delineation using whole genome sequences

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

doi:10.1093/nar/gkv657

Title: Microbial species delineation using whole genome sequences

Journal Article · Mon Jul 06 00:00:00 EDT 2015 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkv657· OSTI ID:1625546

Varghese, Neha J. ^[1]; Mukherjee, Supratim ^[1]; Ivanova, Natalia ^[1]; Konstantinidis, Konstantinos T. ^[2]; Mavrommatis, Kostas ^[3]; Kyrpides, Nikos C. ^[1]; Pati, Amrita ^[1]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial and Metagenome Superprogram
Georgia Inst. of Technology, Atlanta, GA (United States). Dept. of Civil and Environmental Engineering
Celgene Corp., San Francisco, CA (United States)

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625546

Journal Information:: Nucleic Acids Research, Vol. 43, Issue 14; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 401 works

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Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Kaye BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6623-z	journal	March 2020
Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization Moraes, Eduardo C.; Alvarez, Thabata M.; Persinoti, Gabriela F. Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1073-4	journal	March 2018
Domestication of the novel alcohologenic acetogen Clostridium sp. AWRP: from isolation to characterization for syngas fermentation Lee, Joungmin; Lee, Jin Woo; Chae, Cheol Gi Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1570-0	journal	September 2019
New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters Campanaro, Stefano; Treu, Laura; Rodriguez-R, Luis M. Biotechnology for Biofuels, Vol. 13, Issue 1 https://doi.org/10.1186/s13068-020-01679-y	journal	February 2020
Carbapenemases on the move: it’s good to be on ICEs Botelho, João; Roberts, Adam P.; León-Sampedro, Ricardo Mobile DNA, Vol. 9, Issue 1 https://doi.org/10.1186/s13100-018-0141-4	journal	December 2018
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes Alneberg, Johannes; Karlsson, Christofer M. G.; Divne, Anna-Maria Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0550-0	journal	September 2018
Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015) Federhen, Scott; Rossello-Mora, Ramon; Klenk, Hans-Peter Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0134-1	journal	February 2016
High quality draft genome sequences of Pseudomonas fulva DSM 17717T, Pseudomonas parafulva DSM 17004T and Pseudomonas cremoricolorata DSM 17059T type strains Peña, Arantxa; Busquets, Antonio; Gomila, Margarita Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0178-2	journal	September 2016
Draft genome sequence of type strain HBR26T and description of Rhizobium aethiopicum sp. nov. Aserse, Aregu Amsalu; Woyke, Tanja; Kyrpides, Nikos C. Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0220-z	journal	January 2017
High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460 Matrosova, Vera Y.; Gaidamakova, Elena K.; Makarova, Kira S. Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0258-y	journal	July 2017
Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T Aserse, Aregu Amsalu; Woyke, Tanja; Kyrpides, Nikos C. Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0283-x	journal	December 2017
Distinction between Borrelia and Borreliella is more robustly supported by molecular and phenotypic characteristics than all other neighbouring prokaryotic genera: Response to Margos' et al. "The genus Borrelia reloaded" (PLoS ONE 13(12): e0208432) Gupta, Radhey S. PLOS ONE, Vol. 14, Issue 8 https://doi.org/10.1371/journal.pone.0221397	journal	August 2019
Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation Pettengill, Emily A.; Pettengill, James B.; Binet, Rachel Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01573	journal	January 2016
Genome Sequence of Pseudomonas koreensis CRS05-R5, an Antagonistic Bacterium Isolated from Rice Paddy Field Lin, Haiyan; Hu, Shikai; Liu, Ruifang Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01756	journal	November 2016
Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland Daebeler, Anne; Herbold, Craig W.; Vierheilig, Julia Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00193	journal	February 2018
Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data Seol, Donghyeok; Jhang, So Yun; Kim, Hyaekang Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01683	journal	August 2019
The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis Zhang, Pengfan; Jin, Tao; Kumar Sahu, Sunil Molecules, Vol. 24, Issue 7 https://doi.org/10.3390/molecules24071411	journal	April 2019
Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa Amoako, Daniel Gyamfi; Somboro, Anou M.; Abia, Akebe Luther King Pathogens, Vol. 8, Issue 4 https://doi.org/10.3390/pathogens8040166	journal	September 2019
Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences Hahn, Martin W.; Jezberová, Jitka; Koll, Ulrike The ISME Journal, Vol. 10, Issue 7 https://doi.org/10.1038/ismej.2015.237	journal	March 2016
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J. Nature Biotechnology, Vol. 35, Issue 7 https://doi.org/10.1038/nbt.3886	journal	June 2017
A new genomic blueprint of the human gut microbiota Almeida, Alexandre; Mitchell, Alex L.; Boland, Miguel Nature, Vol. 568, Issue 7753 https://doi.org/10.1038/s41586-019-0965-1	journal	February 2019
NSimScan: DNA comparison tool with increased speed, sensitivity and accuracy Novichkov, Vladimir; Kaznadzey, Anna; Alexandrova, Natalia Bioinformatics, Vol. 32, Issue 15 https://doi.org/10.1093/bioinformatics/btw126	journal	March 2016
GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models Clarke, Thomas H.; Brinkac, Lauren M.; Sutton, Granger Bioinformatics, Vol. 34, Issue 17 https://doi.org/10.1093/bioinformatics/bty300	journal	April 2018
A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition Kadnikov, Vitaly V.; Mardanov, Andrey V.; Beletsky, Alexey V. FEMS Microbiology Ecology, Vol. 94, Issue 10 https://doi.org/10.1093/femsec/fiy152	journal	August 2018
Genomic Signatures of Honey Bee Association in an Acetic Acid Symbiont Smith, Eric A.; Newton, Irene L. G. Genome Biology and Evolution, Vol. 12, Issue 10 https://doi.org/10.1093/gbe/evaa183	journal	September 2020
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
Streptomyces chitinivorans sp. nov., a chitinolytic strain isolated from estuarine lake sediment Ray, Lopamudra; Mishra, Samir Ranjan; Panda, Ananta Narayan International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 8 https://doi.org/10.1099/ijsem.0.001176	journal	August 2016
Reclassification of strains MAFF 303099T and R7A into Mesorhizobium japonicum sp. nov. Martínez-Hidalgo, Pilar; Ramírez-Bahena, Martha Helena; Flores-Félix, José David International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 12 https://doi.org/10.1099/ijsem.0.001448	journal	December 2016
Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers McFrederick, Quinn S.; Vuong, Hoang Q.; Rothman, Jason A. International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 6 https://doi.org/10.1099/ijsem.0.002758	journal	June 2018
Establishing Genotypic Cutoff Values To Measure Antimicrobial Resistance in Salmonella Tyson, Gregory H.; Zhao, Shaohua; Li, Cong Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 3 https://doi.org/10.1128/AAC.02140-16	journal	December 2016
A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet? Garrity, George M. Journal of Clinical Microbiology, Vol. 54, Issue 8 https://doi.org/10.1128/jcm.00200-16	journal	May 2016
Complete Genome Sequence of Microbacterium sp. Strain SGAir0570, Isolated from Tropical Air Collected in Singapore Kalsi, Namrata; Drautz-Moses, Daniela I.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 34 https://doi.org/10.1128/mra.00613-19	journal	August 2019
Complete Genome Sequence of Streptomyces sp. Strain SGAir0924, an Actinobacterium Isolated from Outdoor Air in Singapore Gupta, Anjali Bansal; Uchida, Akira; Purbojati, Rikky W. Microbiology Resource Announcements, Vol. 8, Issue 35 https://doi.org/10.1128/mra.00899-19	journal	August 2019
Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium Brzoska, Ryann M.; Huntemann, Marcel; Clum, Alicia Microbiology Resource Announcements, Vol. 8, Issue 14 https://doi.org/10.1128/mra.01701-18	journal	April 2019
Genomics of the Uncultivated, Periodontitis-Associated Bacterium Tannerella sp. BU045 (Oral Taxon 808) Beall, Clifford J.; Campbell, Alisha G.; Griffen, Ann L. mSystems, Vol. 3, Issue 3 https://doi.org/10.1128/msystems.00018-18	journal	June 2018
Marine Chitinolytic Pseudoalteromonas Represents an Untapped Reservoir of Bioactive Potential Paulsen, Sara Skøtt; Strube, Mikael Lenz; Bech, Pernille Kjersgaard mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00060-19	journal	June 2019
Integrated Omic Analyses Provide Evidence that a “Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions Camejo, Pamela Y.; Oyserman, Ben O.; McMahon, Katherine D. mSystems, Vol. 4, Issue 1 https://doi.org/10.1128/msystems.00193-18	journal	January 2019
Genomic variation and biogeography of Antarctic haloarchaea Tschitschko, Bernhard; Erdmann, Susanne; DeMaere, Matthew Z. Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0495-3	journal	June 2018
Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment Jiang, Lijing; L’Haridon, Stéphane; Jebbar, Mohamed Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-016-0214-2	journal	January 2017
High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain Osman, Wan Adnawani Meor; van Berkum, Peter; León-Barrios, Milagros Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0270-2	journal	September 2017
Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. Sutton, Granger G.; Brinkac, Lauren M.; Clarke, Thomas H. F1000Research, Vol. 7 https://doi.org/10.12688/f1000research.14566.1	journal	January 2018
Typing and classification of non-tuberculous mycobacteria isolates Clarke, Thomas; Brinkac, Lauren; Manoranjan, Joanna F1000Research, Vol. 9 https://doi.org/10.12688/f1000research.22620.2	journal	January 2020
Genomic features of bacterial adaptation to plants Sarah, Lebeis,; Bryan, Rangel Alvarez,; Freddy, Monteiro, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/z1ym-1m42	text	January 2018
Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification Sant’Anna, Fernando H.; Ambrosini, Adriana; de Souza, Rocheli Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01849	journal	October 2017
Genomic Insights Into the Mycobacterium kansasii Complex: An Update Jagielski, Tomasz; Borówka, Paulina; Bakuła, Zofia Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02918	journal	January 2020
Elizabethkingia Infections in Humans: From Genomics to Clinics Lin, Jiun-Nong; Lai, Chung-Hsu; Yang, Chih-Hui Microorganisms, Vol. 7, Issue 9 https://doi.org/10.3390/microorganisms7090295	journal	August 2019
Anaerobic Hydrocarbon-Degrading Deltaproteobacteria Davidova, Irene A.; Marks, Christopher R.; Suflita, Joseph M. Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes https://doi.org/10.1007/978-3-319-60053-6_12-1	book	January 2018
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries Jain, Chirag; Rodriguez-R, Luis M.; Phillippy, Adam M. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07641-9	journal	November 2018
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy Meier-Kolthoff, Jan P.; Göker, Markus Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10210-3	journal	May 2019
Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil Yao, Qiuming; Li, Zhou; Song, Yang Nature Ecology & Evolution, Vol. 2, Issue 3 https://doi.org/10.1038/s41559-017-0463-5	journal	January 2018
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
New insights from uncultivated genomes of the global human gut microbiome Nayfach, Stephen; Shi, Zhou Jason; Seshadri, Rekha Nature, Vol. 568, Issue 7753 https://doi.org/10.1038/s41586-019-1058-x	journal	March 2019
Viable bacterial colonization is highly limited in the human intestine in utero Rackaityte, E.; Halkias, J.; Fukui, E. M. Nature Medicine, Vol. 26, Issue 4 https://doi.org/10.1038/s41591-020-0761-3	journal	February 2020
CAMITAX: Taxon labels for microbial genomes Bremges, Andreas; Fritz, Adrian; McHardy, Alice C. GigaScience, Vol. 9, Issue 1 https://doi.org/10.1093/gigascience/giz154	journal	January 2020
Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones: Single-cell genomes of anoxic-marine-zone microbes Plominsky, Alvaro M.; Trefault, Nicole; Podell, Sheila Environmental Microbiology, Vol. 20, Issue 8 https://doi.org/10.1111/1462-2920.14109	journal	April 2018
Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta Moeller, Florian U.; Webster, Nicole S.; Herbold, Craig W. Environmental Microbiology, Vol. 21, Issue 10 https://doi.org/10.1111/1462-2920.14732	journal	July 2019
Complete Genome Sequence of Pseudomonas sp. Strain SGAir0191, Isolated from Tropical Air Collected in Singapore Wong, Anthony; Junqueira, Ana Carolina M.; Chaturvedi, Ankur Microbiology Resource Announcements, Vol. 8, Issue 34 https://doi.org/10.1128/mra.00617-19	journal	August 2019
Whole-Genome Sequence of Bacillus megaterium Strain SGAir0080, Isolated from an Indoor Air Sample Kalsi, Namrata; Uchida, Akira; Purbojati, Rikky W. Microbiology Resource Announcements, Vol. 8, Issue 50 https://doi.org/10.1128/mra.01249-19	journal	December 2019
Visualization of consensus genome structure without using a reference genome Tada, Ipputa; Tanizawa, Yasuhiro; Arita, Masanori BMC Genomics, Vol. 18, Issue S2 https://doi.org/10.1186/s12864-017-3499-7	journal	March 2017
Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment Coil, David A.; Jospin, Guillaume; Darling, Aaron E. PLOS ONE, Vol. 14, Issue 6 https://doi.org/10.1371/journal.pone.0214354	journal	June 2019
Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant Fonseca, Bruna Constante; Riaño-Pachón, Diego Mauricio; Guazzaroni, María-Eugenia Genetics and Molecular Biology, Vol. 42, Issue 1 https://doi.org/10.1590/1678-4685-gmb-2017-0315	journal	March 2019
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Kaye Research Square [preprints] https://doi.org/10.21203/rs.2.15865/v5	posted_content	March 2020
Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients Hawley, Alyse K.; Nobu, Masaru K.; Wright, Jody J. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01376-9	journal	November 2017
Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy Hayashi Sant’Anna, Fernando; Bach, Evelise; Porto, Renan Z. Critical Reviews in Microbiology, Vol. 45, Issue 2 https://doi.org/10.1080/1040841x.2019.1569587	journal	March 2019
Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI Ciufo, Stacy; Kannan, Sivakumar; Sharma, Shobha International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 7 https://doi.org/10.1099/ijsem.0.002809	journal	July 2018
Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan Sarfraz, Sohaib; Riaz, Kashif; Oulghazi, Saïd International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 11 https://doi.org/10.1099/ijsem.0.003029	journal	November 2018
How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity? Rodriguez-R, Luis M.; Castro, Juan C.; Kyrpides, Nikos C. Applied and Environmental Microbiology, Vol. 84, Issue 6 https://doi.org/10.1128/aem.00014-18	journal	January 2018
Genome Sequences of Two Cyanobacterial Strains, Toxic Green Microcystis aeruginosa KW (KCTC 18162P) and Nontoxic Brown Microcystis sp. Strain MC19, under Xenic Culture Conditions Jeong, Haeyoung; Chun, Seong-Jun; Srivastava, Ankita Genome Announcements, Vol. 6, Issue 18 https://doi.org/10.1128/genomea.00378-18	journal	May 2018
Draft Genome Sequence of Enterobacter sp. Strain AD2-3, Isolated from a Postmining Site in Benguet, Philippines Zarate, Jocelyn T.; Aquino, Genevieve Mae B.; Cruz, Joana Marie C. Microbiology Resource Announcements, Vol. 8, Issue 30 https://doi.org/10.1128/mra.00563-19	journal	July 2019
Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume Pinto, Otávio H. B.; Silva, Thais F.; Vizzotto, Carla S. BMC Microbiology, Vol. 20, Issue 1 https://doi.org/10.1186/s12866-020-1698-x	journal	January 2020
Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion Jia, Yangyang; Ng, Siu-Kin; Lu, Hongyuan Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1121-0	journal	April 2018
Typing and classification of non-tuberculous mycobacteria isolates Clarke, Thomas; Brinkac, Lauren; Manoranjan, Joanna F1000Research, Vol. 9 https://doi.org/10.12688/f1000research.22620.1	journal	January 2020
Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina Čadež, Neža; Bellora, Nicolas; Ulloa, Ricardo PLOS ONE, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pone.0210792	journal	January 2019
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Research Square [preprints] https://doi.org/10.21203/rs.2.15865/v4	posted_content	February 2020
Ecogenomics and Taxonomy of Cyanobacteria Phylum Walter, Juline M.; Coutinho, Felipe H.; Dutilh, Bas E. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02132	journal	November 2017
Carbapenemases on the move: it's good to be on ICEs Botelho, João; Roberts, Adam P.; Leon Sampedro, Ricardo ETH Zurich https://doi.org/10.3929/ethz-b-000473515	text	January 2018
Freshwater carbon and nutrient cycles revealed through reconstructed population genomes Linz, Alexandra M.; He, Shaomei; Stevens, Sarah L. R. PeerJ, Vol. 6 https://doi.org/10.7717/peerj.6075	journal	January 2018
Widespread soil bacterium that oxidizes atmospheric methane Tveit, Alexander T.; Hestnes, Anne Grethe; Robinson, Serina L. Proceedings of the National Academy of Sciences, Vol. 116, Issue 17 https://doi.org/10.1073/pnas.1817812116	journal	April 2019
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita Genome Research, Vol. 26, Issue 11 https://doi.org/10.1101/gr.201863.115	journal	October 2016
CAMISIM: simulating metagenomes and microbial communities Fritz, Adrian; Hofmann, Peter; Majda, Stephan Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0633-6	journal	February 2019
Assembly of seed-associated microbial communities within and across successive plant generations Rezki, Samir; Campion, Claire; Simoneau, Philippe Plant and Soil, Vol. 422, Issue 1-2 https://doi.org/10.1007/s11104-017-3451-2	journal	October 2017
Genomic features of bacterial adaptation to plants Levy, Asaf; Salas Gonzalez, Isai; Mittelviefhaus, Maximilian Nature Genetics, Vol. 50, Issue 1 https://doi.org/10.1038/s41588-017-0012-9	journal	December 2017
Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough Daas, Mohamed Seghir; Rosana, Albert Remus R.; Acedo, Jeella Z. Standards in Genomic Sciences, Vol. 13, Issue 1 https://doi.org/10.1186/s40793-018-0331-1	journal	October 2018
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil Klonowska, Agnieszka; Moulin, Lionel; Ardley, Julie Research Square [preprints] https://doi.org/10.21203/rs.2.15865/v3	posted_content	March 2020
Rapid Bacterial Species Delineation Based on Parameters Derived From Genome Numerical Representations Maderankova, Denisa; Jugas, Robin; Sedlar, Karel Computational and Structural Biotechnology Journal, Vol. 17 https://doi.org/10.1016/j.csbj.2018.12.006	journal	January 2019
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms10476	journal	January 2016
Substantial expansion of the human gut microbiota genome catalogue Thoma, Clemens Nature Reviews Gastroenterology & Hepatology, Vol. 16, Issue 4 https://doi.org/10.1038/s41575-019-0129-7	journal	March 2019
Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes Alneberg, Johannes; Bennke, Christin; Beier, Sara Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-0856-x	journal	March 2020
The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut Albert, Korin; Rani, Asha; Sela, David A. Microbial Genomics, Vol. 4, Issue 6 https://doi.org/10.1099/mgen.0.000183	journal	June 2018
Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus “ Candidatus Sulfobium” Zecchin, Sarah; Mueller, Ralf C.; Seifert, Jana Applied and Environmental Microbiology, Vol. 84, Issue 5 https://doi.org/10.1128/aem.02224-17	journal	December 2017
Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504 To, Thao T.; Liu, Quanhui; Watling, Michael Genome Announcements, Vol. 4, Issue 2 https://doi.org/10.1128/genomea.00256-16	journal	April 2016
Draft Genome Sequences of Seven 4-Formylaminooxyvinylglycine Producers Belonging to the Pseudomonas fluorescens Species Complex Okrent, Rachel A.; Manning, Viola A.; Trippe, Kristin M. Genome Announcements, Vol. 5, Issue 18 https://doi.org/10.1128/genomea.00277-17	journal	May 2017
An Important Role for Purifying Selection in Archaeal Genome Evolution Lyu, Zhe; Li, Zhi-Gang; He, Fei mSystems, Vol. 2, Issue 5 https://doi.org/10.1128/msystems.00112-17	journal	October 2017
Analysis of Draft Genome Sequence of Pseudomonas sp. QTF5 Reveals Its Benzoic Acid Degradation Ability and Heavy Metal Tolerance Li, Yang; Ren, Yi; Jiang, Nan BioMed Research International, Vol. 2017 https://doi.org/10.1155/2017/4565960	journal	January 2017
On neotypes and nomina nova: commentary on “Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa”, by C.B. Fitzgerald et al. (BMC Genomics (2018) 19:931) Oren, Aharon; Garrity, George M. BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6680-3	journal	April 2020
Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T Proença, Diogo N.; Whitman, William B.; Shapiro, Nicole Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0262-2	journal	September 2017
Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance Castro-Severyn, Juan; Remonsellez, Francisco; Valenzuela, Sandro L. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00456	journal	March 2017
Comparative Genomic Analysis of Vibrio diabolicus and Six Taxonomic Synonyms: A First Look at the Distribution and Diversity of the Expanded Species Turner, Jeffrey W.; Tallman, James J.; Macias, Amanda Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01893	journal	August 2018
Taxonomic Organization of the Family Brucellaceae Based on a Phylogenomic Approach Leclercq, Sébastien O.; Cloeckaert, Axel; Zygmunt, Michel S. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.03083	journal	January 2020
Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena de la Haba, Rafael R.; Minegishi, Hiroaki; Kamekura, Masahiro Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.740909	journal	October 2021
Comparative genomic analysis of a new tellurite-resistantPsychrobacterstrain isolated from the Antarctic Peninsula Muñoz-Villagrán, Claudia Melissa; Mendez, Katterinne N.; Cornejo, Fabian PeerJ, Vol. 6 https://doi.org/10.7717/peerj.4402	journal	February 2018

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