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Pritchard et al. (2016) “Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens” Anal. Methods, 2016, 8, 12-24 DOI: 10.1039/C5AY02550H
@Article{C5AY02550H,
author ="Pritchard, Leighton and Glover, Rachel H. and Humphris, Sonia and Elphinstone, John G. and Toth, Ian K.",
title  ="Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens",
journal  ="Anal. Methods",
year  ="2016",
volume  ="8",
issue  ="1",
pages  ="12-24",
publisher  ="The Royal Society of Chemistry",
doi  ="10.1039/C5AY02550H",
url  ="http://dx.doi.org/10.1039/C5AY02550H",
abstract  ="Soft rot Enterobacteriaceae (SRE) are bacterial plant pathogens that cause blackleg{,} wilt and soft rot
diseases on a broad range of important crop and ornamental plants worldwide. These organisms (spanning the genera Erwinia{,}
Pectobacterium{,} Dickeya{,} and Pantoea) cause significant economic and yield losses in the field{,} and in storage. They
are transmissible through surface water{,} by trade and other movement of plant material and soil{,} and in some cases are
subject to international legislative and quarantine restrictions. Effective detection and diagnosis in support of food
security legislation and epidemiology is dependent on the ability to classify pathogenic isolates precisely. Diagnostics and
classification are made more difficult by the influence of horizontal gene transfer on phenotype{,} and historically complex
and sometimes inaccurate nomenclatural and taxonomic assignments that persist in strain collections and online sequence
databases. Here{,} we briefly discuss the relationship between taxonomy{,} genotype and phenotype in the SRE{,} and their
implications for diagnostic testing and legislation. We present novel whole-genome classifications of the SRE{,}
illustrating inconsistencies between the established taxonomies and evidence from completely sequenced isolates. We conclude
with a perspective on the future impact of widespread whole-genome sequencing and classification methods on detection and
identification of bacterial plant pathogens in support of legislative and policy efforts in food security."}

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2022

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2021

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  • Saati-Santamaría et al. (2021) “Phylogenomic Analyses of the Genus _Pseudomonas_ Lead to the Rearrangement of Several Species and the Definition of New Genera” Biology doi:10.3390/biology10080782
  • Sakiyama et al. (2021) “Complete Genome Sequence of a Clinical Isolate of Acinetobacter baumannii Harboring 11 Plasmids” Microbiol. Res. Ann. doi:10.1128/MRA.00695-21
  • Schlez et al. (2021) “Corynebacterium rouxii, a recently described member of the C. diphtheriae group isolated from three dogs with ulcerative skin lesions” Ant. van Leeuw. doi:10.1007/s10482-021-01605-8
  • Santos et al. (2021) “Phaffia brasiliana sp. nov., a yeast species isolated from soil in a Cerrado–Atlantic Rain Forest ecotone site in Brazil” Int. J. Syst. Evol. Microbiol. doi:10.1099/ijsem.0.005080
  • Saw et al. (2021) “Complete Genome Sequencing of a Novel Gloeobacter Species from a Waterfall Cave in Mexico” Genome Biol. Evol. doi:10.1093/gbe/evab264
  • Schörner et al. (2021) “Genomic analysis of Neisseria elongata isolate from a patient with infective endocarditis” FEBS Open Bio doi:10.1002/2211-5463.13201
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  • Sedaghatjoo et al. (2021) “Development of a loop-mediated isothermal amplification assay for the detection of Tilletia controversa based on genome comparison” Sci. Reports. doi:10.1038/s41598-021-91098-2
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  • Singh et al. (2021) “Enrichment and description of novel bacteria performing syntrophic propionate oxidation at high ammonia level” Env. Micro. doi:10.1111/1462-2920.15388
  • Singh et al. (2021) “Genome-based reclassification of Amycolatopsis eurytherma as a later heterotypic synonym of Amycolatopsis thermoflavaInt. J. Syst. Evol. Microbiol. doi:10.1099/ijsem.0.004642
  • Son et al. (2021) “Serratia rhizosphaerae sp. nov., a novel plant resistance inducer against soft rot disease in tobacco” Int. J. Syst. Evol. Microbiol. doi:10.1099/ijsem.0.004788
  • Sorokin et al. (2021) “Natronoglycomyces albus gen. nov., sp. nov, a haloalkaliphilic actinobacterium from a soda solonchak soil” Int. J. Syst. Evol. Microbiol. doi:10.1099/ijsem.0.004804
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  • Suarez et al. (2021) “Whole-Genome sequencing and comparative genomics of Mycobacterium spp. from farmed Atlantic and coho salmon in Chile” Antonie van Leeuw. doi:10.1007/s10482-021-01592-w
  • Tegopoulos et al. (2021) “Genomic and Phylogenetic Analysis of Lactiplantibacillus plantarum L125, and Evaluation of Its Anti-Proliferative and Cytotoxic Activity in Cancer Cells” biomedicines doi:10.3390/biomedicines9111718
  • Tian et al. (2021) “LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes” PeerJ doi:10.7717/peerj.10906
  • Tian et al. (2021) “Antifungal mechanism of Bacillus amyloliquefaciens strain GKT04 against Fusarium wilt revealed using genomic and transcriptomic analyses” Microbiol. Open doi:10.1002/mbo3.1192
  • Turco et al. (2021) “Draft Genome Sequence of a New Fusarium Isolate Belonging to Fusarium tricinctum Species Complex Collected From Hazelnut in Central Italy” Front. Plant Sci. doi:10.3389/fpls.2021.788584
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2020

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  • Brock et al. (2020) “Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum: Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov” PeerJ doi:10.7717/peerj.9151
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  • Dangel et al. (2020) “Corynebacterium silvaticum sp. nov., a unique group of NTTB corynebacteria in wild boar and roe deer” Int. J. Syst. Evol. Microb. doi:10.1099/ijsem.0.004195
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  • Déraspe et al. (2020) “Genome Sequence of a Klebsiella pneumoniae NDM-1 Producer Isolated in Quebec City” Microbiol. Resour. Announc. doi:10.1128/MRA.00829-19
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  • France et al. (2020) “Complete Genome Sequences of Six Lactobacillus iners Strains Isolated from the Human Vagina” Microbiol. Res. Ann. doi:10.1128/MRA.00234-20
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  • Gramaje et al. (2020) “Comparative Genomic Analysis of Dactylonectria torresensis Strains from Grapevine, Soil and Weed Highlights Potential Mechanisms in Pathogenicity and Endophytic Lifestyle” J. Fungi doi:10.3390/jof6040255
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  • Hempel et al. (2020) “Complete Genome Sequence of Bacillus velezensis Strain S4, Isolated from Biochar-Treated Soil” Microbiol. Res. Ann. doi:10.1128/MRA.00352-20
  • Hinger et al. (2020) “Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov.” Appl. Env. Microbiol. doi:10.1128/AEM.02395-19
  • Hollensteiner et al. (2020) “Genome Sequence of Komagataeibacter saccharivorans Strain JH1, Isolated from Fruit Flies” Microbiol. Res. Announc. doi:10.1128/MRA.00098-20
  • Hulin et al. (2020) “Cherry picking by pseudomonads: after a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits” Plant Pathology doi:10.1111/ppa.13189
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  • Jung et al. (2020) “Genome Analysis of Enterococcus mundtii Pe103, a Human Gut-Originated Pectinolytic Bacterium” Curr. Microbiol. doi:10.1007/s00284-020-01932-5
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  • Ryngajłło et al. (2020) “Towards control of cellulose biosynthesis by Komagataeibacter using systems-level and strain engineering strategies: current progress and perspectives” Appl. Microbil. Biotech. doi:10.1007/s00253-020-10671-3
  • Salgar-Chaparro et al. (2020) “Complete Genome Sequence of Pseudomonas balearica Strain EC28, an Iron-Oxidizing Bacterium Isolated from Corroded Steel” Microbiol. Res. Ann. doi:10.1128/MRA.00275-20
  • Salgar-Chaparro et al. (2020) ” Draft Genome Sequence of Enterobacter roggenkampii Strain OS53, Isolated from Corroded Pipework at an Offshore Oil Production Facility” Microbiol. Res. Ann. doi:10.1128/MRA.00583-20
  • Salgar-Chaparro et al. (2020) “Complete Genome Sequence of Shewanella chilikensis Strain DC57, Isolated from Corroded Seal Rings at a Floating Oil Production System in Australia” Microbiol. Res. Announc. doi:0.1128/MRA.00584-20
  • Shen et al. (2020) “Helicobacter monodelphidis sp. nov. and Helicobacter didelphidarum sp. nov., isolated from grey short-tailed opossums (Monodelphis domestica) with endemic cloacal prolapses” Int. J. Syst. Evol. Micro. doi:10.1099/ijsem.0.004424
  • Strang (2020) “Genomic Insights and Ecological Adaptations of Deep-Subsurface and Near Subsurface Thermococcus Isolates and Near Subsurface Thermococcus Isolates” WWU Graduate School Collection https://cedar.wwu.edu/wwuet/926
  • Taparia et al. (2020) “Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe” BMC Genomics doi:10.1186/s12864-020-06905-3
  • Tardy et al. (2020) “Mycoplasma bovis in Nordic European Countries: Emergence and Dominance of a New Clone” Pathogens doi:10.3390/pathogens9110875
  • Thapa et al. (2020) “Genome‐wide analyses of Liberibacter species provides insights into evolution, phylogenetic relationships, and virulence factors” Mol. Plant Path. doi:10.1111/mpp.12925
  • Tian et al. (2020) “LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa” Nuc. Acids Res. doi:10.1093/nar/gkaa190
  • Tsukimi et al. (2020) “Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals” J. Genomics doi:10.7150/jgen.38516
  • Vijayan et al. (2020) “Bacteria known to induce settlement of larvae of Hydroides elegans are rare in natural inductive biofilm” Aquatic Microb. Ecol. doi:10.3354/ame01925
  • Waleron et al. (2020) “Arthrospiribacter ruber gen. nov., sp. nov., a novel bacterium isolated from Arthrospira cultures” Syst. Appl. Microbiol. doi:10.1016/j.syapm.2020.126072
  • Wang et al. (2020) “Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches” Genes doi:10.3390/genes11010070
  • Wang et al. (2020) “Complete genomic data of Burkholderia glumae strain GX associated with bacterial panicle blight of rice in China” Plant Dis. doi:10.1094/PDIS-10-19-2265-A
  • Weiser et al. (2020) “A Novel Inducible Prophage from Burkholderia Vietnamiensis G4 is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia” Viruses doi:10.3390/v12060601
  • Webster et al. (2020) “Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India” FEMS Microbiol. Ecol. doi:10.1093/femsec/fiaa147/5876344
  • Wist et al. (2020) “Phenotypic and Genotypic Traits of Vancomycin-Resistant Enterococci from Healthy Food- Producing Animals” Microorganisms doi:10.3390/microorganisms8020261
  • Wu et al. (2020) “Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains” Brief. Bioinf. doi:10.1093/bib/bbaa013
  • Yang et al. (2020) “Isolation and Characterization of the Novel Phages vB_VpS_BA3 and vB_VpS_CA8 for Lysing Vibrio parahaemolyticusFront. Microbiol. doi:10.3389/fmicb.2020.00259
  • Zayulina et al. “Complete Genome Sequence of a Hyperthermophilic Archaeon, Thermosphaera sp. Strain 3507, Isolated from a Chilean Hot Spring” Micro. Res. Ann. doi:10.1128/MRA.01262-20
  • Zhang et al. (2020) “A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea.” ISME J. doi:10.1038/s41396-020-0684-5
  • Zhang et al. (2020) “Deinococcus detaillensis sp. nov., isolated from humus soil in Antarctica” Arch. Microbiol. doi:10.1007/s00203-020-01920-0
  • Zhang et al. (2020) “Chloramphenicol biodegradation by enriched bacterial consortia and isolated strain Sphingomonas sp. CL5.1: The reconstruction of a novel biodegradation pathway” Water Res. doi:10.1016/j.watres.2020.116397
  • Zheng et al. (2020) “Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities” Microorganisms doi:10.3390/microorganisms8101614
  • Zhou et al. (2020) “Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa” BMC Genomics doi:10.1186/s12864-020-6527-y

2019

  • Accetto & Avgustin (2019) “The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut Prevotella species: A factor in their ubiquity?” Syst. Appl. Microbiol. doi:j.syapm.2018.10.001
  • Acevedo et al. (2019) “Bacillus clarus sp. nov. is a new Bacillus cereus group species isolated from soil” BioRxiv doi:10.1101/508077
  • Alberoni et al. (2019) “Bifidobacterium xylocopae sp. nov. and Bifidobacterium aemilianum *sp. nov., from the carpenter bee (*Xylocopa violacea) digestive tract” Syst. Appl. Microbiol. doi:10.1016/j.syapm.2018.11.005
  • Alex & Antunes (2019) “Whole-Genome Comparisons Among the Genus Shewanella Reveal the Enrichment of Genes Encoding Ankyrin-Repeats Containing Proteins in Sponge-Associated Bacteria” Front. Microbiol. doi:10.3389/fmicb.2019.00005
  • Alex & Antunes (2019) “Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses” Microorganisms doi:10.3390/microorganisms7120635
  • Barnier et al. (2019) “Description of Palleronia rufa sp. nov., a biofilm-forming and AHL-producing Rhodobacteraceae, reclassification of Hwanghaeicola aestuarii as Palleronia aestuarii comb. nov., Maribius pontilimi as Palleronia pontilimi comb. nov., Maribius salinus as Palleronia salina comb. nov., Maribius pelagius as Palleronia pelagia comb. nov. and emended description of the genus PalleroniaSyst. Appl. Microbiol. doi:10.1016/j.syapm.2019.126018
  • Bayjanov et al. (2019) “Whole genome analysis of Pandoraea species strains from cystic fibrosis patients” Future Microbiology doi:10.2217/fmb-2019-0038
  • Botelho et al. (2019) “Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain” Emerg. Microb. Inf. doi:10.1080/22221751.2019.1648182
  • Boukerb et al. (2019) “Campylobacter armoricus sp. nov., a novel member of the Campylobacter lari group isolated from surface water and stools from humans with enteric infection” Int. J. Syst. Evol. Micro. doi:10.1099/ijsem.0.003836
  • Briand et al. (2019) “A rapid and simple method for assessing and representing genome sequence relatedness” BioRxiv doi:10.1101/569640
  • Cho & Kwak (2019) “Evolution of Antibiotic Synthesis Gene Clusters in the Streptomyces globisporus TFH56, Isolated from Tomato Flower” G3: Genes, Genomes, Genetics doi:10.1534/g3.119.400037
  • Ciok & Dziewit (2019) “Exploring the genome of Arctic Psychrobacter sp. DAB_AL32B and construction of novel Psychrobacter-specific cloning vectors of an increased carrying capacity” Arch. Microbiol. doi:10.1007/s00203-018-1595-y
  • D’Souza et al. (2019) “Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces” Nat. Comm. doi:10.1038/s41467-019-12563-1
  • do Vale et al. (2019) “Draft Genome Sequences of Three Novel Acinetobacter Isolates from an Irish Commercial Pig Farm” Microbiol. Res. Ann. doi:10.1128/MRA.00919-19
  • Doud et al. (2019) “Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere” ISME J. doi:10.1038/s41396-019-0557-y
  • Du et al. (2019) “Characterization of a Linezolid- and Vancomycin-Resistant Streptococcus suis Isolate That Harbors optrA and vanG Operons” Front. Microbiol. doi:10.3389/fmicb.2019.02026
  • Esposito et al. (2019) “Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway” Microbiol. Open doi:10.1002/mbo3.938
  • Falagan et al. (2019) “Acidithiobacillus sulfuriphilus sp. nov.: an extremely acidophilic sulfur-oxidizing chemolithotroph isolated from a neutral pH environment” Int. J. Syst. Evol. Micro. doi:0.1099/ijsem.0.003576
  • Faoro et al. (2019) “Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts” BMC Genomics doi:10.1186/s12864-019-5982-9
  • Feng et al. (2019) “Complete genome sequence of Hahella sp. KA22, a prodigiosin-producing algicidal bacterium” Marine Genomics doi:10.1016/j.margen.2019.04.003
  • Gasparrini et al. (2019) “Metagenomic signatures of early life hospitalization and antibiotic treatment in the infant gut microbiota and resistome persist long after discharge” Nature Microbiol. doi:10.1038/s41564-019-0550-2
  • Ghosh et al. (2019) “Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position” Microorganisms doi:10.3390/microorganisms7110487
  • Hollensteiner et al. (2019) “Complete Genome Sequence of Marinobacter sp. Strain JH2, Isolated from Seawater of the Kiel Fjord” Micro. Res. Ann. doi:10.1128/MRA.00596-19
  • Hornung et al. (2019) “An in silico survey of Clostridioides difficile extrachromosomal elements” BioRxiv doi:10.1101/651539
  • Huang et al. (2019) “Genomic differences within the phylum Marinimicrobia: From waters to sediments in the Mariana Trench” Marine Genomics doi:10.1016/j.margen.2019.100699
  • Ide et al. (2019) “Draft Genome Sequence of Acidovorax sp. Strain NB1, Isolated from a Nitrite-Oxidizing Enrichment Culture” Micro. Res. Ann. doi:10.1128/MRA.00547-19
  • Jeong et al. (2019) “Chronicle of a Soil Bacterium: Paenibacillus polymyxa E681 as a Tiny Guardian of Plant and Human Health” Front. Microbiol. doi:10.3389/fmicb.2019.00467
  • Kaminsky et al. (2019) “Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of SphingopyxisGenes doi:0.3390/genes10090688
  • Khan et al. (2019) “Genomic and physiological analyses reveal that extremely thermophilic Caldicellulosiruptor changbaiensis deploys unique cellulose attachment mechanisms” BioRxiv doi:10.1101/622977
  • Kirmiz et al. (2019) “Comparative genomics guides elucidation of vitamin B12 biosynthesis in novel human associated AkkermansiaBioRxiv doi:10.1101/587527
  • Kiu et al. (2019) “Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis” Animal Microbiome doi:10.1186/s42523-019-0015-1
  • Kiu et al. (2019) “Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids” Micro. Genom. doi:10.1099/mgen.0.000297
  • Lozada et al. (2019) “Phage vB_BmeM-Goe8 infecting Bacillus megaterium DSM319” Arch. Virol. doi:10.1007/s00705-019-04513-5
  • Kochetkova et al. (2019) “Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14” Int. J. Syst. Evol. Microbiol. doi:10.1099/ijsem.0.003902
  • Kovaleva et al. (2019) “Tautonia sociabilis gen. nov., sp. nov., a novel thermotolerant planctomycete, isolated from a 4000 m deep subterranean habitat” Int. J. Syst. Evol. Microbiol. doi:10.1099/ijsem.0.003467
  • Labuda et al. (2019) “Bloodstream Infections With a Novel Nontuberculous Mycobacterium Involving 52 Outpatient Oncology Clinic Patients―Arkansas, 2018” Clin. Inf. Dis. doi:10.1093/cid/ciz1120
  • Lan et al. (2019) “Vogesella urethralis sp. nov., isolated from human urine, and emended descriptions of Vogesella perlucida and Vogesella mureinivoransInt. J. Syst. Evol. Microbiol. doi:10.1099/ijsem.0.003802
  • Lawson et al. (2019) “Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem” ISME J. doi:0.1038/s41396-019-0553-2
  • Ma et al. (2019) “First report of Dickeya fangzhongdai causing soft rot of onion in New York State” Plant Dis. doi:10.1094/PDIS-09-19-1940-PDN
  • Matteo-Estrada et al. (2019) “Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for AcinetobacterGenome Biol. Evol. doi:10.1093/gbe/evz178
  • McIntyre et al. (2019) “Single-molecule sequencing detection of N6-methyladenine in microbial reference materials” Nat. Comm. doi:10.1038/s41467-019-08289-9
  • Nordmann et al. (2019) “Complete genome sequence of the virus isolate vB_BthM-Goe5 infecting Bacillus thuringiensisArch. Virol. doi:10.1007/s00705-019-04187-z
  • Paim et al. (2019) “Evaluation of niche adaptation features by genome data mining approach of Escherichia coli urinary and gastrointestinal strains” PeerJ Preprints doi:10.7287/peerj.preprints.27720v1
  • Park et al (2019) “Complete genome sequence of acetate-producing Klebsiella pneumoniae L5-2 isolated from infant feces” 3Biotech doi:10.1007/s13205-019-1578-y
  • Pedron & van Gijsegem (2019) “Diversity in the Bacterial Genus Dickeya Grouping Plant Pathogens and Waterways Isolates” OBM Genetics doi:10.21926/obm.genet.1904098
  • Portier et al. (2019) “Elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov., proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., emended description of Pectobacterium carotovorum and description of Pectobacterium versatile sp. nov., isolated from streams and symptoms on diverse plants” Int. J Syst. Evol. Biol doi:10.1099/ijsem.0.003611
  • Potter et al. (2019) “In Silico Analysis of Gardnerella Genomospecies Detected in the Setting of Bacterial Vaginosis” Clin. Chem. doi:10.1373/clinchem.2019.305474
  • Reichler et al. (2019) “A century of gray: A genomic locus found in 2 distinct Pseudomonas spp. is associated with historical and contemporary color defects in dairy products worldwide” J. Dairy Sci. doi:10.3168/jds.2018-16192
  • Royo-Llonch et al. “Ecological and functional capabilities of an uncultured Kordia sp” Syst. Appl. Microbiol. doi:10.1016/j.syapm.2019.126045
  • Ruiz et al. (2019) “Microbiota of human precolostrum and its potential role as a source of bacteria to the infant mouth” Sci. Rep. doi:10.1038/s41598-019-42514-1
  • Sant’Anna et al. (2019) “Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy” Crit. Rev. Microbiol. doi:10.1080/1040841X.2019.1569587
  • Schmuhl et al. (2019) “Comparative Transcriptomic Profiling of Yersinia enterocolitica O:3 and O:8 Reveals Major Expression Differences of Fitness- and Virulence-Relevant Genes Indicating Ecological Separation” mSystems doi:10.1128/mSystems.00239-18
  • Spirina et al. (2019) “Draft Genome Sequence of Microbacterium sp. Gd 4-13, Isolated from Gydanskiy Peninsula Permafrost Sediments of Marine Origin” Microb. Res. Announce. doi:10.1128/MRA.00889-19
  • Stefanic et al. (2019) “Intra-species DNA exchange: Bacillus subtilis prefers sex with less related strains” BioRxiv doi:10.1101/756569
  • Stevens et al. (2019) “Whole-genome-based phylogeny of Bacillus cytotoxicus reveals different clades within the species and provides clues on ecology and evolution” Sci. Rep. doi:10.1038/s41598-018-36254-x
  • Tanaka et al. (2019) “Draft Genome Sequences of Enterococcus faecalis Strains Isolated from Healthy Japanese Individuals” Microb. Res. Announce. doi:10.1128/MRA.00832-19
  • Thorell et al. (2019) “Isolates from colonic spirochaetosis in humans show high genomic divergence and carry potential pathogenic features but are not detected by 16S amplicon sequencing using standard primers for the human microbiota” BioRxiv doi:doi.org/10.1101/544502
  • Tian et al. (2019) “LINbase: A Web service for genome-based identification of microbes as members of crowdsourced taxa” BioRxiv doi:10.1101/752212
  • Tohno et al. (2019) “Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom substrates” Int. J Syst. Evol. Biol doi:10.1099/ijsem.0.003224
  • Vazquez-Campos et al. (2019) “Genomic insights into the Archaea inhabiting an Australian radioactive legacy site” BioRxiv doi:10.1101/728089
  • Vincent et al. (2019) “A Mesophilic Aeromona salmonicida Strain Isolated from an Unsuspected Host, the Micratory Bird Pied Avocet” Microorganisms doi:10.3390/microorganisms7120592
  • Vincent et al. (2019) “Investigation of the virulence and genomics of Aeromonas salmonicida strains isolated from human patients” Inf. Genet. Evol. doi:10.1016/j.meegid.2018.11.019
  • Vincent et al. (2019) “Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics” PLoS Neg. Trop. Dis. doi:10.1371/journal.pntd.0007270
  • Wallner et al. (2019) “Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans” BMC Genomics doi:10.1186/s12864-019-6186-z
  • Wang et al. (2019) “Occurrence of CTX-M-123-producing Salmonella Indiana in chicken carcasses: a new challenge for the poultry industry and food safety” J. Antimicrob. Chemo. doi:10.1093/jac/dkz386
  • Webster et al. (2019) “Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments” Microbiol. Res. Ann. doi:10.1128/MRA.00342-19
  • Webster et al. (2019) “The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential” Microbiol. Res. Ann. doi:10.1128/MRA.00778-19
  • Wiegand et al. (2019) “Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology” Nat. Microbiol. doi:10.1038/s41564-019-0588-1
  • Wittouck et al. (2019) ” A genome-based species taxonomy of the Lactobacillus genus complex” mSystems doi:10.1128/mSystems.00264-19
  • Yin et al. (2019) “A hybrid sub-lineage of Listeria monocytogenes comprising hypervirulent isolates” Nat. Comm. doi:10.1038/s41467-019-12072-1
  • Yin et al. (2019) “Genetic Diversity of Listeria monocytogenes Isolates from Invasive Listeriosis in China” Foodborne Path. Dis. doi:10.1089/fpd.2019.2693
  • Zabel et al. (2019) “Novel Genes and Metabolite Trends in Bifidobacterium longum subsp. infantis Bi-26 Metabolism of Human Milk Oligosaccharide 2′-fucosyllactose” Sci. Rep. doi:10.1038/s41598-019-43780-9
  • Zakham et al. (2019) “Molecular diagnosis and enrichment culture identified a septic pseudoarthrosis due to an infection with Erysipelatoclostridium ramosumInt. J. Inf. Dis. doi:10.1016/j.ijid.2019.02.001
  • Zhu et al. (2019) “First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China” Front. Vet. Sci. doi:10.3389/fvets.2019.00128
  • Zhu et al. (2019) “Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands” Func. Int. Genom doi:10.1007/s10142-019-00715-x

2018

  • Alex & Antunes (2018) “Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts” PLoS One doi:10.1371/journal.pone.0194368
  • Beaton et al. (2018) “Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies” FEMS Micro. Lett. doi:10.1093/femsle/fny069
  • Bogema et al. (2018) “Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes” BMC Genomics doi:10.1186/s12864-018-4701-2
  • Brand et al. (2018) “Niche Differentiation among Three Closely Related Competibacteraceae Clades at a Full-Scale Activated Sludge Wastewater Treatment Plant and Putative Linkages to Process Performance” App. Env. Micro. doi:10.1128/AEM.02301-18
  • Bridel et al. (2018) “Comparative Genomics of Tenacibaculum dicentrarchi and “Tenacibaculum finnmarkense” Highlights Intricate Evolution of Fish-Pathogenic Species” Genome Biol. Evol. doi:10.1093/gbe/evy020
  • Carlos et al. (2018) “Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers” Front. Microbiol. doi:10.3389/fmicb.2018.00364
  • Covarrubias et al. (2018) “Occurrence, integrity and functionality of Aca*ML1–like viruses infecting extreme acidophiles of the *Acidithiobacillus species complex” Res. Microbiol. doi:10.1016/j.resmic.2018.07.005
  • da Gama et al. (2018) “Taxonomic Repositioning of Xanthomonas campestris pv. viticola (Nayudu 1972) Dye 1978 as Xanthomonas citri pv. viticola (Nayudu 1972) Dye 1978 comb. nov. and Emendation of the Description of Xanthomonas citri pv. anacardii to Include Pigmented Isolates Pathogenic to Cashew Plant” Phytopath. doi:10.1094/PHYTO-02-18-0037-R
  • Ferretti et al. (2018) “Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome” Cell Host Microbe doi:10.1016/j.chom.2018.06.005
  • Fontana et al. (2018) “Genetic Signatures of Dairy Lactobacillus casei Group” Front. Microbiol. doi:10.3389/fmicb.2018.02611
  • Freschi et al. (2018) “The Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity” Genome Biol. Evol. doi:10.1093/gbe/evy259
  • Gillis et al. (2018) “Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar israelensisFEMS Micro. Rev. doi:10.1093/femsre/fuy034
  • Gragna-Miraglia et al. (2018) “Phylogenomics picks out the par excellence markers for species phylogeny in the genus StaphylococcusPeerJ doi:10.7717/peerj.5839
  • Hubbard et al. (2018) “Comparison of the first whole genome sequence of ‘Haemophilus quentini’ with two new strains of ‘Haemophilus quentini’ and other species of HaemophilusGenome doi:10.1139/gen-2017-0195
  • Issotta et al. (2018) “Insights into the biology of acidophilic members of the Acidiferrobacteraceae family derived from comparative genomic analyses” Res. Microbiol. doi:10.1016/j.resmic.2018.08.001
  • Jangam et al. (2018) “Draft Genome Sequence of Vibrio parahaemolyticus Strain VP14, Isolated from a Penaeus vannamei Culture Farm” Micro. Res. Ann. doi:10.1128/genomeA.00149-18
  • Jarett et al. (2018) “Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis” Microbiome doi:10.1186/s40168-018-0539-8
  • Jung et al. (2018) “Complete genome sequence of Bifidobacterium choerinum FMB-1, a resistant starch-degrading bacterium” J. Biotech. doi:10.1016/j.jbiotec.2018.03.009
  • Lazarte et al. (2018) “Bacillus wiedmannii biovar thuringiensis: A Specialized Mosquitocidal Pathogen with Plasmids from Diverse Origins” Genome Biol. Evol. doi:10.1093/gbe/evy211
  • Li et al. (2018) “A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains” Front. Microbiol. doi:10.3389/fmicb.2018.00973
  • Lima et al. “Genome sequencing and functional characterization of the non-pathogenic Klebsiella pneumoniae KpGe bacteria* Microbes Inf. doi:10.1016/j.micinf.2018.04.001
  • McCann et al. (2018) “Viromes of one year old infants reveal the impact of birth mode on microbiome diversity” PeerJ doi:10.7717/peerj.4694
  • Morales-Covarrubias (2018) “Streptococcus penaeicida sp. nov., isolated from a diseased farmed Pacific white shrimp (Penaeus vannamei)” Int. J Syst. Evol. Biol doi:10.1099/ijsem.0.002693
  • Munoz-Villagran et al. (2018) “Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula” PeerJ doi:10.7717/peerj.4402
  • Nascimento et al. (2018) “From plants to nematodes: Serratia grimesii BXF1 genome reveals an adaptation to the modulation of multi-species interactions” Microb. Genom. doi:10.1099/mgen.0.000178
  • Orr et al. (2018) “De novo assembly of the Pasteuria penetrans genome reveals high plasticity, host dependency, and BclA-like collagens” BioRxiv doi:10.1101/485748
  • Pinto et al. (2018) “Draft Genome Sequences of Novel Pseudomonas, Flavobacterium, and Sediminibacterium Strains from a Freshwater Ecosystem” Micro. Res. Ann. doi:10.1128/genomeA.00009-18
  • Potter et al. (2018) “Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella variicolamBio doi:10.1128/mBio.02481-18
  • Potter et al. (2018) “Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum β-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces” Front. Microbiol. doi:10.3389/fmicb.2018.01629
  • Samad et al. (2017) “Comparative genome analysis of the vineyard weed endophyte Pseudomonas viridiflava CDRTc14 showing selective herbicidal activity” Sci. Rep. doi:10.1038/s41598-017-16495-y
  • Sant’Anna et al. (2018) “Genome-based reclassification of Paenibacillus dauci as a later heterotypic synonym of Paenibacillus shenyangensisInt. J. Syst. Evol. Micro. doi:10.1099/ijsem.0.003127
  • Schilling et al. (2018) “Genomic Analysis of the Recent Viral Isolate vB_BthP-Goe4 Reveals Increased Diversity of φ29-Like Phages” Viruses doi:10.3390/v10110624
  • Stevens et al. (2018) “Massive Diversity in Whole-Genome Sequences of Streptococcus suis Strains from Infected Pigs in Switzerland” Microbiol. Res. Ann. doi:10.1128/MRA.01656-18
  • Tanizawa et al. (2018) “Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses” Int. J Syst. Evol. Biol doi:10.1099/ijsem.0.003020
  • Vincent & Charette (2018) “Completion of genome of Aeromonas salmonicida subsp. salmonicida 01-B526 reveals how sequencing technologies can influence sequence quality and result interpretations” New Microb. New Inf. doi:10.1016/j.nmni.2018.05.007
  • Wilhelm (2018) “Following the terrestrial tracks of Caulobacter - redefining the ecology of a reputed aquatic oligotroph” ISME J doi:10.1038/s41396-018-0257-z
  • Wittwer et al. (2018) “Population Genomics of Francisella tularensis subsp. holarctica and its Implication on the Eco-Epidemiology of Tularemia in Switzerland” Front. Cell. Inf. Microbiol. doi:10.3389/fcimb.2018.00089
  • Zhang et al. (2018) “Draft Genome Sequence of Komagataeibacter maltaceti LMG 1529T, a Vinegar-Producing Acetic Acid Bacterium Isolated from Malt Vinegar Brewery Acetifiers” Micro. Res. Ann. doi:10.1128/genomeA.00330-18

2017

  • Anderson et al. (2017) “Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents” Nat. Comm. doi:10.1038/s41467-017-01228-6
  • Ding et al. (2017) “Loss of the ssrA genome island led to partial debromination in the PBDE respiring Dehalococcoides mccartyi strain GY50” Env. Micro. doi:10.1111/1462-2920.13817
  • Edgington et al. (2017) “Genome Sequences of Chancellor, Mitti, and Wintermute, Three Subcluster K4 Phages Isolated Using Mycobacterium smegmatis mc^{2}155” Microbiol. Res. Ann. doi:10.1128/genomeA.01070-17
  • Esposito et al. (2017) “Evolution of Stenotrophomonas maltophilia in Cystic Fibrosis Lung over Chronic Infection: A Genomic and Phenotypic Population Study” Front. Microbiol. doi:10.3389/fmicb.2017.01590
  • Jeukens et al. (2017) “A Pan-Genomic Approach to Understand the Basis of Host Adaptation in AchromobacterGenome Biol. Evol. doi:10.1093/gbe/evx061
  • Ke et al. (2017) “Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade” Sci. Rep. doi:10.1038/srep41394
  • Kumar et al. (2017) “Draft Genome Sequence of the Luminescent Strain Vibrio campbellii LB102, Isolated from a Black Tiger Shrimp (Penaeus monodon) Broodstock Rearing System” Micro. Res. Ann. doi:10.1128/genomeA.00342-17
  • Pelve et al. (2017) “Bacterial Succession on Sinking Particles in the Ocean’s Interior” Front. Microbiol. doi:10.3389/fmicb.2017.02269
  • Poehlein et al. (2017) “Microbial solvent formation revisited by comparative genome analysis” Biotech. Biofuels doi:10.1186/s13068-017-0742-z
  • Ruiz-Valdeviezo et al. (2017) “Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere” Micro. Res. Ann. doi:10.1128/genomeA.01280-17
  • Tada et al. (2017) “Revealing the genomic differences between two subgroups in Lactobacillus gasseriBiosci. Microb. Food Health doi:10.12938/bmfh.17-006
  • Tanizawa et al. (2017) “Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiriBiosci. Microb. Food Health doi:10.12938/bmfh.16-026
  • Tohno et al. (2017) “Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from silage” Int. J Syst. Evol. Biol doi:10.1099/ijsem.0.002196
  • Vincent et al. (2017) “Study of mesophilic Aeromonas salmonicida A527 strain sheds light on the species’ lifestyles and taxonomic dilemma” FEMS Micro. Lett. doi:10.1093/femsle/fnx239
  • Vollmers et al. (2017) “Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning” Front. Microbiol. doi:10.3389/fmicb.2017.00472
  • Wang et al. (2017) “Genomic sequence of ‘Candidatus Liberibacter solanacearum’ haplotype C and its comparison with haplotype A and B genomes” PLoS One doi:10.1371/journal.pone.0171531

2016

  • Burstein et al. (2016) “New CRISPR–Cas systems from uncultivated microbes” Nature doi:10.1038/nature21059
  • Gupta et al. (2016) “Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach” Sci. Rep. doi:10.1038/srep29043
  • Haack et al. (2016) “Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearumFront. Microbiol. doi:10.3389/fmicb.2016.01668
  • Maeno et al. (2016) “Genomic characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation” Syst. Appl. Microbiol. doi:10.1016/j.syapm.2016.09.006
  • Pritchard et al. (2016) “Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens” Anal. Methods doi:10.1039/C5AY02550H
  • Rodriguez-Rojas et al. (2016) “Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica” Front. Microbiol. doi:10.3389/fmicb.2016.01777
  • Tanizawa et al. (2016) “DFAST and DAGA: web-based integrated genome annotation tools and resources” Biosci. Microb. Food Health doi:10.12938/bmfh.16-003
  • Zheng et al. (2016) “Metabolism of Toxic Sugars by Strains of the Bee Gut Symbiont Gilliamella apicolamBio doi:10.1128/mBio.01326-16