All Stories

  1. Sequencing depth (coverage) can bias microbial intraspecies diversity estimates and how to account for it
  2. GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs
  3. Microbial Response to Natural Disturbances: Rare Biosphere often plays a role
  4. Why and how to use the SeqCode
  5. An ANI gap within bacterial species that advances the definitions of intra-species units
  6. Towards estimating the number of strains that make up a natural bacterial population
  7. Wood decay fungi and their bacterial interaction partners in the built environment – A systematic review on fungal bacteria interactions in dead wood and timber
  8. Towards estimating the number of strains that make up a natural bacterial population
  9. GSearch: Ultra-Fast and Scalable Microbial Genome Search by Combining Kmer Hashing with Hierarchical Navigable Small World Graphs
  10. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation
  11. Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database
  12. SeqCode: a nomenclatural code for prokaryotes described from sequence data
  13. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type
  14. Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling
  15. A natural definition for a bacterial strain and clonal complex
  16. ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes
  17. FastAAI: Efficient Estimation of Genome Average Amino Acid Identity and Phylum-level relationships using Tetramers of Universal Proteins
  18. Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms
  19. Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions
  20. Novel municipal sewage-associated bacterial genomes and their potential in source tracking
  21. Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species”
  22. Beach sand oil spills select for generalist microbial populations
  23. Transcriptomic and rRNA:rDNA signatures of environmental vs. enteric Enterococcus faecalis isolates under oligotrophic freshwater conditions
  24. How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample
  25. The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility
  26. Identification and Classification of Prokaryotes using whole-genome sequences.
  27. The Type VI Secretion System of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility
  28. Rocker Models for Reliable Detection and Typing of Short Read Sequences Carrying β-lactamases
  29. Classifying prokaryotic genomes using the Microbial Genomes Atlas (MiGA) webserver
  30. Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies over 400 Novel Species and their Ecologic Preferences
  31. Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes
  32. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters
  33. Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes
  34. Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations
  35. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri
  36. Genome Repository of Oiled Systems (GROS): an interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes
  37. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri
  38. Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies of over Four Hundred Novel Species and their Ecologic Preferences
  39. Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California
  40. Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus “Candidatus Fonsibacter” and proposal of Ca. Fonsibacter lacus sp. nov
  41. The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production
  42. “Candidatus Macondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments
  43. Analysis of Whole-Genome Sequences for the Prediction of Penicillin Resistance and β-Lactamase Activity inBacillus anthracis
  44. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
  45. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient
  46. imGLAD: accurate detection and quantification of target organisms in metagenomes
  47. Genomic Characterization and Copy Number Variation ofBacillus anthracisPlasmids pXO1 and pXO2 in a Historical Collection of 412 Strains
  48. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level
  49. Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity
  50. imGLAD: Accurate detection and quantification of target organisms in metagenomes
  51. imGLAD: Accurate detection and quantification of target organisms in metagenomes
  52. How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?
  53. High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries
  54. Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids
  55. Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem
  56. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores
  57. SAR11 bacteria linked to ocean anoxia and nitrogen loss
  58. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem
  59. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes
  60. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes
  61. Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections
  62. Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill
  63. New Multilocus Variable-Number Tandem-Repeat Analysis Tool for Surveillance and Local Epidemiology of Bacterial Leaf Blight and Bacterial Leaf Streak of Rice Caused by Xanthomonas oryzae
  64. Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities
  65. Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle
  66. On the importance of coverage in metagenomics
  67. Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics
  68. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences
  69. Bypassing Cultivation To Identify Bacterial Species
  70. Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics
  71. Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen Xanthomonas axonopodis pv. Manihotis Strain CIO151
  72. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets
  73. An Improved Method for TAL Effectors DNA-Binding Sites Prediction Reveals Functional Convergence in TAL Repertoires of Xanthomonas oryzae Strains
  74. Reply to Smith and Griffin: Methods, air flows, and conclusions are robust in the DeLeon-Rodriguez et al. study
  75. Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications
  76. A User’s Guide to Quantitative and Comparative Analysis of Metagenomic Datasets
  77. Development of a Variable Number of Tandem Repeats Typing Scheme for the Bacterial Rice Pathogen Xanthomonas oryzae pv. oryzicola
  78. Genomes-based phylogeny of the genus Xanthomonas
  79. Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease
  80. A new method for designing degenerate primers and its use in the identification of sequences in Brachiaria showing similarity to apomixis-associated genes
  81. Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions
  82. Discovery of Phytophthora infestans Genes Expressed in Planta through Mining of cDNA Libraries
  83. An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1
  84. Computational Biology in Colombia