All Stories

  1. Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it

    Article • ISME Communications, December 2025, Oxford University Press (OUP)

    Luis M Rodriguez-R

  2. Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance

    Article • Scientific Reports, October 2025, Springer Science + Business Media

    Luis M Rodriguez-R

  3. A practical guide on environmental genomics for prokaryotic systematics

    Article • Systematic and Applied Microbiology, September 2025, Elsevier

    Luis M Rodriguez-R

  4. FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins

    Article • Nucleic Acids Research, April 2025, Oxford University Press (OUP)

    Luis M Rodriguez-R

  5. The ecological success of freshwater microorganisms is mediated by streamlining and biotic interactions

    Article • March 2025, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  6. Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination

    Article • Nature Communications, November 2024, Springer Science + Business Media

    Luis M Rodriguez-R

  7. Options and considerations for validation of prokaryotic names under the SeqCode

    Article • Systematic and Applied Microbiology, November 2024, Elsevier

    Luis M Rodriguez-R

  8. Sequencing depth (coverage) can bias microbial intraspecies diversity estimates and how to account for it

    Article • July 2024, Springer Science + Business Media

    Luis M Rodriguez-R

  9. GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs

    Article • Nucleic Acids Research, July 2024, Oxford University Press (OUP)

    Luis M Rodriguez-R

  10. Microbial Response to Natural Disturbances: Rare Biosphere often plays a role

    Article • March 2024, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  11. Why and how to use the SeqCode

    Article • mLife, February 2024, Tsinghua University Press

    William Whitman, Luis M Rodriguez-R

  12. An ANI gap within bacterial species that advances the definitions of intra-species units

    Article • mBio, January 2024, ASM Journals

    Luis M Rodriguez-R

  13. Towards estimating the number of strains that make up a natural bacterial population

    Article • Nature Communications, January 2024, Springer Science + Business Media

    Luis M Rodriguez-R

  14. Wood decay fungi and their bacterial interaction partners in the built environment – A systematic review on fungal bacteria interactions in dead wood and timber

    Article • Fungal Biology Reviews, September 2023, Elsevier

    Luis M Rodriguez-R

  15. Towards estimating the number of strains that make up a natural bacterial population

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  16. GSearch: Ultra-Fast and Scalable Microbial Genome Search by Combining Kmer Hashing with Hierarchical Navigable Small World Graphs

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  17. Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation

    Article • ISME Communications, September 2022, Springer Science + Business Media

    Luis M Rodriguez-R

  18. Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database

    Article • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, September 2022, Society for General Microbiology

    Luis M Rodriguez-R

  19. SeqCode: a nomenclatural code for prokaryotes described from sequence data

    Article • Nature Microbiology, September 2022, Springer Science + Business Media

    Luis M Rodriguez-R

  20. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

    Article • Systematic and Applied Microbiology, September 2022, Elsevier

    Luis M Rodriguez-R

  21. Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling

    Article • ISME Communications, August 2022, Springer Science + Business Media

    Luis M Rodriguez-R

  22. A natural definition for a bacterial strain and clonal complex

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  23. ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes

    Article • mSystems, May 2022, ASM Journals

    Luis M Rodriguez-R

  24. FastAAI: Efficient Estimation of Genome Average Amino Acid Identity and Phylum-level relationships using Tetramers of Universal Proteins

    Article • March 2022, Research Square

    Luis M Rodriguez-R

  25. Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms

    Article • Water Research, February 2022, Elsevier

    Luis M Rodriguez-R

  26. Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions

    Article • Microbiology Spectrum, October 2021, ASM Journals

    Luis M Rodriguez-R

  27. Novel municipal sewage-associated bacterial genomes and their potential in source tracking

    Article • July 2021, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  28. Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species”

    Article • Nature Communications, July 2021, Springer Science + Business Media

    Luis M Rodriguez-R

  29. Beach sand oil spills select for generalist microbial populations

    Article • The ISME Journal, June 2021, Springer Science + Business Media

    Luis M Rodriguez-R

  30. Transcriptomic and rRNA:rDNA signatures of environmental vs. enteric Enterococcus faecalis isolates under oligotrophic freshwater conditions

    Article • May 2021, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  31. How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample

    Article • Applied and Environmental Microbiology, January 2021, ASM Journals

    Luis M Rodriguez-R

  32. The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

    Article • BMC Microbiology, January 2021, Springer Science + Business Media

    Luis M Rodriguez-R

  33. Identification and Classification of Prokaryotes using whole-genome sequences.

    Article • January 2021, CABI Publishing

    Luis M Rodriguez-R

  34. The Type VI Secretion System of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

    Article • December 2020, Research Square

    Luis M Rodriguez-R

  35. Rocker Models for Reliable Detection and Typing of Short Read Sequences Carrying β-lactamases

    Article • November 2020, Research Square

    Luis M Rodriguez-R

  36. Classifying prokaryotic genomes using the Microbial Genomes Atlas (MiGA) webserver

    Article • September 2020, Wiley

    Luis M Rodriguez-R

  37. Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies over 400 Novel Species and their Ecologic Preferences

    Article • Environmental Microbiology, June 2020, Wiley

    Luis M Rodriguez-R

  38. Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes

    Article • Environmental Microbiology, March 2020, Wiley

    Luis M Rodriguez-R

  39. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

    Article • Biotechnology for Biofuels, February 2020, Springer Science + Business Media

    Luis M Rodriguez-R

  40. Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes

    Article • Scientific Reports, February 2020, Springer Science + Business Media

    Luis M Rodriguez-R

  41. Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

    Article • Applied and Environmental Microbiology, January 2020, ASM Journals

    Luis M Rodriguez-R

  42. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri

    Article • BMC Genomics, December 2019, Springer Science + Business Media

    Luis M Rodriguez-R

  43. Genome Repository of Oiled Systems (GROS): an interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  44. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri

    Article • November 2019, Research Square

    Luis M Rodriguez-R

  45. Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies of over Four Hundred Novel Species and their Ecologic Preferences

    Article • October 2019, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  46. Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  47. Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus “Candidatus Fonsibacter” and proposal of Ca. Fonsibacter lacus sp. nov

    Article • Systematic and Applied Microbiology, July 2019, Elsevier

    Luis M Rodriguez-R

  48. The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  49. “Candidatus Macondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments

    Article • The ISME Journal, April 2019, Springer Science + Business Media

    Luis M Rodriguez-R

  50. Analysis of Whole-Genome Sequences for the Prediction of Penicillin Resistance and β-Lactamase Activity inBacillus anthracis

    Article • mSystems, December 2018, ASM Journals

    Luis M Rodriguez-R

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

    Article • Nature Communications, November 2018, Springer Science + Business Media

    Luis M Rodriguez-R

  52. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient

    Article • The ISME Journal, November 2018, Springer Science + Business Media

    Luis M Rodriguez-R, Professor Konstantinos (Kostas) Kormas

  53. imGLAD: accurate detection and quantification of target organisms in metagenomes

    Article • PeerJ, November 2018, PeerJ

    Luis M Rodriguez-R

  54. Genomic Characterization and Copy Number Variation ofBacillus anthracisPlasmids pXO1 and pXO2 in a Historical Collection of 412 Strains

    Article • mSystems, August 2018, ASM Journals

    Luis M Rodriguez-R, Konstantinos Konstantinidis

  55. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

    Article • Nucleic Acids Research, June 2018, Oxford University Press (OUP)

    Luis M Rodriguez-R

  56. Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

    Article • mSystems, April 2018, ASM Journals

    Luis M Rodriguez-R

  57. imGLAD: Accurate detection and quantification of target organisms in metagenomes

    Article • February 2018, PeerJ

    Luis M Rodriguez-R

  58. imGLAD: Accurate detection and quantification of target organisms in metagenomes

    Article • February 2018, PeerJ

    Luis M Rodriguez-R

  59. How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

    Article • Applied and Environmental Microbiology, January 2018, ASM Journals

    Luis M Rodriguez-R, Konstantinos Konstantinidis, Dr Nikos C Kyrpides

  60. High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries

    Article • November 2017, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  61. Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids

    Article • Genome Announcements, April 2017, ASM Journals

    Luis M Rodriguez-R

  62. Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem

    Article • Applied and Environmental Microbiology, March 2017, ASM Journals

    Konstantinos Konstantinidis, Luis M Rodriguez-R

  63. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

    Article • Nucleic Acids Research, October 2016, Oxford University Press (OUP)

    Luis M Rodriguez-R

  64. SAR11 bacteria linked to ocean anoxia and nitrogen loss

    Article • Nature, August 2016, Springer Science + Business Media

    Luis M Rodriguez-R

  65. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

    Article • Frontiers in Microbiology, April 2016, Frontiers

    Luis M Rodriguez-R

  66. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes

    Article • March 2016, PeerJ

    Luis M Rodriguez-R

  67. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes

    Article • March 2016, PeerJ

    Luis M Rodriguez-R

  68. Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

    Article • Applied and Environmental Microbiology, March 2016, ASM Journals

    Konstantinos Konstantinidis, Luis M Rodriguez-R

  69. Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

    Article • The ISME Journal, February 2015, Nature

    Luis M Rodriguez-R

  70. 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

    Article • Applied and Environmental Microbiology, November 2014, ASM Journals

    Dr Ralf Koebnik, Luis M Rodriguez-R

  71. Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities

    Article • Environmental Microbiology Reports, June 2014, Wiley

    Luis M Rodriguez-R

  72. Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle

    Article • mBio, June 2014, ASM Journals

    Konstantinos Konstantinidis, Luis M Rodriguez-R

  73. On the importance of coverage in metagenomics

    Article • The ISME Journal, May 2014, Nature

    Luis M Rodriguez-R

  74. Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

    Article • PLOS One, April 2014, PLOS

    Luis M Rodriguez-R

  75. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

    Article • Nucleic Acids Research, March 2014, Oxford University Press (OUP)

    Luis M Rodriguez-R

  76. Bypassing Cultivation To Identify Bacterial Species

    Article • Microbe Magazine, March 2014, ASM Journals

    Luis M Rodriguez-R

  77. Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

    Article • Applied and Environmental Microbiology, December 2013, ASM Journals

    Konstantinos Konstantinidis, Luis M Rodriguez-R

  78. Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen Xanthomonas axonopodis pv. Manihotis Strain CIO151

    Article • PLOS One, November 2013, PLOS

    Dr Ralf Koebnik, Luis M Rodriguez-R

  79. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

    Article • Bioinformatics, October 2013, Oxford University Press (OUP)

    Luis M Rodriguez-R

  80. An Improved Method for TAL Effectors DNA-Binding Sites Prediction Reveals Functional Convergence in TAL Repertoires of Xanthomonas oryzae Strains

    Article • PLOS One, July 2013, PLOS

    Dr Ralf Koebnik, Luis M Rodriguez-R

  81. Reply to Smith and Griffin: Methods, air flows, and conclusions are robust in the DeLeon-Rodriguez et al. study

    Article • Proceedings of the National Academy of Sciences, April 2013, Proceedings of the National Academy of Sciences

    Luis M Rodriguez-R

  82. Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications

    Article • Proceedings of the National Academy of Sciences, January 2013, Proceedings of the National Academy of Sciences

    Luis M Rodriguez-R

  83. A User’s Guide to Quantitative and Comparative Analysis of Metagenomic Datasets

    Article • January 2013, Elsevier

    Luis M Rodriguez-R

  84. Development of a Variable Number of Tandem Repeats Typing Scheme for the Bacterial Rice Pathogen Xanthomonas oryzae pv. oryzicola

    Article • Phytopathology, October 2012, Scientific Societies

    Dr Ralf Koebnik, Luis M Rodriguez-R

  85. Genomes-based phylogeny of the genus Xanthomonas

    Article • BMC Microbiology, January 2012, Springer Science + Business Media

    Luis M Rodriguez-R

  86. Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease

    Article • The ISME Journal, September 2011, Nature

    Luis M Rodriguez-R

  87. A new method for designing degenerate primers and its use in the identification of sequences in Brachiaria showing similarity to apomixis-associated genes

    Article • Bioinformatics, June 2010, Oxford University Press (OUP)

    Luis M Rodriguez-R

  88. Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions

    Article • Briefings in Bioinformatics, March 2010, Oxford University Press (OUP)

    Luis M Rodriguez-R

  89. Discovery of Phytophthora infestans Genes Expressed in Planta through Mining of cDNA Libraries

    Article • PLOS One, March 2010, PLOS

    Luis M Rodriguez-R

  90. An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1

    Article • Virology Journal, January 2010, Springer Science + Business Media

    Luis M Rodriguez-R

  91. Computational Biology in Colombia

    Article • PLoS Computational Biology, October 2009, PLOS

    Luis M Rodriguez-R, Maria Mercedes Zambrano