All Stories

  1. Metagenomics reveal unrestricted dispersal of extreme halophiles and higher connectivity among coastal vs. inland solar salterns and hypersaline lakes

    Article • ISME Communications, June 2026, Oxford University Press (OUP)

    Luis M Rodriguez-R

  2. Maximal Transparency for Online Recommender Systems

    Article • Philosophy & Technology, April 2026, Springer Science + Business Media

    Luis M Rodriguez-R

  3. An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations

    Article • ISME Communications, March 2026, Oxford University Press (OUP)

    Luis M Rodriguez-R

  4. Request for public discussion and ballot to add rules on paratypes to the SeqCode and amend recommendations on name formation

    Article • ISME Communications, January 2026, Oxford University Press (OUP)

    Luis M Rodriguez-R

  5. 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

  6. Author Correction: A roadmap for equitable reuse of public microbiome data

    Article • Nature Microbiology, November 2025, Springer Science + Business Media

    Dr Robert A Edwards, Luis M Rodriguez-R, Professor Konstantinos (Kostas) Kormas

  7. 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

  8. Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns

    Article • October 2025, openRxiv

    Luis M Rodriguez-R

  9. A roadmap for equitable reuse of public microbiome data

    Article • Nature Microbiology, September 2025, Springer Science + Business Media

    Gareth Trubl, Dr Robert A Edwards, Luis M Rodriguez-R, Professor Konstantinos (Kostas) Kormas

  10. A practical guide on environmental genomics for prokaryotic systematics

    Article • Systematic and Applied Microbiology, September 2025, Elsevier

    Luis M Rodriguez-R

  11. Determinism and stochasticity drive microbial community assembly and microbial interactions in calcareous glacier forefields

    Article • Applied and Environmental Microbiology, June 2025, ASM Journals

    Luis M Rodriguez-R

  12. 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

  13. Earth's most needed uncultivated aquatic prokaryotes

    Article • Water Research, April 2025, Elsevier

    Luis M Rodriguez-R

  14. 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

  15. Probiotic Potential of Yeast, Mold, and Intermediate Morphotypes of Geotrichum candidum in Modulating Gut Microbiota and Body Physiology in Mice

    Article • Probiotics and Antimicrobial Proteins, March 2025, Springer Science + Business Media

    Luis M Rodriguez-R

  16. Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence

    Article • The ISME Journal, January 2025, Oxford University Press (OUP)

    Luis M Rodriguez-R

  17. Differences in metagenome coverage may confound abundance-based and diversity conclusions and how to deal with them

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

    Luis M Rodriguez-R

  18. Global dominance of Haloquadratum walsbyi by a single genomovar with distinct gene content and viral cohorts from close relatives

    Article • The ISME Journal, January 2025, Oxford University Press (OUP)

    Luis M Rodriguez-R

  19. Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean

    Article • The ISME Journal, January 2025, Oxford University Press (OUP)

    Luis M Rodriguez-R

  20. Quantifying the contribution of the rare biosphere to natural disturbances

    Article • The ISME Journal, January 2025, Oxford University Press (OUP)

    Luis M Rodriguez-R

  21. 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

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

    Article • Systematic and Applied Microbiology, November 2024, Elsevier

    Luis M Rodriguez-R

  23. 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

  24. 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

  25. Quis custodiet ipsos custodes? A call for community participation in the governance of the SeqCode

    Article • Systematic and Applied Microbiology, May 2024, Elsevier

    Luis M Rodriguez-R

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

    Article • March 2024, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  27. Why and how to use the SeqCode

    Article • mLife, February 2024, Tsinghua University Press

    William Whitman, Luis M Rodriguez-R

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

    Article • mBio, January 2024, ASM Journals

    Luis M Rodriguez-R

  29. 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

  30. A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection

    Article • International Journal of Food Microbiology, January 2024, Elsevier

    Luis M Rodriguez-R

  31. Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes

    Article • Systematic and Applied Microbiology, January 2024, Elsevier

    Luis M Rodriguez-R

  32. Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement

    Article • The ISME Journal, January 2024, Oxford University Press (OUP)

    Luis M Rodriguez-R

  33. 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

  34. Comparative Genomics Identifies Conserved and Variable TAL Effectors in African Strains of the Cotton Pathogen Xanthomonas citri pv. malvacearum

    Article • Phytopathology, August 2023, Scientific Societies

    Luis M Rodriguez-R

  35. Corrigendum: 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, May 2023, Society for General Microbiology

    Luis M Rodriguez-R

  36. 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

  37. 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

  38. 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

  39. 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

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

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

    Luis M Rodriguez-R

  41. 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

  42. 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

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

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  44. 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

  45. 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

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

    Article • Water Research, February 2022, Elsevier

    Luis M Rodriguez-R

  47. RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity

    Article • Frontiers in Bioinformatics, January 2022, Frontiers

    Luis M Rodriguez-R

  48. 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

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

    Article • July 2021, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  50. 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

  51. Beach sand oil spills select for generalist microbial populations

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

    Luis M Rodriguez-R

  52. 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

  53. 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

  54. 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

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

    Article • January 2021, CABI Publishing

    Luis M Rodriguez-R

  56. 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

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

    Article • November 2020, Research Square

    Luis M Rodriguez-R

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

    Article • September 2020, Wiley

    Luis M Rodriguez-R

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. “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

  72. 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

  73. 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

  74. 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

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

    Article • PeerJ, November 2018, PeerJ

    Luis M Rodriguez-R

  76. 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

  77. 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

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

    Article • mSystems, April 2018, ASM Journals

    Luis M Rodriguez-R

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

    Article • February 2018, PeerJ

    Luis M Rodriguez-R

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

    Article • February 2018, PeerJ

    Luis M Rodriguez-R

  81. 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

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

    Article • November 2017, Cold Spring Harbor Laboratory Press

    Luis M Rodriguez-R

  83. 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

  84. 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

  85. 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

  86. SAR11 bacteria linked to ocean anoxia and nitrogen loss

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

    Luis M Rodriguez-R

  87. 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

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

    Article • March 2016, PeerJ

    Luis M Rodriguez-R

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

    Article • March 2016, PeerJ

    Luis M Rodriguez-R

  90. 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

  91. 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

  92. 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

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

    Article • Environmental Microbiology Reports, June 2014, Wiley

    Luis M Rodriguez-R

  94. 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

  95. On the importance of coverage in metagenomics

    Article • The ISME Journal, May 2014, Nature

    Luis M Rodriguez-R

  96. 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

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

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

    Luis M Rodriguez-R

  98. Bypassing Cultivation To Identify Bacterial Species

    Article • Microbe Magazine, March 2014, ASM Journals

    Luis M Rodriguez-R

  99. 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, Kai Xue

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

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

    Article • January 2013, Elsevier

    Luis M Rodriguez-R

  106. 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

  107. Genomes-based phylogeny of the genus Xanthomonas

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

    Luis M Rodriguez-R

  108. 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

  109. 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

  110. 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

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

    Article • PLOS One, March 2010, PLOS

    Luis M Rodriguez-R

  112. 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

  113. Computational Biology in Colombia

    Article • PLoS Computational Biology, October 2009, PLOS

    Luis M Rodriguez-R, Maria Mercedes Zambrano