All Stories

  1. The Oral Microbiome Is a Population-Scale Readout of the Exposome, Age, and Systemic Health

    Article • February 2026, openRxiv

    Dr Aleksandar D Kostic

  2. Veillonella atypica supplementation reduces fatigue interference and increases voluntary physical activity: A randomized controlled trial with mechanistic validation in mice

    Article • November 2025, Cold Spring Harbor Laboratory Press

    Dr Aleksandar D Kostic

  3. Specification curve analysis of the TEDDY study reveals large variation in microbiome-based T1D predictive performance

    Article • Nature Communications, October 2025, Springer Science + Business Media

    Dr Aleksandar D Kostic

  4. Portal vein-enriched metabolites as intermediate regulators of the gut microbiome in insulin resistance

    Article • Cell Metabolism, October 2025, Elsevier

    Dr Aleksandar D Kostic

  5. Adipose tissue–gut microbiome crosstalk in inflammation and thermogenesis

    Article • Trends in Endocrinology and Metabolism, August 2025, Elsevier

    Dr Aleksandar D Kostic

  6. Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin

    Article • Nature Communications, July 2025, Springer Science + Business Media

    Dr Aleksandar D Kostic

  7. Single-cell RNA-seq reveals disease-specific CD8+ T cell clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in diabetic NOD mice

    Article • PLOS One, March 2025, PLOS

    Dr Aleksandar D Kostic

  8. A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population

    Article • Microbiome, January 2025, Springer Science + Business Media

    Dr Aleksandar D Kostic

  9. Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin.

    Article • November 2024, openRxiv

    Dr Aleksandar D Kostic

  10. Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice

    Article • January 2024, Springer Science + Business Media

    Dr Aleksandar D Kostic

  11. Impact of probiotic Veillonella atypica FB0054 supplementation on anaerobic capacity and lactate

    Article • iScience, January 2024, Elsevier

    Dr Aleksandar D Kostic

  12. DNA characterization reveals potential operon-unit packaging of extracellular vesicle cargo from a gut bacterial symbiont

    Article • December 2023, Springer Science + Business Media

    Dr Aleksandar D Kostic

  13. Whole mitogenome analysis highlights demographic history and shared connections among distal Indigenous groups of Mexico Complete mitogenome sequencing from 60 Mexican Native American groups

    Article • September 2023, openRxiv

    Dr Aleksandar D Kostic

  14. Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Dr Aleksandar D Kostic

  15. Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems

    Article • mSystems, April 2023, ASM Journals

    Dr Aleksandar D Kostic

  16. Erratum for Proctor et al., “Resources To Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model To Study Microbiome Function”

    Article • mSystems, April 2023, ASM Journals

    Dr Aleksandar D Kostic

  17. Editorial: Gut microbiome, metabolites, and immune response in lupus, rheumatoid arthritis, and Sjögren syndrome

    Article • Frontiers in Immunology, January 2023, Frontiers

    Dr Aleksandar D Kostic

  18. Reproducible and opposing gut microbiome signatures distinguish autoimmune diseases and cancers: a systematic review and meta-analysis

    Article • Microbiome, December 2022, Springer Science + Business Media

    Dr Aleksandar D Kostic

  19. Unraveling Signatures of Local Adaptation among Indigenous Groups from Mexico

    Article • Genes, November 2022, MDPI AG

    Dr Aleksandar D Kostic

  20. Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function

    Article • mSystems, October 2022, ASM Journals

    Dr Aleksandar D Kostic

  21. Quantifying shared and unique gene content across 17 microbial ecosystems

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Dr Aleksandar D Kostic

  22. The human microbiome: A coming of age story

    Article • Cell Host & Microbe, April 2022, Elsevier

    Dr Aleksandar D Kostic

  23. Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research

    Article • PLoS Biology, March 2022, PLOS

    Dr Aleksandar D Kostic

  24. The impact of multigenerational high-fat diet feeding on the gut microbiome and host metabolism

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Dr Aleksandar D Kostic

  25. E. coli Nissle 1917 modulates host glucose metabolism without directly acting on glucose

    Article • Scientific Reports, December 2021, Springer Science + Business Media

    Dr Aleksandar D Kostic

  26. Using Cartesian Doubt To Build a Sequencing-Based View of Microbiology

    Article • mSystems, October 2021, ASM Journals

    Dr Aleksandar D Kostic

  27. The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas

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

    Dr Aleksandar D Kostic

  28. Leveraging vibration of effects analysis for robust discovery in observational biomedical data science

    Article • PLoS Biology, September 2021, PLOS

    Chirag Patel, Dr Aleksandar D Kostic

  29. Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators

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

    Dr Aleksandar D Kostic

  30. Reconstruction of ancient microbial genomes from the human gut

    Article • Nature, May 2021, Springer Science + Business Media

    Dr Aleksandar D Kostic

  31. Circulating short and medium chain fatty acids are associated with normoalbuminuria in type 1 diabetes of long duration

    Article • Scientific Reports, April 2021, Springer Science + Business Media

    Dr Aleksandar D Kostic

  32. Activation of adenosine receptor A2a by gut symbionts promotes immune tolerance

    Article • April 2021, Springer Science + Business Media

    Dr Aleksandar D Kostic

  33. Mechanisms of microbial–neuronal interactions in pain and nociception

    Article • Neurobiology of Pain, January 2021, Elsevier

    Dr Aleksandar D Kostic

  34. An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint

    Article • Cell, June 2020, Elsevier

    Dr Aleksandar D Kostic

  35. A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type

    Article • PLoS Computational Biology, May 2020, PLOS

    Chirag Patel, Dr Aleksandar D Kostic

  36. Reply to “Is physical performance (in mice) increased by Veillonella atypica or decreased by Lactobacillus bulgaricus?”

    Article • Journal of Sport and Health Science, May 2020, Elsevier

    Dr Aleksandar D Kostic

  37. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

    Article • PeerJ, April 2020, PeerJ

    Dr Aleksandar D Kostic

  38. The predictive power of the microbiome exceeds that of genome-wide association studies in the discrimination of complex human disease

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Dr Aleksandar D Kostic

  39. The Landscape of Genetic Content in the Gut and Oral Human Microbiome

    Article • Cell Host & Microbe, August 2019, Elsevier

    Dr Aleksandar D Kostic

  40. Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences

    Article • Nature Communications, July 2019, Springer Science + Business Media

    Dr Aleksandar D Kostic

  41. Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism

    Article • Nature Medicine, June 2019, Springer Science + Business Media

    Dr Aleksandar D Kostic

  42. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis

    Article • Cell Host & Microbe, May 2019, Elsevier

    Dr Aleksandar D Kostic

  43. A perfect storm: Genetics and anticommensal antibodies shore up type 1 diabetes

    Article • Science Immunology, February 2019, American Association for the Advancement of Science

    Dr Aleksandar D Kostic

  44. The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response

    Article • eLife, January 2019, eLife

    Dr Aleksandar D Kostic

  45. Understanding the growing epidemic of type 2 diabetes in the Hispanic population living in the United States

    Article • Diabetes/Metabolism Research and Reviews, December 2018, Wiley

    Dr Aleksandar D Kostic

  46. Correction for Zhao et al., Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

    Article • Proceedings of the National Academy of Sciences, November 2018, Proceedings of the National Academy of Sciences

    Dr Aleksandar D Kostic

  47. Diets That Promote Colon Inflammation Associate With Risk of Colorectal Carcinomas That Contain Fusobacterium nucleatum

    Article • Clinical Gastroenterology and Hepatology, October 2018, Elsevier

    Dr Aleksandar D Kostic

  48. Fusobacterium nucleatum in Colorectal Cancer Relates to Immune Response Differentially by Tumor Microsatellite Instability Status

    Article • Cancer Immunology Research, September 2018, American Association for Cancer Research (AACR)

    Dr Aleksandar D Kostic

  49. Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites

    Article • Cell Reports, March 2018, Elsevier

    Dr Aleksandar D Kostic

  50. Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing

    Article • GigaScience, December 2017, Oxford University Press (OUP)

    Dr Aleksandar D Kostic

  51. Aether: leveraging linear programming for optimal cloud computing in genomics

    Article • Bioinformatics, December 2017, Oxford University Press (OUP)

    Dr Aleksandar D Kostic

  52. Aether: Leveraging Linear Programming For Optimal Cloud Computing In Genomics

    Article • July 2017, Cold Spring Harbor Laboratory Press

    Dr Aleksandar D Kostic

  53. Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

    Article • Proceedings of the National Academy of Sciences, July 2017, Proceedings of the National Academy of Sciences

    Dr Aleksandar D Kostic

  54. Association of Dietary Patterns With Risk of Colorectal Cancer Subtypes Classified by Fusobacterium nucleatum in Tumor Tissue

    Article • JAMA Oncology, July 2017, American Medical Association (AMA)

    Dr Aleksandar D Kostic

  55. Gut Microbiota: Small Molecules Modulate Host Cellular Functions

    Article • Current Biology, April 2017, Elsevier

    Dr Aleksandar D Kostic

  56. A Microbiome Foundation for the Study of Crohn’s Disease

    Article • Cell Host & Microbe, March 2017, Elsevier

    Dr Aleksandar D Kostic

  57. Abstract PR01: Fusobacterium nucleatum and mutational landscape of colorectal cancer in whole-exome sequencing analysis

    Article • Cancer Research, January 2017, American Association for Cancer Research (AACR)

    Dr Aleksandar D Kostic

  58. Emerging Concepts and Technologies for the Discovery of Microorganisms Involved in Human Disease

    Article • Annual Review of Pathology Mechanisms of Disease, January 2017, Annual Reviews

    Dr Aleksandar D Kostic

  59. Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location

    Article • Clinical and Translational Gastroenterology, November 2016, Nature

    Dr Aleksandar D Kostic

  60. Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease

    Article • Genome Medicine, July 2016, Springer Science + Business Media

    Dr Aleksandar D Kostic

  61. The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

    Article • Cell Host & Microbe, July 2016, Elsevier

    Dr Aleksandar D Kostic

  62. Research Highlights

    Article • Transplantation, July 2016, Wolters Kluwer Health

    Dr Aleksandar D Kostic

  63. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

    Article • Cell, June 2016, Elsevier

    Dr Aleksandar D Kostic

  64. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

    Article • Cell, May 2016, Elsevier

    Dr Aleksandar D Kostic

  65. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis

    Article • Gut, August 2015, BMJ

    Dr Aleksandar D Kostic

  66. Fusobacterium nucleatumand T Cells in Colorectal Carcinoma

    Article • JAMA Oncology, August 2015, American Medical Association (AMA)

    Dr Aleksandar D Kostic

  67. An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases

    Article • Cell Host & Microbe, May 2015, Elsevier

    Dr Aleksandar D Kostic

  68. The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

    Article • Cell Host & Microbe, February 2015, Elsevier

    Dr Aleksandar D Kostic

  69. Correction: Human Genome-Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type-I Interferon Response

    Article • PLoS Pathogens, October 2014, PLOS

    Dr Aleksandar D Kostic

  70. Inflammatory Bowel Disease as a Model for Translating the Microbiome

    Article • Immunity, June 2014, Elsevier

    Dr Aleksandar D Kostic

  71. The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

    Article • Gastroenterology, May 2014, Elsevier

    Dr Aleksandar D Kostic

  72. The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

    Article • Cell Host & Microbe, March 2014, Elsevier

    Dr Aleksandar D Kostic

  73. Human Genome-Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type-I Interferon Response

    Article • PLoS Pathogens, February 2014, PLOS

    Dr Aleksandar D Kostic

  74. Microbes and Inflammation in Colorectal Cancer

    Article • Cancer Immunology Research, September 2013, American Association for Cancer Research (AACR)

    Dr Aleksandar D Kostic

  75. Sequence-Based Discovery ofBradyrhizobium entericain Cord Colitis Syndrome

    Article • The New England Journal of Medicine and Surgery and the Collateral Branches of Science, August 2013, New England Journal of Medicine (NEJM/MMS)

    Dr Aleksandar D Kostic, Dr Francisco M Marty

  76. Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment

    Article • Cell Host & Microbe, August 2013, Elsevier

    Dr Aleksandar D Kostic

  77. Exploring host-microbiota interactions in animal models and humans

    Article • Genes & Development, April 2013, Cold Spring Harbor Laboratory Press

    Dr Aleksandar D Kostic

  78. Sequence-Based Discovery of Novel Bacteria, Bradyrhizobium Enterica, in Cord Colitis Syndrome

    Article • Biology of Blood and Marrow Transplantation, February 2013, Elsevier

    Dr Aleksandar D Kostic

  79. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma

    Article • Journal of Clinical Investigation, December 2012, American Society for Clinical Investigation

    Dr Aleksandar D Kostic

  80. Keystone microbiome meeting 2012: a mountain top experience

    Article • EMBO Reports, May 2012, EMBO

    Dr Aleksandar D Kostic

  81. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

    Article • Genome Research, October 2011, Cold Spring Harbor Laboratory Press

    Dr Aleksandar D Kostic

  82. The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

    Article • Science, July 2011, American Association for the Advancement of Science

    Dr Jorge Melendez-Zajgla, Dr Aleksandar D Kostic, Dr Alfredo Hidalgo-Miranda

  83. PathSeq: software to identify or discover microbes by deep sequencing of human tissue

    Article • Nature Biotechnology, May 2011, Nature

    Dr Aleksandar D Kostic

  84. Abstract 949: PathSeq: A comprehensive computational tool for pathogen discovery by deep sequencing of human cancer tissues

    Article • Cancer Research, April 2011, American Association for Cancer Research (AACR)

    Dr Aleksandar D Kostic

  85. The TPR-containing domain within Est1 homologs exhibits species-specific roles in telomerase interaction and telomere length homeostasis

    Article • BMC Molecular Biology, January 2011, Springer Science + Business Media

    Dr Aleksandar D Kostic