Alm, Eric J.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology

Scientific Computing and Data ManagementGut microbiota and health

Cited by 23,742

Salt-responsive gut commensal modulates TH17 axis and disease

Wilck, N., Matus, M. G., Kearney, S. M., Olesen, S. W., Forslund, K., Bartolomaeus, H., Haase, S., Mähler, A., Balogh, A., Markó, L., et al. (2017) · Nature

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 1,310

Host lifestyle affects human microbiota on daily timescales

David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., Erdman, S. E., & Alm, E. J. (2014) · Genome biology

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 950

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

Vich Vila, A., Imhann, F., Collij, V., Jankipersadsing, S. A., Gurry, T., Mujagic, Z., Kurilshikov, A., Bonder, M. J., Jiang, X., Tigchelaar, E. F., et al. (2018) · Science Translational Medicine

Gut microbiota and healthInflammatory Bowel Disease

Cited by 587

Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study

Youngster, I., Sauk, J., Pindar, C., Wilson, R. G., Kaplan, J. L., Smith, M. B., Alm, E. J., Gevers, D., Russell, G. H., & Hohmann, E. L. (2014) · Clinical Infectious Diseases

Clostridium difficile and Clostridium perfringens researchGut microbiota and health

Cited by 467

A practical guide to methods controlling false discoveries in computational biology

Korthauer, K., Kimes, P. K., Duvallet, C., Reyes, A., Subramanian, A., Teng, M., Shukla, C., Alm, E. J., & Hicks, S. C. (2019) · Genome Biology

Statistical Methods in Clinical TrialsBioinformatics and Genomic Networks

Cited by 436

Adaptive Evolution within Gut Microbiomes of Healthy People

Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe

Gut microbiota and healthEvolution and Genetic Dynamics

Cited by 434

Microbial symbionts accelerate wound healing via the neuropeptide hormone oxytocin

Poutahidis, T., Kearney, S. M., Levkovich, T., Qi, P., Varian, B. J., Lakritz, J. R., Ibrahim, Y. M., Chatzigiagkos, A., Alm, E. J., & Erdman, S. E. (2013) · PLoS ONE

Wound Healing and TreatmentsGut microbiota and health

Cited by 310

Mobile genes in the human microbiome are structured from global to individual scales

Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Smillie, C. S., Wortman, J. R., et al. (2016) · Nature

Gut microbiota and healthBacteriophages and microbial interactions

Cited by 288

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

Zheng, W., Zhao, S., Yin, Y., Zhang, H., Needham, D. M., Evans, E. D., Dai, C. L., Lu, P. J., Alm, E. J., & Weitz, D. A. (2022) · Science

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 283

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles

Sinha, T., Vich Vila, A., Garmaeva, S., Jankipersadsing, S. A., Imhann, F., Collij, V., Bonder, M. J., Jiang, X., Gurry, T., Alm, E. J., et al. (2019) · Gut Microbes

Gut microbiota and healthAntibiotic Resistance in Bacteria

Cited by 208

Probiotic Microbes Sustain Youthful Serum Testosterone Levels and Testicular Size in Aging Mice

Poutahidis, T., Springer, A., Levkovich, T., Qi, P., Varian, B. J., Lakritz, J. R., Ibrahim, Y. M., Chatzigiagkos, A., Alm, E. J., & Erdman, S. E. (2014) · PLoS ONE

Probiotics and Fermented FoodsSperm and Testicular Function

Cited by 177

Methanogenic burst in the end-Permian carbon cycle

Rothman, D. H., Fournier, G. P., French, K. L., Alm, E. J., Boyle, E. A., Cao, C., & Summons, R. E. (2014) · Proceedings of the National Academy of Sciences

Paleontology and Stratigraphy of FossilsMethane Hydrates and Related Phenomena

Cited by 169

Unlocking short read sequencing for metagenomics

Rodrigue, S., Materna, A. C., Timberlake, S. C., Blackburn, M. C., Malmstrom, R. R., Alm, E. J., & Chisholm, S. W. (2010) · PLoS ONE

Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity Studies

Cited by 168

Microbial Reprogramming Inhibits Western Diet-Associated Obesity

Poutahidis, T., Kleinewietfeld, M., Smillie, C., Levkovich, T., Perrotta, A., Bhela, S., Varian, B. J., Ibrahim, Y. M., Lakritz, J. R., Kearney, S. M., et al. (2013) · PLoS ONE

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 164

Dysbiosis is not an answer

Olesen, S. W., & Alm, E. J. (2016) · Nature Microbiology

Gut microbiota and healthMicrobial Community Ecology and Physiology

Cited by 154

Microbial lysate upregulates host oxytocin

Varian, B. J., Poutahidis, T., DiBenedictis, B. T., Levkovich, T., Ibrahim, Y., Didyk, E., Shikhman, L., Cheung, H. K., Hardas, A., Ricciardi, C. E., et al. (2017) · Brain Behavior and Immunity

Neuroendocrine regulation and behaviorProbiotics and Fermented Foods

Cited by 153

Policy: how to regulate faecal transplants

Smith, M. B., Kelly, C., & Alm, E. J. (2014) · Nature

Biomedical Ethics and RegulationHealthcare Regulation

Cited by 140

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

Kearney, S. M., Gibbons, S. M., Poyet, M., Gurry, T., Bullock, K., Allegretti, J. R., Clish, C. B., & Alm, E. J. (2018) · The ISME Journal

Gut microbiota and healthClostridium difficile and Clostridium perfringens research

Cited by 59

Structured community transitions explain the switching capacity of microbial systems

Long, C., Deng, J., Nguyen, J., Liu, Y.-Y., Alm, E. J., Solé, R., & Saavedra, S. (2024) · Proceedings of the National Academy of Sciences

Microbial Community Ecology and PhysiologyEcosystem dynamics and resilience

Cited by 19