Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,013 · see citing works

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 20,966 · see citing works

Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894 · see citing works

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116 · see citing works

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227 · see citing works

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,010 · see citing works

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015) · Nature · doi:10.1038/nature13828 · Cited by 1,872 · see citing works

Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome

Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009836 · Cited by 1,160 · see citing works

Enteric defensins are essential regulators of intestinal microbial ecology

Salzman, N. H., Hung, K., Haribhai, D., Chu, H., Karlsson-Sjöberg, J., Amir, E., Teggatz, P., Barman, M., Hayward, M., Eastwood, D., et al. (2010) · Nature Immunology · doi:10.1038/ni.1825 · Cited by 1,156 · see citing works

Decreased Diversity of the Fecal Microbiome in Recurrent<i>Clostridium difficile</i>–Associated Diarrhea

Chang, J. Y., Antonopoulos, D. A., Kalra, A., Tonelli, A., Khalife, W. T., Schmidt, T. M., & Young, V. B. (2008) · The Journal of Infectious Diseases · doi:10.1086/525047 · Cited by 1,010 · see citing works

Experimental and analytical tools for studying the human microbiome

Kuczynski, J., Lauber, C. L., Walters, W. A., Parfrey, L. W., Clemente, J. C., Gevers, D., & Knight, R. D. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3129 · Cited by 710 · see citing works

Effect of Antibiotic Therapy on the Density of Vancomycin-Resistant Enterococci in the Stool of Colonized Patients

Donskey, C. J., Chowdhry, T. K., Hecker, M. T., Hoyen, C. K., Hanrahan, J., Hujer, A. M., Hutton‐Thomas, R., Whalen, C. C., Bonomo, R. A., & Rice, L. B. (2000) · New England Journal of Medicine · doi:10.1056/nejm200012283432604 · Cited by 691 · see citing works

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

Stein, R. R., Bucci, V., Toussaint, N. C., Buffie, C. G., Rätsch, G., Pamer, E. G., Sander, C., & Xavier, J. B. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003388 · Cited by 604 · see citing works

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

Pérez‐Cobas, A. E., Gosalbes, M. J., Friedrichs, A. K., Knecht, H., Artacho, A., Eismann, K., Otto, W., Rojo, D., Bargiela, R., von Bergen�, M., et al. (2012) · Gut · doi:10.1136/gutjnl-2012-303184 · Cited by 603 · see citing works

Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

Antonopoulos, D. A., Huse, S. M., Morrison, H. G., Schmidt, T. M., Sogin, M. L., & Young, V. B. (2009) · Infection and Immunity · doi:10.1128/iai.01520-08 · Cited by 545 · see citing works

Proton Pump Inhibitor Use and the Risk of Small Intestinal Bacterial Overgrowth: A Meta-analysis

Lo, W., & Chan, W. W. (2013) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2012.12.011 · Cited by 353 · see citing works

Antibiotic Treatment of <i>Clostridium difficile</i> Carrier Mice Triggers a Supershedder State, Spore-Mediated Transmission, and Severe Disease in Immunocompromised Hosts

Lawley, T. D., Clare, S., Walker, A. W., Goulding, D., Stabler, R. A., Croucher, N., Mastroeni, P., Scott, P., Raisen, C., Mottram, L., et al. (2009) · Infection and Immunity · doi:10.1128/iai.00558-09 · Cited by 349 · see citing works

Resilience of the Dominant Human Fecal Microbiota upon Short-Course Antibiotic Challenge

Cochetiere, M. F. D. L., Durand, T., Lepage, P., Bourreille, A., Galmiche, J. P., & Dore, J. M. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.11.5588-5592.2005 · Cited by 333 · see citing works

Performance of a short tool to assess dietary intakes of fruits and vegetables, percentage energy from fat and fibre

Thompson, F. E., Midthune, D., Subar, A. F., Kahle, L., Schatzkin, A. G., & Kipnis, V. (2004) · Public Health Nutrition · doi:10.1079/phn2004642 · Cited by 218 · see citing works

The Prevalence of Overgrowth by Aerobic Bacteria in the Small Intestine by Small Bowel Culture: Relationship with Irritable Bowel Syndrome

Pyleris, E., Giamarellos‐Bourboulis, E. J., Tzivras, D. M., Koussoulas, V., Barbatzas, C., & Pimentel, M. (2012) · Digestive Diseases and Sciences · doi:10.1007/s10620-012-2033-7 · Cited by 189 · see citing works

Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility

Seto, C. T., Jeraldo, P., Orenstein, R., Chia, N., & DiBaise, J. K. (2014) · Microbiome · doi:10.1186/2049-2618-2-42 · Cited by 163 · see citing works

Comparative Metagenomic Study of Alterations to the Intestinal Microbiota and Risk of NosocomialClostridum difficile–Associated Disease

Manges, A. R., Labbe, A., Loo, V. G., Atherton, J., Behr, M. A., Masson, L., Tellis, P. A., & Brousseau, R. (2010) · The Journal of Infectious Diseases · doi:10.1086/657319 · Cited by 151 · see citing works

Systems biology analysis of omeprazole therapy in cirrhosis demonstrates significant shifts in gut microbiota composition and function

Bajaj, J. S., Cox, I. J., Betrapally, N. S., Heuman, D. M., Schubert, M. L., Ratneswaran, M., Hylemon, P. B., White, M. B., Daita, K., Noble, N. A., et al. (2014) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00268.2014 · Cited by 143 · see citing works

Dietary intake estimates in the National Health Interview Survey, 2000: Methodology, results, and interpretation

Thompson, F. E., Midthune, D., Subar, A. F., McNeel, T. S., Berrigan, D. A., & Kipnis, V. (2005) · Journal of the American Dietetic Association · doi:10.1016/j.jada.2004.12.032 · Cited by 125 · see citing works

Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection

Vincent, C., Stephens, D. A., Loo, V. G., Edens, T. J., Behr, M. A., Dewar, K., & Manges, A. R. (2013) · Microbiome · doi:10.1186/2049-2618-1-18 · Cited by 123 · see citing works

16S Community Profiling Identifies Proton Pump Inhibitor Related Differences in Gastric, Lung, and Oropharyngeal Microflora

Rosen, R., Hu, L., Amirault, J. P., Khatwa, U., Ward, D. V., & Onderdonk, A. B. (2015) · The Journal of Pediatrics · doi:10.1016/j.jpeds.2014.12.067 · Cited by 105 · see citing works

Changes in Gastric and Lung Microflora With Acid Suppression

Rosen, R., Amirault, J. P., Liu, H., Mitchell, P. D., Hu, L., Khatwa, U., & Onderdonk, A. B. (2014) · Archives of Pediatrics and Adolescent Medicine · doi:10.1001/jamapediatrics.2014.696 · Cited by 102 · see citing works

Clinical evaluation of the RapID-ANA II panel for identification of anaerobic bacteria

Celig, D. M., & Schreckenberger, P. C. (1991) · Journal of Clinical Microbiology · doi:10.1128/jcm.29.3.457-462.1991 · Cited by 51 · see citing works

Gastroesophageal Reflux in Infants

Rosen, R. (2013) · Archives of Pediatrics and Adolescent Medicine · doi:10.1001/jamapediatrics.2013.2911 · Cited by 47 · see citing works

Microbiota Transfer Therapy Alters Gut Ecosystem and Improves Gastrointestinal and Autism Symptoms: An Open-Label Study

Kang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., et al. (2017) · Microbiome · doi:10.1186/s40168-016-0225-7 · Cited by 1,391 · see citing works

European consensus conference on faecal microbiota transplantation in clinical practice

Cammarota, G., Ianiro, G., Tilg, H., Rajilić-Stojanović, M., Kump, P., Satokari, R., Sokol, H., Arkkila, P., Pintus, C., Hart, A., et al. (2017) · Gut · doi:10.1136/gutjnl-2016-313017 · Cited by 1,207 · see citing works

Akkermansia muciniphila and its role in regulating host functions

Derrien, M., Belzer, C., & de Vos, W. M. (2017) · Microbial Pathogenesis · doi:10.1016/j.micpath.2016.02.005 · Cited by 1,044 · see citing works

Proton pump inhibitors alter the composition of the gut microbiota

Jackson, M. A., Goodrich, J. K., Maxan, M.-E., Freedberg, D. E., Abrams, J. A., Poole, A. C., Sutter, J. L., Welter, D., Ley, R. E., Bell, J. T., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-310861 · Cited by 895 · see citing works

The Human Gut Microbiome: From Association to Modulation

Schmidt, T. S. B., Raes, J., & Bork, P. (2018) · Cell · doi:10.1016/j.cell.2018.02.044 · Cited by 845 · see citing works

Microbiota-Brain-Gut Axis and Neurodegenerative Diseases

Quigley, E. M. M. (2017) · Current Neurology and Neuroscience Reports · doi:10.1007/s11910-017-0802-6 · Cited by 804 · see citing works

Mechanisms and consequences of intestinal dysbiosis

Weiss, G. A., & Hennet, T. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2509-x · Cited by 775 · see citing works

Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection

Ducarmon, Q. R., Zwittink, R. D., Hornung, B. V. H., van Schaik, W., Young, V. B., & Kuijper, E. J. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00007-19 · Cited by 566 · see citing works

Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease

van Kessel, S. P., Frye, A. K., El-Gendy, A. O., Castejon, M., Keshavarzian, A., van Dijk, G., & El Aidy, S. (2019) · Nature Communications · doi:10.1038/s41467-019-08294-y · Cited by 521 · see citing works

Microbiota-Gut-Brain Axis: New Therapeutic Opportunities

Long-Smith, C., O'Riordan, K. J., Clarke, G., Stanton, C., Dinan, T. G., & Cryan, J. F. (2020) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010919-023628 · Cited by 419 · see citing works

Alzheimer’s disease microbiome is associated with dysregulation of the anti-inflammatory p-glycoprotein pathway

Haran, J. P., Bhattarai, S. K., Foley, S. E., Dutta, P., Ward, D. V., Bucci, V., & McCormick, B. A. (2019) · mBio · doi:10.1128/mbio.00632-19 · Cited by 412 · see citing works

Proton-pump inhibitors: understanding the complications and risks

Malfertheiner, P., Kandulski, A., & Venerito, M. (2017) · Nature Reviews Gastroenterology &amp; Hepatology · doi:10.1038/nrgastro.2017.117 · Cited by 297 · see citing works

Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications

Le Bastard, Q., Al‐Ghalith, G. A., Grégoire, M., Chapelet, G., Javaudin, F., Dailly, E., Batard, E., Knights, D., & Montassier, E. (2018) · Alimentary Pharmacology &amp; Therapeutics · doi:10.1111/apt.14451 · Cited by 263 · see citing works

Proton pump inhibitors and dysbiosis: current knowledge and aspects to be clarified

Bruno, G., Zaccari, P., Rocco, G., Scalese, G., Panetta, C., Porowska, B., Pontone, S., & Severi, C. (2019) · World Journal of Gastroenterology · doi:10.3748/wjg.v25.i22.2706 · Cited by 258 · see citing works

Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients

Ticinesi, A., Milani, C., Lauretani, F., Nouvenne, A., Mancabelli, L., Lugli, G. A., Turroni, F., Duranti, S., Mangifesta, M., Viappiani, A., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10734-y · Cited by 211 · see citing works

Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health

Koch, C. D., Gladwin, M. T., Freeman, B. A., Lundberg, J. O., Weitzberg, E., & Morris, A. (2017) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.12.015 · Cited by 186 · see citing works

A comparison of the gut microbiome between long‐term users and non‐users of proton pump inhibitors

Clooney, A. G., Bernstein, C. N., Leslie, W. D., Vagianos, K., Sargent, M., Laserna‐Mendieta, E. J., Claesson, M. J., & Targownik, L. E. (2016) · Alimentary Pharmacology &amp; Therapeutics · doi:10.1111/apt.13568 · Cited by 166 · see citing works

Systematic review: the effects of proton pump inhibitors on the microbiome of the digestive tract—evidence from next‐generation sequencing studies

Macke, L., Schulz, C., Koletzko, L., & Malfertheiner, P. (2020) · Alimentary Pharmacology &amp; Therapeutics · doi:10.1111/apt.15604 · Cited by 118 · see citing works

The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes

Aydin, Ö., Nieuwdorp, M., & Gerdes, V. (2018) · Current Diabetes Reports · doi:10.1007/s11892-018-1020-6 · Cited by 124 · see citing works

The influence of long-term use of proton pump inhibitors on the gut microbiota: an age-sex-matched case-control study

Takagi, T., Naito, Y., Inoue, R., Kashiwagi, S., Uchiyama, K., Mizushima, K., Tsuchiya, S., Okayama, T., Dohi, O., Yoshida, N., et al. (2018) · Journal of Clinical Biochemistry and Nutrition · doi:10.3164/jcbn.17-78 · Cited by 121 · see citing works

Gut Microbiota Composition Before and After Use of Proton Pump Inhibitors

Hojo, M., Asahara, T., Nagahara, A., Takeda, T., Matsumoto, K., Ueyama, H., Matsumoto, K., Asaoka, D., Takahashi, T., Nomoto, K., et al. (2018) · Digestive Diseases and Sciences · doi:10.1007/s10620-018-5122-4 · Cited by 114 · see citing works

Proton Pump Inhibitors Are Associated With Minimal and Overt Hepatic Encephalopathy and Increased Mortality in Patients With Cirrhosis

Nardelli, S., Gioia, S., Ridola, L., Farcomeni, A., Merli, M., & Riggio, O. (2019) · Hepatology · doi:10.1002/hep.30304 · Cited by 109 · see citing works

“With a little help from my friends”—the role of microbiota in thyroid hormone metabolism and enterohepatic recycling

Virili, C., & Centanni, M. (2017) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2017.01.053 · Cited by 105 · see citing works

Biomarkers for oralization during long-term proton pump inhibitor therapy predict survival in cirrhosis

Horvath, A., Rainer, F., Bashir, M., Leber, B., Schmerboeck, B., Klymiuk, I., Groselj-Strele, A., Durdevic, M., Freedberg, D. E., Abrams, J. A., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-48352-5 · Cited by 93 · see citing works

Oral microbiome alterations of healthy volunteers with proton pump inhibitor

Mishiro, T., Oka, K., Kuroki, Y., Takahashi, M., Tatsumi, K., Saitoh, T., Tobita, H., Ishimura, N., Sato, S., Ishihara, S., et al. (2018) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.14040 · Cited by 96 · see citing works

Targeting the Microbiota in Pharmacology of Psychiatric Disorders

Pascale, A., Marchesi, N., Govoni, S., & Barbieri, A. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.104856 · Cited by 67 · see citing works

Anti-Acid Drug Treatment Induces Changes in the Gut Microbiome Composition of Hemodialysis Patients

Lin, Y.-T., Lin, T.-Y., Hung, S.-C., Liu, P.-Y., Wu, P.-H., Chuang, Y.-S., Hung, W.-C., Chiu, Y.-W., Kuo, M.-C., & Wu, C.-Y. (2021) · Microorganisms · doi:10.3390/microorganisms9020286 · Cited by 22 · see citing works

Pharmacomicrobiomics of Non-Antibiotic Drugs: Mechanisms and Clinical Consequences of Gut Microbiota Alterations

Dumitru, C. N., Dumitru, A. O., Goroftei, L., Niculet, E., Ignat, M. D., Baroiu, L., Nechita, A., & Balan, G. (2026) · Pharmaceutics · doi:10.3390/pharmaceutics18060651 · Cited by 4 · see citing works

The Two-Period Crossover Design in Medical Research

Woods, J. R., Williams, J. G., & Tavel, M. (1989) · Annals of Internal Medicine · doi:10.7326/0003-4819-110-7-560 · Cited by 139 · see citing works

Considerations for crossover design in clinical study

Lim, C., & In, J. (2021) · Korean Journal of Anesthesiology · doi:10.4097/kja.21165 · Cited by 243 · see citing works

Crossover Designs in Lower Extremity Wounds

REED, J. F. (2003) · The International Journal of Lower Extremity Wounds · doi:10.1177/1534734603258476 · Cited by 2 · see citing works

An optimal multi-period crossover design for an application in paediatric nephrologyPreprint

Matthews, J. N. S. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1210.6260

BMC322- A RATIONALLY-DESIGNED LIVE BACTERIAL CONSORTIUM BASED ON MICROBIOME FUNCTIONAL GENOMIC ANALYSIS FOR TREATMENT OF IBD

Polonsky, O., Meshner, S., Eshar, S., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.01.140 · Cited by 1 · see citing works