An overview of the microbiome and the effects of antibiotics

Linking long-term dietary patterns with gut microbial enterotypes

Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works

The human microbiome project

Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091 · see citing works

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579 · see citing works

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774 · see citing works

<i>Faecalibacterium prausnitzii</i> is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermúdez-Humarán, L. G., Gratadoux, J.-J., Blugeon, S., Bridonneau, C., Furet, J.-P., Corthier, G., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804812105 · Cited by 4,413 · see citing works

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000322 · Cited by 3,058 · cited 1× · see citing works

Development of the Human Infant Intestinal Microbiota

Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050177 · Cited by 2,877 · see citing works

Succession of microbial consortia in the developing infant gut microbiome

Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540 · see citing works

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

Dethlefsen, L., & Relman, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000087107 · Cited by 2,421 · see citing works

The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing

Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · see citing works

Effect of antibiotic prescribing in primary care on antimicrobial resistance in individual patients: Systematic review and meta-analysis

Costelloe, C., Metcalfe, C., Lovering, A., Mant, D., & Hay, A. D. (2010) · BMJ · doi:10.1136/bmj.c2096 · Cited by 1,981 · see citing works

The Amygdaloid Complex: Anatomy and Physiology

SAH, P., FABER, E. S. L., LOPEZ DE ARMENTIA, M., & POWER, J. (2003) · Physiological Reviews · doi:10.1152/physrev.00002.2003 · Cited by 1,745 · see citing works

Defining the human microbiome

Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00493.x · Cited by 1,255 · 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

Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection

Gough, E., Shaikh, H., & Manges, A. R. (2011) · Clinical Infectious Diseases · doi:10.1093/cid/cir632 · Cited by 1,003 · see citing works

The microbiome-gut-brain axis: from bowel to behavior

Cryan, J. F., & O’Mahony, S. M. (2011) · Neurogastroenterology &amp; Motility · doi:10.1111/j.1365-2982.2010.01664.x · Cited by 990 · see citing works

Intestinal microbiota in functional bowel disorders: a Rome foundation report

Simrén, M., Barbara, G., Flint, H. J., Spiegel, B. M. R., Spiller, R. C., Vanner, S., Verdu, E. F., Whorwell, P. J., & Zoetendal, E. G. (2013) · Gut · doi:10.1136/gutjnl-2012-302167 · Cited by 939 · see citing works

Chronic Gastrointestinal Inflammation Induces Anxiety-Like Behavior and Alters Central Nervous System Biochemistry in Mice

Bercik, P., Verdu, E. F., Foster, J. A., Macri, J., Potter, M., Huang, X., Malinowski, P., Jackson, W., Blennerhassett, P., Neufeld, K. A., et al. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.06.063 · Cited by 674 · see citing works

Probiotics for the prevention of pediatric antibiotic-associated diarrhea

Goldenberg, J. Z., Lytvyn, L., Steurich, J., Parkin, P. C., Mahant, S., & Johnston, B. C. (2015) · Cochrane Database of Systematic Reviews · doi:10.1002/14651858.cd004827.pub4 · Cited by 635 · see citing works

Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics

Ajslev, T. A., Andersen, C. S., Gamborg, M., Sørensen, T. I. A., & Jess, T. (2011) · International Journal of Obesity · doi:10.1038/ijo.2011.27 · Cited by 534 · see citing works

Antibiotic Prescription Rates for Acute Respiratory Tract Infections in US Ambulatory Settings

Grijalva, C. G. (2009) · JAMA · doi:10.1001/jama.2009.1163 · Cited by 513 · see citing works

Antibiotic Prescribing in Ambulatory Pediatrics in the United States

Hersh, A. L., Shapiro, D. J., Pavia, A. T., & Shah, S. S. (2011) · PEDIATRICS · doi:10.1542/peds.2011-1337 · Cited by 510 · see citing works

Antibiotic use and inflammatory bowel diseases in childhood

Hviid, A. P., Svanström, H., & Frisch, M. (2010) · Gut · doi:10.1136/gut.2010.219683 · Cited by 492 · see citing works

Probiotics and Prebiotics in Pediatrics

Thomas, D. W., & Greer, F. R. (2010) · PEDIATRICS · doi:10.1542/peds.2010-2548 · Cited by 422 · see citing works

Impact of maternal probiotic-supplemented dietary counselling on pregnancy outcome and prenatal and postnatal growth: a double-blind, placebo-controlled study

Luoto, R., Laitinen, K., Nermes, M., & Isolauri, E. (2010) · British Journal Of Nutrition · doi:10.1017/s0007114509993898 · Cited by 369 · see citing works

Fecal microbiota transplantation: past, present and future

Aroniadis, O. C., & Brandt, L. J. (2013) · Current Opinion in Gastroenterology · doi:10.1097/mog.0b013e32835a4b3e · Cited by 336 · see citing works

The Emerging Infectious Challenge of Clostridium difficile-Associated Disease in Massachusetts Hospitals: Clinical and Economic Consequences

O’Brien, J. A., Lahue, B. J., Jaime, J., & Davidson, D. M. (2007) · Infection Control and Hospital Epidemiology · doi:10.1086/522676 · Cited by 315 · see citing works

The Human Microbiome and Its Potential Importance to Pediatrics

Johnson, C. L., & Versalovic, J. A. (2012) · PEDIATRICS · doi:10.1542/peds.2011-2736 · Cited by 310 · see citing works

Effect of probiotic mix (Bifidobacterium bifidum, Bifidobacterium lactis, Lactobacillus acidophilus) in the primary prevention of eczema: a double‐blind, randomized, placebo‐controlled trial

Kim, J. Y., Kwon, J. H., Ahn, S. H., Lee, S. I., Han, Y. S., Choi, Y. O., Lee, S., Ahn, K. M., & Ji, G. E. (2009) · Pediatric Allergy and Immunology · doi:10.1111/j.1399-3038.2009.00958.x · Cited by 266 · see citing works

Probiotics for the prevention of pediatric antibiotic-associated diarrhea

Johnston, B. C., Goldenberg, J. Z., Vandvik, P. O., Sun, X., & Guyatt, G. H. (2011) · Cochrane Database of Systematic Reviews · doi:10.1002/14651858.cd004827.pub3 · Cited by 258 · see citing works

Effect of Intestinal Microbial Ecology on the Developing Brain

Douglas‐Escobar, M., Elliott, E., & Neu, J. (2013) · Archives of Pediatrics and Adolescent Medicine · doi:10.1001/jamapediatrics.2013.497 · Cited by 207 · see citing works

Neural Circuitry of Anxiety: Evidence from Structural and Functional Neuroimaging Studies

Cannistraro, P. A., Rauch, S. L., Rauch, A. S. L., & MD (2025) · Psychopharmacology Bulletin · doi:10.64719/pb.4161 · Cited by 199 · see citing works

Potentially Inappropriate Treatment of Urinary Tract Infections in Two Rhode Island Nursing Homes

Rotjanapan, P., Dosa, D. M., & Thomas, K. S. (2011) · Archives of Internal Medicine · doi:10.1001/archinternmed.2011.13 · Cited by 168 · see citing works

Antibiotic Prescribing to Adults With Sore Throat in the United States, 1997-2010

Barnett, M. L., & Linder, J. A. (2013) · JAMA Internal Medicine · doi:10.1001/jamainternmed.2013.11673 · Cited by 157 · see citing works

Commensal microbiota induce LPS hyporesponsiveness in colonic macrophages via the production of IL-10

Ueda, Y., Kayama, H., Jeon, S. G., Kusu, T., Isaka, Y., Rakugi, H., Yamamoto, M., & Takeda, K. (2010) · International Immunology · doi:10.1093/intimm/dxq449 · Cited by 138 · see citing works

On communication between gut microbes and the brain

Forsythe, P., Kunze, W. A., & Bienenstock, J. (2012) · Current Opinion in Gastroenterology · doi:10.1097/mog.0b013e3283572ffa · Cited by 137 · see citing works

Microbiome and immunological interactions

Kelly, D., & Mulder, I. E. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00498.x · Cited by 127 · see citing works

Fermentation potential of the gut microbiome: implications for energy homeostasis and weight management

Arora, T., & Sharma, R. K. (2011) · Nutrition Reviews · doi:10.1111/j.1753-4887.2010.00365.x · Cited by 110 · see citing works

Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: part III – convergence toward clinical trials

Bested, A. C., Logan, A. C., & Selhub, E. M. (2013) · Gut Pathogens · doi:10.1186/1757-4749-5-4 · Cited by 84 · see citing works

The human microbiome and autoimmunity

Proal, A. D., Albert, P. J., & Marshall, T. G. (2013) · Current Opinion in Rheumatology · doi:10.1097/bor.0b013e32835cedbf · Cited by 78 · see citing works

Fecal Transplantation for Recurrent C lostridium difficile Infection in Older Adults: A Review

Burke, K. E., & LaMont, J. T. (2013) · Journal of the American Geriatrics Society · doi:10.1111/jgs.12378 · Cited by 70 · see citing works

The use of antibacterials in children: a report of the Specialist Advisory Committee on Antimicrobial Resistance (SACAR) Paediatric Subgroup

Sharland, M. (2007) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkm153 · Cited by 66 · see citing works

At least it won’t hurt: the personal risks of antibiotic exposure

Stewardson, A. J., Huttner, B. D., & Harbarth, S. (2011) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2011.06.011 · Cited by 43 · see citing works

Trends in Emergency Department Antibiotic Prescribing for Acute Respiratory Tract Infections

Thorpe, J. M., Smith, S. R., & Trygstad, T. K. (2004) · Annals of Pharmacotherapy · doi:10.1345/aph.1d380 · Cited by 35 · see citing works

Signalling cognition: The gut microbiota and hypothalamic-pituitary-adrenal axis

Rusch, J. A., Layden, B. T., & Dugas, L. R. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1130689 · Cited by 415 · see citing works

Guts Imbalance Imbalances the Brain: A Review of Gut Microbiota Association With Neurological and Psychiatric Disorders

Mitrea, L., Nemeș, S. A., Szabo, K., Teleky, B., & Vodnar, D. C. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.813204 · Cited by 242 · see citing works

Combating antibiotic resistance, mitigating future threats and ongoing initiatives

Velez, R., & Sloand, E. (2016) · Journal of Clinical Nursing · doi:10.1111/jocn.13246 · Cited by 43 · see citing works

Antibiotic-induced dysbiosis effects on the murine gastrointestinal tract and their systemic repercussions

Rosa, C. P., Brancaglion, G. A., Miyauchi-Tavares, T. M., Corsetti, P. P., & de Almeida, L. A. (2018) · Life Sciences · doi:10.1016/j.lfs.2018.06.030 · Cited by 41 · see citing works

The Microbiota‐Gut‐Brain Connection: A New Horizon in Neurological and Neuropsychiatric Disorders

Faysal, M. F., Zehravi, M., Sutradhar, B., Amin, M. A., Shanmugarajan, T. S., Arjun, U. V. N. V., Ethiraj, S., Durairaj, A., Dayalan, G., Ahamad, S. K., et al. (2025) · CNS Neuroscience & Therapeutics · doi:10.1111/cns.70593 · Cited by 37 · see citing works

Fecal Microbiota Transplant to Treat Recurrent Clostridium difficile Infections

Boyle, M. L., Ruth-Sahd, L. A., & Zhou, Z. (2015) · Critical Care Nurse · doi:10.4037/ccn2015356 · Cited by 20 · see citing works

Psychological Impact of Probiotics and Fermented Foods on Mental Health of Human in Integrated Healthy Lifestyle

Nasr, N. (2018) · International Journal of Current Microbiology and Applied Sciences · doi:10.20546/ijcmas.2018.708.296 · Cited by 19 · see citing works

Cyclodextrin subject-object recognition-based aptamer sensor for sensitive and selective detection of tetracycline

Wu, Y., Bi, H., Ge, N., Xu, Z., Liu, G., Wang, Y., & Zhao, Y. (2020) · Journal of Solid State Electrochemistry · doi:10.1007/s10008-020-04751-7 · Cited by 19 · see citing works

Antibiotic use but not gastrointestinal infection frequently precedes first diagnosis of functional gastrointestinal disorders

Jones, M., Shah, A., Walker, M. M., Koloski, N. A., Holtmann, G., & Talley, N. J. (2021) · United European Gastroenterology Journal · doi:10.1002/ueg2.12164 · Cited by 10 · see citing works

İnsan Mikrobiyomu: Beslenme ve Sağlık Üzerindeki Etkileri

Cetinbas, S., Kemeriz, F., Göker, G., Biçer, İ., & Velioğlu, Y. S. (2017) · Akademik Gıda · doi:10.24323/akademik-gida.370267 · Cited by 9 · see citing works

An Update on the Relationship Between the Gut Microbiome and Obsessive-Compulsive Disorder

Turna, J., Patterson, B. A., & Ameringen, M. V. (2017) · Psychiatric Annals · doi:10.3928/00485713-20171013-01 · Cited by 8 · see citing works

Updates and Current Challenges in Reproductive Microbiome: A Comparative Analysis between Cows and Women

Zangirolamo, A. F., Souza, A. K., Yokomizo, D. N., Miguel, A. K. A., Costa, M., Alfieri, A. A., & Seneda, M. M. (2024) · Animals · doi:10.3390/ani14131971 · Cited by 7 · see citing works

The Human Microbiota: The Importance and Relevance of its Incorportation into Anatomy and Physiology Curricula

Oh-McGinnis, R., Sigola, L. B., Fuentes, A., Vapenik, J., & Millis, L. (2015) · HAPS Educator · doi:10.21692/haps.2015.023

Human Microbiome: Effects on Nutrition and HealthPreprint

Alsaeedi, S. (2023) · doi:10.14293/pr2199.000523.v1

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

Bonilla-Carrero, P. I., Mader, H., Meier, N. F., Olivas, I., Boyle, B., & Bonilla-Carrero, P. I. (2020) · Springer eBooks · doi:10.1007/978-3-030-47384-6_10

Effects of Antibiotics upon the Gut Microbiome: A Review of the Literature

Konstantinidis, T. G., Tsigalou, C., Karvelas, A., Stavropoulou, E., Voidarou, C. C., & Bezirtzoglou, E. (2020) · Biomedicines · doi:10.3390/biomedicines8110502 · Cited by 169 · see citing works

Antibiotics and the gut microbiome: Understanding the impact on human health

Lathakumari, R. H., Vajravelu, L. K., Satheesan, A., Ravi, S. S. S., & Thulukanam, J. (2024) · Medicine in Microecology · doi:10.1016/j.medmic.2024.100106 · Cited by 160 · see citing works

Antibiotics in early life: dysbiosis and the damage done

Neuman, H., Forsythe, P., Uzan-Yulzari, A., Avni, O., & Koren, O. (2018) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuy018 · Cited by 258 · see citing works

Understanding Gut Microbiota and Antibiotics Complex Interplay and Clinical Implications

Karim, M. M., Paswan, S., Bhairam, M., & Mishra, S. (2024) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.14635348 · Cited by 9 · see citing works