Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice
Open accessAbstract
Shifts in microbial populations of the intestinal tract have been associated with a multitude of nutritional, autoimmune, and infectious diseases. The limited diversity following antibiotic treatments creates a window for opportunistic pathogens, diarrhea, and inflammation as the microbiome repopulates. Depending on the antibiotics used, microbial diversity can take weeks to months to recover. To alleviate this loss of diversity in the intestinal microbiota, supplementation with probiotics has become increasingly popular. However, our understanding of the purported health benefits of these probiotic bacteria and their ability to shape the microbiome is significantly lacking. This study examined the impact of probiotics concurrent with antibiotic treatment or during the recovery phase following antibiotic treatment of mice. We found that probiotics did not appear to colonize the intestine themselves or shift the overall diversity of the intestinal microbiota. However, the probiotic supplementation did significantly change the types of bacteria which were present. In particular, during the recovery phase the probiotic caused a suppression of Enterobacteriaceae outgrowth (Shigella and Escherichia) while promoting a blooming of Firmicutes, particularly from the Anaerotruncus genus. These results indicate that probiotics have a significant capacity to remodel the microbiome of an individual recovering from antibiotic therapy.
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Probiotics-treated hosts after antibiotics have a lower number of observed species in gut microbiota.
“This study and others also demonstrated a lower number of observed species in the gut microbiota of probiotics-treated hosts after antibiotics.93–95”
From Emerging issues in probiotic safety: 2023 perspectives (2023) · cites this paper as [94]
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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
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,633 · see citing works
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785 · see citing works
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823 · see citing works
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
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533 · see citing works
Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease
The International IBD Genetics Consortium (IIBDGC), Jostins, L., Ripke, S., Weersma, R. K., Duerr, R. H., McGovern, D. P., Hui, K. Y., Lee, J. C., Philip Schumm, L., Sharma, Y., et al. (2012) · Nature · doi:10.1038/nature11582 · Cited by 4,722 · see citing works
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788 · see citing works
Duodenal Infusion of Donor Feces for Recurrent <i>Clostridium difficile</i>
van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F. W. M., Tijssen, J. G. P., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1205037 · Cited by 3,708 · see citing works
Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota
Atarashi, K., Tanoue, T., Oshima, K., Suda, W., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., et al. (2013) · Nature · doi:10.1038/nature12331 · Cited by 2,872 · see citing works
Microbiota-mediated colonization resistance against intestinal pathogens
Buffie, C. G., & Pamer, E. G. (2013) · Nature reviews. Immunology · doi:10.1038/nri3535 · Cited by 1,564 · see citing works
Stenotrophomonas maltophilia: an Emerging Global Opportunistic Pathogen
Brooke, J. S. (2012) · Clinical Microbiology Reviews · doi:10.1128/cmr.00019-11 · Cited by 1,434 · see citing works
Gut immune maturation depends on colonization with a host-specific microbiota
Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., Reading, N. C., Villablanca, E. J., Wang, S., Mora, J. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.037 · Cited by 1,241 · see citing works
Symbiotic gut microbes modulate human metabolic phenotypes
Li, M., Wang, B., Zhang, M., Rantalainen, M., Wang, S., Zhou, H., Zhang, Y., Shen, J., Pang, X., Zhang, M., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712038105 · Cited by 1,144 · see citing works
Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2007) · The ISME Journal · doi:10.1038/ismej.2007.3 · Cited by 1,134 · see citing works
Long-term impacts of antibiotic exposure on the human intestinal microbiota
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2010) · Microbiology · doi:10.1099/mic.0.040618-0 · Cited by 1,067 · see citing works
Towards the human intestinal microbiota phylogenetic core
Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J., Ugarte, E., Muñoz‐Tamayo, R., Paslier, D. L. E., Nalin, R., et al. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01982.x · Cited by 927 · see citing works
McFarland, L. V. (2006) · The American Journal of Gastroenterology · doi:10.1111/j.1572-0241.2006.00465.x · Cited by 872 · see citing works
Newberry, S. J. (2012) · JAMA · doi:10.1001/jama.2012.3507 · Cited by 870 · see citing works
Human intestinal bacteria as reservoirs for antibiotic resistance genes
Salyers, A. A., GUPTA, A., & WANG, Y. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.07.004 · Cited by 847 · see citing works
Safety assessment of probiotics for human use
Sanders, M. E., Akkermans, L. M. A., Haller, D., Hammerman, C., Heimbach, J. T., Hörmannsperger, G., & Huys, G. (2010) · Gut Microbes · doi:10.4161/gmic.1.3.12127 · Cited by 816 · see citing works
Goodman, A. L., Kallstrom, G., Faith, J. J., Reyes, A., Moore, A. M., Dantas, G. A., & Gordon, J. I. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102938108 · Cited by 779 · see citing works
Janssen, P. H., Yates, P. S., Grinton, B. E., Taylor, P., & Sait, M. L. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.5.2391-2396.2002 · Cited by 729 · see citing works
Intestinal microbiota in human health and disease: the impact of probiotics
Gerritsen, J., Smidt, H., Rijkers, G. T., & de Vos, W. M. (2011) · Genes & Nutrition · doi:10.1007/s12263-011-0229-7 · Cited by 724 · see citing works
<i>Lactobacillus</i> Sepsis Associated With Probiotic Therapy
Land, M. H., Rouster-Stevens, K., Woods, C. R., Cannon, M. L., Cnota, J., & Shetty, A. K. (2005) · Pediatrics · doi:10.1542/peds.2004-2137 · Cited by 599 · see citing works
Buffie, C. G., Jarchum, I., Equinda, M., Lipuma, L., Gobourne, A., Viale, A., Ubeda, C., Xavier, J., & Pamer, E. G. (2012) · Infection and Immunity · doi:10.1128/iai.05496-11 · Cited by 596 · see citing works
Stenotrophomonas maltophilia: an emerging opportunist human pathogen
Looney, W. J., Narita, M., & Mühlemann, K. (2009) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(09)70083-0 · Cited by 553 · 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
McNulty, N. P., Yatsunenko, T., Hsiao, A., Faith, J. J., Muegge, B. D., Goodman, A. L., Henrissat, B., Oozeer, R., Cools-Portier, S., Gobert, G., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3002701 · Cited by 544 · see citing works
Bacterial contributions to mammalian gut development
Hooper, L. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.01.001 · Cited by 541 · see citing works
Lawley, T. D., Clare, S., Walker, A. W., Stares, M. D., Connor, T. R., Raisen, C., Goulding, D., Rad, R., Schreiber, F., Brandt, C., et al. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002995 · Cited by 540 · see citing works
Alander, M., Satokari, R. M., Korpela, R., Saxelin, M., Vilpponen-Salmela, T., Mattila, T., & von Wright, A. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.1.351-354.1999 · Cited by 531 · see citing works
Matsuki, T., Watanabe, K., Fujimoto, J., Kado, Y., Takada, T., Matsumoto, K., & Tanaka, R. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.1.167-173.2004 · Cited by 498 · see citing works
Sekirov, I., Tam, N. M., Jogova, M., Robertson, M. L., Li, Y., Lupp, C., & Finlay, B. B. (2008) · Infection and Immunity · doi:10.1128/iai.00319-08 · Cited by 483 · see citing works
Improvement of phylum- and class-specific primers for real-time PCR quantification of bacterial taxa
Gregoris, T. B. D., Aldred, N., Clare, A. S., & Burgess, J. G. (2011) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2011.06.010 · Cited by 431 · see citing works
Quantitative Analysis of Diverse Lactobacillus Species Present in Advanced Dental Caries
Byun, R., Nadkarni, M. A., Chhour, K.-L., Martin, F. E., Jacques, N. A., & Hunter, N. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.7.3128-3136.2004 · Cited by 382 · see citing works
Liver Abscess Due to aLactobacillus rhamnosusStrain Indistinguishable fromL. rhamnosusStrain GG
Rautio, M., Jousimies-Somer, H. R., Kauma, H., Pietarinen, I., Saxelin, M., Tynkkynen, S., & Koskela, M. (1999) · Clinical Infectious Diseases · doi:10.1086/514766 · Cited by 327 · see citing works
Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data
Rosa, P. S. L., Brooks, J. P., Deych, E., Boone, E. L., Edwards, D., Wang, Q., Sodergren, E. J., Weinstock, G. M., & Shannon, W. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052078 · Cited by 325 · see citing works
Antibiotics promote inflammation through the translocation of native commensal colonic bacteria
Knoop, K. A., McDonald, K. G., Kulkarni, D. H., & Newberry, R. D. (2015) · Gut · doi:10.1136/gutjnl-2014-309059 · Cited by 273 · see citing works
Schubert, A. M., Sinani, H., & Schloss, P. D. (2015) · mBio · doi:10.1128/mbio.00974-15 · Cited by 269 · see citing works
Krych, Ł., Hansen, C. H. F., Hansen, A. K., van den Berg, F. W. J., & Nielsen, D. S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062578 · Cited by 250 · see citing works
Masco, L., Huys, G., De Brandt, E., Temmerman, R., & Swings, J. (2005) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2004.11.018 · Cited by 247 · see citing works
Veiga, P., Gallini, C. A., Beal, C., Michaud, M., Delaney, M. L., DuBois, A. M., Khlebnikov, A., Vlieg, J. E. T. V. H., Punit, S., Glickman, J. N., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011737107 · Cited by 220 · see citing works
Regulatory Oversight and Safety of Probiotic Use
Venugopalan, V., Shriner, K. A., & Wong-Beringer, A. (2010) · Emerging Infectious Diseases · doi:10.3201/eid1611.100574 · Cited by 216 · see citing works
Lahti, L., Salonen, A., Kekkonen, R. A., Salojärvi, J., Jalanka, J., Palva, A., Orešič, M., & de Vos, W. M. (2013) · PeerJ · doi:10.7717/peerj.32 · Cited by 196 · see citing works
Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract
Koenigsknecht, M. J., Theriot, C. M., Bergin, I. L., Schumacher, C. A., Schloss, P. D., & Young, V. B. (2014) · Infection and Immunity · doi:10.1128/iai.02768-14 · Cited by 172 · see citing works
Huys, G. R. B., Vancanneyt, M., D'Haene, K., Vankerckhoven, V., Goossens, H., & Swings, J. (2006) · Research in Microbiology · doi:10.1016/j.resmic.2006.06.006 · Cited by 164 · see citing works
Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption
Eloe-Fadrosh, E. A., Brady, A., Crabtree, J., Drabek, E. F., Ma, B., Mahurkar, A., Ravel, J., Haverkamp, M., Fiorino, A.-M., Botelho, C., et al. (2015) · mBio · doi:10.1128/mbio.00231-15 · Cited by 160 · see citing works
Waters, V. J., Atenafu, E. G., Lu, A., Yau, Y. C. W., Tullis, E. D., & Ratjen, F. A. (2013) · Journal of Cystic Fibrosis · doi:10.1016/j.jcf.2012.12.006 · Cited by 136 · see citing works
Watterlot, L., Rochat, T., Sokol, H., Cherbuy, C., Bouloufa, I., Lefèvre, F., Gratadoux, J., Honvo‐Houeto, E., Chilmonczyk, S., Blugeon, S., et al. (2010) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2010.03.037 · Cited by 134 · see citing works
The “Microflora Hypothesis” of Allergic Disease
Shreiner, A. B., Huffnagle, G. B., & Noverr, M. C. (2009) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-09550-9_10 · Cited by 112 · see citing works
Lamousé-Smith, E. S. N., Tzeng, A., & Starnbach, M. N. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027662 · Cited by 107 · see citing works
Ballal, S. A., Veiga, P., Fenn, K., Michaud, M., Kim, J. H., Gallini, C. A., Glickman, J. N., Quéré, G., Garault, P., Beal, C., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1501897112 · Cited by 104 · see citing works
Anaerotruncus colihominis gen. nov., sp. nov., from human faeces
Lawson, P. A., Song, Y., Liu, C., Molitoris, D. R., Väisänen, M., Collins, M. D., & Finegold, S. M. (2004) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.02653-0 · Cited by 97 · see citing works
Lee, Y. K., Ho, P. S., Low, C., Arvilommi, H. S., & Salminen, S. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.2.670-674.2004 · Cited by 87 · see citing works
Bacteraemia caused by Anaerotruncus colihominis and emended description of the species
Lau, S. K. P., Woo, P. C. Y., Woo, G. K. S., Fung, A. M. Y., Ngan, A. H. Y., Song, Y., Liu, C., Summanen, P., Finegold, S. M., & Yuen, K. (2006) · Journal of Clinical Pathology · doi:10.1136/jcp.2005.031773 · Cited by 57 · see citing works
Satokari, R. M., Fuentes, S., Mattila, E. J., Jalanka, J., de Vos, W. M., & Arkkila, P. E. T. (2014) · Case Reports in Medicine · doi:10.1155/2014/913867 · Cited by 49 · see citing works
Replenishing our defensive microbes
Ursell, L. K., Treuren, W. V., Metcalf, J. L., Pirrung, M., Gewirtz, A. T., & Knight, R. D. (2013) · BioEssays · doi:10.1002/bies.201300018 · Cited by 43 · see citing works
Probiotic-Associated Aspiration Pneumonia Due to Lactobacillus rhamnosus
Doern, C. D., Nguyen, S. T., Afolabi, F., & Burnham, C.-A. D. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.01065-14 · Cited by 41 · see citing works
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Suez, J., Zmora, N., Zilberman-Schapira, G., Mor, U., Dori-Bachash, M., Bashiardes, S., Zur, M., Regev-Lehavi, D., Ben-Zeev Brik, R., Federici, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.047 · Cited by 1,184 · see citing works
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- Authors
- Grazul, H., Kanda, L. L., & Gondek, D.
- Affiliations
- Ithaca College (US)
- Corresponding author
- Gondek, David
- ORCID
- Gondek, David
- Venue
- Gut Microbes
- Publisher
- Informa UK Limited
- Published
- 2016-03-03
- Volume
- 7
- Issue
- 2
- Pages
- 101-114
- ISSN
- 1949-0976 (ISSN-L)
- 1949-0984
- PMC
- PMC4856465
- OpenAlex
- W2302109531
- Cited by
- 135
- References
- 59
- Citations by year
- 2026: 7 · 2025: 20 · 2024: 10 · 2023: 19 · 2022: 17 · 2021: 17 · 2020: 20 · 2019: 8 · 2018: 15 · 2016: 2
- FWCI
- 4.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Gut Microbes (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Digital Collections - Ithaca College Library (Ithaca College) (submittedVersion, public-domain)
- Digital Collections - Ithaca College Library (Ithaca College) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Keywords
- probiotics, gut microbiota, microbiome diversity, antibiotic therapy, antibiotic-associated diarrhea, microbiome recovery, Enterobacteriaceae, Escherichia, Shigella, Firmicutes, Anaerotruncus, probiotic colonization, mice
- MeSH terms
- Gastrointestinal Microbiome, Animals, Anti-Bacterial Agents, Bacteria, Diarrhea, Female, Humans, Male, Mice, Inbred C57BL, Dietary Supplements, Probiotics, Gastrointestinal Tract, Biodiversity, Mice
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