Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Apr 13;8(1):39.
doi: 10.1186/s13073-016-0294-z.

The Effects of Antibiotics on the Microbiome Throughout Development and Alternative Approaches for Therapeutic Modulation

Free PMC article

The Effects of Antibiotics on the Microbiome Throughout Development and Alternative Approaches for Therapeutic Modulation

Amy Langdon et al. Genome Med. .
Free PMC article


The widespread use of antibiotics in the past 80 years has saved millions of human lives, facilitated technological progress and killed incalculable numbers of microbes, both pathogenic and commensal. Human-associated microbes perform an array of important functions, and we are now just beginning to understand the ways in which antibiotics have reshaped their ecology and the functional consequences of these changes. Mounting evidence shows that antibiotics influence the function of the immune system, our ability to resist infection, and our capacity for processing food. Therefore, it is now more important than ever to revisit how we use antibiotics. This review summarizes current research on the short-term and long-term consequences of antibiotic use on the human microbiome, from early life to adulthood, and its effect on diseases such as malnutrition, obesity, diabetes, and Clostridium difficile infection. Motivated by the consequences of inappropriate antibiotic use, we explore recent progress in the development of antivirulence approaches for resisting infection while minimizing resistance to therapy. We close the article by discussing probiotics and fecal microbiota transplants, which promise to restore the microbiota after damage of the microbiome. Together, the results of studies in this field emphasize the importance of developing a mechanistic understanding of gut ecology to enable the development of new therapeutic strategies and to rationally limit the use of antibiotic compounds.


Fig. 1
Fig. 1
Health consequences linked to the disruption of human-associated microbiota involving antibiotic use during development and adulthood. Red lines indicate that a single dose of antibiotics within the time period has been linked to a health consequence, whereas a dotted red line indicates that multiple doses of antibiotics within the time period are required to observe a link

Similar articles

See all similar articles

Cited by 142 articles

See all "Cited by" articles


    1. Kinch MS, Patridge E, Plummer M, Hoyer D. An analysis of FDA-approved drugs for infectious disease: antibacterial agents. Drug Discov Today. 2014;19:1283–7. doi: 10.1016/j.drudis.2014.07.005. - DOI - PubMed
    1. Review on Antimibrobial Resistance. Antimicrobial resistance: tackling a crisis for the health and wealth of nations. 2014. Accessed 5 Apr 2016.
    1. Guarner F, Malagelada J-R. Gut flora in health and disease. Lancet. 2003;361:512–9. doi: 10.1016/S0140-6736(03)12489-0. - DOI - PubMed
    1. Holmes E, Loo RL, Stamler J, Bictash M, Yap IKS, Chan Q, et al. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature. 2008;453:396–400. doi: 10.1038/nature06882. - DOI - PMC - PubMed
    1. Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science. 2013;339:548–54. doi: 10.1126/science.1229000. - DOI - PMC - PubMed

Publication types

MeSH terms


LinkOut - more resources