Antibiotics & Gut microbiota

What effect do antibiotics have on the gut microbiome?

Antibiotics (J01) esp. broad-spectrum antibiotics use can have several adverse effects on the gut microbiota, including induction of intestinal dysbiosis through the diminution of the abundance of critical species or the complete eradication of important commensals (dysbiosis), altered metabolic activity, and the selection of antibiotic-resistant organisms, which can lead to Diarrhea / Diarrhoea (antibiotic-induced) and recurrent Clostridioides difficile infections (1, 2, 3)

Depletion of gut microbes in conventional mice via antibiotic treatment significantly impacts the immune system- it reduces spleen size, decreases immune cell numbers and alters expression of genes regulating inflammatory responses and production of antimicrobial factors such that these animals more closely resemble germfree mice than those with a conventional microbiota (34, 35)

Frequent antibiotic use significantly alters the developing gut microbiota by rapidly changing its composition.

Perturbations caused by antibiotics or acute infections disrupt the resident microbes and colonization resistance (26)

The long-term effects of antibiotics on the gut microbiota are increasingly gaining attention. Studies suggest that antibiotics can disrupt gut microbiota, which in turn affects energy metabolism, fat deposition, and immune homeostasis. Such disruptions may contribute to the development of obesity (4)

Commensal gut bacteria escape systemically in antibiotic-treated mice (18)

How strong is the effect of broad-spectrum antibiotics on the gut microbiome?

Manichanh et al., 2010 observed a 10-fold decrease in the bacterial load and reduced bacterial phylotype richness after three days of broad-spectrum antibiotic administration in a preclinical study (36). One to four months after antibiotic therapy discontinuation, the fecal samples regained a partial but incomplete recovery in richness with shifts in the overall microbiome profile (1).

Are specific taxa affected by the administration of antibiotics?

Antibiotics reduce the alfa-diversity and influence beta-diversity. Antibiotics reduce Bifidobacteriaceae, Bifidobacterium, Bifidobacterium longum, Bifidobacterium adolescentis, Prevotellaceae, Peptococcaceae, Odoribacteraceae, Clostridiaceae, Alcaligenaceae, Anaeroplasmataceae,unclassified Lachnospiraceae (7, 22, 23, 24)

Antibiotics use decreased Bifidobacterium and Bacteroides species, increased Campylobacter (32, 33)

Antibiotics reduce the amount of butyrate-producing bacteria in the colon, impairing the epithelial barrier and increasing susceptibility to pathogens (27)

What are the varying ways using different antibiotics?

Different antibiotics impact the gut microbiota in varying ways. Broad-spectrum antibiotics, such as macrolides and fluoroquinolones, cause significant and prolonged changes. In contrast, some beta-lactam antibiotics have more transient effects (4)

Broad-spectrum antibiotics (ATBs) capable of destroying the gut microbiota in healthy mice consist of a cocktail of vancomycin, neomycin, metronidazole, and Ampicillin (J01CA01) (31)

Also, there are differences depending on the region: different baseline microbiome, different antibiotic resistance genes, different use of antibiotics, differences in diet. Most studies come from North America and Europe, which means limited knowledge. Especially in non-Western countries, including low-income countries, the use of antibiotics is increasing (5)

Human microbiotas were resilient and recovered rapidly during antibiotic administration (28). The fecal community is depleted to a low-diversity consortium during severe perturbations such as antibiotic treatment. However, membership and relative abundance largely resemble the pretreatment state after a recovery period (11)

What are diseases associated with antibiotic-induced dysbiosis?

Diseases associated with antibiotic-induced dysbiosis (rapid “microbiome shifts”) are well documented in dynamic populations such as adults with inflammatory bowel disease and traveler’s diarrhea (6, 7, 8, 9).

Disruption of the intestinal microbiota by antibiotics plays a causal role in C. difficile infection of the gut (19). Antibiotics (J01) produce an environment that permits germination of Clostridioides (Clostridium) difficile spores and expansion of the pathogen (30)

Antibiotics (J01) perturb the microbiota composition (11), and reduce the density of strict anaerobes that are associated with resistance to pathogen colonization (12, 13). They lead to dominations by antibiotic-resistant bacteria that increase the risk of bacteremia in immune-compromised patients (14, 15, 16, 17).

The dominations of the gut microbiome that happen after antibiotics are strongly associated with higher risks of bacteremia in cancer patients receiving systemic chemotherapy (14, 16, 20)

Broad-spectrum Antibiotics that can, together with chemotherapy, promote intestinal dysbiosis and expansion of antibiotic-resistant pathogens (29)

Why can antibiotic use promote antibiotic resistance via the gut microbiome?

Antibiotic use leads to increased bacteriophage activation in the gut microbiota and increased selection of single-nucleotide polymorphism (SNP) required for resistance development. In addition, growth rates of intestinal bacteria are modulated, and changes in composition are triggered (10)

What is the relevance of Maternal antibiotic exposure?

Maternal antibiotic exposure in rats resulted in lasting effects on select offspring microbiota including a lower relative abundance of Streptococcus, Lactococcus, and Eubacterium at 10 weeks of age (21)

What are consequences of antibiotic treatment early in life?

Microbiome disturbances incurred by antibiotic treatment early in life were sufficient to induce leukemia in genetically predisposed mice (25)

References

(1) Elkrief et al. 2019 Annals of Oncology 30(10): 1572-1579
(2) Kelly et al. 2022 Science 376(6596): 932
(3) Ramirez-Olea et al. 2022 Front. Microbiol. 13: 993451
(4) Zhu et al. 2026 Front Microbiol 17: 1782016
(5) Jaya & Brito 2025 Trends in Microbiology 33(11): 1224-1236
(6) Gibson et al. 2016 Nat. Microbiol. 1: 16024
(7) Lloyd-Price et al. 2019
(8) Boolchandani et al. 2022 Nat. Commun. 13: 7485
(9) Schwartz et al. 2023 Sci. Transl. Med. 15: eadg5562
(10) Münch et al. 2023 Cell Host & Microbe 31: 1007-1020
(11) Dethlefsen & Relman 2011 Proc Natl Acad Sci USA 108(Suppl 1): 4554-61
(12) Buffie et al. 2019 Nature 517: 205–208
(13) Morjaria et al. 2019 Infect. Immun. 87: e00206–e00219
(14) Taur et al. 2012 Clin Infect Dis 55(7): 905-914
(15) Djukovic et al., 2020 Antimicrob. Agents Chemother. 64: e01415-01419
(16) Stoma et al. 2021 Clin. Infect. Dis. 73: e4627–e4635
(17) Bernard-Raichon et al. 2022 Nat. Commun. 13: 5926
(18) Drummond et al. 2022 Cell Host & Microbe 30(7): 1020-1033.E6
(19) Schlechte et al. 2022 Mucosal Immunology doi.org/10.1038/s41385-022-00539-2
(20) Tamburini et al. 2018 Nat. Med. 24: 1809–1814
(21) Cho et al. 2020c
(22) Thomas et al. 2019a Nat Med 25: 667-78
(23) Zhou et al. 2019h Nature 569: 663-71
(24) Petersen et al. 2020 Nat Struct Mol Biol 27: 49-61
(25) Vincente-Dueñas et al. 2020a Blood 136(18): 2003-2017
(26) Daniel & McQuade 2019
(27) Guinan et al. 2019 Sci. Rep. 9: 8872
(28) Ng et al. 2019
(29) Kim et al. 2017 Immunol Rev. 279(1): 90-105
(30) Britton & Young 2014
(31) Borody et al. 2013 Curr Gastroenterol Rep 15: 337
(32) Penders et al. 2006 Pediatrics. 118: 511-21
(33) McKenna et al. 2008 PLoS Pathog. 4:e20
(34) Reikvam et al. 2011 PLoS One 6: e17996
(35) Hill et al. 2012 Nat Med. 18: 538-546
(36) Manichanh et al. 2010 Genome Res 20(10): 1411-1419

see also:
Antibiotics & Dysbiosis
Antibiotics & Early Childhood / Neonates
Antibiotics & Immune Checkpoint Inhibitors (ICIs)
Antimicrobial resistance (AMR / AR)
Childbirth / Perinatal & Development of Gut Microbiota
Ciprofloxacin & Gut microbiota
Cisplatin & Gut microbiota
Development of Gut Microbiota & Early Childhood / Neonates
Fucoidan
Gut microbiota & Preterm infants / Preterm labor (PL)
Gut microbiota & Race / Ethnicity
Tetracyclines