Facing a New Challenge: The Adverse Effects of Antibiotics on Gut Microbiota and Host Immunity
Mammals have existed on Earth for millions of years, during which they have coevolved and coadapted with their gut commensal microbes, forming a complex and inseparable interrelationship often referred to as “superorganisms.” This relationship is shaped by the food and gut environment, which influence the composition and function of gut microbiota. In turn, gut microbiota actively participates in host nutrition metabolism and profoundly affects host immunity. However, this natural coevolving process has been significantly disrupted in recent decades by the widespread use of antibiotics. While antibiotic therapy has been a milestone in fighting infectious diseases, its negative effects on gut microbiota and host health are increasingly recognized. This article explores the unfavorable effects and underlying mechanisms of antibiotics on gut microbiota and host immunity, as well as potential solutions to mitigate these adverse effects.
The gut is the largest reservoir for microbiota in mammals and humans. For a long time, our understanding of gut microbes was limited because most of them could not be identified using traditional culture techniques. However, the advent of high-throughput sequencing technologies, such as metagenomics, metatranscriptomics, and metaproteomics, has provided powerful tools to study the composition and function of gut microbiota. It is estimated that approximately 100 trillion microbes from over 1000 species and more than 7000 strains reside in the gut. While the gut microbiota includes various organisms such as helminths, protozoa, archaea, viruses, phages, yeast, and fungi, bacteria remain the dominant participants in maintaining gut and host homeostasis. The five major bacterial phyla in the gut are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia, accounting for more than 90% of the total bacterial population. The remaining bacteria belong to less abundant phyla, such as Fusobacteria and Fibrobacteres. These microbial communities are distributed with varying density across different segments of the gut and play crucial roles in physiological processes, including food digestion, energy utilization, vitamin synthesis, essential amino acid production, immune system development, maintenance of the gut mucosal barrier, and protection against enterogenous pathogens.
The discovery of penicillin by Alexander Fleming in 1928 marked the beginning of the antibiotic era. Since then, thousands of antibiotic substances have been extracted from natural sources or synthesized artificially. Antibiotics have saved millions of lives by protecting against pathogenic bacteria. However, their extensive use has also led to significant negative impacts on human health. A growing body of research indicates that antibiotics can cause microbial dysbiosis, and the disruption of gut microbiota in both neonates and adults is associated with numerous diseases, including diabetes, obesity, inflammatory bowel disease, asthma, rheumatoid arthritis, depression, autism, and superinfection in critically ill patients.
Antibiotics affect gut microbiota through both direct and indirect mechanisms. Directly, antibiotics are administered to eliminate pathogenic bacteria, but their broad-spectrum activity often results in the indiscriminate killing or inhibition of commensal microbes. Different antibiotics or their combinations have varying antimicrobial spectra, leading to different changes in the microbiome. For example, vancomycin reduces fecal microbial diversity and the absolute number of gram-positive bacteria, particularly those in the Firmicutes phylum, while amoxicillin does not significantly alter total bacterial numbers or microbial diversity. A combination of antibiotics, including ampicillin, gentamicin, metronidazole, neomycin, and vancomycin, not only reduces the total number of bacteria but also dramatically shifts the composition of gut microbiota. Therefore, when using antibiotics to study the effects of microbiota on host health, it is essential to choose appropriate antibiotics and understand how they will reshape the gut microbiome.
Indirectly, antibiotics can impair gut microbiota by disrupting the symbiotic and codependent relationships among different microbial species. Under normal conditions, the microbiota maintains a homeostatic state, where the secondary metabolites produced by some species serve as necessary nutrients for others. For instance, Bifidobacterium adolescentis can utilize fructooligosaccharides and starch to produce lactate and acetate, which are then used as growth substrates by butyrate-producing anaerobes. This cross-feeding-dependent symbiotic relationship is also observed in other microbial pairs, such as Rhodopseudomonas palustris and Escherichia coli, Methanobrevibacter smithii and Bacteroides thetaiotaomicron, and Eubacterium rectale and B. thetaiotaomicron. Additionally, some metabolites accumulated in the gut may be toxic to other microbes, and their biotransformation is often restricted to specific species. For example, conjugated bile acids inhibit bacterial growth in the duodenum and jejunum, but their deconjugation by Lactobacilli, Bifidobacteria, Clostridium, and Bacteroides reduces their toxicity. Deconjugated bile acids can be further utilized by bacteria or reabsorbed by the liver for bile acid enterohepatic circulation. Thus, the loss of specific microbial populations can alter metabolites and the gut microenvironment, affecting the growth of other microbiota members.
The administration of antibiotics can lead to several unfavorable effects on host health. One direct adverse effect is the generation and spread of antibiotic-resistance genes in gut microbiota. Under selective pressure from antibiotics, sensitive strains are eliminated, giving antibiotic-resistant strains a growth advantage. Antibiotic-resistance genes can then be horizontally transferred among bacteria through conjugation, transduction, and transformation. Among the horizontally transmitted genes in the human gut microbiome, approximately 6% are antibiotic-resistance genes, which is 4.8-fold higher than the percentage of antimicrobial peptide-resistance genes. Moreover, antibiotic-resistance genes are more readily transmitted across bacterial species, leading to rapid dissemination of antibiotic resistance within the gut microbiota.
Antibiotics also impact host immunity by altering bacterial metabolites and the signals transmitted from gut microbiota to the host, particularly those recognized by intestinal epithelial cells and immune cells. Metabonomic analysis has revealed that antibiotics profoundly affect lipids, bile acids, amino acids, and amino acid-related substances in the gut. Short-chain fatty acids (SCFAs), produced by bacterial fermentation of fibers in the large intestine, play a crucial role in maintaining epithelial integrity, regulating Treg differentiation and accumulation, and modulating inflammatory and immune responses. Depletion of commensal bacteria by antibiotics reduces SCFA production, leading to a lower frequency of Th17 and Treg cells and increased gut inflammation during oral Candida albicans infections in mice. SCFA administration promotes C. albicans clearance and inflammation resolution in antibiotic-treated mice. Clostridium difficile, a leading cause of antibiotic-associated diarrhea, is significantly inhibited by secondary bile acids. A combination of cefoperazone, clindamycin, and vancomycin reduces the transformation of primary bile acids to secondary bile acids in the large intestine, increasing the risk of C. difficile infection. Additionally, antibiotic-induced alteration of amino acids, particularly proline, has been identified as a key factor in C. difficile colonization.
Beyond affecting bacterial metabolites, antibiotics profoundly impact the interaction between the host and gut microbiota. Gut microbes communicate with the host through pattern-recognition receptors (PRRs), including toll-like receptors (TLRs) and NOD-like receptors. Depletion of gram-negative bacteria by antibiotics reduces TLR4- and MyD88-mediated signaling, diminishing the expression of Reg3g, a C-type lectin antimicrobial peptide that kills gram-positive bacteria. This compromises the clearance of vancomycin-resistant Enterococci (VRE) in mice. Oral administration of LPS, a TLR4 agonist, restores Reg3g production and corrects the VRE-clearance defect. Similarly, depletion of gram-positive bacteria decreases TLR2 activation, reducing the expression of Reg3b, another C-type lectin antimicrobial peptide targeting gram-negative bacteria. Reg3b-deficient mice exhibit impaired defense against gram-negative Salmonella translocation and dissemination. NOD1, which recognizes peptidoglycan from gram-negative bacteria, primes neutrophil function and enhances their ability to kill Streptococcus pneumoniae and Staphylococcus aureus. Depletion of gut microbiota by antibiotics decreases peptidoglycan concentration, impairing neutrophil function and increasing susceptibility to early pneumococcal-induced sepsis. NOD2, recognizing peptidoglycan from both gram-negative and gram-positive bacteria, induces the expression of α-defensins in Paneth cells. NOD2 deficiency is associated with increased susceptibility to S. pneumoniae, S. aureus, and Listeria monocytogenes infections.
Antibiotic-induced perturbation of the microbiota also compromises the development and function of gut immune cells. Tissue-resident group 3 innate lymphoid cells, prevalent in the intestinal lamina propria, are essential for retaining microbes in the gut lumen and preventing bacterial translocation via an interleukin (IL)-22-dependent pathway. Depletion of gut microbiota with antibiotics impacts group 3 innate lymphoid cells’ recruitment and development, reducing IL-22 production and increasing susceptibility to invading pathogens. Additionally, disruption of gut microbiota by antibiotics affects other gut immune cells, leading to a dysregulated ratio of type 1 T-helper cells to type 2 T-helper cells, perturbed differentiation of naive T cells into regulatory T cells, and reduced frequency of type 17 T-helper cells. These changes alter gut immune homeostasis and may increase susceptibility to enterogenic infections.
The adverse effects of antibiotics are not confined to the gut; they also affect systemic immunity. Administration of antibiotics to maternal mice decreases IL-17A production, plasma granulocyte-colony stimulating factor levels, and the number of neutrophils in bone marrow and circulation in neonatal mice, increasing susceptibility to E. coli K1 and Klebsiella pneumoniae sepsis in the early neonatal period. Depletion of gut microbiota with antibiotics also impairs pulmonary defense against pathogens. Altered metabolism within alveolar macrophages correlates with diminished phagocytic capacity and compromised responses to lipopolysaccharide and lipoteichoic acid stimulation. Loss of gut microbiota dysregulates TLRs signaling, reducing the expression of a proliferation-inducing ligand (APRIL) and pulmonary immunoglobulin A (IgA) production in mice and critically ill patients. IgA deficiency in the lungs predisposes the host to Pseudomonas aeruginosa pneumonia. Gut-derived IgA+ plasma cells can access the central nervous system and attenuate neuroinflammation via an IL-10-dependent mechanism in mouse models and patients with multiple sclerosis. Depletion of gut microbiota by antibiotics also impairs adaptive immunity against hepatitis B virus (HBV) infection, as patients treated with antibiotics show decreased interferon-γ (IFN-γ) production and impaired HBV clearance.
Given the adverse effects of antibiotics, measures to restrict their overuse are imperative. Procalcitonin protocols have been shown to reduce antibiotic exposure and side effects while improving survival in patients with acute respiratory infections. Other biomarkers and clinical algorithms, such as C-reactive protein-based algorithms, clinical pulmonary infection score evaluations, routine bronchoscopy, and microbiologic examinations, have also been effective in reducing antibiotic exposure. However, completely abandoning antibiotics is unrealistic, especially for patients with severe infections. Therefore, several strategies have been proposed to mitigate antibiotic-induced microbial dysbiosis and immune disorders, although most studies have been conducted under laboratory conditions.
One strategy is the administration of PRRs agonists locally or systemically. Oral administration of LPS partially reverses postnatal granulocytopenia through a TLR4- and MyD88-dependent pathway in neonatal mice receiving antibiotics. Systemic administration of flagellin or oral delivery of resiquimod upregulates Reg3g expression via an IL-22-dependent pathway, enhancing defense against VRE infection in antibiotic-treated mice. However, using a single PRRs agonist cannot restore the complex signaling network orchestrated by various resident microbes in the gut. Therefore, another method involves using bacterial lysates or products containing multiple PRRs ligands to restore immune homeostasis. Incubation of peripheral B cells and T lymphocytes with gut-resident antigen-presenting cells and gut microbial products at a physiological aerobe-to-anaerobe ratio induces the expression of signaling lymphocyte-activation molecule family member 4, which protects against enteric pathogens such as L. monocytogenes and Citrobacter rodentium.
Probiotics are another strategy to restore gut microbiota balance. The most commonly used probiotics belong to the genera Lactobacillus, Saccharomyces, Bacillus, Bifidobacterium, and Enterococcus. Experimental studies suggest that probiotics benefit the host by inhibiting pathogen growth, stimulating host immunity, inducing antimicrobial peptides, and maintaining epithelial barrier integrity. However, the effectiveness of probiotics in preventing or treating antibiotic-induced microbial dysbiosis remains controversial. A meta-analysis indicated that probiotic intervention reduces the risk of antibiotic-associated diarrhea, but due to significant heterogeneity among studies, this conclusion should be interpreted cautiously. Probiotics may specifically prevent C. difficile infection in patients receiving antibiotics.
Fecal microbiota transplantation (FMT) is another promising method. FMT can control intestinal inflammation and restore homeostasis by increasing IL-10 production, restoring secondary bile acid metabolism, providing signals for epithelial regeneration, and stimulating antimicrobial peptide secretion. FMT has been highly successful in treating recurrent or refractory Clostridium difficile infection, with a cure rate of 87% to 90%. Selective transfer of a single bacterial species, Clostridium scindens, increases host resistance to C. difficile infection by converting primary bile salts to secondary bile salts, which inhibit C. difficile colonization. While it is unclear whether microbiota transplantation is as effective for other superinfections, it holds promise for counteracting the negative effects of antibiotics on gut microbiota and host homeostasis.
As microbial omics technologies continue to advance, our understanding of the adverse effects of antibiotics on gut microbiota and host immunity will become more comprehensive. Future studies should evaluate the impact of antibiotics on the composition and functionality of gut microbiota and host immunity. Probiotics and FMT are promising therapeutic approaches for managing antibiotic-induced gut microbial dysbiosis. However, long-term follow-up is needed to assess the safety, impacts on intestinal microbiota and host immunity, and effects on nutrient metabolism.
doi.org/10.1097/CM9.0000000000000245
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