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Table 2 Examples of antibiotic-induced changes in microbiota that lead to disease

From: The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

Feature Effect of antibiotics Pathological consequence
Antibiotic resistance Enrichment for resistance genes and resistant organisms [73]. In some cases, the rates of genetic exchange between microbes increase [178] Multidrug-resistant tuberculosis. Carbapenem-resistant Escherichia coli infection [79]
Vitamin production Depletion of vitamin-producing bacteria Broad-spectrum antibiotic use (especially β-lactams with an N-methylthiotetrazole moiety) can cause vitamin K deficiency leading to hypoprothrombinemia and uncontrolled bleeding [179]
Digestion Changes in the proportions of relevant metabolic functions in the microbiome [180] Altered efficiency of nutrient extraction from food that can contribute to obesity [45, 59]
Diversity Reduced number of different microbes [68] Lower diversity reduces ecological stability and resistance to pathogens. Increased susceptibility to infection and diarrhea [34, 46, 77, 78]
Resilience Decreased availability of microbes to take over newly open niches Each course of antibiotic acts on a new ecology. Recovery to a stable state, and to a particular stable state, is highly individual [63]
Immune regulation Increased inappropriate immune activity Asthma, allergies and autoimmune diabetes have all been linked to antibiotic use [6, 10, 61]
Composition Varying effects across taxa and for different durations See Table 1 [41, 6769, 72]