Antibiotic resistance
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Enrichment for resistance genes and resistant organisms [73]. In some cases, the rates of genetic exchange between microbes increase [178]
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Multidrug-resistant tuberculosis. Carbapenem-resistant Escherichia coli infection [79]
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Vitamin production
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Depletion of vitamin-producing bacteria
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Broad-spectrum antibiotic use (especially β-lactams with an N-methylthiotetrazole moiety) can cause vitamin K deficiency leading to hypoprothrombinemia and uncontrolled bleeding [179]
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Digestion
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Changes in the proportions of relevant metabolic functions in the microbiome [180]
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Altered efficiency of nutrient extraction from food that can contribute to obesity [45, 59]
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Diversity
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Reduced number of different microbes [68]
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Lower diversity reduces ecological stability and resistance to pathogens. Increased susceptibility to infection and diarrhea [34, 46, 77, 78]
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Resilience
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Decreased availability of microbes to take over newly open niches
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Each course of antibiotic acts on a new ecology. Recovery to a stable state, and to a particular stable state, is highly individual [63]
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Immune regulation
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Increased inappropriate immune activity
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Asthma, allergies and autoimmune diabetes have all been linked to antibiotic use [6, 10, 61]
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Composition
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Varying effects across taxa and for different durations
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See Table 1 [41, 67–69, 72]
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