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

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, 67–69, 72]