Many clinically useful antibiotics interfere with the life of pathogenic bacteria by paralyzing their ribosomes, the universal cellular machines that translate the genetic code into proteins. Structures of ribosomes from non-pathogenic eubacteria, used as models for genuine pathogens, illuminated common properties such as antibiotics binding modes, inhibitory actions, synergism, the distinction between patients vs. pathogens and mechanisms leading to resistance. As species specific diversity was detected in susceptibility to infectious diseases, we extended our structural studies to ribosomes from multi-resistant pathogens. These structure highlighted subtle, albeit meaningful structural elements that can account partially or fully for species specificity and may lead to the design of species specific drug, thus preserving the microbiome.