The human gut microbiota is linked to a variety of human health issues and implicated in antibiotic resistance gene dissemination. Most of these associations rely on culture-independent methods, since it is commonly believed that gut microbiota cannot be easily or sufficiently cultured. Here, we show that carefully designed conditions enable cultivation of a representative proportion of human gut bacteria, enabling rapid multiplex phenotypic profiling. We use this approach to determine the phylogenetic distribution of antibiotic tolerance phenotypes for 16 antibiotics in the human gut microbiota. Based on the phenotypic mapping, we tailor antibiotic combinations to specifically select for previously uncultivated bacteria. Utilizing this method we cultivate and sequence the genomes of four isolates, one of which apparently belongs to the genus Oscillibacter; uncultivated Oscillibacter strains have been previously found to be anti-correlated with Crohn's disease.
Nature Communications, 2014, Vol 5, Issue 4714
Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteria  Oscillibacter genus; Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae  human common adult; antibiotic antibacterial-drug, antiinfective-drug; 12512, Pathology - Therapy; 14004, Digestive system - Physiology and biochemistry; 14006, Digestive system - Pathology; 31000, Physiology and biochemistry of bacteria; 34508, Immunology - Immunopathology, tissue immunology; 38502, Chemotherapy - General, methods and metabolism; 38504, Chemotherapy - Antibacterial agents; Digestive System; Methods and Techniques; Crohn's disease digestive system disease, immune system disease; phylogenetic distribution; Ingestion and Assimilation; gut digestive system; cultivation-based multiplex phenotyping laboratory techniques; MULTIDISCIPLINARY; GASTROINTESTINAL-TRACT MICROBIOTA; ANTIBIOTIC-RESISTANCE RESERVOIR; FUNCTIONAL-CHARACTERIZATION; HUMAN MICROFLORA; PURE CULTURE; HUMAN FECES; DIVERSITY; MICROORGANISMS; DISEASE; SOIL