Culture-enriched human gut microbiomes reveal core and accessory resistance genes

In this study, we used culture enrichment of stools to reveal lower abundance bacteria by high-throughput sequencing. We sequenced fecal bacteria growing under four culture conditions from 24 individuals, before and after use of antibiotics (day 0 and day 7). Overall, 187 species of bacteria had an assembly size greater than 1 million nucleotides, 67 species achieved it only under culture conditions and 22 only in culture-independent fecal microbiomes.The four culture conditions are : (i) MCDA maximum enrichment broth anaerobic culture (MEB-ANA)(ii) MCDA maximum enrichment broth aerobic culture (air enriched with 5% CO2) (MEB-CO2), (iii) MCDA anaerobic culture in presence of 32µg/ml cefoxitin (FOX-ANA)(iv) MCDA aerobic (with 5% CO2) culture in presence of 32µg/ml cefoxitin (FOX-CO2)