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

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)

本研究采用粪便培养富集法结合高通量测序技术，以检出低丰度细菌。我们对24名受试者在使用抗生素前（第0天）及使用后（第7天）的、四种培养条件下生长的粪便细菌进行了测序。总体而言，共有187种细菌的基因组组装序列总长度超过100万核苷酸；其中67种仅在培养条件下可获得该组装长度，另有22种仅在非培养依赖性粪便微生物组中可获得该组装长度。本研究所设置的四种培养条件如下：(i) MCDA最大富集肉汤厌氧培养（MEB-ANA）；(ii) MCDA最大富集肉汤需氧培养（通入5% CO₂的空气环境，MEB-CO₂）；(iii) 含32μg/ml头孢西丁的MCDA厌氧培养（FOX-ANA）；(iv) 含32μg/ml头孢西丁且通入5% CO₂的MCDA需氧培养（FOX-CO₂）