The human gut microbiota is a reservoir of antibiotic resistance genes, but little is known about their diversity and richness within the gut. Here we analyse the antibiotic resistance genes of gut microbiota from 162 individuals. We identify a total of 1,093 antibiotic resistance genes and find that Chinese individuals harbour the highest number and abundance of antibiotic resistance genes, followed by Danish and Spanish individuals. Single-nucleotide polymorphism-based analysis indicates that antibiotic resistance genes from the two European populations are more closely related while the Chinese ones are clustered separately. We also confirm high abundance of tetracycline resistance genes with this large cohort study. Our study provides a broad view of antibiotic resistance genes in the human gut microbiota.

Segmented filamentous bacteria (SFB) are indigenous gut commensal bacteria. They are commonly detected in the gastrointestinal tracts of both vertebrates and invertebrates. Despite the significant role they have in the modulation of the development of host immune systems, little information exists regarding the presence of SFB in humans. The aim of this study was to investigate the distribution and diversity of SFB in humans and to determine their phylogenetic relationships with their hosts. Gut contents from 251 humans, 92 mice and 72 chickens were collected for bacterial genomic DNA extraction and subjected to SFB 16S rRNA-specific PCR detection. The results showed SFB colonization to be age-dependent in humans, with the majority of individuals colonized within the first 2 years of life, but this colonization disappeared by the age of 3 years. Results of 16S rRNA sequencing showed that multiple operational taxonomic units of SFB could exist in the same individuals. Cross-species comparison among human, mouse and chicken samples demonstrated that each host possessed an exclusive predominant SFB sequence. In summary, our results showed that SFB display host specificity, and SFB colonization, which occurs early in human life, declines in an age-dependent manner.

The transition from a sterile gut environment to the development of microbiota in the newborns is not fully understood. The objective of this study was to investigate the impact of exposure to bacterial communities on the development of gut microbiota in the newly hatched chicken. A total of 90 as-hatched chicks were divided into three groups. Groups A and B were treated with inocula of the cecal origin, whereas group C was fed with sterile water. The major bacteria in Inoculum-I to treat group A included Bacteroides (20.7%), Lachnospiraceae (17.2%) and unclassified Ruminococcaceae (16.1%), whereas group B was introduced with Inoculum-II composed of Prevotella (37.9%), Acidaminococcus (16.1%) and Dorea (12.6%). Analyses of the ileal and cecal contents over a period of 15 days showed that Inoculum-I resulted in a higher rate of colonization than Inoculum-II, but the colonization was predominantly in the cecum. The influence of Inoculum-II on group B was similar to that of water on group C, showing only a marginal effect on colonization. Microarray analysis showed that each group presented a distinct pattern of gene expression in the ileum. In group A, the most obvious changes were noted in genes controlling the function of ion transport, cell cycle and chromosome maintenance, suggesting that the inocula influenced gene expression. Our findings indicate that initial exposure to different bacterial communities could lead to the development of distinct microbiota and gene expression in the gut. It is possible to manipulate the gut microbiota by feeding to a proper bacterial composition at an early age.