Diversity Of Infant Gut Microbiome And The Effects Of Antibiotic Treatment

Infant gut microbiome plays an important role in the nutrition absorption,metabolism,immunity and digestive system.The early life is the key period for the colonization of gut microbiome.The disorder of gut microbiome can lead to inflammatory bowel disease,allergy,necrotizing enterocolitis and various diseases.The diversity of infant gut microbiome was influence by many environmental factors,such as mode of delivery,feeding mode,antibiotic treatment,regional factors and food culture.Therefore,it is significant for studying the infant gut microbiome.At present,the combination of traditional cultivation-based method and high throughput sequencing techniques method has been widely used to analyze the diversity of infant gut microbiome.This study took the infant gut microbiome as the object,exploring the structure of infant gut and investigating whether different parameters can affect the diversity of infant gut microbiome.In the one hand,the DNA was extracted from the single isolated strain and run the PCR process based on the universal primers,then the sequencing results of PCR product was submitted to NCBI database to definite the taxonomic levels using BLAST for initial exploring whether usage of antibiotics had effects on the diversity of infant gut microbiome.On the other hand,the 16 S full-length rDNA was sequenced by the SMRT either in healthy or antibiotic ones,and the sequencing results were analyzed by the bioinformatics analysis.The influences of antibiotics used in the infant gut microbiome were clarified by the Alpha diversity analysis,taxonomic analysis,Beta diversity analysis and PICRUSt analysis.The results were as follows:(1)By using the traditional cultivation-based method based on selective and broad-range media,a total of 305 strains were isolated from 51 infant fecal samples,and the strains were divided into three phylum,ten genus and 27 species,including Firmicutes as the dominant phylum(84.92%),Enterococcus as the dominant genus and E.faecium as the dominant species.A total of 26 species were obtained in the healthy group,the diversity of microbiome in antibiotic group was lower than the healthy ones,and only 9 species were isolated from the antibiotic group.The dominate species of healthy and antibiotic group was E.faecium.The abundance of Lactobacillus in breast-feeding and vaginal-delivered infants was higher than the mixed-feeding and C-section ones,the abundance of Enterococcus was higher in the gut microbiome of mixed-feeding and C-section infants.(2)The structure of infant gut microbiome was analyzed by the SMRT,the diversity of infant gut microbiome in the antibiotic group was lower than the healthy ones,and meropenem had stronger effects on the infant gut microbiome.The abundance of Proteobacteria in antibiotic group(60.96%)was higher than the healthy ones(51.21%).For detailed subgroups,the dominate units of each taxonomic level in the amoxicillin group were: Firmicutes(69.77%),Enterococcus(64.52%)and E.faecium Aus0004(33.16%);and in meropenem group were: Proteobacteria(92.03%),Escherichia(91.50%)and E.fergusonii(91.48%);and in the healthy group were Proteobacteria(51.17%),Veillonella(17.52%)and R.ornithinolytica B6(17.28%).(3)The alpha and beta diversity analysis were used to explore the differences between the antibiotic and healthy groups.Except S1,all of the alpha diversity indices of antibiotic group were lower than the healthy group without a significant difference(P>0.05).The indices of Simpson and Shannon in meropenem group was lower than that in the healthy group(P<0.05).The beta diversity analysis based on the PCA? NMDS? UPGMA and PLS-DA showed that there were differences between the healthy and antibiotic groups,meropenem had larger effects on the infant gut microbiome and the effect of this antibiotic showed consistency.(4)The PICRUSt analysis was used to predict the function of gut microbiome in each group.It was found that amoxicillin group was more enriched in the pathway of xenobiotic biodegradation and metabolism,which to some extent indicated that the gut microbiome of infants had the ability to metabolize amoxicillin.