Metagenomics Study On The Gut Microbiota Of Children With Hand,Foot And Mouth Disease

BackgroundHFMD is an acute infectious disease caused by various enteroviruses that are prevalent in the neonatal and paediatric populations,and its etiology is complex and cannot be clarified by existing studies.As the largest micro-ecosystem in the human body,the intestinal flora can maintain environmental homeostasis in the human body through metabolic pathways and immune responses.It has been confirmed that intestinal flora dysbiosis is closely related to the development of HFMD,but the related mechanism is still unclear.ObjectiveIn this study,we intended to further analyze intestinal microecology of children with HFMD and different enterovirus infection using metagenomic techniques,to clarify the differences in species composition,gene function and pathways between the HFMD group and the control group,to compare the changes in species composition of various types of enterovirus,and to explore the characteristics of intestinal microecological changes in children with HFMD based on the previous study of HFMD based on 16S rRNA gene sequencing.MethodsWe conducted a case-control study of HFMD in Xinhui District of Jiangmen City and Longchuan County of Heyuan City in Guangdong Province from May to July 2017.The case group consisted of 69 children diagnosed with HFMD at three hospitals and the control group consisted of 69 hospital/community-matched children without diarrhea,gastroenteritis,history of suffering from HFMD,herpangina or other related diseases.The participants were required to complete a disease risk-factor questionnaire and provide their fecal samples.The collected stool samples were subjected to metagenomic sequencing.The obtained dataset was used to analyze the structure,relative abundance,gene function and pathways of the intestinal flora using a metagenomic approach.Results1.There was statistically significant difference in the case exposure history between the HFMD and healthy groups(P<0.05).2.Differential analysis of species between the HFMD and control groups.At the phylum level,Firmicutes,Bacteroidetes,Proteobacteria,Verrucomicrobia and Actinobacteria were the main intestinal flora in both the HFMD and healthy groups.At the genus level,Prevotella,Megamonas,Lachnospiraceae_unclassified,Streptococcus,Coprococcus,Dorea,Ruminococcaceae_unclassified and Clostridium were higher in the HFMD group than in the control group and the abundance of Bacteroides,,Klebsiella and Flavonifractor was lower.At the species level,the species that were enriched in the HFMD group were Eubacterium_rectale,Megamonas_funiformis,Megamonas_hypermegale,Dorea_formicigenerans,Odoribacter_splanchnicus and Ruminococcus_torques.The species that clustered in the control group were Bacteroides_thetaiotaomicron,Bacteroides_fragilis,Blautia_producta and Ruminococcus bromii.3.Differential analysis of species among the various enterovirus groups.At the phylum level,the F/B ratio was elevated in the EV-A71 group.At the genus level,the marker genera of the EV-A71 group were Megamonas,Lachnospiraceae_unclassified,Coprococcus and Lactobacillus.The marker genera of the CoxA16 group were Dorea.And the marker genera of the CoxA6 group were Erysipelatoclostridium,Citrobacter and Eggerthella.At the species level,the marker species of the EV-A71 group were Eubacterium_rectale、Ruminococcus_torques、Dorea_formicigenerans and Megamonas_hypermegale.The marker species of the CoxA16 group was Ruminococcus_gnavus.And the marker species of the CoxA6 group were Eubacterium_hallii and Clostridium_innocuum.4.Analysis of gene function and pathways for the HFMD and control groups.Compared with the control group,the gene functions that were significantly up-regulated in the HFMD group were chitinase activity,the integral component of membrane and the dUMP biosynthetic process,and the gene functions that were significantly down-regulated were 3’-5’ exonuclease activity,ribosome and the teichoic acid biosynthetic process.The differential gene functional pathways between the HFMD and control groups was mainly focused on cofactor biosynthesis.All differences were statistically significant(P<0.05)Conclusions1.The gut microbiota of the HFMD and control groups differed in species composition,gene function and pathways,suggesting a degree of imbalance in the intestinal microecology of children with HFMD.2.The gut microbiota changes caused by each type of enterovirus were different,and EV-A71 caused the greatest degree disorder of intestinal flora compared to CoxA6 and CoxA16 types..