Sample Collection,DNA Extraction,and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project

The human microbiome plays a crucial role in human health.In the past decade,advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome.However,most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection,handling,and processing procedures,which impedes obtaining valid and timely microbial taxonomic and functional results.This protocol provides detailed operation methods of human microbial sample collection,DNA extraction,and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity,oral cavity,and skin,as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult par-ticipants.This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples.

The gut microbiome and microbial metabolites in acute myocardial infarction

Emerging evidence has highlighted the role of gut microbiome in human health.However,the integrative role of gut microbiome and microbial metabolites in acute myocardial infarction(AMI)remains unclear.The current study profiles the microbial community through 16S rRNA gene sequencing and shotgun metagenomic sequencing and measures fecal short-chain fatty acids and circulating choline pathway metabolites among 117 new-onset AMI cases and 78 controls.Significant microbial alternations are observed in AMI patients compared with controls(P=0.001).The abundances of nine species(e.g.,Streptococcus salivarius and Klebsiella pneumoniae)are positively associated,and one species(Roseburia hominis)is inversely associated with AMI status and severity.A gut microbial score at disease onset is associated with the risk of major adverse cardiovascular events in 3.2 years(hazard ratio[95%CI]:2.01[1.04-4.24])in AMI patients.The molar proportions of fecal acetate and butyrate are higher,and the circulating levels of choline and carnitine are lower in AMI patients than in controls.In addition,disease classifiers show that AMI cases and controls have a more distinct pattern in taxonomical composition than in pathways or metabolites.Our findings suggest that microbial composition and functional potentials are associated with AMI status and severity.