Human Microbiome Environment Metagenome

The samples within this Bioproject represent the third phase (Phase III) of metagenomic sequencing (whole genome shotgun (WGS) sequencing) of microbial communities from specimens collected as a part of the NIH-supported Human Microbiome Project (HMP Consortium A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209). The sample collection represents a unique reference resource of microbiome samples from healthy adults largely residing in the USA at the time of sample collection. In the HMP Phase III component the goal has been to supplement previous WGS sequencing by generating additional sequence from as many of the specimens in the HMP collection as possible that had not been sequenced in the previous HMP Phase I and Phase II sequencing. In Phase III, a focus was placed on six of the 18 body sites: Stool (gut), Buccal mucosa (oral), Supragingival plaque (oral), Tongue dorsum (oral), Anterior nares (nasal), Posterior fornix (vaginal) and the goal was to further capture as many of the longitudinal samples (second and third visits by the same individual) as possible. From genomic DNA extracted from the collected specimens, WGS sequence was produced from libraries constructed from using a NexteraXT library construction protocol. All libraries were sequenced using a 100bp paired end approach using the Illumina HiSeq 2000 platform.