NIAID Microbiome Program: Sequencing

NIAID’s microbiome sequencing facility studies the structure and function of the microbiome associated with various hosts and body sites. This facility has one dedicated staff member and is equipped with an Ilumina MiSeq, which can sequence whole genomes or specific amplicons. Whole genome sequencing is regularly used to characterize entire genomes from complex microbial communities or unique fungal or bacterial isolates in an unbiased manner. This approach allows the investigator to compare microbial communities and their gene content in different environments.

The facility caters to a variety of research collaborators undertaking small to large sequencing projects.

Main Areas of Focus

  • To allow investigators to compare microbial communities and their gene content in different environments
  • Using amplicon sequencing, to target the prokaryotic or fungal eukaryotic ribosomes of the different members of the microbiota for species identification and allow researchers to determine the structure of complex communities
  • Using whole genome sequencing, to provide a broad idea of the potential functional capacity of the communities or single species sequenced

Support Services

  • Amplicion and metagenomic sequencing
  • Expertise, intrastructures, and tools for next generation microbiome sequencing and downstream analysis
  • Expertise in bioinformatics and computational biology methods related to microbiome projects


  • Data management and analysis tools have been baked into the BCBB-developed Nephele platform

How To Get Started

  • Before beginning a project, a project proposal must be submitted to an oversight committee to be reviewed for scientific rationale and feasibility. 
Content last reviewed on February 27, 2018