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HSPH Microbiome Analysis Core

Director: Huttenhower, Curtis, Ph.D.

Location: Biostatistics Department, Bldg SPH1, 4th Floor, Room 412H, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115

Core Summary:

The HSPH Microbiome Analysis Core (HMAC) provides analyses of microbial amplicon (16S rDNA and ITS), metagenomic, metatranscriptomic, and metaproteomic sequence data. The HMAC offers support at all stages of research, from study design through proposal drafting to data analysis and interpretation. Core activities include consultation, provision of services, and fully collaborative grant-funded investigations.

The HMAC has extensive experience with large cohort-based multi’omic data collections, from bioinformatics processing to systems biology and integrative data analysis. We also carry out analysis of individual microbial genomes, and maintain a richly annotated catalog of all currently available microbial genomes as well as a large database of cross-species microbial functional data.

  • Harvard T.H. Chan School of Public Health
Personnel/Contact Information:

Director: Huttenhower, Curtis, Ph.D.

Member: Abu-Ali, Galeb, Ph.D., D.V.M.
Role: Associate Director, HSPH Microbiome Analysis Core
Phone: (617) 432-4927

Facilities and Equipment:

Location of Core: Biostatistics Department, Bldg SPH1, 4th Floor, Room 412H, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115

Major Equipment:

  • bioBakery - an easy to use computing environment for analyses of microbiome data
  • Computing infrastructure - Odyssey FAS Computing Cluster
  • Wet Laboratory - small-scale sample handling and sequencing on an Illumina MiSeq platform
  • Data analysis and interpretation

    - Quality control (QC) processing of raw sequence data using the KNEAD bioinformatics workflow, an implementation of open-source sequence filtering algorithms.
    - Meta-omic data analysis using Huttenhower Lab Tools (https://bitbucket.org/biobakery/biobakery/wiki/Home).
    - Amplicon (16S rDNA and ITS) data QC and analysis: QIIME, mothur, UPARSE, RDP Classifier.
    - Multivariate analysis, network analysis and integration of high-dimensional microbial data using publicly available statistical libraries (e.g. MaAsLin, Vegan, phyloseq, mixOmics, NeAT, etc.)
    - Custom implementation of algorithms for analysis of microbial datasets.

  • Data handling

    For computing infrastructure, the Core is using Odyssey, the FAS Research Computing cluster. Your meta’omic data is housed on dedicated and regularly backed-up network storage drives.

  • Free consultation on study design and data analysis

  • Grant proposal review, drafting, and power analysis

  • Manuscript: review, drafting response to reviewers

  • Wet lab services – small-scale

    - Extraction of microbial RNA/DNA from host and environmental samples.
    - Sequencing of metagenomic, metatranscriptomic, and amplicon libraries.

    Service models: fee-for-service ($150/h), grant percent effort.

Departmental Web Link(s):

Last updated: 2014-09-22T13:46:12.401-05:00