Metagenomics


The metagenomics team focuses on analyses of microbes and microbial communities including metagenomics, metatranscriptomics, and integrations of other 'omics data. We collaborate on research directly with investigators in NIAID labs, as well as through the NIAID Microbiome Program. Some of these collaborations have led to the development of bioinformatic pipelines for public use - see the Related tools developed by BCBB (right panel) to learn about some of these tools.

We are available for research collaborations, short consultations to answer questions, one-on-one or group trainings, and pipeline development. See below for examples and selected publications.

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Metagenomics Collaboration Areas


  • Amplicon metagenomics (16S, 18S, ITS, etc.)
  • Shotgun metagenomics including compositional and functional analyses of multi-kingdom mixed communities using short and long read data.
  • Community and diversity analyses.
  • Viral meta-transcriptomics.
  • Viral genome assembly and variant calling.
  • Comparative genomics.
  • Viral phylodynamics and molecular evolution.
  • Integration of other omics data with microbiome data.
  • Pathogen detection.
  • Development of custom pipelines and scripts for individual labs, including optimization for small and large-scale computation on microbiome datasets and databases in specific environments (HPC, containerization, cloud, etc.)

Metagenomics Team


  • Poorani Subramanian, Ph.D. (Group coordinator)
  • Angelina Angelova, Ph.D.
  • Mariam Quinones, Ph.D.
  • David Stern, Ph.D.

Selected Publications


  • Kupritz, J; Angelova, A;Nutman, T; Gazzinelli-Guimaraes, P. "Helminth-induced human gastrointestinal dysbiosis: a systematic review and meta-analysis reveals insights into altered taxa diversity and microbial gradient collapse," mBio, (Manuscript accepted).
  • Ozen, A.; Kasap, N.; Vujkovic-Cvijin, I.; Apps, R.; Cheung, F.; Karakoc-Aydiner, E.; Akkelle, B.; Sari, S.; Tutar, E.; Ozcay, F.; Uygun, D. K.; Islek, A.; Akgun, G.; Selcuk, M.; Sezer, O. B.; Zhang, Y.; Kutluk, G.; Topal, E.; Sayar, E.; Celikel, C.; Houwen, R. H. J.; Bingol, A.; Ogulur, I.; Eltan, S. B.; Snow, A. L.; Lake, C.; Fantoni, G.; Alba, C.; Sellers, B.; Chauvin, S. D.; Dalgard, C. L.; Harari, O.; Ni, Y. G.; Wang, M.-D.; Devalaraja-Narashimha, K.; Subramanian, P.; Ergelen, R.; Artan, R.; Guner, S. N.; Dalgic, B.; Tsang, J.; Belkaid, Y.; Ertem, D.; Baris, S.; Lenardo, M. J. "Broadly Effective Metabolic and Immune Recovery with C5 Inhibition in CHAPLE Disease." Nature Immunology 2021, 22 (2), 128–139. https://doi.org/10.1038/s41590-020-00830-z.
  • Stern, D. B.; Castro Nallar, E.; Rathod, J.; Crandall, K. A. "DNA Barcoding Analysis of Seafood Accuracy in Washington, D.C. Restaurants." PeerJ 2017, 5, e3234. https://doi.org/10.7717/peerj.3234.
  • Sortino, O.; Phanuphak, N.; Schuetz, A.; Ortiz, A. M.; Chomchey, N.; Belkaid, Y.; Davis, J.; Mystakelis, H. A.; Quiñones, M.; Deleage, C.; Ingram, B.; Rerknimitr, R.; Pinyakorn, S.; Rupert, A.; Robb, M. L.; Ananworanich, J.; Brenchley, J.; Sereti, I.; RV254/SEARCH010 Study Group. "Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome." Open Forum Infectious Diseases 2020, 7 (12).https://doi.org/10.1093/ofid/ofz367.
  • Chascsa, D. M.; Ferré, E. M. N.; Hadjiyannis, Y.; Alao, H.; Natarajan, M.; Quiñones, M.; Kleiner, D. E.; Simcox, T. L.; Chitsaz, E.; Rose, S. R.; Hallgren, A.; Kampe, O.; Marko, J.; Ali, R. O.; Auh, S.; Koh, C.; Belkaid, Y.; Lionakis, M. S.; Heller, T. "APECED-Associated Hepatitis: Clinical, Biochemical, Histological and Treatment Data From a Large, Predominantly American Cohort." Hepatology 2021, 73 (3), 1088–1104. https://doi.org/10.1002/hep.31421.
Related tools developed by BCBB

Nephele 

Cloud application for microbial analysis. Pipelines for sequence QC, amplicon and shotgun metagenomics (WGSA)


METAGENOTE 

Cloud application for metadata annotation and SRA submission of sequence data