Metagenomics at BCBB

The microbiome and meta-omics team at the Bioinformatics Computational Biosciences Branch (BCBB) focuses on analyses of microbes and microbial ecology including metagenomics, metatranscriptomics, metabolomics, 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 a list of these tools below.

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.

Areas of expertise include:

• Amplicon metagenomics (16S, 18S, ITS, etc.)
• Shotgun metagenomics including assembly, compositional and functional analyses of multi-kingdom mixed communities using short and long read data.
• Community and diversity analyses.
• Metabolomics
• Viral and microbial 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 general bioinformatics processing, optimization for small and large-scale computation on microbiome datasets and databases in specific environments (HPC, containerization, cloud, etc.)

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. 2021 Dec 21;12(6):e0289021.

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.