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.
We are available for research collaborations, support sessions to answer questions, one-on-one and group trainings, and pipeline development.
Areas of Expertise
- 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.
The metagenomics team at BCBB specializes in the 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.
Research Team
Team Lead
Poorani Subramanian, Ph.D.
(Contractor)
Education:
Ph.D., Applied Mathematics and Scientific Computing, 2010, University of Maryland, College Park, MD
B.A., Applied Mathematics in Economics, 2002, Northwestern University, Evanston, IL
Poorani collaborates with NIAID investigators on analysis of microbiome data and integrating it with other multi-omics data to explore research questions. She is also the lead for the Nephele project, which is a NIAID web application for microbial genomics and metagenomics analysis.
Team Members
Angelina G. Angelova, Ph.D.
(Contractor)
Education:
Ph.D., Heriot-Watt University, Edinburgh, Scotland
M.Sc., University of Arizona, Tucson, AZ
B.Sc., University of Arizona, Tucson, AZ
Dr. Angelina Angelova is a molecular and microbiologist turned bioinformatician and metagenomics analyst.
She earned her Ph.D. in Marine Microbial Ecology from Heriot-Watt University in Scotland. She received her M.Sc. in Soil, Water, and Environmental Science and B.Sc. in Biochemistry and Molecular Biophysics from the University of Arizona. Angelina was involved in genomic library constructions...
Lauren E. Krausfeldt, Ph.D.
(Contractor)
Education:
B.Sc., Biology, 2012, Elmhurst University
Ph.D., Microbiology, 2018, University of Tennessee Knoxville
Dr. Lauren Krausfeldt is a microbiologist with expertise in microbial and viral ecology and bioinformatics. She applies multi-omics approaches to study both human and environmental health problems through the lens of microbial biodiversity and genomics. In her position as a Metagenomics Specialist in the Science Support section of Bioinformatics and Computational Bioscience Branch (BCBB) at NIAID...
Kathryn McCauley, M.P.H.
(Contractor)
Education:
M.P.H., 2015, University of California Berkeley, Berkeley, CA
B.A., 2012, University of California Berkeley, Berkeley, CA
Katie joined Bioinformatics and Computational Biosciences Branch (BCBB) as a Metagenomics Specialist in December 2022 and works remotely in California. She received her Master's of Public Health in Epidemiology and Biostatistics from University of California, Berkeley where she studied associations between childhood leukemia, early-life exposures, and genetics. During her studies, she became...
