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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Parasitic Diseases Laboratory » Research » Publications at this Location » Publication #371766
Research Project: Molecular Approaches to Control Intestinal Parasites that Affect the Microbiome in Swine and Small Ruminants

Location: Animal Parasitic Diseases Laboratory

Title: Tools and resources enabling marker gene-based microbiome studies

Author
item LIU, JIANAN - US Department Of Agriculture (USDA)
item Li, Robert

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 2/10/2022
Publication Date: 12/16/2022
Citation: Liu, J., Li, R.W. 2022. Tools and resources enabling marker gene-based microbiome studies. In: Wu, V.C.H., editor. The Gut Microbiome: Bench to Table. 1st edition. Boca Raton, FL: CRC Press. p. 3-44. https://doi.org/10.1201/b22970.
DOI: https://doi.org/10.1201/b22970

Interpretive Summary: N/A

Technical Abstract: The gut microbiome, the collective community of microorganisms residing in the gastrointestinal tract, plays important roles in host nutrition and the development of the host immune system and disease. The advent of next-generation sequencing technologies and the rapid development of computational tools and reference databases have revolutionized microbiome studies. The aggregate genetic material and environmental interactions in a specific environment have been the focus of intensive studies using marker gene-based approaches. In the past few years, numerous algorithms and computational resources have been developed to address unique characteristics of the count data, such as compositionality, sparseness, and high dimensionality, derived from the most widely used marker genes, small subunits (SSUs) of the ribosomal RNA gene. In this chapter, we summarized recent advances in the development of computational tools and methods and discussed their practical implications in microbiology ecology and microbiome analyses.