91. probabilities to balances: an alternative approach

Department: Computer Science & Engineering
Research Institute Affiliation: Agile Center for Microbiome Innovation
Faculty Advisor(s): Rob Knight

Primary Student
Name: James Tong Morton
Email: jmorton@ucsd.edu
Phone: 513-907-9853
Grad Year: 2019

Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples.

Industry Application Area(s)
Life Sciences/Medical Devices & Instruments | Software, Analytics | Statistics

Related Links:

  1. http://msystems.asm.org/content/2/1/e00162-16
  2. https://www.youtube.com/watch?v=HAULM1WQkew

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