Eric Allen

About

Eric E. Allen is a Professor of Marine Biology and Molecular Biology within the Biological Sciences department at UC San Diego. He is based at the Scripps Institution of Oceanography, where his research focuses on the molecular genetics and genomics of marine microbial communities. His work includes studying the biosynthesis of microbial omega-3 polyunsaturated fatty acids and long-chain hydrocarbons, as well as the community systems biology of marine fish gut microbial ecosystems. Professor Allen's research integrates metagenomic and metabolomic approaches to understand marine sponge holobionts and explores the diversity, activity, and dynamics of marine microbial communities, including microbiomes of marine fish and mollusks. His expertise extends to microbial oceanography, bioinformatics, and the development of bioinformatic tools to analyze host-associated marine microbial communities and microbial horizontal gene transfer dynamics. His research topics broadly cover phytoplankton biology, algal biofuels, marine microbiology, genomics, metagenomics, and bioinformatics.

Research topics

• Computer Science
• Ecology
• Biology
• Philosophy
• Computational biology
• Data science
• Bioinformatics
• Genetics
• Evolutionary biology

Selected publications

• Defining and quantifying the core microbiome: Challenges and prospects

  Proceedings of the National Academy of Sciences · 2021 · 586 citations

  The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is littl…

  PublisherOA PDFDOI

• Visualizing ’omic feature rankings and log-ratios using Qurro

  NAR Genomics and Bioinformatics · 2020 · 179 citations

  Many tools for dealing with compositional ' 'omics' data produce feature-wise values that can be ranked in order to describe features' associations with some sort of variation. These values include differentials (which describe features' associations with specified covariates) and feature loadings (which describe features' associations with variation along a given axis in a biplot). Although prior work has discussed the use of these 'rankings' as a starting point for exploring the log-ratios of…

  DOI

• Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

  Nature Communications · 2022-11-17 · 110 citations

  articleOpen accessSenior author

  Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, represent…

  PublisherOA PDFDOI

• The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function

  Journal of Biological Chemistry · 2022-09-12 · 67 citations

  articleOpen access

  The Natural Product Domain Seeker (NaPDoS) webtool detects and classifies ketosynthase (KS) and condensation domains from genomic, metagenomic, and amplicon sequence data. Unlike other tools, a phylogeny-based classification scheme is used to make broader predictions about the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes in which these domains are found. NaPDoS is particularly useful for the analysis of incomplete biosynthetic genes or gene clusters, as are often ob…

  PublisherDOI

• Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

  Animal Microbiome · 2022-05-23 · 45 citations

  articleOpen access

  BACKGROUND: Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively un…

  PublisherOA PDFDOI

Recent grants

• MTM 1: Experimental framework for marine fish microbiomes through synthetic communities and multi-omic approaches

  NSF · $499k · 2020–2024

• CAREER: Genetic and Functional Characterization of Microbial Secondary Lipid Biosynthesis - a Biomes to Biotechnology Investigation

  NSF · $865k · 2012–2018

• NIH Grant R21HG005107

  NIH · $380k · 2012

Frequent coauthors

• Jeremiah J. Minich

  143 shared

• Sheila Podell

  University of California, San Diego

  100 shared

• Rob Knight

  University of California, San Diego

  98 shared

• Emily Kunselman

  Scripps Institution of Oceanography

  68 shared

• Todd P. Michael

  Salk Institute for Biological Studies

  52 shared

• Benjamin W. Frable

  46 shared

• Joseph Vechinski

  Hubbs-Sea World Research Institute

  46 shared

• Zachary R. Skelton

  University of California, San Diego

  46 shared

Labs

• Eric Allen LabPI

Education

• Ph.D., Marine Biology, Scripps Institution of Oceanography

  University of California San Diego

  2002

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