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

• Erratum for Levesque et al., “Complete genome sequence of bacteriophages Merry and Sunny infecting <i>Microbacterium chocolatum</i> strain GAI20246-6 isolated from an outdoor commercial algal pond”

  Microbiology Resource Announcements · 2026-02-26

  articleOpen access
  PublisherDOI

• Overturning circulation structures the microbial functional seascape of the South Pacific

  Science · 2025-07-10 · 3 citations

  article

  Global overturning circulation partitions the deep ocean into regions, each with different physicochemical characteristics, but the extent to which these water masses represent distinct ecosystems remains unknown. In this work, we integrate extensive genomic information with hydrography and water mass age to delineate microbial taxonomic and functional boundaries across the South Pacific. Prokaryotic richness steeply increases with depth in the surface ocean, which forms a so-called phylocline, below which, richness is consistently high, dipping slightly in highly aged water. Reconstructed genomes self-organize into six spatially distinct taxonomic cohorts and 10 functionally distinct biomes that are primarily structured by wind-driven circulation at the surface and density-driven circulation at depth. Overall, water physicochemistry, modulated at depth by water age, drives microbial diversity patterns and functional potential in the pelagic ocean.

  PublisherDOI

• Complete genome sequence of bacteriophages Merry and Sunny infecting <i>Microbacterium chocolatum</i> strain <i>GAI20246-6</i> isolated from an outdoor commercial algal pond

  Microbiology Resource Announcements · 2025-10-20

  articleOpen access

  ABSTRACT We report the isolation of two virulent phages from an outdoor algal pond infecting the bacteria Microbacterium chocolatum strain GAI20246-6. Their genomes are both 53.6kb with a GC content of 67.8%. Some genomic features are described as well as morphological characteristics based on transmission electron microscopy (TEM) micrographs.

  PublisherDOI

• Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of a generalist macro-algivorous fish

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-05

  preprintOpen accessSenior authorCorresponding

  ABSTRACT The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgae polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, macroalgae polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens , to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing were employed to distinguish the natural active fraction from transient gut microbiome taxa. Four media combinations were able to propagate between 96% to 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo . Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation. IMPORTANCE Seaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes to propagate these active microbial communities in vitro . This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.

  PublisherOA PDFDOI

• Overturning circulation structures the microbial functional landscape of the South Pacific

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-13 · 1 citations

  preprintOpen access

  Global overturning circulation partitions the deep ocean into regions with unique physicochemical characteristics, but the extent to which these water masses represent distinct ecosystems remains unknown. Here, we integrate extensive genomic information with hydrography and water mass age to delineate microbial taxonomic and functional boundaries across the South Pacific. Prokaryotic richness steeply increases with depth in the surface ocean, forming a "phylocline", below which richness is consistently high, dipping slightly in highly aged water. Reconstructed genomes self-organize into six spatially-distinct taxonomic cohorts and ten functionally-distinct biomes that are primarily structured by wind-driven circulation at the surface and density-driven circulation at depth. Overall, water physicochemistry, modulated at depth by water age, drives microbial diversity and functional potential in the pelagic ocean.

  PublisherOA PDFDOI

• Soil depth determines the microbial communities in <i>Sorghum bicolor</i> fields within a uniform regional environment

  Microbiology Spectrum · 2025-04-16 · 6 citations

  articleOpen access

  ABSTRACT Sorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a stratified soil microbiome that plays a crucial role in plant health, growth, and carbon storage. Microbiome studies on agricultural soils, particularly fields growing S. bicolor , have been mostly limited to surface soils (&lt;30 cm). Here we investigated the abiotic factors of soil properties, field location, depth, and the biotic factors of sorghum type across 38 genotypes of the soil microbiome. Utilizing 16S rRNA gene amplicon sequencing, our analysis reveals significant changes in microbial composition and decreasing diversity at increasing soil depths within S. bicolor fields, regardless of genotype or field, with microbial richness and diversity declining to a minimum at the 60–90 cm layer and increasing beyond the 90 cm depth. Notably, specific microbial families, such as Thermogemmatisporaceae and an unclassified family within the ABS-6 order, were enriched in deeper soil layers beyond 30 cm. These findings highlight the importance of soil depth in agricultural soil microbiome studies. IMPORTANCE Sorghum bicolor is a valuable model for studying the microbiome in deep soils, which is crucial for enhancing carbon sequestration in agricultural systems. As we look to crops with deeper roots for improved carbon storage, it is essential to move beyond the traditional focus on surface soils in agricultural settings. This study shifts that focus by investigating microbial dynamics at greater soil depths, revealing significant changes in microbial composition and diversity with increasing depth, revealing the critical role of deep-soil microbiomes in nutrient cycling and carbon sequestration in agricultural fields with the deep-rooted crop S. bicolor . By exploring these processes beyond surface soils, this research supports the development of sustainable agricultural practices that can better harness the potential of deep-rooted crops for long-term carbon storage.

  PublisherDOI

• State Department of Health’s Equitable Funding Allocation Methodology to Address COVID-19 Health Disparities Among High-Risk and Underserved Populations

  American Journal of Public Health · 2024-08-28 · 2 citations

  articleOpen access

  The Washington State Department of Health developed an equitable funding allocation methodology incorporating quantitative and qualitative decision-making components. We describe the methodology and an implementation evaluation performed by an external evaluation team using the RE-AIM (Reach, Effectiveness, Adoption, Implementation, and Maintenance) evaluation framework. The evaluation team concluded that the methodology was developed in a way that used a racial equity lens and prioritized intersectionalities in the communities that the funding was intended to serve. ( Am J Public Health. 2024;114(S7):S575–S579. https://doi.org/10.2105/AJPH.2024.307833 )

  PublisherOA PDFDOI

• Soil depth determines the microbial communities in <i>Sorghum bicolor</i> fields

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-02

  preprintOpen access

  Abstract Sorghum bicolor , an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a unique and stratified soil microbiome that plays a crucial role in plant health, growth, and carbon storage. Microbiome studies on agricultural soils, particularly fields growing S. bicolor , have been mostly limited to surface soils (&lt;30 cm). Here we investigated the abiotic factors of soil properties, field location, depth, and the biotic factors of sorghum type across 38 genotypes on the soil microbiome. Utilizing 16S rRNA gene amplicon sequencing, our analysis reveals significant changes in microbial composition and decreasing diversity at increasing soil depths within S. bicolor regardless of genotype or fields. Notably, specific microbial families, such as Thermogemmatisporaceae and an unclassified family within the ABS-6 order, were enriched in deeper soil layers beyond 30 cm. Additionally, microbial richness and diversity declined with depth, reaching a minimum at the 60 - 90 cm layer, with layers beyond 90 cm increasing in alpha diversity. These findings highlight the importance of soil depth in agricultural soil microbiome studies.

  PublisherOA PDFDOI

• Microbiome divergence of marine gastropod species separated by the Isthmus of Panama

  Applied and Environmental Microbiology · 2024-10-31

  articleOpen access

  ABSTRACT The rise of the Isthmus of Panama separated the populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and the Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped the compositions of their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera Cerithium and Cerithideopsis to those of congeneric outgroups. Our results suggest that the effects of ~3 million years of separation and isolation on microbiome composition varied among host genera and between sample types within the same hosts. In the whole-body samples, microbiome compositions of geminate species pairs tended to be similar, likely due to host filtering, although the strength of this relationship varied among the two groups and across similarity metrics. Shell-surface microbiomes show contrasting patterns, with co-divergence between the host taxa and a small number of microbial clades evident in Cerithideopsis but not Cerithium . These results suggest that (i) isolation of host populations after the rise of the Isthmus of Panama affected microbiomes of geminate hosts in a complex and host-specific manner, and (ii) host-associated microbial taxa respond differently to vicariance events than the hosts themselves. IMPORTANCE While considerable work has been done on evolutionary divergences of marine species in response to the rise of the Isthmus of Panama, which separated two previously connected oceans, how this event shaped the microbiomes of these marine hosts remains poorly known. Using whole-body and shell-surface microbiomes of closely related gastropod species from opposite sides of the Isthmus, we show that divergences of microbial taxa after the formation of the Isthmus are often not concordant with those of their gastropod hosts. Our results show that evolutionary responses of marine gastropod-associated microbiomes to major environmental perturbations are complex and are shaped more by local environments than host evolutionary history.

  PublisherOA PDFDOI

• Adaptation to high pressure; insights from the genome of an evolved <i>Escherichia coli</i> strain with increased piezotolerance

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-09-25 · 1 citations

  preprintOpen access

  Abstract Pressure is a key environmental parameter that influences the activity and distribution of microbial life on our planet. Despite its key role there is still not a definitive list of essential genes for microbial adaptation to life under increasing pressure. In this study we used a previously characterized Escherichia coli strain (AN62) evolved to grow at pressure (60 MPa) non-permissive to the parental strain and performed comparative genomics in order to identify the genome-level adaptations that might allowed the observed pressure-adapted phenotype. We identified 18 mutations in total of which 3 mutations were present in both the parental and evolved strain, 3 mutations were only present in the parental strain, and 12 mutations were observed only in the evolved AN62 strain. Among the characterized mutations we observed a point mutation in the acyl carrier protein ( acp P V43G ). Complementation experiments revealed that the observed V43G mutation in AcpP is responsible for increased levels of cis-vaccenic acid but is not alone responsible for the pressure adapted phenotype. Further molecular dynamics and docking simulations suggested that the V43G mutation promoted stronger binding of the AcpP protein to partner enzymes of the fatty acid biosynthesis pathway involved in fatty acid unsaturation. Data Summary Escherichia coli reads from the parental and evolved strain have been deposited in the Sequence Read Archive (SRA) under accession number RJNA600359. All software used in the bioinformatic analysis is publicly available. Impact Statement Pressure is a key environmental parameter. Two-thirds of our planet is covered by oceans with an average depth of 3800m, which means that the majority of the marine life experiences deep sea conditions. Our results offer a list of gene mutations that could contribute to an improved pressure growth phenotype in Escherichia coli , offering a unique insight on the genome level adaptations that might contribute to high pressure adaptation.

  PublisherDOI

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

• Natural Sources and Microbial Transformation of Marine Halogenated Pollutants

  NIH · $669k · 2018–2024

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