Research Areas

Do bacteria isolated from metal-contaminated environments have higher predicted metal tolerance scores than bacteria from uncontaminated environments?

Can BacDive-measured bacterial phenotypes (Gram stain, oxygen tolerance, metabolite utilization, enzyme activities) predict metal tolerance as measure...

When bacteria are exposed to metal salts (CoCl₂, NiCl₂, CuCl₂), how much of the observed fitness effect is caused by the metal cation versus the count...

Is the genetic architecture of metal cross-resistance conserved across phylogenetically diverse bacteria, or is it rewired species by species?

Across diverse bacteria subjected to genome-wide fitness profiling under metal stress, what is the genetic architecture of metal tolerance — is it enc...

Where on Earth are metal-resistant environmental bacteria most abundant, and where are the gaps in public metagenomic sampling that prevent us from kn...

Among the 12,838 metal-important genes identified by the Metal Fitness Atlas, which are specifically required for metal tolerance vs general stress su...

Do metal-resistance functions in the global microbiome reflect phylogenetic constraint (conserved in lineages) or environmental selection (enriched in...

Which microbial functional gene categories (COGs) are significantly associated with soil metal concentrations at global scale, and do these associatio...

How does a gene's importance for bacterial survival relate to its evolutionary conservation, and what does the conserved genome actually look like?

Are essential genes preferentially conserved in the core genome, and what functional categories distinguish essential-core from essential-auxiliary ge...

What characterizes genes that are simultaneously burdensome (fitness improves when deleted) and not conserved in the pangenome? Are they mobile elemen...

Which essential genes are conserved across bacteria, which are context-dependent, and can we predict function for uncharacterized essential genes usin...

Which biochemical reactions are universally essential across bacteria, and what does the essential metabolome reveal about the minimal core metabolism...

Is there a continuous gradient from essential genes (core) to dispensable genes (accessory) across the full fitness spectrum, and what does the fitnes...

Do species with open pangenomes show different COG functional enrichment patterns than species with closed pangenomes?

Do open pangenomes show different patterns of environmental vs phylogenetic effects compared to closed pangenomes?

How do pangenome characteristics (open vs. closed) correlate with metabolic pathway completeness, phylogenetic distances, and species ecology?

Do pangenome characteristics (open vs. closed) correlate with metabolic pathway diversity and biogeographic distribution patterns?

Can we systematically identify and resolve metabolic annotation gaps in bacterial genomes by integrating experimental growth phenotypes, gene fitness ...

Just because a bacterium's genome encodes a complete metabolic pathway (metabolic *capability*), does the organism actually depend on it? Can we disti...

When a bacterium's genome encodes a complete biosynthetic or catabolic pathway, does the organism actually depend on it? Can we use fitness data to di...

Do genes with correlated fitness profiles (co-fit) tend to co-occur in the same genomes across a species' pangenome? Does functional coupling constrai...

Can we decompose RB-TnSeq fitness compendia into latent functional modules via robust ICA, align them across organisms using orthology, and use module...

Are ICA fitness modules enriched in core pangenome genes, and do cross-organism module families map to the core genome?

What drives gene content similarity between bacterial genomes: environmental similarity or phylogenetic relatedness?

Does the environment effect on gene content become stronger when analysis is restricted to genuinely environmental samples, excluding human-associated...

What do AlphaEarth environmental embeddings capture, and how do they relate to geographic coordinates and NCBI environment labels?

At pangenome scale (293K genomes, 27K species), are antibiotic resistance genes preferentially located within or adjacent to prophage regions, and doe...

Which microbial species and ecological environments show the highest concentration of antibiotic resistance genes, and can we predict resistance accum...

Within the Bacillota_B phylum (Desulfosporosinus, BRH-c8a Peptococcaceae, BRH-c4a Desulfotomaculales, and other obligate-anaerobe deep-subsurface Firm...

Do BERDL's cultured bacterial genomes from clay-confined deep-subsurface environments recapitulate the genomic signatures the recent literature has id...

How do COG functional category distributions differ across core, auxiliary, and novel genes in bacterial pangenomes?

Do gene-content ecotypes within bacterial species differ in their COG functional profiles, showing differentiation in adaptive functions while sharing...

Does environmental selection shape the distribution of plant growth-promoting (PGP) bacterial genes across the BERDL pangenome (293K genomes, 27K spec...

How prevalent are SNIPE (Surface-associated Nuclease Inhibiting Phage Entry) homologues across the 293K-genome BERDL pangenome, and does their taxonom...

Do antimicrobial resistance gene profiles differ between ecological niches across 27,000 bacterial species? Using 83K AMR gene clusters mapped to 293K...

What is the distribution, conservation, phylogenetic structure, functional context, and environmental association of antimicrobial resistance (AMR) ge...

What genes are co-regulated with antimicrobial resistance (AMR) genes across growth conditions, and do these "support networks" explain the uniform fi...

Do antimicrobial resistance (AMR) genes impose a fitness cost in the absence of antibiotic selection pressure? Using genome-wide RB-TnSeq fitness data...

Which genes matter for survival under environmentally-realistic conditions but appear dispensable in the lab, and vice versa? Do field-relevant fitnes...

Do lab-measured fitness effects under contaminant stress predict the field abundance of Fitness Browser organisms across Oak Ridge groundwater sites w...

Why are core genome genes MORE likely to show positive fitness effects when deleted, and what functions and conditions drive this burden paradox?

How does core genome composition change over sampling time, and do genes transition in and out of core status?

What does the `kescience_paperblast` collection contain, how current is it, and what are its coverage patterns across organisms, domains of life, and ...

What does the `kescience_webofmicrobes` exometabolomics collection contain, which organisms overlap with the Fitness Browser, and how well do metaboli...

Which genes of unknown function across 48 bacteria have strong fitness phenotypes, and can biogeographic patterns, pathway gap analysis, and cross-org...

Among the ~6,400 Fitness Browser genes that remain functionally unannotated even after bakta v1.12.0 reannotation, what distinguishes them from "annot...

What is the scope and structure of a comprehensive ADP1 database, and how do its annotations, metabolic models, and phenotype data intersect with BERD...

What is the condition-dependent structure of gene essentiality in *Acinetobacter baylyi* ADP1, as revealed by the de Berardinis single-gene deletion c...

Among genes that TnSeq says are dispensable in *Acinetobacter baylyi* ADP1, does FBA correctly predict which ones have growth defects? Can direct muta...

Does AlphaFold MSA depth predict functional annotation richness in the bacterial pangenome, and is structural novelty (low MSA depth) systematically e...

Within a species, how does the AMR repertoire vary between strains, and what drives that variation?

Why does aromatic catabolism in *Acinetobacter baylyi* ADP1 require Complex I (NADH dehydrogenase), iron acquisition, and PQQ biosynthesis when growth...

What data is available in BERDL (across tenants, agencies, and programs), what biological topics does it cover, and where do datasets amplify each oth...

Why does inactivation of *fur* (the ferric uptake regulator) permit the loss of lipid A in *Caulobacter crescentus*, when no equivalent connection to ...

Can we build a multi-criterion framework that explains measured *P. aeruginosa* PA14 inhibition from metabolic competition, growth kinetics, and patie...

For 83 groundwater- and necromass-derived carbon compounds proposed for community enrichment and isolate phenotyping, what is known about (1) their en...

Do high-contamination Oak Ridge groundwater communities show enrichment for taxa with higher inferred stress-related functional potential compared wit...

Does 16S community similarity across the 9 ENIGMA SSO wells (3x3 grid, ~4 m span at Oak Ridge) recapitulate the spatial arrangement in X, Y, and Z? Wh...

For *Pseudomonas fluorescens* FW300-N2E3 (ENIGMA groundwater isolate), how consistent are exometabolomic outputs (Web of Microbes), genome-wide gene f...

Across the prokaryotic tree (GTDB r214; 293,059 genomes / 27,690 species), build a multi-resolution **innovation + acquisition-depth atlas of bacteria...

Can we predict bacterial growth phenotype — at multiple resolutions from binary growth through continuous kinetics to complex dynamics — from genome c...

After ~25 years of +5°C experimental soil warming at the Harvard Forest Barre Woods plot, does the functional transcript pool (metatranscriptome KO/Pf...

Which bacterial pathobionts are **enriched, ubiquitous, and non-protective** in IBD, UC, and Crohn's disease patients — considered both across indicat...

Across BERDL's 293K-genome pangenome, what is the phylogenomic distribution and cassette-completeness of the lanthanide-dependent methanol/ethanol oxi...

How does sequential enrichment on lignin, with or without labile carbon supplementation, shape bacterial and fungal community composition — and does e...

Do the GapMind-predicted pathway completeness profiles of community resident taxa predict or correlate with observed metabolomics profiles in NMDC env...

How are polyhydroxybutyrate (PHB) granule-forming pathways distributed across bacterial clades and environments, and does this distribution support th...

What is the genomic basis for plant-microbe associations across different plant compartments (rhizosphere, root, phyllosphere, endophyte)? Can we clas...

How are prophage gene modules and terminase-defined prophage lineages distributed across bacterial phylogeny and environmental gradients, and which mo...

Among free-living *Pseudomonas* clades, does the carbon source utilization profile predict the soil ecosystem type from which strains were isolated — ...

How is *Acinetobacter baylyi* ADP1's branched respiratory chain wired across carbon sources — which NADH dehydrogenases and terminal oxidases are requ...

Do Type IV secretion systems (T4SS) in environmental bacteria physically co-localise with carbohydrate-active enzyme (CAZy) genes in a manner consiste...