Knowledge Base Index

Documents

• Web of Microbes Data Explorer (short) — Summary of the Web of Microbes Data Explorer project, which characterized a 2018 Web of Microbes exometabolomics snapshot and assessed its links to Fitness Browser, ModelSEED, GapMind and pangenome collections.
• Truly Dark Genes — What Remains Unknown After Modern Annotation? (short) — Summary of the truly_dark_genes project, which separates Fitness Browser dark genes into annotation-lag, truly dark and unlinked sets after Bakta reannotation, characterizes the truly dark genes’ structural, evolutionary and phenotypic properties, and ranks candidates for experimental characterization.
• T4SS–CAZy Environmental HGT (short) — Preliminary analysis of type IV secretion system (T4SS) machinery in environmental MAGs, its genomic co-localization with carbohydrate-active enzyme (CAZy) genes, cross-phylum horizontal transfer of GT2 glycosyltransferases, and an association with metal-resistance genes.
• Soil Metal Concentrations Drive Functional Gene Shifts (short) — Preliminary analysis of associations between nine soil metal concentrations and microbial COG functional gene content across 51,748 samples, with its confounding, effect-size and spatial-validation caveats.
• Soil Microbial Dark Matter and the Clay Shield Null Result (short) — Preliminary global soil analysis of 5,441 samples finding no support for the clay shield hypothesis, and introducing a Genomic Discovery Index that flags forest, cropland and alkaline soils as genomically under-represented.
• SNIPE Defense System in the KBase Data Lakehouse Pangenome (short) — Project report evaluating the SNIPE phage-defense system across the KBase Data Lakehouse pangenome, covering its corrected PF13250/PF13455 domain architecture, ManXYZ fitness trade-off, prevalence and mobility, environmental association, and phage-host and Klebsiella evidence.
• Condition-Specific Respiratory Chain Wiring in ADP1 (short) — Summary of the respiratory_chain_wiring project, which reports that carbon source selects qualitatively different respiratory-chain configurations in Acinetobacter baylyi ADP1, proposes an NADH flux-rate explanation, and records a null cross-species NDH-2 compensation test and standard-condition proteomics.
• Carbon Source Utilization Predicts Ecology and Lifestyle in Pseudomonas (short) — Summary of a GapMind carbon-pathway analysis of 12,732 Pseudomonas genomes showing strong plant-sugar pathway loss in the P. aeruginosa group and a significant but modest ecological signal in carbon profiles among free-living species.
• Prophage Gene Modules and Terminase-Defined Lineages Across Bacterial Phylogeny and Environmental Gradients (short) — Summary of the prophage_ecology project, which maps eggNOG-annotated prophage gene modules and TerL lineages across 27,702 bacterial species and tests their environmental, phylogenetic, genome-size and NMDC metagenomic associations.
• Prophage-AMR Co-mobilization Atlas (short) — Pangenome-scale analysis of how antimicrobial-resistance genes co-localize with prophage markers across GTDB species, finding a strong species-level link between prophage density and AMR repertoire breadth but only a modest, heterogeneous gene-level proximity effect.
• Plant Microbiome Ecotypes — Compartment-Specific Functional Guilds and Their Genetic Architecture (short) — Summary of the plant_microbiome_ecotypes project, which tests compartment effects, beneficial-versus-pathogenic genome architecture, HGT, complementarity, plant-enriched gene families, dual-nature classification and within-species subclade structure across 293,059 GTDB genomes, including its Phase 2b adversarial-review corrections.
• pitfalls (short) — Cross-project reference of practical pitfalls when querying and analyzing KBase Data Lakehouse databases, covering access, joins, typing, Spark scale limits, database-specific schema rules, statistical design, and reproducibility.
• Polyhydroxybutyrate Granule Formation Pathways — Distribution Across Clades and Environmental Selection (short) — Summary of the phb_granule_ecology project, which surveys polyhydroxybutyrate (PHB) pathway distribution across 27,690 GTDB species and tests environmental selection, genome-size confounding, and horizontal transfer of phaC.
• Pan-Bacterial Anti-Phage Defense Arsenal (short) — Summary of the phage_defense_arsenal report, which surveys seven anti-phage defense-system families across the KBase Data Lakehouse pangenome and covers prevalence, the prophage-burden association, co-occurrence syndromes, accessory-pangenome enrichment and detection caveats.
• PGP Gene Distribution Across Environments & Pangenomes (short) — Summary of a KBase Data Lakehouse pangenome analysis of plant-growth-promoting gene co-occurrence, soil/rhizosphere enrichment, core/accessory status and tryptophan-pathway coupling to ipdC.
• Metabolic Capability vs Dependency (short) — Summary of the pathway_capability_dependency project, which separates GapMind-predicted pathway capability from RB-TnSeq-observed dependency in 7 model bacteria and links pathway variation to pangenome openness and metabolic ecotypes across 2,810 GTDB species.
• PaperBLAST Data Explorer — Literature Coverage Bias in Protein Sequence Space (short) — Summary of the paperblast_explorer project, which quantifies how unevenly literature covers organisms, genes and MMseqs2 protein families in the KBase Data Lakehouse PaperBLAST collection and identifies dark protein families.
• Pangenome Openness Analysis (short) — Summary of the pangenome_openness project, which found no significant correlation between species pangenome openness and environment or phylogeny effects on gene content.
• NMDC Context Audit (short) — Audit of the KBase Data Lakehouse resources labeled nmdc, showing that 20 database names resolve to 7 maintained resources that differ in provenance, tenant placement, scale, currency and authority.
• Community Metabolic Ecology via NMDC × Pangenome Integration (short) — Summary of a project integrating NMDC community taxonomy and metabolomics with GTDB pangenome GapMind pathway completeness to test community-scale Black Queen dynamics and Soil–Freshwater differentiation of metabolic potential.
• Fitness Modules × Pangenome Conservation (short) — Summary of the module_conservation project, which tests whether genes in ICA fitness modules and cross-organism module families are enriched in the bacterial core genome.
• Metal Resistance Ecology — Phylogenetic Conservation vs. Environmental Selection (short) — Summary of the microbeatlas_metal_ecology project, which links genus-level metal-resistance type diversity from pangenome AMR annotations to global MicrobeAtlas niche breadth using phylogenetic comparative methods, with groundwater and ENIGMA ORFRC field validation and extensive sensitivity caveats.
• Metal-Specific vs General Stress Genes (short) — Summary of the metal_specificity project, which classifies metal-important fitness genes from 24 organisms as metal-specific, metal+stress, or general sick, and tests their conservation, functional enrichment, candidate families, and module behavior.
• Global Biogeography of Environmental Bacterial Metal Resistance (short) — Preliminary global map of metal-resistance prevalence in 22,356 geolocated environmental MGnify MAGs, with 5° grid hotspots, biome enrichment and depletion, and ENA coordinate-coverage limits.
• Pan-Bacterial Metal Fitness Atlas (short) — Cross-species atlas of bacterial gene fitness under metal stress, showing that metal-important genes are enriched in the core genome and proposing a two-tier core-stress versus accessory-resistance model.
• Gene-Resolution Metal Cross-Resistance Across Diverse Bacteria (short) — Summary of the metal_cross_resistance project, which used gene-level fitness data across 28 bacteria to show universally positive metal cross-resistance, a three-tier gene conservation gradient, and a null BacDive isolation-environment validation at Fitness Browser scale.
• Metabolic Capability vs Metabolic Dependency (short) — Summary of a 48-organism study comparing GapMind metabolic pathway completeness with Fitness Browser fitness dependency, and relating fitness-neutral latent pathways to pathway conservation, pangenome openness and within-species metabolic ecotypes.
• Lignin Enrichment and Ecological Memory in Microbial Communities (short) — Summary of a 16S and ITS amplicon study of how lignin enrichment, labile-carbon co-supplementation and sequential passaging restructure bacterial and fungal communities, including a quantified bacterial ecological-memory effect.
• Lanthanide Methylotrophy Atlas — Summary (short) — A 293,059-genome atlas of lanthanide-dependent methanol oxidation in the KBase Data Lakehouse pangenome, covering xoxF predominance over mxaF, clade-restricted lanmodulin, soil/sediment enrichment, REE-AMD MAGs, PQQ annotation gaps and eggNOG-versus-Bakta marker calibration.
• Lab Fitness Predicts Field Ecology at Oak Ridge (short) — Project report testing whether Fitness Browser laboratory metal-tolerance fitness predicts genus abundance and community composition across a uranium gradient in 108 Oak Ridge groundwater sites.
• Metagenome-Prioritized Phage Cocktails for Crohn’s Disease and IBD (short) — Project report compiling four gut-microbiome ecotypes, rigor-controlled Tier-A pathobiont prioritization, pathway/BGC/metabolite/strain/serology mechanism analyses, three layers of phage evidence and per-patient hybrid phage-cocktail drafts for 23 UC Davis Crohn’s disease patients.
• Harvard Forest Long-Term Warming — DNA vs RNA Functional Response (short) — Summary of a 25-year +5°C Harvard Forest soil-warming study comparing DNA- and RNA-pool functional responses, community composition, carbon-cycling genes and metabolite richness across organic and mineral horizons.
• Genotype × Condition to Phenotype Prediction from ENIGMA Growth Curves (short) — Summary of the ENIGMA genotype × condition project that predicts bacterial growth phenotypes from KEGG-ortholog content, finding binary growth partly predictable but growth kinetics not, and proposing field-relevant active-learning experiments for Oak Ridge.
• Gene Function Ecological Agora (short) — Summary of the Gene Function Ecological Agora project, a GTDB-r214-scale Producer × Participation and Sankoff-parsimony atlas of clade × KO gene-function innovation and acquisition depth, with its pre-registered hypothesis verdicts, ecological grounding, methodology revisions and caveats.
• Metabolic Consistency of Pseudomonas FW300-N2E3 Across Four KBase Data Lakehouse Databases (short) — Cross-database consistency of Pseudomonas FW300-N2E3 metabolism across Web of Microbes exometabolomics, Fitness Browser gene fitness, BacDive species-level utilization and GapMind pathway predictions, with sample-size-aware grading of discordances.
• Functional Dark Matter — Experimentally Prioritized Novel Genetic Systems (short) — Summary of the functional_dark_matter project, which integrates fitness, essentiality, pangenome, environmental, pathway and reannotation evidence to prioritize experimentally actionable bacterial genes of unknown function across 48 Fitness Browser organisms.
• Pan-bacterial Fitness Modules via Independent Component Analysis (short) — Summary of the fitness_modules project, which used independent component analysis on RB-TnSeq fitness data from 32 bacteria to find co-regulated fitness modules, align them into cross-organism module families, and give hypothetical proteins process-level function context.
• Fitness Effects vs Conservation — Quantitative Analysis (short) — Quantitative comparison of Fitness Browser mutant fitness effects with pangenome conservation across ~194,000 genes from 43 bacteria, showing a weak but robust gradient in which fitness-important genes are more often core.
• Field vs Lab Gene Importance in *Desulfovibrio vulgaris* Hildenborough (short) — A single-organism analysis of Desulfovibrio vulgaris Hildenborough testing whether field-relevant versus lab-condition RB-TnSeq fitness importance predicts pangenome core status, finding that fitness importance itself matters more than ecological condition class.
• Metadata Correlates of Eukaryotic Contamination in NMDC Prokaryote-Targeted Metagenomes (short) — Summary of a project that quantified eukaryotic read fractions in 2,759 NMDC prokaryote-targeted metagenome runs and showed that cross-study environmental correlates of eukaryotic signal are confounded with study batch, while vegetation and geography predict it within one batch-controlled soil study.
• Essential Metabolome: GapMind Pathway Analysis Across Essential-Gene Organisms (short) — Pilot GapMind analysis of amino-acid biosynthesis and carbon-source pathway completeness across 7 Fitness Browser organisms with essential-gene data, including an apparent Desulfovibrio vulgaris serine gap and E. coli coverage loss.
• The Pan-Bacterial Essential Genome (short) — Summary of the essential_genome project, which uses RB-TnSeq essentiality calls from the Fitness Browser, bidirectional-best-hit orthology, pangenome conservation links and ICA fitness modules across 48 organisms to classify universally, variably and orphan essential gene families and predict functions for hypothetical essentials.
• AlphaEarth Embeddings, Geography & Environment Explorer (short) — Characterization of 64-dimensional AlphaEarth satellite-derived environmental embeddings for 83,287 pangenome genomes, covering geographic distance-decay, human-associated sampling bias, coordinate quality, metadata harmonization, and UMAP/DBSCAN structure.
• SSO Subsurface Community Ecology — Spatial Structure, Functional Gradients, and Hydrogeological Drivers (short) — Summary of the ENIGMA SSO subsurface 16S ASV study testing spatial structure, hydrogeological depth zonation, inferred biogeochemical gradients, groundwater–sediment differentiation, guild co-occurrence and short-term temporal stability across a 3×3 well grid.
• Contamination Gradient vs Functional Potential in ENIGMA Communities (short) — Summary of an ENIGMA project linking groundwater metal-contamination gradients to genus-bridged pangenome functional proxies, in which confirmatory contamination–defense tests were null and exploratory coverage-aware associations were sensitive to coverage, covariates, taxonomic resolution and FDR correction.
• ENIGMA Carbon Census — Tiered Knowledge Census of 83 Enrichment Compounds (short) — Summary of the ENIGMA Carbon Census, a tiered knowledge census of 83 groundwater and necromass enrichment compounds that links compound identity, pathways, ENIGMA-isolate utilizers, GTDB placement and environmental occurrence, and finds 74 of the 83 compounds organism-dark.
• Ecotype Functional Differentiation (short) — Summary of a 15-species KBase Data Lakehouse pangenome study finding that within-species gene-content ecotypes are common and differ in COG functional categories, with larger effect sizes in adaptive than housekeeping categories.
• Ecotype Reanalysis — Environmental vs Human-Associated Species (short) — Reanalysis testing whether environmental species show stronger environment–gene content correlations than human-associated species in the AlphaEarth subset, finding a null result despite confirmed clinical sampling bias.
• Ecotype Correlation Analysis (short) — Summary of the ecotype_analysis project, which tested across 172 bacterial species whether environmental (AlphaEarth embedding) or phylogenetic similarity better predicts pangenome gene-content similarity.
• discoveries (short) — Cross-project digest of 2026 BERIL research findings — direct measurements, methodological corrections, null results, contradictions and reusable analytical rules spanning microbial fitness, pangenome evolution, metabolic modeling, resistance and defense, subsurface ecology, microbiome analysis and research-quality practice.
• Counter Ion Effects on Metal Fitness Measurements (short) — Summary of the counter_ion_effects project, which tested whether chloride from metal salts confounds genome-wide metal-fitness measurements and found substantial metal–NaCl shared-stress overlap but no chloride dose effect, with Metal Fitness Atlas core enrichment robust to correction.
• The 5,526 Costly + Dispensable Genes (short) — Cross-organism characterization of 5,526 bacterial genes that are costly in laboratory fitness assays yet dispensable in the pangenome, showing they are dominated by mobile genetic elements and poorly annotated, taxonomically restricted DNA that the report interprets as horizontally acquired.
• Core Gene Paradox — Why Are Core Genes More Burdensome? (short) — Summary of the core_gene_tradeoffs project, which links Fitness Browser RB-TnSeq fitness burden to pangenome conservation and finds a function-specific core-gene burden paradox, enrichment of condition-dependent trade-off genes among core genes, and a costly-versus-conserved selection-signature matrix.
• Conservation vs Fitness — Linking FB Genes to Pangenome Clusters (short) — Summary of the conservation_vs_fitness project, which links Fitness Browser essentiality calls to KBase pangenome clusters across 33 bacteria and finds a modest enrichment of putative essential genes in core clusters.
• Gene Conservation, Fitness, and the Architecture of Bacterial Genomes (short) — Summary of a synthesis that combines RB-TnSeq fitness and pangenome conservation across 43 organisms, covering a modest conservation gradient, a core-genome burden paradox, selection signatures, and core-enriched fitness modules.
• COG Functional Category Analysis (short) — Cross-species analysis of COG functional categories across 32 bacterial species that contrasts conserved core-gene functions with mobile-, defense- and unknown-function enrichment among novel or singleton genes.
• Co-fitness and Co-inheritance in Bacterial Pangenomes (short) — Summary of the cofitness_coinheritance project, which tested whether Fitness Browser gene co-fitness predicts gene co-occurrence across bacterial pangenomes at pairwise and ICA-module levels.
• Self-Sufficiency, Anaerobic Toolkit, and Cultivation Bias in Clay-Confined Cultured Bacterial Genomes (short) — Summary of the clay_confined_subsurface project, which tests biosynthetic self-sufficiency, an anaerobic toolkit, and porewater-versus-rock-attached cultivation bias in cultured deep-clay, shallow-clay, and soil-baseline bacterial genomes.
• Rational Design of Protective Microbiome Formulations for Competitive Exclusion of *Pseudomonas aeruginosa* in Cystic Fibrosis Airways (short) — Design of commensal consortia to competitively exclude Pseudomonas aeruginosa from cystic-fibrosis airways, integrating inhibition assays, carbon-utilization and growth-kinetics profiling, patient meta-omics, PA pangenome and virulence typing, and multi-criterion formulation optimization.
• Regulatory and proteomic architecture of Δfur-permitted lipid A loss in *Caulobacter crescentus* (short) — Integration of transcriptomics, single-replicate outer-membrane proteomics, RB-TnSeq fitness, published regulons and comparative annotation explaining how Δfur ΔsspB permits lipid A loss in Caulobacter crescentus.
• BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergies (short) — Summary of the BERDL Data Atlas project, which inventories the KBase Data Lakehouse’s tables, agency and topic coverage, cross-tenant join bridges, realized project use, and a sample-validated FitnessBrowser-to-AlphaFold join.
• Subsurface Bacillota_B Specialization — What Distinguishes Deep-Clay Lineages from Soil Congeners? (short) — Summary of a comparison of 10 deep-clay and 62 soil-baseline Bacillota_B genomes that finds 547 anchor-enriched orthologous groups and larger deep-clay genomes, and that corrects the clay project’s iron-reduction marker analysis.
• BacDive Phenotype Signatures of Metal Tolerance (short) — BacDive phenotypes add no predictive power beyond taxonomy for metal tolerance
• BacDive Isolation Environment × Metal Tolerance Prediction (short) — Summary of the bacdive_metal_validation project, which tested whether BacDive isolation environments independently support genome-based metal-tolerance scores from GTDB pangenome species.
• Aromatic Catabolism Support Network in ADP1 (short) — Summary of the aromatic_catabolism_network project, which defines a 51-gene quinate-specific support network around the β-ketoadipate pathway in Acinetobacter baylyi ADP1 spanning aromatic degradation, Complex I, iron acquisition, PQQ biosynthesis and regulation.
• Annotation-Gap Discovery via Phenotype-Fitness-Pangenome-Gapfilling Integration (short) — Summary of the annotation_gap_discovery project, which triangulated gapfilling, Fitness Browser fitness, pangenome, GapMind and BLAST evidence to assign candidate genes to gapfilled metabolic reactions across 14 bacteria.
• Within-Species AMR Strain Variation (short) — Within-species antimicrobial-resistance gene variation across 1,305 bacterial species and 180,025 genomes, covering prevalence classes, resistance islands, phylogenetic signal, AMR ecotypes, temporal nulls and environment associations.
• Pan-Bacterial AMR Gene Landscape (short) — Pan-bacterial atlas of AMRFinderPlus antimicrobial-resistance genes across 27,690 pangenome species, covering core-versus-accessory conservation, mechanisms, taxonomic hotspots, environment associations, Fitness Browser fitness effects, caveats and proposed follow-up analyses.
• Fitness Cost of Antimicrobial Resistance Genes (short) — Summary of a Fitness Browser RB-TnSeq meta-analysis across 25 organisms that finds a small relative baseline fitness cost for antimicrobial-resistance genes, independent of mechanism and core/accessory status, with mechanism-dependent importance under antibiotic exposure.
• Environmental Resistome at Pangenome Scale (short) — Pangenome-scale analysis of how antimicrobial-resistance gene-cluster counts, core/accessory composition and resistance mechanisms vary with ecological environment across 14,723 bacterial species, with its caveats, literature context and proposed follow-up work.
• AMR Co-Fitness Support Networks (short) — Pan-bacterial analysis of antimicrobial-resistance gene cofitness support networks across 28 Fitness Browser organisms, covering ICA module membership, InterProScan GO enrichment, organism-versus-mechanism specificity, and the unresolved split between co-regulation and shared dispensability.
• AlphaFold MSA Depth as a Lens on the Bacterial Annotation Gap (short) — Summary of a project that used AlphaFold MSA depth as a proxy for functional annotation richness across bacterial pangenome gene clusters, covering the core/accessory gradient and conserved low-MSA-depth core ‘paradox’ proteins.
• Triple Essentiality Concordance Analysis for *Acinetobacter baylyi* ADP1 (short) — Summary of a two-stage Acinetobacter baylyi ADP1 analysis comparing FBA, RB-TnSeq, knockout, mutant growth and proteomics evidence for gene essentiality, including null FBA–growth results and systematic TnSeq–knockout discordance.
• ADP1 Deletion Collection Phenotype Analysis (short) — Analysis of Acinetobacter baylyi ADP1 single-gene deletion growth across 8 carbon sources, integrated with TnSeq essentiality, functional annotation and pangenome status, showing a continuous condition-dependent phenotype gradient with one discrete quinate module.
• Acinetobacter baylyi ADP1 Data Explorer (short) — Summary of the Acinetobacter baylyi ADP1 Data Explorer project, which analyzes a multi-omics SQLite database for ADP1 and 13 related genomes and links it to the KBase Data Lakehouse pangenome, biochemistry and fitness collections.

Concepts

• active-learning-experiment-selection — Active learning picks the next growth experiments by ranking candidate conditions on model error, model uncertainty and field relevance; this ENIGMA proposal has not yet been validated against random selection.
• adaptive-versus-housekeeping-functional-differentiation — Cross-project assessment of whether adaptive functional categories differentiate more strongly than housekeeping categories among gene-content ecotypes, with significance rates, effect sizes, replication attempts in gut and plant-associated systems, and the annotation, ontology and phylogenetic limits on the contrast.
• adversarial-research-quality-assurance — Why computational-biology claims in this corpus need an adversarial review layer, and the citation, statistical, leakage, provenance and code-level failure classes it catches.
• analysis-provenance-and-reproducible-outputs — What counts as a reproducible analysis record in this corpus: committed figures and data files are not enough without committed code history and retained execution outputs.
• antimicrobial-resistance-fitness-cost — Evidence that antimicrobial-resistance genes carry a modest, mechanism-independent relative fitness burden in transposon-knockout data while becoming more important under antibiotic exposure, with the measurement, annotation, and sampling limits that constrain that reading.
• biosynthetic-prototrophy-and-auxotrophy — How pathway completeness, fitness, and nutrient dependence relate
• biosynthetic-self-sufficiency-and-cultivation — Synthesis of why cultured-genome collections, such as the clay-associated subsurface cohorts, may miss the most biosynthetically self-sufficient lineages, and how pathway completeness, genome expansion and fitness evidence bear on that question.
• callability-limited-comparative-inference — Why unequal evidence callability across resources, strata, assays and reference databases can render ecological and clinical contrasts untestable rather than merely underpowered, and how BERIL projects reported such gaps.
• capability-versus-kinetic-predictability — Cross-project argument that gene content predicts whether an organism can grow under a condition far better than it predicts growth rate, lag, or yield, and that measured kinetics, codon usage bias, and flux models each bound that asymmetry differently.
• carriage-prevalence-versus-within-carrier-function — Why a species-level disease association must be decomposed into carriage prevalence, within-carrier pathway-level function, and strain content, worked through CD-associated gut species whose signals sit at different levels.
• chromosomal-and-integrative-gene-transfer — How chromosomal neighborhoods, integrative elements, and conjugative machinery rather than plasmid carriage account for gene dissemination in environmental and resistance-gene datasets, and what evidence can and cannot identify the transfer route.
• circularity-in-metabolic-model-validation — How gapfilling genome-scale metabolic models can make knockout-based validation circular and tie the accuracy of growth predictions to the quality of the added reactions.
• classifier-database-compatibility-in-taxonomic-quantification — Classifier databases constrain cross-study taxonomic comparisons and ecological inference.
• cofitness-network-architecture — How cofitness networks and ICA fitness modules organize bacterial gene phenotypes across organisms, and whether their structure reflects co-regulation, organism-specific architecture, or shared conditional dispensability.
• community-metabolic-interdependence — Cross-project synthesis of evidence for and against Black Queen-style community metabolic interdependence, spanning community metabolomics, latent pathway capability, pangenome openness, plant-associated complementarity tests, and gut cross-feeding disambiguation.
• comparative-conservation-metric-calibration — How ortholog-breadth, species-count, pangenome-reference and core/accessory definitions change conservation-based interpretation and prioritization of unknown bacterial genes.
• competitive-exclusion-consortium-design — Multi-objective design of protective microbial consortia against Pseudomonas aeruginosa, where inhibition, niche coverage, safety, member compatibility and engraftability trade off against one another.
• composite-functional-annotation — Composite or multi-category functional annotations, such as multi-letter COG assignments and KOs spanning both regulatory and metabolic pathways, can carry biological signal about multifunctional genes rather than annotation noise.
• composite-resistance-score-limitations — Why composite and repertoire-based metal-resistance scores support prioritization and ecological association but cannot by themselves identify metal-specific tolerance mechanisms.
• compositional-robustness-of-differential-abundance-calls — How normalization choice (raw relative abundance vs CLR/LinDA) and contrast design (pooled vs within-substudy, ecotype-stratified) can reverse, erase or re-rank differential-abundance calls in gut microbiome data.
• computational-pathway-prediction-validation — When computational pathway-completeness predictions (chiefly GapMind) are supported by measured growth, fitness and utilization phenotypes, how accurate they are where accuracy has been measured, and how scoring, thresholds and gene-mapping choices bound those validations.
• condition-dependent-gene-tradeoffs — Synthesis of evidence that bacterial genes can be costly in some conditions and beneficial in others, and how such condition-dependent fitness trade-offs relate to pangenome conservation, antibiotic and phage resistance, and pathway retention.
• condition-space-dimensionality — How many independent condition axes are needed to describe gene-dependent growth effects, and how general growth sensitivity separates from substrate-specific metabolic requirements across ADP1 deletion phenotypes and comparative pathway-dependency analyses.
• condition-specific-fitness — Concept page synthesizing how gene fitness effects, pathway dependence and conservation patterns change across carbon-source, nutrient, metal, stress and environmental conditions.
• confirmatory-exploratory-ecological-association-discordance — How predeclared or confirmatory ecological association tests compare across BERIL projects with exploratory, coverage-adjusted, robustness and broad-screen signals, and how evidence should be graded by test status, correction tier, sample size and effect size.
• contaminant-selection-of-subsurface-communities — Contaminant concentration, especially uranium together with low pH and metals, as an axis that selects subsurface microbial community composition, distinct from hydrogeological zonation.
• core-gene-annotation-paradox — Synthesis of evidence that broadly conserved core, essential, and pan-bacterial genes can still lack deep sequence representation, structural characterization, or functional annotation.
• core-genome-burden-paradox — Genes conserved across bacterial genomes can be costly to retain under laboratory conditions, where deleting them can improve mutant growth; the pattern varies by functional category and links to natural selection only by interpretation.
• costly-dispensable-gene-loss — Synthesis of evidence that genes which are burdensome in laboratory fitness assays yet not conserved across pangenomes are mostly horizontally acquired, poorly annotated accessory DNA that is a candidate for ongoing evolutionary loss.
• credential-and-tenant-access-lifecycle — Tenant-group membership and authentication-token expiry are recurring preconditions and failure modes for data access in analysis sessions on the KBase Data Lakehouse.
• cross-cohort-microbiome-portability — How microbiome classifiers, ecotype frameworks and metabolomics features do or do not retain their biological meaning when moved across cohorts, laboratories, feature namespaces and study designs.
• cross-condition-metabolic-comparability — How exometabolomics, mutant fitness, phenotype databases, pathway predictions and metabolic models measure different metabolic capabilities under different conditions, limiting direct cross-assay comparison.
• cross-species-fitness-transferability — How far gene-level fitness phenotypes and ortholog-based function predictions transfer between organisms, and how recipient network architecture, ortholog-graph scope, annotation error, and condition context limit that transfer.
• cross-tenant-data-bridging — How shared schema keys across the KBase Data Lakehouse tenants differ from validated value-space overlap, executable joins and interpretable cross-resource evidence, with recorded identifier, type and provenance traps.
• cultivation-collection-bias-in-ecological-genomics — How cultivation, collection and metadata bias in public genome and occurrence collections constrains ecological genomic inference, with per-project coverage audits, failed bias predictions, and diagnostics of which habitat fraction a collection represents.
• data-landscape-ownership-and-coverage-bias — How agency, tenant and name-based ownership structure determines what biological data the KBase Data Lakehouse covers, and how organism- and resource-level gaps hide behind inventory breadth.
• driver-side-result-collection-limits — In several documented genome-scale analyses on the KBase Data Lakehouse, failures occurred when distributed Spark results were pulled into one driver process, either by hitting the driver-result size cap or by exhausting driver memory; the page also covers the reported staging, batching, push-down and algebraic remedies.
• dual-nature-plant-associated-bacteria — Genome-based cohort assignment places most plant-associated bacterial species in a dual-nature cohort that carries both beneficial and pathogenic signatures, rather than a clean beneficial or pathogenic class.
• ec-less-reaction-annotation — Gapfilled metabolic reactions that lack EC numbers are much harder to link to genes than EC-annotated reactions, so they form a distinct barrier to functional annotation.
• ecological-cost-of-microbiome-target-depletion — Why candidate microbiome depletion targets need per-target ecological-cost annotations, instantiated by a bile-acid 7α-dehydroxylation network whose active members cannot be removed without predicted metabolic collateral.
• ecological-memory — Ecological memory is the persistence of community-composition differences from prior environmental exposure, shown quantitatively for bacteria in a lignin-enrichment carbon-history experiment, with weaker and preliminary fungal evidence.
• ecotype-clustering-validity — Why principal-component/KMeans, density-based, pathway-presence and community-composition clustering of bacterial genomes and microbiomes yields weakly separated, threshold- and feature-dependent ecotypes whose biological validity remains unsettled.
• ecotype-environment-gene-content — Cross-project synthesis of how far environmental context, rather than phylogeny, explains bacterial gene content and pathway differentiation, and where subsystem-specific exceptions and sampling artifacts qualify the broad null.
• environment-embedding-geography — Cross-project synthesis of how satellite embeddings, environmental metadata, coordinate quality and sampling composition shape inferences about geographic and environmental structure in microbial genomes and gene content.
• environmental-distribution-of-lanthanide-methylotrophy — How the genomic capacity for lanthanide-dependent methylotrophy, marked by xoxF, is distributed across habitats, and how weakly that distribution lines up with rare-earth-element-rich environments such as REE acid mine drainage.
• environmental-resistome — Cross-project synthesis of how bacterial antimicrobial- and metal-resistance gene repertoires vary in abundance, mechanism, conservation, mobility, and phylogenetic signal across ecological settings, and of the limits on inferring environmental causation from these associations.
• essentiality-assay-discordance — Why RB-TnSeq insertion-mutant essentiality calls and complete-gene-knockout lethality disagree, and what continuous fitness, conservation, FBA and condition matching add to that comparison.
• eukaryotic-dna-admixture-in-prokaryotic-metagenomes — How much eukaryotic and plastid DNA appears in prokaryote-targeted metagenomes, where it comes from by habitat, and what that means for interpreting metagenomic profiles.
• evidence-triangulation-for-functional-annotation — Combining metabolic-model gapfilling, fitness phenotypes, pangenome conservation, pathway evidence, homology and multiple annotation pipelines resolves more microbial gene-function gaps than any single signal, with resolution limited by reference, assay and phylogenetic coverage.
• execution-environment-dependent-access-paths — How the REST interface, direct Spark SQL, hosted notebooks, cluster scripts and local machines each impose different access paths, failure signatures and limits on the same KBase Data Lakehouse analysis.
• experimental-prioritization-of-functional-dark-matter — How the corpus turns unknown bacterial genes into ranked, testable experimental hypotheses by weighing fitness, essentiality, conservation, context, annotation and environmental evidence, and where those rankings remain uncertain or internally inconsistent.
• feature-attribution-with-correlated-genomic-features — Why SHAP-style feature attributions over correlated genomic features (KEGG orthologs, genome-scale traits) indicate that a correlated block matters rather than that a specific gene matters, and how fitness-data concordance tests probe their mechanistic grounding.
• fitness-condition-coverage-prioritization-bias — How uneven experimental condition coverage across organisms, condition classes and experiment counts biases fitness-based gene prioritization and threshold-based fitness calls.
• fitness-matched-null-models — Why functional-enrichment and threshold tests on fitness and genomic data need null models or comparators matched to the background fitness or catalog structure of the genes being tested.
• fitness-module-detection-sensitivity — How ICA-based fitness-module discovery depends on membership thresholds, annotation settings, experiment depth, component caps, orthology scope, activity normalization and condition space.
• foreign-dump-ingestion-fidelity — How the documented MySQL dumps and SQLite files lose fidelity at ingestion through headerless data, literal null markers, unparseable DDL and non-UTF-8 text, and the preprocessing proposed to repair them.
• functional-marker-validation — Why gene, domain and annotation markers must be validated for biological identity, specificity, source agreement and scale before their presence is read as ecological evidence.
• gene-cooccurrence-ecological-guilds — How co-occurrence of genes across genomes, and of guilds across communities, can indicate shared ecological selection without establishing physical linkage, direct interaction, or complementary function.
• gene-essentiality — Cross-project synthesis of how bacterial gene essentiality is defined, measured, and predicted across conditions, assays, conservation classes, and annotation status.
• gene-function-acquisition-depth — How phylogenetic depth of gene-function acquisition, clade-specific and ecological distribution, phylogenetic signal of traits, pathway capability and annotation quality jointly explain whether microbial functions are widespread, specialized, exchanged, or stably inherited.
• genetic-perturbation-coverage-bias — Cross-project synthesis of how perturbation collections and fitness panels over- or under-represent genes and organisms, and how that coverage bias constrains downstream inference.
• genome-wide-versus-locus-specific-ecological-adaptation — Whether bacterial ecological adaptation registers as genome-wide gene-content similarity or is concentrated at particular loci, pathways, functional categories, or within-species subclades.
• genomic-dispersal-functional-coupling — Cross-project synthesis of how genes at separate genomic loci can form tightly coupled metabolic systems, set against operon and neighborhood clustering as complementary signals of functional linkage.
• genomic-under-representation — How uneven genome sampling, reference-database coverage and annotation depth limit inference about microbial functional potential across BERIL projects.
• gut-microbiome-ecotypes-as-patient-strata — A four-ecotype K=4 consensus over 8,489 human gut metagenomes, its sample counts and diagnosis distributions, and how far those community states survive as usable patient strata when projected onto a small independent clinical cohort.
• habitat-structured-community-metabolic-potential — Community-level predicted metabolic pathway completeness separates soil from freshwater communities, with carbon-utilization pathways on the main ordination axis and amino-acid biosynthesis on a secondary axis.
• homology-search-negative-evidence — Why zero-hit homology, domain, name and literature searches across the corpus must be validated against known positives, query format and annotation substrate before they are read as biological absence.
• horizontal-gene-transfer-driven-innovation — Cross-project synthesis of evidence that horizontal gene transfer and mobile elements generate bacterial gene novelty, covering COG enrichments, acquisition-depth inference, positive-control calibration, transfer proxies and their limits.
• join-strategy-and-table-partitioning-cost — How physical table layout (partitioning) and join strategy (broadcast vs. shuffle, partition-aligned filters vs. pagination) affect the cost of billion-row genomic joins in Spark queries over the KBase Data Lakehouse.
• lab-field-fitness-concordance — Cross-project synthesis of whether laboratory fitness phenotypes and genome-predicted tolerances predict where genes and organisms occur in natural environments, and of the conditional, partly underpowered evidence for that concordance.
• laboratory-fitness-versus-natural-selection — Synthesis of evidence that laboratory fitness assays such as RB-TnSeq track the natural selection reflected in pangenome conservation, field abundance and ecological resistance costs only partly and with confounding.
• lanmodulin-narrow-distribution — Bakta-validated lanmodulin, a lanthanide-binding protein, is confined to three α-Proteobacterial methylotroph families and does not reliably co-occur with xoxF, so chelator presence cannot be read off lanthanide-dependent dehydrogenase presence.
• lanthanide-dependent-methanol-dehydrogenase-predominance — Across a genome-scale atlas, annotations for the lanthanide-dependent methanol dehydrogenase xoxF far outnumber those for the calcium-dependent mxaF, globally and within every adequately sampled phylum carrying either gene.
• long-running-analysis-execution-reliability — Interactive notebook kernels are an unreliable container for long-running analyses, so long jobs need explicit timeouts, detached script execution and on-disk checkpointing.
• long-term-soil-warming-microbial-response — How long-term experimental soil warming at Harvard Forest shifts microbial community composition with FDR support while gene-content, transcript and metabolite signals remain weak or nominal.
• metabolic-capacity-specialization — Cross-project synthesis of evidence that microbial carbon-utilization and related metabolic capacities are concentrated in particular lineages and dominated by specialists, with caveats on callability, conditional denominators and fitness realization.
• metabolic-model-gapfilling — How metabolic-model gapfilling, flux balance analysis predictions, and pathway-completeness calls compare against experimental essentiality, knockout, and growth evidence, and where that validation chain breaks down.
• metabolite-class-signatures-of-gut-inflammation — How aggregating paired-cohort metabolomics into pre-specified chemical-class themes reads a Crohn’s-disease contrast, with polyamines and long-chain PUFAs passing the enrichment gate, most themes not passing it, and taurine-conjugated bile acids signalling at the compound level inside a theme that fails at class level.
• metal-cross-resistance — Cross-project synthesis of how bacterial gene-fitness responses to different metals share a broadly positive direction, vary in magnitude with metal chemistry, split into general-stress and metal-specific gene tiers, and connect only weakly and observationally to environmental occurrence.
• module-level-coinheritance — Coordinated ICA fitness modules, especially accessory modules, show stronger pangenome co-occurrence than pairwise co-fitness, although most modules are core and prevalence ceilings limit what can be detected.
• multi-omics-integration — Cross-project synthesis of how BERIL projects combine genomic, fitness, model, proteomic, metabolomic and ecological modalities, and what their concordances, method limits and contradictions support.
• null-results-under-limited-statistical-resolution — How to tell FDR-corrected null results caused by incomplete metadata or sample-size p-value floors apart from real evidence that an effect is absent, using AMR temporal trends and per-OTU lignin enrichment as examples.
• numeric-type-fidelity-across-engine-boundaries — How Spark SQL numeric types and Arrow-backed pandas columns change or fail when data moves between the query engine and the analysis frame, and the casting and query-design practices that avoid it.
• occurrence-versus-catabolic-activity — Why detecting an organism, an enriched taxon, a complete pathway, or a shifted metabolite pool is not evidence that a compound was catabolized in situ, and what each measurement type does support.
• ontology-and-category-schema-sensitivity — How ontologies, category schemas, membership thresholds and identifier vocabularies shape the biological conclusions drawn across BERIL projects.
• organism-dark-compounds — Carbon compounds in the ENIGMA carbon census whose utilization the queried resources cannot link to any organism, how they are stratified by why they are dark, and the proposed routes to making them callable.
• outer-membrane-lipid-homeostasis — How Caulobacter crescentus maintains outer-membrane integrity when lipid A is lost, synthesizing lipid substitution, shared Lpt transport, Tol-Pal and peptidoglycan remodeling, phased ChvI regulation, and the fitness and proteomic limits on each claim.
• pangenome-conservation-fitness-decoupling — How pangenome core/accessory status relates to, and often fails to predict, measured gene fitness effects across AMR, essential-gene, metal-stress and pathway-level analyses.
• pangenome-core-boundary-and-clade-size-bias — How pangenome core/auxiliary classifications depend on clade sampling depth, prevalence thresholds, counting conventions, denominators and join coverage, and what that implies for conservation-fitness comparisons.
• pangenome-integration — How BERIL projects reconcile gene, cluster, genome, strain and species identifiers across pangenome, fitness, phenotype, metabolite and ecological datasets, and the coverage losses, schema rules and caveats that limit those joins.
• pangenome-openness-determinants — Cross-project synthesis of the metabolic, ecological, phylogenetic and sampling factors associated with bacterial pangenome openness, and of the metric choices and coverage limits that shape those associations.
• pathobiont-biosynthetic-gene-cluster-repertoires — Why a MIBiG-anchored biosynthetic gene cluster catalog assigns a named chemical virulence mechanism to Escherichia coli alone among six actionable Crohn’s-disease pathobiont targets, and which mechanisms of the other five it leaves unlabelled.
• pathway-versus-reaction-evidence-resolution — Why pathway-level, organism-level and module-level evidence (GapMind calls, co-occurrence, fitness modules, catabolic pathway calls) cannot by itself assign specific genes to specific reactions or pathway steps, and what additional evidence such assignment requires.
• phage-defense-syndromes-and-arms-race — Cross-project synthesis of whether bacterial anti-phage defense systems co-occur as recurring syndromes and whether defense-repertoire breadth tracks prophage burden, environment and mobile-element carriage.
• phage-therapy-evidence-translation — How phage host-range, phage-availability and ecological-cost evidence is combined into patient-specific Crohn’s-disease cocktail designs, and what that chain of inference does not establish.
• phb-granule-ecology — Cross-project synthesis of how the polyhydroxybutyrate (PHB) pathway is distributed across bacterial and archaeal species, covering enrichment in feast/famine environments, genome-size confounding of niche breadth, accessory-genome evidence for horizontal transfer, and NMDC metagenomic cross-validation.
• phenotype-database-coverage-bias — How uneven sampling, sparse and heterogeneous phenotype fields, matching attrition, and lineage composition in microbial phenotype and metadata databases such as BacDive shape, inflate, or hide apparent phenotype–genotype and ecological associations.
• phylogenetic-confounding-of-pangenome-associations — How shared ancestry and uneven taxonomic sampling can create, hide, reverse or inflate cross-species associations between genome content and traits or habitats, and how far different phylogenetic controls go in correcting them.
• pooled-run-pseudoreplication-and-metadata-label-noise — How pooled sequencing runs, aggregated replicates and repeated samples from one subject change the correct statistical unit, and how inherited or inferred metadata labels add predictor noise in microbiome association analyses.
• provenance-aware-resource-discovery — Concept page arguing that resource discovery in the KBase Data Lakehouse must expose provenance, authority, scale, tenant placement, access status, content gaps, and data currency together rather than relying on resource names.
• proxy-assays-for-community-state-assignment — Whether clinical covariates or a small targeted qPCR panel can replace shotgun metagenomics for assigning gut samples to IBD ecotypes, and the evidence that they cannot yet.
• reference-strain-representativeness — How the Pseudomonas aeruginosa PA14 reference strain diverges in effector, biofilm and regulatory genotype from the CF isolate population it is used to model, and what that implies for generalizing assay results.
• research-attention-inequality — Synthesis of how research attention, literature coverage and functional annotation are unevenly distributed across organisms, genes and protein families, and how literature darkness differs from annotation darkness.
• resistance-island-coinheritance — Synthesis of evidence on whether co-occurring antimicrobial-resistance genes form co-inherited resistance islands, and how far that co-occurrence supports physical, functional, or co-selective linkage.
• respiratory-capacity-and-nadh-load — Respiratory-chain component dependence in Acinetobacter baylyi ADP1 and related bacteria appears to track NADH-generating load and proposed flux-rate limits rather than aromatic substrate identity, while the NDH-2 compensation hypothesis remains unresolved.
• runtime-budgeted-resampling-and-embedding — How resampling and dimension-reduction steps in corpus analyses are run under explicit compute budgets, trading exactness for feasibility, and why that trade should be declared.
• sample-size-aware-phenotype-consensus — Why species-level phenotype and utilization claims must be reported with per-strain consensus, explicit strain and genome denominators, defined record categories, and lineage or coverage structure.
• sampling-depth-and-downsampling-effects — How genome sampling depth, downsampling, minimum-genome filters, rarefaction, prevalence filtering and missingness change comparative-genomic and ecological association estimates across BERIL projects.
• scale-dependent-mobile-element-associations — How associations between mobile-element markers and resistance, defense, photosynthesis, plant-interaction and carbohydrate-active genes change with genomic scale and measurement proxy, and what each scale can support about mobilization.
• selection-on-outcome-leakage — How reusing the same features to define groups and then to test outcomes inflates microbiome and genomic associations, what it forced to be retracted, and which designs remove it.
• shared-stress-versus-stressor-specific-fitness — How fitness profiles under metal and other stressors decompose into a shared cellular-stress component and stressor-specific requirements, and how thresholds, salt controls and record sets shape that split.
• silent-failure-modes-in-distributed-queries — How distributed queries on the KBase Data Lakehouse can fail quietly, returning plausible empty results or authorization errors that may not clearly identify the cause, and why empty results must be verified rather than trusted.
• soil-horizon-response-heterogeneity — In stratified soils, depth horizon explains more community variance than experimental treatment and is associated with different treatment responses between layers, suggesting that organic and mineral compartments should not be pooled.
• spatial-sampling-effort-confounding — How uneven sampling effort, missing or low-quality coordinates, institutional-address clusters, study concentration and spatial autocorrelation can confound geographic hotspot and habitat analyses of environmental microbial genomes.
• species-cooccurrence-modules-as-intervention-units — Whether species co-occurrence modules detected in gut metagenomes can serve as units for microbiome intervention, given that they concentrate phage-target candidates but shift membership between community states.
• structural-annotation-gap — How sequence-space (MSA) depth, reference-database coverage and literature attention together shape how richly bacterial gene clusters are functionally annotated.
• study-batch-confounding-of-environmental-associations — How study, cohort, site and batch structure can make an environmental or clinical association non-portable, structurally unadjustable, or sign-reversed, and which validation designs separate real signal from batch structure.
• subsurface-bacillota-specialization — Cross-project synthesis of how deep-clay subsurface Bacillota_B differ from soil-baseline relatives in accessory gene content, genome size and anaerobic respiratory markers, and how phylogeny, cohort size, compartment bias and marker correction limit those inferences.
• subsurface-hydrogeological-zonation — How hydrogeological depth zones, inferred contamination-plume flow, sample habitat and temporal persistence structure subsurface microbial communities at the SSO and Oak Ridge sites, and which of these claims rest on measurement versus composition-based inference.
• taxonomic-nomenclature-reconciliation — Concept page on aligning taxonomic names, accessions, taxonomy versions and identifier formats across microbial databases, and on the analytical artifacts that arise when they are not reconciled.
• taxonomic-resolution-dependent-functional-inference — How the taxonomic rank and reference coverage chosen for an analysis determine which genotype-to-function associations can be detected, synthesized across ENIGMA bridges, pangenome propagation, multi-rank innovation scores, taxonomy-inferred metagenome scores and clinical microbiome attribution.
• transposon-callability-bias — Transposon callability bias is the risk that absent or uninterpretable transposon insertions are mistaken for gene essentiality or neutrality, and it shapes which genes downstream fitness analyses can see.
• two-speed-bacterial-genome — Cross-project synthesis of the two-speed bacterial genome model, in which a conserved core carries metabolism and housekeeping while a variable accessory fraction carries mobile, defense, and poorly characterized functions, together with the evidence that qualifies that split.
• vectorization-versus-row-wise-iteration — Row-wise pandas iteration over large genomic tables has been reported to run for long periods without completing, while vectorized merges finished the same operations in seconds.
• within-species-conservation-between-species-functional-divergence — How functions conserved within species, such as core metal-tolerance and amino-acid catabolic genes, coexist with between-species or between-clade divergence in functional breadth, gene content and ecological association.

Entities

• 16s-amplicon-sequencing (method) — Microbial-community profiling method using 16S rRNA amplicons
• 3 hydroxybenzoic acid (compound) — A callable ENIGMA-isolate carbon source in the aromatic compound census.
• 4 hydroxybenzaldehyde (compound) — A census-tracked aromatic compound with ENIGMA-isolate utilization predictions.
• abscisic acid (compound) — Abscisic acid was an ENIGMA-isolate-callable terpenoid compound.
• acds (gene_or_pathway) — Plant-growth-promoting gene marker enriched in soil and rhizosphere genomes
• acea icl (gene_or_pathway) — Glyoxylate-cycle isocitrate lyase gene detected in warmed Harvard Forest soil
• aceb glcb (gene_or_pathway) — Malate synthase gene aceB/glcB, KO K01638, in the glyoxylate cycle
• acetate (compound) — Carbon-source substrate linked to demanding growth and respiratory-chain requirements.
• acetatifactor intestinalis (organism) — Organism showing metabolic ecotype clustering in the study
• aciad2176 (gene_or_pathway) — ACIAD2176 is a DUF2280 candidate Complex I accessory factor in ADP1.
• aciad3137 (gene_or_pathway) — ADP1 DUF-associated candidate Complex I accessory factor
• aciad3522 (gene_or_pathway) — ACIAD3522 is an NADH-FMN oxidoreductase with acetate-specific fitness effects in ADP1.
• acidobacteria (organism) — Acidobacteria is a bacterial phylum with warming and methylotrophy-associated genomic evidence.
• acinetobacter baumannii (organism) — Comparator bacterium with reported alternative lipid A-loss routes.
• acinetobacter baylyi adp1 data explorer database (dataset) — Integrated SQLite dataset for multi-omics analysis of Acinetobacter baylyi ADP1
• acinetobacter-baylyi-adp1 (organism) — Acinetobacter baylyi ADP1 genome, fitness, metabolism, and respiratory wiring
• actinobacteria (organism) — Bacterial phylum enriched in long-term warmed organic soil
• adp1-single-gene-deletion-collection (dataset) — Published complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1, whose growth phenotypes on several carbon sources are reused by BERIL ADP1 projects.
• aeromonas (organism) — Labile-carbon-enriched bacterial genus in lignin-amended communities
• alistipes-onderdonkii (organism) — Alistipes onderdonkii, a gut commensal bacterium that is one of the two species with the most inferred metabolic ecotypes in the corpus’s pathway-profile clustering.
• alph-aearth (dataset) — Environmental embedding dataset for ecological context in microbial genomes
• alteromonas (organism) — Alteromonas macleodii showed a two-cluster metabolic ecotype structure.
• aluminum (compound) — Aluminum and its condition-specific bacterial fitness responses
• aminobacter (organism) — Aminobacter is a genus enriched in Round-2 lignin-history communities.
• amrfinderplus (method) — AMRFinderPlus annotates antimicrobial- and metal-resistance genes.
• anaeromyxobacter (organism) — Anaeromyxobacter, an SSO-associated inferred iron-reducing organism
• arabidopsis thaliana (organism) — Model plant included among PaperBLAST’s five most represented organisms.
• arabinose (compound) — Pentose proposed as a selective prebiotic for two commensals
• arcobacter (organism) — Arcobacter, an SSO sediment-associated sulfur-oxidizing genus
• arginine (compound) — Arginine evidence across fitness, utilization, pathway, and community datasets
• aromatic amino acid biosynthesis (gene_or_pathway) — ADP1 aromatic amino acid pathway modifications and proteomics context
• arsenic (compound) — Arsenic and its microbial resistance and soil-gene associations
• asparagine (compound) — Asparagine is a tested carbon source in ADP1 deletion phenotyping.
• atacama desert (place) — Chilean region identified as the strongest metal-resistance hotspot
• average-nucleotide-identity (method) — Genome-comparison method for estimating relatedness through nucleotide identity.
• azospirillum-brasilense (organism) — Model bacterium used in metabolic, fitness, and ecology studies
• bacdive (dataset) — Bacterial strain database linking phenotypes and isolation metadata to genome analyses
• bacillota-b (organism) — Bacillota_B lineages compared across deep-clay and soil habitats
• bacillus safensis (organism) — Bacterial species represented by a three-ecotype pangenome analysis.
• bacillus-subtilis (organism) — Bacillus subtilis 168, the Gram-positive model bacterium proposed in the corpus as a priority genetic-library addition and used as a prophage validation species.
• bacteroides-thetaiotaomicron (organism) — Bacteroidetes organism with low gapfilling resolution and distinctive co-inheritance patterns
• bacteroides xylanisolvens (organism) — Bacteroides species with six gene-content ecotypes in the KBase Data Lakehouse analysis
• bacteroides (organism) — Bacteroides genus detected in Oak Ridge groundwater and positively associated with uranium.
• bacteroidota (organism) — Bacteroidota is a bacterial phylum with diverse ecological and functional profiles.
• bakta (method) — Bacterial genome annotation method used for AMR and functional discovery.
• barnesiella-intestinihominis (organism) — Barnesiella intestinihominis is a gut commensal bacterium that ties with Alistipes onderdonkii for the most inferred metabolic ecotypes in the BERIL pathway-capability analysis.
• benjamini-hochberg-fdr (method) — Multiple-testing correction controlling false discovery rates across microbial ecology analyses
• beta-ketoadipate-pathway (gene_or_pathway) — Aromatic degradation pathway converting quinate-derived intermediates to TCA-cycle inputs
• beta lactamases (gene_or_pathway) — Gene-function class showing a recent-acquisition signature in the atlas
• beyelii yar (place) — Russian borehole site represented in the Bacillota_B subsurface comparison
• bidirectional-best-hit-orthology (method) — Orthology-inference method based on reciprocal best-hit gene relationships
• bile-acid-7alpha-dehydroxylation (gene_or_pathway) — Gut-microbial bai-operon bile-acid transformation whose active taxa, metabolite signature, and ecological cost shape IBD phage-cocktail design.
• bonferroni-correction (method) — Bonferroni correction is a family-wise multiple-testing correction that divides the significance level by the number of tests in a family; in this corpus it sets confirmatory thresholds in the gene-function agora, MicrobeAtlas metal-ecology and SNIPE defense-system projects.
• bradyrhizobium (organism) — Root-associated bacterial genus with limited phylogenetic coverage
• bray curtis dissimilarity (method) — Dissimilarity measure used to compare prophage-module compositions
• brex (gene_or_pathway) — BREX is a bacterial anti-phage defense system enriched in accessory genomes.
• butanediol (compound) — 2,3-butanediol is a carbon source used to measure ADP1 deletion fitness.
• cadaverine (compound) — Cadaverine, a metabolite positively associated with E. coli in IBD data.
• cadmium (compound) — Cadmium, a metal linked to specific and environmental stress responses
• canonical correlation analysis (method) — Method linking two data modalities through maximally correlated canonical variates
• carbon source phenotypes (dataset) — Genome-by-condition corpus for predicting bacterial growth capability
• card (dataset) — CARD (Comprehensive Antibiotic Resistance Database) is an external antibiotic-resistance reference resource; the corpus names its Antibiotic Resistance Ontology (ARO) as a classification standard and its gene groups as a source of known horizontal gene transfer (HGT) controls.
• caulobacter-crescentus (organism) — Model alphaproteobacterium studied for envelope and lipid A-loss adaptation
• caulobacter vibrioides (organism) — Caulobacter vibrioides pathway-completeness profile in the essential-metabolome pilot
• cazy (dataset) — CAZy families used to study carbohydrate-active enzyme genes and HGT
• cbass (gene_or_pathway) — CBASS is a bacterial anti-phage defense-system family.
• centrifuge (method) — Taxonomic classifier with genus-level ambiguity in this NMDC deployment
• checkm (method) — CheckM is a tool that estimates genome completeness and contamination; BERIL projects use it to filter genomes by quality, to rescale genome-content measures, and to check whether genome-size and pathway-count contrasts are quality artefacts.
• chemotaxis (gene_or_pathway) — Bacterial chemotaxis signaling associated with AMR cofitness neighborhoods.
• chromium (compound) — Metal associated with fitness specificity and soil functional-gene shifts
• chrysosporium (organism) — Fungal genus dominant under lignin plus labile-carbon enrichment
• chvg (gene_or_pathway) — Caulobacter-restricted sensor-regulator partner in the ChvG–ChvI circuit
• chvi (gene_or_pathway) — Caulobacter response regulator associated with early and late envelope-remodeling phases
• clostridium-scindens (organism) — Human gut bacterium whose apparent Crohn’s-disease enrichment in IBD metagenome re-analyses moved from a flagged protective-species paradox to a confound-free CD-up call after feature-leakage repair.
• cobalt (compound) — Cobalt and its conserved, environment-dependent microbial fitness responses
• cobrapy (method) — Python framework for constructing and analyzing constraint-based metabolic models
• cog-functional-categories (dataset) — COG-based functional categories for comparing microbial gene content and ecology
• cog0443 (gene_or_pathway) — COG0443 is a pan-bacterial ortholog group that the functional dark matter analyses rank among the most broadly conserved yet functionally uncharacterized gene families.
• cog0468 (gene_or_pathway) — COG0468 is a pan-bacterial ortholog group that ranks first among functionally uncharacterized (‘dark’) gene families by the conservation × ignorance importance score.
• cog3569 (gene_or_pathway) — Plant-enriched COG ortholog group retained after phylogenetic control
• comamonas (organism) — Bacterial genus enriched during sequential lignin passage
• complex-i (gene_or_pathway) — Respiratory Complex I links NADH flux to condition-specific fitness in ADP1
• copper (compound) — Copper evidence spans metal fitness, cross-resistance, and soil functional genomics.
• crispr-cas (gene_or_pathway) — CRISPR-Cas microbial defense-system gene category and anti-phage defense system
• crispri (method) — CRISPRi method for testing essential and functionally dark genes
• curatedmetagenomicdata (dataset) — Cross-cohort microbiome dataset used for ecotype and IBD analyses
• cyanobacteriia (organism) — Cyanobacteriia is a cyanobacterial class associated with photic-aquatic ecology.
• cytochrome bo3 (gene_or_pathway) — Respiratory-chain cytochrome bo3 with carbon-source-specific fitness requirements
• dbscan (method) — Density-based clustering method for identifying embedding and ecotype clusters
• desulfovibrio-vulgaris-hildenborough (organism) — Anaerobic sulfate-reducing bacterium studied for metal fitness and gene function.
• diamond (method) — DIAMOND sequence-comparison method for fitness, pangenome, and annotation linking
• disarm (gene_or_pathway) — Defense-system family detected across bacterial pangenomes
• dissimilatory-sulfate-reduction (gene_or_pathway) — The dissimilatory sulfate reduction pathway (Sat–AprAB–DsrAB), and how strongly its genomic markers are enriched in clay-confined deep-subsurface genomes, both within Bacillota_B and after a later marker correction.
• distance-based-redundancy-analysis (method) — Multivariate method for relating distance-based functional profiles to explanatory variables
• drosophila melanogaster (organism) — Fruit fly species included among PaperBLAST’s most-studied organisms
• duf1043 yhcb (gene_or_pathway) — DUF1043/YhcB is a candidate metal-specific gene family.
• eggerthella lenta (organism) — Eggerthella lenta, a Tier-A IBD pathobiont target
• eggnog (dataset) — Cross-project synthesis of eggNOG orthology, annotation coverage, and interpretation limits.
• enigma-coral (dataset) — ENIGMA CORAL is an Oak Ridge field-sample dataset for geochemistry and microbial communities.
• enigma-genome-depot (dataset) — Dataset linking ENIGMA isolates, genomes, annotations, and utilization phenotypes
• enigma growth curves (dataset) — ENIGMA growth curves linking bacterial strains, conditions, and kinetics
• enterobacter cloacae m (organism) — Enterobacter cloacae M represented by four gene-content ecotypes.
• enterobacter cloacae (organism) — Bacterium analyzed for gene-content ecotype differentiation
• enterobacter kobei (organism) — Bacterial species represented by a two-ecotype KBase Data Lakehouse analysis
• enterocloster bolteae (organism) — Enterocloster bolteae, an IBD-associated Tier-A pathobiont
• enterococcus d gallinarum (organism) — Organism represented by 95 genomes in the ecotype analysis.
• entner-doudoroff-pathway (gene_or_pathway) — Glucose-associated pathway supporting condition-specific metabolism in ADP1
• erwinia amylovora (organism) — Bacterium with the clearest ecotype separation in this study ₁
• escherichia-coli (organism) — Escherichia coli reference strain with fitness, pangenome, and disease-ecology evidence
• european nucleotide archive (dataset) — ENA archive used for sample-coordinate retrieval
• fishers-exact-test (method) — Exact test for categorical enrichment, depletion, and association
• flagellar-motility (gene_or_pathway) — Bacterial flagellar motility and assembly functions enriched in AMR networks
• flavobacterium (organism) — Lignin-enriched bacterial genus with a carbon-dependent response.
• flavonifractor plautii (organism) — IBD-associated Tier-A pathobiont with bile-acid coupling costs and a phage coverage gap
• flux-balance-analysis (method) — Metabolic-modeling method that predicts fluxes and growth from stoichiometric constraints
• franzosa (dataset) — Franzosa cohort used for cross-cohort metabolomics validation
• fucose (compound) — Fucose, a glycan-derived sugar tracked across BERIL projects as a candidate selective prebiotic, a Pseudomonas carbon-pathway feature, and one of the most frequently gapped carbon pathways in GapMind predictions.
• fur (gene_or_pathway) — Iron-responsive regulator linked to Caulobacter transport and respiratory changes
• fusarium (organism) — Fungal genus enriched in base and lignin communities
• gabija (gene_or_pathway) — Gabija anti-phage defense system
• gallionella (organism) — Gallionella, a groundwater-enriched iron-oxidizer-associated genus
• gapmind (dataset) — Dataset for assessing metabolic pathway completeness across genomes and communities
• gemella sanguinis (organism) — Candidate commensal inhibitor of Pseudomonas aeruginosa
• gemmatimonadota (organism) — Bacterial phylum with high xoxF prevalence in the atlas
• gene-knockout (method) — Complete-gene deletion method for testing essentiality and growth defects
• gene-ontology (dataset) — Gene Ontology annotations and their provenance in the KBase Data Lakehouse and NMDC holdings
• genomad (method) — geNomad is a mobile-genetic-element prediction tool that BERIL projects used for mobilome detection or named as a dedicated alternative for prophage identification.
• genomic discovery index (method) — Index for identifying spatial gaps in soil genomic representation
• geobacter (organism) — Geobacter is an iron-reducing bacterial genus that this corpus places on Opalinus clay rock surfaces at Mont Terri and finds at trace levels in ENIGMA groundwater.
• gh23 (gene_or_pathway) — GH23 is a CAZy family associated with GT2–T4SS neighborhoods.
• glucarate (compound) — Glucarate, a robust carbon source in ADP1 deletion phenotyping
• gluconate (compound) — Gluconate is a carbon-source compound whose predicted utilization pathways are reduced in cystic fibrosis lung Pseudomonas aeruginosa genomes and recur as a utilization gap in functional dark-matter analyses.
• glucose (compound) — Carbon source associated with ADP1’s Entner–Doudoroff metabolism and respiratory redundancy.
• glycine (compound) — Glycine, an amino acid and strongly ecosystem-differentiated biosynthesis pathway
• glyoxylate-shunt (gene_or_pathway) — Acetate-associated pathway supporting growth through central metabolism
• gottcha2 (method) — GOTTCHA2 is a taxonomic classifier used to estimate eukaryotic read fractions.
• groupkfold (method) — Grouped cross-validation method for testing generalization across studies.
• gt2 glycosyltransferases (gene_or_pathway) — GT2 glycosyltransferases linked to T4SS-proximal environmental HGT
• gtdb (dataset) — GTDB is a versioned genome-taxonomy and pangenome dataset for microbial analysis.
• harvard forest (place) — Harvard Forest site of a 25-year, +5°C soil-warming experiment
• hcnc (gene_or_pathway) — PGP-associated gene marker enriched in soil and rhizosphere species
• hdbscan (method) — Density-based clustering method considered for ecotype analysis
• herbaspirillum seropedicae (organism) — Herbaspirillum seropedicae evaluated for annotation-gap resolution.
• herbaspirillum (organism) — Herbaspirillum genus associated with higher uranium abundance
• histidine biosynthesis (gene_or_pathway) — Histidine biosynthesis enrichment in AMR cofitness networks
• hmp2 (dataset) — IBD-associated human microbiome and metabolomics dataset
• homo sapiens (organism) — Homo sapiens, the human organism most represented in PaperBLAST literature links.
• humann3 (method) — HUMAnN3, the metagenomic functional profiler whose MetaCyc pathway-abundance outputs (unstratified and species-stratified) are analysed in this corpus and whose pathway categories depend on the class hierarchy used to annotate them.
• hungatella hathewayi (organism) — Hungatella hathewayi, an IBD-associated Tier-A pathobiont
• icefinder (method) — Method for detecting integrative conjugative elements and related mobile elements
• independent-component-analysis (method) — Independent component analysis for discovering bacterial fitness modules
• interproscan (method) — Domain and functional annotation method for gene clusters and proteins
• ipdc (gene_or_pathway) — ipdC plant-growth-promoting gene associated with aromatic amino-acid pathways
• iron (compound) — Iron (Fe), a metal condition associated with conserved fitness responses.
• isoleucine (compound) — Isoleucine is an amino acid that appears in the corpus as a Pseudomonas aeruginosa PA14 growth substrate and as a biosynthetic pathway that showed no signal in NMDC community metabolic ecology.
• its amplicon sequencing (method) — ITS amplicon sequencing method for profiling fungal communities
• jaccard distance (method) — A method for measuring gene-content dissimilarity between genomes
• kaiju (method) — Kaiju, the NCBI-NR read-based taxonomic classifier used for the Kuehl_WGS (UC Davis) IBD cohort, and the reliability and classifier-mismatch limits that follow from using it alongside MetaPhlAn3-trained references.
• kbase-ke-pangenome (dataset) — KBase Data Lakehouse pangenome dataset linking genomes, gene clusters, annotations, and phenotypes
• kbase-msd-biochemistry (dataset) — KBase Data Lakehouse biochemistry dataset used to validate ADP1 reactions and compounds
• kegg (dataset) — Dataset for genes, pathways, and functional annotations
• kescience-alphafold (dataset) — Structural-protein dataset connecting AlphaFold models, MSA depth, and fitness data.
• kescience-fitnessbrowser (dataset) — KBase Data Lakehouse dataset of comparative microbial mutant-growth fitness measurements
• kescience-paperblast (dataset) — KBase Data Lakehouse dataset linking protein sequences, genes, annotations, and literature.
• kescience pubmed (dataset) — KEScience PubMed is a literature-record dataset in the BERDL Data Atlas.
• klebsiella-michiganensis (organism) — Klebsiella michiganensis, an organism with high annotation-gap resolution and latent capability.
• klebsiella-oxytoca (organism) — Klebsiella oxytoca studied for co-fitness, pangenome co-inheritance, and essential dark genes
• klebsiella-pneumoniae (organism) — AMR-variable bacterial pathogen with extensive accessory resistance
• klebsiella (organism) — Klebsiella strains with DUF4041 and mannose-transporter components
• kmeans-clustering (method) — Partitioning method used to identify gene-content and metabolic ecotypes
• kraken2 (method) — Prokaryote-restricted classifier evaluated for eukaryotic read detection.
• kruskal-wallis-test (method) — The Kruskal-Wallis test, a rank-based test for differences among three or more groups, as applied across BERIL projects to resistome, fitness-cost, eukaryotic-admixture, growth-rate and metabolic-pathway comparisons.
• lactate (compound) — Lactate links condition-specific respiration with microbial metabolite production.
• lactiplantibacillus-plantarum (organism) — Plant- and gut-associated Firmicute that appears in this corpus both as a genetically tractable candidate host for dark-gene experiments and as a proposed probiotic reported to enhance Pseudomonas aeruginosa pathogenicity in a cystic fibrosis model.
• lanmodulin (gene_or_pathway) — Lanmodulin is a clade-restricted lanthanide-handling protein marker.
• lauric acid (compound) — A necromass-derived fatty acid with a measured-fitness carbon call.
• lead (compound) — Lead (Pb), a soil metal linked to functional gene shifts
• leucine (compound) — Amino acid linked to community biosynthesis and accessory pathway variation
• lightgbm (method) — Gradient-boosted tree method for genome-by-condition growth prediction
• lignin (compound) — Complex aromatic polymer that selectively restructures microbial communities
• limivicinus (organism) — Limivicinus sp. in metabolic capability ecotype analysis
• limosilactobacillus fermentum (organism) — Organism analyzed for gene-content ecotype functional differentiation
• linda (method) — LinDA, a compositional differential-abundance method (linear CLR regression with bias correction) used in this corpus as the second-method concordance check for gut-microbiome differential-abundance calls.
• lipid a biosynthesis (gene_or_pathway) — Envelope lipid A pathway examined in Caulobacter lipid A-loss rescue
• lpxc (gene_or_pathway) — LpxC is a lipid A biosynthesis enzyme linked to Caulobacter lipid A loss.
• lysine (compound) — Lysine, an amino acid linked to pathway completeness and utilization evidence
• malassezia (organism) — Malassezia is a variable dominant fungal genus in Round-2 communities.
• malate (compound) — Malate, a metabolite with four-way evidence consistency for FW300-N2E3
• manganese (compound) — Essential metal associated with strongly core-enriched and partly metal-specific fitness determinants.
• mann-whitney-u-test (method) — Statistical method for rank-based comparisons of cofitness and pathway completeness
• mantel-test (method) — Distance-matrix correlation method used for ecological and genomic comparisons
• manxyz (gene_or_pathway) — Mannose/glucosamine PTS transporter linked to SNIPE phage defense
• marinobacter (organism) — Marinobacter, a bacterial genus studied through annotation and fitness analyses.
• mediterraneibacter gnavus (organism) — IBD-associated pathobiont prioritized for state-dependent targeting
• mercury (compound) — Mercury, a metal assessed in fitness and soil functional-genomics studies
• mesorhizobium (organism) — Root-associated genus with evidence of host-linked subclade structure.
• metacyc (dataset) — MetaCyc is a curated metabolic-pathway database whose class hierarchy, distributed through ModelSEEDDatabase, was used in this corpus to categorize HUMAnN3 pathway outputs for theme-enrichment tests.
• metal-fitness-atlas (dataset) — Genome-derived resource and cross-species atlas of bacterial metal-fitness and tolerance.
• metaphlan3 (method) — MetaPhlAn3 taxonomic profiling method and cross-cohort microbiome namespace
• methanococcus-maripaludis (organism) — Archaeal methanogen represented by Fitness Browser and SNIPE analyses
• methanoperedens (organism) — Methanoperedens, an SSO sediment-associated methanotrophic taxon
• methionine (compound) — Methionine showed the largest negative association but limited statistical power.
• methylobacterium-extorquens (organism) — Organism associated with lanmodulin and plant-microbiome phylogenetic coverage gaps
• methylomirabilota (organism) — Phylum with a 28.7% xoxF rate in the atlas
• mgnify (dataset) — Metagenomic dataset supporting global and soil functional ecology analyses
• microbacterium (organism) — Microbacterium, an informative genus for model-error follow-up
• microbial-atlas (dataset) — Global environmental 16S dataset for habitat and genomic-representation analysis
• micrococcus luteus (organism) — Commensal with broad substrate coverage but no observed lung engraftability.
• mmseqs2 (method) — Sequence-search and clustering method used for protein-family and TerL lineage analysis
• modelseed (dataset) — Metabolic reconstruction, reaction, and compound resource used in the KBase Data Lakehouse workflows.
• molybdenum (compound) — Molybdenum (Mo), an essential metal with conserved stress-associated fitness determinants.
• mont-terri (place) — Mont Terri site for deep-clay borehole and rock-porewater sampling.
• moraxella catarrhalis (organism) — Moraxella catarrhalis comparator in Caulobacter lipid A-loss analysis
• multi-heme-cytochrome-detection (method) — Method for detecting multi-heme cytochrome signals with PFAM and CXXCH evidence
• mus musculus (organism) — Organism ranked among PaperBLAST’s top five literature-covered taxa
• mxaf (gene_or_pathway) — Ca-dependent methanol dehydrogenase marker contrasted with xoxF
• mycobacteriaceae (organism) — Mycobacteriaceae, a bacterial family linked to mycolic-acid innovation and PHB enrichment
• mycobacterium avium (organism) — Organism represented by 249 genomes in a six-ecotype functional differentiation analysis
• mycobacterium-tuberculosis (organism) — Tuberculosis pathogen with accessory AMR and extensive literature coverage.
• mycolic acid (compound) — Compound analyzed through Mycobacteriaceae gene-function patterns.
• myoinositol (compound) — Proposed selective prebiotic predicted to support Rothia dentocariosa.
• ncbi biosample (dataset) — NCBI BioSample harvest re-hosted as nmdc.ncbi_biosamples
• ncbi-environment-metadata (dataset) — Genome-associated environmental metadata used for habitat classification and ecological analysis
• ndh 2 (gene_or_pathway) — Alternative NADH dehydrogenase identified as ACIAD_RS16420 (KO K03885).
• neisseria-gonorrhoeae (organism) — Neisseria gonorrhoeae, the organism whose initial analysis generated the predictions later tested across species in the COG analysis project.
• neisseria meningitidis (organism) — Comparator bacterium for alternative lipid A-loss routes
• neisseria mucosa (organism) — Leading Neisseria mucosa candidate for CF airway microbiome formulations
• neon (dataset) — National Ecological Observatory Network (NEON), a dataset distinct from NMDC.
• nickel (compound) — Nickel, a metal linked to broad and condition-specific microbial stress
• nife-hydrogenase (gene_or_pathway) — [NiFe]-hydrogenase, studied in this corpus as group 1 [NiFe]-hydrogenase markers in deep-clay subsurface genomes, where its apparent enrichment reflects Bacillota_B lineage background rather than habitat.
• nifh (gene_or_pathway) — nifH, a PGP-associated gene marking a distinct diazotrophic guild
• nitrate (compound) — Nitrate (NO₃⁻) is a groundwater contaminant in the Oak Ridge plume that shapes the SSO well grid, and a candidate compound in proposed ENIGMA growth experiments.
• nitrosotalea (organism) — Nitrosotalea-associated nitrifier detected in SSO groundwater ecology
• nmdc-arkin (dataset) — Arkin-derived NMDC dataset with environmental and multi-omics products
• nmdc mags (dataset) — KBase-hosted NMDC-derived catalog containing 62,346 MAGs.
• nmdc-metadata (dataset) — Canonical NMDC biosample metadata resource and its provenance boundaries
• nmdc-results (dataset) — NMDC analysis-results dataset and its provenance-aware access boundary
• nmdc (other) — National Microbiome Data Collaborative dataset ecosystem and provenance authority
• nmds (method) — NMDS ordination method used to assess SSO community structure
• oak-ridge-field-research-center (place) — Oak Ridge groundwater research site and ENIGMA field-study location
• paenisporosarcina (organism) — Paenisporosarcina, a genus associated with inferred fermentation at SSO.
• palsa 747 (organism) — PALSA-747 sp., a species-level ecotype-analysis organism
• partial-correlation (method) — Method for measuring associations while controlling for confounding variables
• pcac (gene_or_pathway) — pcaC (locus ACIAD1710) encodes 4-carboxymuconolactone decarboxylase (EC 4.1.1.44), a core protocatechuate (pca) pathway enzyme that a keyword annotation pass misclassified and co-fitness analysis recovered.
• pectobacterium carotovorum (organism) — Bacterial species with two gene-content ecotypes in the study
• pedobacter (organism) — Pedobacter declined with uranium across Oak Ridge groundwater sites.
• pelagibacter (organism) — Pelagibacter sp. showing metabolic clustering without environment association
• permanova (method) — Permutational multivariate analysis of variance for multivariate composition tests
• permdisp (method) — Method for testing multivariate dispersion heterogeneity.
• pf13250 duf4041 (gene_or_pathway) — SNIPE-associated Pfam domain marker DUF4041
• pf13455 mug113 (gene_or_pathway) — SNIPE-associated nuclease family in Pfam family PF13455
• pfam (dataset) — Protein-family domain database used for gene annotation and functional interpretation
• phaa (gene_or_pathway) — Upstream PHB-pathway gene represented by phaA clusters.
• phab (gene_or_pathway) — PHB-related gene involved in pathway-completeness analysis
• phac (gene_or_pathway) — PHA synthase gene central to PHB biosynthesis and ecological distribution
• phagefoundry (dataset) — Dataset of phage, mobile-element, and strain-susceptibility records
• phenylethylamine (compound) — An alkaloid compound with predicted utilization in ENIGMA isolates.
• phenylobacterium (organism) — Phenylobacterium group with environment-associated metabolic clustering
• phi coefficient (method) — Binary association statistic used to compare gene co-occurrence.
• photosystem ii (gene_or_pathway) — Photosystem II complex and its Cyanobacteriia-associated gene functions
• phthalic acid (compound) — Compound callable in ENIGMA isolate predictions and sourced from necromass
• phylogenetic-generalized-least-squares (method) — Phylogeny-aware regression for testing trait associations
• planet microbe (dataset) — Marine metagenomic dataset used for environmental abundance comparisons
• pleurotus (organism) — Fungal genus detected at 50.0% in the LC-LC passage condition
• pmoa (gene_or_pathway) — pmoA gene associated with particulate methane monooxygenase
• pmob (gene_or_pathway) — Methane monooxygenase subunit B gene tracked as KO K10945.
• polyhydroxybutyrate biosynthesis (gene_or_pathway) — PHB pathway defined by phaA, phaB, and phaC
• polysaccharide utilization loci (gene_or_pathway) — Polysaccharide-utilization loci and their qualified HGT signal
• pqq-biosynthesis (gene_or_pathway) — PQQ biosynthesis pathway and its condition-specific, ecological, and pangenome evidence
• pqqc (gene_or_pathway) — PGP marker gene linked to rhizosphere-associated gene co-occurrence
• pqqd (gene_or_pathway) — PGP gene with relatively high accessory and singleton fractions
• prescottella (organism) — Prescottella genus prioritized for low-growth active-learning experiments
• principal-component-analysis (method) — Dimensionality-reduction method for detecting ecosystem-associated pathway structure
• prochlorococcus a (organism) — Prochlorococcus A sp., a marine organism with a metabolic ecotype profile
• protect-genomedepot (dataset) — Pathogen-genome data collection supporting PROTECT and KBase Data Lakehouse analyses
• protect-gold (dataset) — PROTECT Gold is a curated data collection of isolate, assay, growth-kinetic, patient-metagenomic and pairwise-interaction tables used in cystic fibrosis formulation-design analyses.
• protein-data-bank (dataset) — The Protein Data Bank (PDB), the collection of experimental macromolecular structures available in the KBase Data Lakehouse and used by PaperBLAST, with its query pitfalls.
• proteomics (method) — Protein-expression measurement used to interpret essentiality and respiratory-chain wiring
• protocatechuate (compound) — Aromatic intermediate cleaved during ADP1 quinate catabolism
• pseudomonadota (organism) — Bacterial phylum with high xoxF and PHB pathway prevalence
• pseudomonas-aeruginosa (organism) — Cystic-fibrosis pathogen and intensively studied Pseudomonas model.
• pseudomonas e avellanae (organism) — Plant-associated species with significant subclade structure
• pseudomonas e (organism) — GTDB Pseudomonas_E clade retaining broad carbon-use pathways
• pseudomonas-fluorescens (organism) — Pseudomonas fluorescens utilization phenotypes and carbon-ecology context
• pseudomonas-fw300-n2e3 (organism) — ENIGMA groundwater Pseudomonas isolate linked across the KBase Data Lakehouse fitness and metabolite resources
• pseudomonas gw456 l13 (organism) — ENIGMA groundwater isolate with direct Fitness Browser overlap
• pseudomonas-putida (organism) — Pseudomonas putida evidence spans co-fitness, metabolism, and ecological carbon use
• pseudomonas-stutzeri-rch2 (organism) — Pseudomonas stutzeri RCH2 strain and its fitness–pangenome outlier profile
• pseudomonas-syringae-b728a (organism) — Pseudomonas syringae B728a in co-fitness and pangenome analyses
• pseudomonas (organism) — Pseudomonas carbon-pathway ecology and lifestyle test organism
• pubchem (dataset) — Chemical-identity database used to resolve all 83 census compounds
• quinate-degradation-pathway (gene_or_pathway) — Aromatic pathway converting quinate and protocatechuate to TCA-cycle intermediates
• quinate (compound) — Quinate is an aromatic carbon source with distinctive Complex I dependence in ADP1.
• ralstonia (organism) — Ralstonia is a bacterial genus, including plant pathogens, that appears in BERIL work as a conservation–fitness gradient example, as an organism excluded from co-fitness analysis, and as a member of an acid-associated co-occurrence cluster.
• random forest (method) — Random Forest method for predicting Pseudomonas isolation environments
• rast (method) — Automated genome-annotation system used to build draft metabolic models
• rattus norvegicus (organism) — Rat organism included among PaperBLAST’s most-covered organisms
• reeb76 (organism) — Uncharacterised REE-AMD-associated bacterial clade in a 37-MAG set
• restriction modification type i (gene_or_pathway) — Type I restriction-modification defense system against phages
• restriction modification type ii (gene_or_pathway) — Type II restriction-modification defense system and phage-resistance pathway
• retron (gene_or_pathway) — Anti-phage defense-system candidates detected through reverse-transcriptase markers
• rhamnose (compound) — Rhamnose, a plant-derived sugar that appears in this corpus both as a genomic pathway marker for Pseudomonas environment classification and as a candidate selective prebiotic, with the caveat that its selectivity is predicted from pathway completeness rather than measured growth.
• rhizobium (organism) — Rhizobium, a dominant genus among plant root-associated genomes
• rhodanobacter (organism) — ENIGMA genus associated with denitrification and environmental partitioning
• rothia dentocariosa (organism) — Lung-adapted commensal prioritized for a two-species PA formulation.
• ruminococcus e (organism) — Ruminococcus E sp., a species-level metabolic ecotype-analysis organism
• salicylic acid (compound) — Salicylic acid, an ENIGMA-isolate-callable enrichment compound
• salmonella-enterica (organism) — Host-associated species with extensive accessory AMR and metabolic ecotype structure
• sankoff parsimony (method) — Parsimony method used to infer ancestral states and rank-attributed gains
• seed (dataset) — SEED is a functional annotation and pathway-membership resource.
• selenium (compound) — Selenium, a metal assessed for microbial fitness and stress specificity.
• serine (compound) — Amino acid with a predicted biosynthesis gap in D. vulgaris
• shap (method) — SHAP explains feature contributions in predictive models.
• shewanella-oneidensis (organism) — Shewanella oneidensis MR1, a model organism for fitness and pathway analysis.
• sideroxydans (organism) — Sideroxydans, an iron-oxidizing genus detected in SSO groundwater
• silva (dataset) — SILVA is a ribosomal RNA reference sequence database that BERIL amplicon projects used for 16S rRNA taxonomy assignment.
• sinorhizobium-meliloti (organism) — Rhizobial model organism used in fitness, pathway, and pangenome analyses.
• snipe-defense-system (gene_or_pathway) — Mobile SNIPE phage-defense system with PF13250 and PF13455 domains
• sodium chloride (compound) — Sodium chloride used as a stress comparator in metal-fitness analysis
• sorbitol (compound) — Sorbitol, a sugar alcohol that appears in this corpus as a predicted carbon-utilization pathway — frequently gap-flagged by pathway prediction across genomes and reduced in lung-adapted Pseudomonas aeruginosa genomes.
• spark sql (method) — Spark SQL is KBase Data Lakehouse’s preferred interface for large and complex queries.
• spearman correlation (method) — Rank-based method used to test metal–gene associations
• sphingolipid biosynthesis (gene_or_pathway) — Caulobacter pathway substituting sphingolipids for lipid A
• sphingomonas (organism) — Environmental bacterial genus associated with Oak Ridge and plant-associated ecology
• spirochaeta (organism) — Spirochaeta, a genus associated with inferred fermentation at SSO
• sso (dataset) — Groundwater and field-occurrence dataset used in ENIGMA subsurface ecology studies.
• sspb (gene_or_pathway) — SspB-associated buffering of Caulobacter respiratory genes
• staphylococcus-aureus (organism) — Organism with predominantly accessory AMR and clinical-associated genomic variation
• staphylococcus simulans (organism) — Organism represented by a gene-content ecotype analysis
• streptococcus-pneumoniae (organism) — Clinical-dominant pathogen with a highly accessory AMR repertoire
• streptococcus pseudopneumoniae (organism) — Organism analyzed for within-species gene-content ecotype differentiation
• streptococcus salivarius (organism) — Commensal candidate with strong inhibition and conserved metabolic pathways
• stutzerimonas (organism) — Bacterial lineage represented by Stutzerimonas stutzeri in metabolic ecotype analysis
• succinate (compound) — Succinate is a non-aromatic, high-NADH-flux comparison substrate.
• swiss-prot (dataset) — Reviewed protein-sequence dataset used for homology and integrated annotation evidence.
• synechococcus-elongatus (organism) — Synechococcus elongatus (SynE) is a cyanobacterium in the BERIL fitness corpus that is notably sensitive to metals and is the outlier in NaCl dose-response experiments that inflates shared-stress overlap statistics.
• terephthalic acid (compound) — A necromass-sourced aromatic compound with ENIGMA-isolate utilization predictions.
• terl (gene_or_pathway) — TerL terminase marker used to define prophage lineages
• thiobacillus (organism) — Thiobacillus, a sulfur-oxidizing genus detected in SSO sediments
• threonine (compound) — Amino acid whose biosynthetic capacity depends partly on accessory genes
• tigrfam (dataset) — TIGRFam annotation dataset used for fitness-module predictions
• tnseq (method) — Transposon sequencing for gene essentiality and condition-specific fitness
• tol pal system (gene_or_pathway) — Envelope system implicated in phospholipid transport after lipid A loss
• trehalose (compound) — Trehalose, a produced metabolite with limited species-level utilization evidence
• tryptophan-biosynthesis (gene_or_pathway) — Tryptophan biosynthesis pathway with AMR and FW300-N2E3 fitness evidence
• tryptophan (compound) — Aromatic amino acid linked to microbial metabolism and ipdC distribution
• tungsten (compound) — Essential metal associated with conserved and metal-specific fitness effects.
• two component system histidine kinases (gene_or_pathway) — Two-component histidine kinases that mediate bacterial signal transduction
• type iii secretion system (gene_or_pathway) — Refined T3SS markers linked to plant association, but sensitive to analytical scale.
• type-iv-secretion-system (gene_or_pathway) — Type IV secretion system markers and machinery involved in microbial transfer.
• tyrosine (compound) — Tyrosine, an amino acid whose community biosynthesis completeness in NMDC metagenomes was an outlier both in Black Queen Hypothesis tests and in ecosystem-type differentiation.
• ucp030820 (gene_or_pathway) — Metal-specific candidate family UCP030820 (OG01015)
• umap (method) — UMAP is a nonlinear method for visualizing structure in genome embeddings.
• uniprot (dataset) — Protein sequence dataset used for cross-dataset identification and annotation.
• uranium (compound) — Uranium’s ecological associations and metal-specific fitness determinants
• urea (compound) — Nitrogenous compound used as a demanding ADP1 growth condition
• urease complex (gene_or_pathway) — Urease pathway complex selected by urea-dependent growth phenotypes
• urobilin (compound) — Urobilin, a metabolite decreased in Crohn’s disease samples
• valine (compound) — A branched-chain amino acid with cross-database pathway evidence.
• web-of-microbes (dataset) — Exometabolomics database linking microbial compounds to organism observations
• wood-ljungdahl-pathway (gene_or_pathway) — The Wood–Ljungdahl pathway as a genomic marker in this corpus, whose apparent enrichment in deep clay-confined subsurface isolates turns out to track the Bacillota_B lineage rather than the habitat.
• xanthine (compound) — Xanthine, an enrichment compound misclassified as carbon-catabolic
• xanthomonas campestris (organism) — Plant-associated bacterium with a Brassica-linked genomic subclade
• xanthomonas vasicola (organism) — Plant-associated bacterium with strong maize-linked subclade segregation
• xgboost (method) — XGBoost method for predicting genome-based metal tolerance
• xoxf (gene_or_pathway) — REE-dependent methanol dehydrogenase marker
• xoxj (gene_or_pathway) — xoxJ is a marker for lanthanide-dependent methanol oxidation.
• xylitol (compound) — Proposed selective prebiotic sugar alcohol for commensal support
• xylose (compound) — Xylose is a proposed selective prebiotic substrate for commensals over Pseudomonas aeruginosa.
• yebc (gene_or_pathway) — YebC is a candidate metal-specific fitness determinant.
• zinc (compound) — Zinc, a metal linked to shared stress, cross-resistance, and environmental gene shifts.