Recurring ideas. Each page gathers evidence from every project in the corpus that speaks to it.
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Concepts
AI-generated wiki from AI-conducted research reports. Partially reviewed by scientists. See About This Wiki.
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126 items under this folder.
Pangenome Integration Across Identifier SystemsHow 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.Condition-Specific Mutant FitnessConcept page synthesizing how gene fitness effects, pathway dependence and conservation patterns change across carbon-source, nutrient, metal, stress and environmental conditions.Environmental structuring of the bacterial resistomeCross-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.Gene Essentiality Across Conditions and PredictorsCross-project synthesis of how bacterial gene essentiality is defined, measured, and predicted across conditions, assays, conservation classes, and annotation status.Multi-Omics IntegrationCross-project synthesis of how BERIL projects combine genomic, fitness, model, proteomic, metabolomic and ecological modalities, and what their concordances, method limits and contradictions support.Metabolic Model Gapfilling and Prediction ReliabilityHow 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.Environmental Context and Functional Gene-Content DifferentiationCross-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.Cofitness Network Architecture, Organism Specificity, and Shared DispensabilityHow 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.Geographic and environmental structure in microbial genomic patternsCross-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.Schema-Level Bridges and Validated Cross-Tenant Data IntegrationHow 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.Phylogenetic Confounding of Pangenome AssociationsHow 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.Metal cross-resistance across bacterial fitness landscapesCross-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.Ontology and Category-Schema Dependence of Biological ConclusionsHow ontologies, category schemas, membership thresholds and identifier vocabularies shape the biological conclusions drawn across BERIL projects.Phylogenetic acquisition depth and ecological distribution of gene functionsHow 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.Genomic under-representation limits inference about microbial functional potentialHow uneven genome sampling, reference-database coverage and annotation depth limit inference about microbial functional potential across BERIL projects.Taxonomic Resolution Controls Detectable Functional AssociationsHow 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.Validating Functional Markers Before Ecological InferenceWhy gene, domain and annotation markers must be validated for biological identity, specificity, source agreement and scale before their presence is read as ecological evidence.Cultivation and collection bias constrain ecological genomic inferenceHow 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.Sampling Depth and Downsampling EffectsHow genome sampling depth, downsampling, minimum-genome filters, rarefaction, prevalence filtering and missingness change comparative-genomic and ecological association estimates across BERIL projects.Evidence Triangulation Improves Functional Annotation Beyond Any Single SignalCombining 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.Two-Speed Bacterial Genomes Separate Conserved Metabolism from Accessory InnovationCross-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.Pangenome Core Boundaries and Clade-Size BiasHow 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.Evidence-weighted experimental prioritization of unknown bacterial genesHow 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.Negative homology-search results require sensitivity validationWhy 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.Cluster assumptions and weak separation limit inference about bacterial gene-content ecotypesWhy 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.Confirmatory Nulls and Exploratory Signals in Ecological Association TestingHow 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.Provenance, scale, and currency must be exposed during resource discoveryConcept 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.Unequal evidence callability can make ecological contrasts untestableWhy 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.Study and batch confounding can reverse environmental generalizationHow 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.Testing whether laboratory fitness phenotypes predict environmental gene distributionsCross-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.Decoupling between pangenome conservation and fitness costHow 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.Coverage and Study Bias in Microbial Phenotype DatabasesHow 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.Community Metabolic Interdependence and Black Queen PredictionsCross-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.Horizontal Gene Transfer as a Driver of Bacterial Gene NoveltyCross-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.Defense-system syndromes and prophage-associated anti-phage arms racesCross-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.Pathway-completeness predictions gain support from matched growth phenotypesWhen 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.Perturbation-Collection Coverage BiasCross-project synthesis of how perturbation collections and fitness panels over- or under-represent genes and organisms, and how that coverage bias constrains downstream inference.Taxonomic nomenclature and identifier reconciliation across databasesConcept 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.Uneven Experimental Condition Coverage Biases Fitness-Based Gene PrioritizationHow uneven experimental condition coverage across organisms, condition classes and experiment counts biases fitness-based gene prioritization and threshold-based fitness calls.Adversarial Validation of Computational Biology ClaimsWhy computational-biology claims in this corpus need an adversarial review layer, and the citation, statistical, leakage, provenance and code-level failure classes it catches.Cross-Cohort Portability of Microbiome Classifiers and MetabolomicsHow 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.Environmental occurrence does not establish compound catabolismWhy 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.Metabolic evidence is condition-dependent across assays and databasesHow exometabolomics, mutant fitness, phenotype databases, pathway predictions and metabolic models measure different metabolic capabilities under different conditions, limiting direct cross-assay comparison.Fitness-Module Discovery Depends on Thresholds and Decomposition ConstraintsHow ICA-based fitness-module discovery depends on membership thresholds, annotation settings, experiment depth, component caps, orthology scope, activity normalization and condition space.Metabolic and Sampling Determinants of Pangenome OpennessCross-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.Sequence-space depth predicts functional annotation richnessHow sequence-space (MSA) depth, reference-database coverage and literature attention together shape how richly bacterial gene clusters are functionally annotated.Subsurface Bacillota_B specialization and genome expansionCross-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.Selection-on-outcome leakage in microbiome and genomic inferenceHow 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.Transposon Callability Bias in Essentiality InferenceTransposon 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.Fitness costs and conditional benefits of antimicrobial-resistance genesEvidence 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.Separating Shared Stress Responses from Stressor-Specific Fitness RequirementsHow 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.Classifier database compatibility limits cross-study taxonomic quantificationHow differences in taxonomic classifiers, reference databases, feature namespaces and taxon-name keys limit cross-study comparison of taxonomic abundances and the conclusions drawn from them.Condition-space dimensionality separates general sensitivity from substrate-specific requirementsHow 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.Designing Protective Microbial Consortia Requires Joint Optimization of Inhibition, Coverage, Safety, and EngraftabilityMulti-objective design of protective microbial consortia against Pseudomonas aeruginosa, where inhibition, niche coverage, safety, member compatibility and engraftability trade off against one another.Laboratory Fitness as an Imperfect Proxy for Natural SelectionSynthesis 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.Limits of Composite Resistance Scores for Mechanistic InferenceWhy composite and repertoire-based metal-resistance scores support prioritization and ecological association but cannot by themselves identify metal-specific tolerance mechanisms.Ortholog-transferred fitness phenotypes are constrained by organism-specific network architectureHow 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.Pathway-Level Evidence Does Not Map Directly to Reaction-Level Gene AssignmentsWhy 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.Gene co-occurrence can reveal ecological guilds without proving physical linkageHow 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.Hydrogeological depth and flow structure subsurface microbial communitiesHow 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.Polyhydroxybutyrate pathway ecology, genome size, and horizontal transferCross-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.Research-Attention Inequality and Functional DarknessSynthesis 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.Scale-Dependent Mobile-Element Associations and Mobilization InferenceHow 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.Conserved Core Genes Can Remain Structurally and Functionally UncharacterizedSynthesis of evidence that broadly conserved core, essential, and pan-bacterial genes can still lack deep sequence representation, structural characterization, or functional annotation.Translating Phage Host-Range Evidence into Patient-Specific TherapyHow 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.Biosynthetic Prototrophy, Auxotrophy, and Nutrient DependenceHow pathway completeness, fitness, and nutrient dependence relategut-microbiome-ecotypes-as-patient-strataA 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.Multi-gene fitness modules predict pangenome co-inheritance better than pairwise linksCoordinated 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.Species-level utilization claims require sample-size-aware strain consensusWhy 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.Agency and Tenant Ownership Shape Biological Data CoverageHow 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.Chromosomal and Integrative Routes of Horizontal Gene TransferHow 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.Condition-Dependent Gene Fitness Trade-OffsSynthesis 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.Conserved Within-Species Functions Can Coexist with Between-Species Functional DivergenceHow 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.Evolutionary loss of costly, non-conserved genesSynthesis 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.Genome-Wide Versus Locus-Specific Ecological AdaptationWhether bacterial ecological adaptation registers as genome-wide gene-content similarity or is concentrated at particular loci, pathways, functional categories, or within-species subclades.null-results-under-limited-statistical-resolutionHow 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.Why transposon fitness and complete-knockout essentiality disagreeWhy 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.Fitness-Matched Null Models for Functional EnrichmentWhy 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.Utilization capacities are phylogenetically concentrated and specialist-dominatedCross-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.Adaptive Functions Differentiate More Strongly Than Housekeeping Functions Among Gene-Content EcotypesCross-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.Calibrating Conservation Metrics for Unknown Bacterial GenesHow ortholog-breadth, species-count, pangenome-reference and core/accessory definitions change conservation-based interpretation and prioritization of unknown bacterial genes.Cultured genomes do not necessarily capture extreme biosynthetic self-sufficiencySynthesis 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.Physically Dispersed Genes Can Form Tightly Coupled Metabolic SystemsCross-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 Capability Is More Predictable Than Continuous Growth KineticsCross-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.Respiratory-chain dependence tracks reducing-equivalent load rather than substrate identityRespiratory-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.Composite Functional Categories Can Represent Multifunctional GenesComposite 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.Distributed Queries Can Return Plausible Empty Results Instead of ErrorsHow 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.ecological-cost-of-microbiome-target-depletionWhy 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.Most Plant-Associated Species Carry Both Beneficial and Pathogenic Genomic SignaturesGenome-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.Resistance-Island Co-inheritance and Mechanistic LinkageSynthesis 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.Spatial Sampling Effort and Geographic Hotspot ConfoundingHow 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.The Core-Genome Burden ParadoxGenes 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.EC-Less Reactions Are a Distinct Annotation-Resolution BarrierGapfilled 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.Gapfilled Models Can Make Their Own Validation CircularHow 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.Outer-membrane lipid homeostasis after lipid A lossHow 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.Pooled sequencing runs complicate the statistical unit and metadata assignmentHow 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.compositional-robustness-of-differential-abundance-callsHow 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.Long-Running Analyses Outlive the Interactive Sessions That Launch ThemInteractive notebook kernels are an unreliable container for long-running analyses, so long jobs need explicit timeouts, detached script execution and on-disk checkpointing.Habitat Enrichment of Lanthanide Methylotrophy Does Not Track Rare-Earth-Rich EnvironmentsHow 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.metabolite-class-signatures-of-gut-inflammationHow 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.Single-Driver Result Collection as a Recurring Failure Point in Documented Genome-Scale AnalysesIn 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.Biosynthetic Gene Cluster Catalogs Explain Only Some Pathobiont AssociationsWhy 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.Cheap Proxies Do Not Yet Substitute for Metagenomic Community-State AssignmentWhether 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.Ecological memory preserves community differences across changing environmentsEcological 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.Lanthanide-Chelator Machinery Is Far Narrower Than Lanthanide-Dependent Dehydrogenase DistributionBakta-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.Organism-Dark Compounds: Compounds Not Linked to a Degrading Organism in Queried ResourcesCarbon 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.analysis-provenance-and-reproducible-outputsWhat 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.execution-environment-dependent-access-pathsHow 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.Join Strategy and Table Partitioning, Not Query Logic, Set the Cost of Billion-Row Genomic JoinsHow 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.lanthanide-dependent-methanol-dehydrogenase-predominanceAcross 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.species-cooccurrence-modules-as-intervention-unitsWhether 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.Credential Expiry and Tenant Membership Are Analysis-Session Failure ModesTenant-group membership and authentication-token expiry are recurring preconditions and failure modes for data access in analysis sessions on the KBase Data Lakehouse.Eukaryotic and Plastid DNA Admixture in Prokaryotic MetagenomesHow much eukaryotic and plastid DNA appears in prokaryote-targeted metagenomes, where it comes from by habitat, and what that means for interpreting metagenomic profiles.habitat-structured-community-metabolic-potentialCommunity-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.long-term-soil-warming-microbial-responseHow 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.Numeric and Array Types Do Not Survive Transfers Between Query Engine and Analysis FrameHow 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.Resampling and Embedding Analyses Are Budgeted, Not ExactHow 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.Row-Wise Iteration Versus Vectorized Merges in Large Genomic DataFrame OperationsRow-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.soil-horizon-response-heterogeneityIn 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.Active-Learning Selection of Next Experiments from Model Error and UncertaintyActive 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.Contaminant Gradients Select Subsurface Community CompositionContaminant concentration, especially uranium together with low pH and metals, as an axis that selects subsurface microbial community composition, distinct from hydrogeological zonation.Decomposing Species-Level Disease Association into Carriage, Within-Carrier Function, and Strain ContentWhy 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.Feature Attribution Is Not Gene-Level Evidence When Genomic Features Are CorrelatedWhy 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.foreign-dump-ingestion-fidelityHow 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.Laboratory Reference Strains May Not Represent the Populations They Are Used to ModelHow 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.Iron and Heme Acquisition as a Convergent Pathobiont SignatureEvidence that iron and heme acquisition is the dominant Crohn's-disease-enriched functional theme in gut metagenomes and a genomically concentrated Escherichia coli specialization, together with the comparator, interaction-test, mouse and clinical limits on reading it as a uniform iron effect.