BERIL Knowledge Wiki

BERIL Knowledge Wiki

AI-generated wiki from AI-conducted research reports. Partially reviewed by scientists. See About This Wiki.

Most of these projects analysed data already in the KBase Data Lakehouse; a few brought their own. See About This Wiki for what that means for citing anything here.

This wiki compiles the reports of the BERIL Research Observatory. In this observatory, AI agents conduct microbial-biology research over the KBase Data Lakehouse. Each project report records one investigation. Two cross-project digests collect the discoveries and the pitfalls that recur across projects.

Start with the topics. Each topic hub introduces a research question and links to the concept pages that argue it across projects. Concept pages synthesize evidence from several reports and cite each claim to its source project. Entity pages describe specific organisms, genes, compounds, methods and datasets. Summary pages condense a single report and list the concepts it feeds.

The corpus

73
Project reports the primary evidence
2
Cross-project digests discoveries and pitfalls
126
Concepts synthesised across them
185
Entities organisms, genes, datasets, methods
152
Recorded conflicts with the evidence on both sides
15
Topics gathering the rest

Every figure counts pages on this site, not a claim about the field.

Start here

Ways in, depending on what you came for.

The map

Each of the 15 topics sits at the middle of the concepts that belong to it, 126 in all, sized by how linked each one is. Click any point to open the page.

Ecotypes and Environmental Gene-Content Differentiation and Metabolic Models and Pathway-Level Evidence: 1 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Lanthanide-Dependent Methylotrophy: 1 wikilinks between their conceptsLaboratory Fitness Versus Natural Selection and Gene Conservation and Subsurface and Soil Community Ecology: 1 wikilinks between their conceptsLanthanide-Dependent Methylotrophy and Pangenome Structure and Genome Evolution: 1 wikilinks between their conceptsLanthanide-Dependent Methylotrophy and Resistance, Defense Systems, and Mobile Elements: 1 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Lanthanide-Dependent Methylotrophy: 1 wikilinks between their conceptsMetabolic Models and Pathway-Level Evidence and Translational Microbiome and Phage Therapeutics: 1 wikilinks between their conceptsLanthanide-Dependent Methylotrophy and Metabolic Traits, Auxotrophy, and Community Dependence: 1 wikilinks between their conceptsMetabolic Models and Pathway-Level Evidence and Pangenome Structure and Genome Evolution: 1 wikilinks between their conceptsGene Fitness Landscapes and Cofitness Modules and Subsurface and Soil Community Ecology: 1 wikilinks between their conceptsMetabolic Traits, Auxotrophy, and Community Dependence and Subsurface and Soil Community Ecology: 1 wikilinks between their conceptsMetabolic Models and Pathway-Level Evidence and Subsurface and Soil Community Ecology: 1 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Laboratory Fitness Versus Natural Selection and Gene Conservation: 2 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Gene Essentiality and Perturbation-Assay Validity: 2 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Gene Fitness Landscapes and Cofitness Modules: 2 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Lanthanide-Dependent Methylotrophy: 2 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Subsurface and Soil Community Ecology: 2 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Laboratory Fitness Versus Natural Selection and Gene Conservation: 2 wikilinks between their conceptsMetabolic Traits, Auxotrophy, and Community Dependence and Resistance, Defense Systems, and Mobile Elements: 2 wikilinks between their conceptsGene Fitness Landscapes and Cofitness Modules and Sampling Coverage and Statistical Confounding: 2 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Subsurface and Soil Community Ecology: 2 wikilinks between their conceptsLanthanide-Dependent Methylotrophy and Translational Microbiome and Phage Therapeutics: 2 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Subsurface and Soil Community Ecology: 3 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Lanthanide-Dependent Methylotrophy: 3 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Pangenome Structure and Genome Evolution: 3 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Translational Microbiome and Phage Therapeutics: 3 wikilinks between their conceptsLaboratory Fitness Versus Natural Selection and Gene Conservation and Metabolic Traits, Auxotrophy, and Community Dependence: 3 wikilinks between their conceptsMetabolic Models and Pathway-Level Evidence and Sampling Coverage and Statistical Confounding: 3 wikilinks between their conceptsMetabolic Models and Pathway-Level Evidence and Resistance, Defense Systems, and Mobile Elements: 3 wikilinks between their conceptsResistance, Defense Systems, and Mobile Elements and Translational Microbiome and Phage Therapeutics: 3 wikilinks between their conceptsGene Fitness Landscapes and Cofitness Modules and Translational Microbiome and Phage Therapeutics: 3 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Resistance, Defense Systems, and Mobile Elements: 4 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Gene Essentiality and Perturbation-Assay Validity: 4 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Laboratory Fitness Versus Natural Selection and Gene Conservation: 4 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Resistance, Defense Systems, and Mobile Elements: 4 wikilinks between their conceptsLaboratory Fitness Versus Natural Selection and Gene Conservation and Sampling Coverage and Statistical Confounding: 4 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Gene Fitness Landscapes and Cofitness Modules: 5 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Metabolic Traits, Auxotrophy, and Community Dependence: 5 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Distributed Computation and Analysis Execution: 5 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Functional Dark Matter and Annotation Resolution: 5 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Resistance, Defense Systems, and Mobile Elements: 5 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Resistance, Defense Systems, and Mobile Elements: 5 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Translational Microbiome and Phage Therapeutics: 5 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Metabolic Models and Pathway-Level Evidence: 5 wikilinks between their conceptsGene Fitness Landscapes and Cofitness Modules and Metabolic Models and Pathway-Level Evidence: 5 wikilinks between their conceptsLanthanide-Dependent Methylotrophy and Sampling Coverage and Statistical Confounding: 5 wikilinks between their conceptsPangenome Structure and Genome Evolution and Subsurface and Soil Community Ecology: 5 wikilinks between their conceptsPangenome Structure and Genome Evolution and Translational Microbiome and Phage Therapeutics: 5 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Metabolic Traits, Auxotrophy, and Community Dependence: 6 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Metabolic Traits, Auxotrophy, and Community Dependence: 6 wikilinks between their conceptsMetabolic Traits, Auxotrophy, and Community Dependence and Sampling Coverage and Statistical Confounding: 6 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Ecotypes and Environmental Gene-Content Differentiation: 7 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Metabolic Models and Pathway-Level Evidence: 7 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Translational Microbiome and Phage Therapeutics: 7 wikilinks between their conceptsLaboratory Fitness Versus Natural Selection and Gene Conservation and Resistance, Defense Systems, and Mobile Elements: 7 wikilinks between their conceptsPangenome Structure and Genome Evolution and Sampling Coverage and Statistical Confounding: 7 wikilinks between their conceptsSampling Coverage and Statistical Confounding and Subsurface and Soil Community Ecology: 7 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Pangenome Structure and Genome Evolution: 8 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Sampling Coverage and Statistical Confounding: 8 wikilinks between their conceptsGene Fitness Landscapes and Cofitness Modules and Metabolic Traits, Auxotrophy, and Community Dependence: 8 wikilinks between their conceptsLaboratory Fitness Versus Natural Selection and Gene Conservation and Pangenome Structure and Genome Evolution: 8 wikilinks between their conceptsMetabolic Traits, Auxotrophy, and Community Dependence and Translational Microbiome and Phage Therapeutics: 8 wikilinks between their conceptsMetabolic Traits, Auxotrophy, and Community Dependence and Pangenome Structure and Genome Evolution: 8 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Metabolic Traits, Auxotrophy, and Community Dependence: 9 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Laboratory Fitness Versus Natural Selection and Gene Conservation: 9 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Translational Microbiome and Phage Therapeutics: 10 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Gene Fitness Landscapes and Cofitness Modules: 10 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Gene Essentiality and Perturbation-Assay Validity: 10 wikilinks between their conceptsResistance, Defense Systems, and Mobile Elements and Sampling Coverage and Statistical Confounding: 10 wikilinks between their conceptsSampling Coverage and Statistical Confounding and Translational Microbiome and Phage Therapeutics: 10 wikilinks between their conceptsMetabolic Models and Pathway-Level Evidence and Metabolic Traits, Auxotrophy, and Community Dependence: 11 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Functional Dark Matter and Annotation Resolution: 13 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Metabolic Models and Pathway-Level Evidence: 13 wikilinks between their conceptsData Infrastructure, Provenance, and Research Practice and Sampling Coverage and Statistical Confounding: 14 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Pangenome Structure and Genome Evolution: 14 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Pangenome Structure and Genome Evolution: 14 wikilinks between their conceptsFunctional Dark Matter and Annotation Resolution and Sampling Coverage and Statistical Confounding: 14 wikilinks between their conceptsGene Fitness Landscapes and Cofitness Modules and Pangenome Structure and Genome Evolution: 14 wikilinks between their conceptsGene Fitness Landscapes and Cofitness Modules and Laboratory Fitness Versus Natural Selection and Gene Conservation: 14 wikilinks between their conceptsPangenome Structure and Genome Evolution and Resistance, Defense Systems, and Mobile Elements: 14 wikilinks between their conceptsEcotypes and Environmental Gene-Content Differentiation and Sampling Coverage and Statistical Confounding: 16 wikilinks between their conceptsGene Essentiality and Perturbation-Assay Validity and Gene Fitness Landscapes and Cofitness Modules: 16 wikilinks between their conceptsGene Fitness Landscapes and Cofitness Modules and Resistance, Defense Systems, and Mobile Elements: 16 wikilinks between their conceptsValidating Functional Markers Before Ecological Inference also belongs to Lanthanide-Dependent MethylotrophyCultivation and collection bias constrain ecological genomic inference also belongs to Sampling Coverage and Statistical ConfoundingAdversarial Validation of Computational Biology ClaimsAdversarial Validation of Computational Biolo…Agency and Tenant Ownership Shape Biological Data CoverageAgency and Tenant Ownership Shape Biological…analysis-provenance-and-reproducible-outputsanalysis-provenance-and-reproducible-outputsforeign-dump-ingestion-fidelityforeign-dump-ingestion-fidelityMulti-Omics IntegrationMulti-Omics IntegrationProvenance, scale, and currency must be exposed during resource discoveryProvenance, scale, and currency must be expos…Schema-Level Bridges and Validated Cross-Tenant Data IntegrationSchema-Level Bridges and Validated Cross-Tena…Taxonomic nomenclature and identifier reconciliation across databasesTaxonomic nomenclature and identifier reconci…Data Infrastructure, Provenance, and Research PracticeData Infrastructure,Provenance, and Research Prac…Credential Expiry and Tenant Membership Are Analysis-Session Failure ModesCredential Expiry and Tenant Membership Are A…Distributed Queries Can Return Plausible Empty Results Instead of ErrorsDistributed Queries Can Return Plausible Empt…execution-environment-dependent-access-pathsexecution-environment-dependent-access-pathsJoin Strategy and Table Partitioning, Not Query Logic, Set the Cost of Billion-Row Genomic JoinsJoin Strategy and Table Partitioning, Not Que…Long-Running Analyses Outlive the Interactive Sessions That Launch ThemLong-Running Analyses Outlive the Interactive…Numeric and Array Types Do Not Survive Transfers Between Query Engine and Analysis FrameNumeric and Array Types Do Not Survive Transf…Resampling and Embedding Analyses Are Budgeted, Not ExactResampling and Embedding Analyses Are Budgete…Row-Wise Iteration Versus Vectorized Merges in Large Genomic DataFrame OperationsRow-Wise Iteration Versus Vectorized Merges i…Single-Driver Result Collection as a Recurring Failure Point in Documented Genome-Scale AnalysesSingle-Driver Result Collection as a Recurrin…Distributed Computation and Analysis ExecutionDistributed Computationand Analysis ExecutionAdaptive Functions Differentiate More Strongly Than Housekeeping Functions Among Gene-Content EcotypesAdaptive Functions Differentiate More Strongl…Cluster assumptions and weak separation limit inference about bacterial gene-content ecotypesCluster assumptions and weak separation limit…Environmental Context and Functional Gene-Content DifferentiationEnvironmental Context and Functional Gene-Con…Gene co-occurrence can reveal ecological guilds without proving physical linkageGene co-occurrence can reveal ecological guil…Genome-Wide Versus Locus-Specific Ecological AdaptationGenome-Wide Versus Locus-Specific Ecological…Geographic and environmental structure in microbial genomic patternsGeographic and environmental structure in mic…Most Plant-Associated Species Carry Both Beneficial and Pathogenic Genomic SignaturesMost Plant-Associated Species Carry Both Bene…Ecotypes and Environmental Gene-Content DifferentiationEcotypes andEnvironmental Gene-Content Di…Composite Functional Categories Can Represent Multifunctional GenesComposite Functional Categories Can Represent…Conserved Core Genes Can Remain Structurally and Functionally UncharacterizedConserved Core Genes Can Remain Structurally…Evidence Triangulation Improves Functional Annotation Beyond Any Single SignalEvidence Triangulation Improves Functional An…Evidence-weighted experimental prioritization of unknown bacterial genesEvidence-weighted experimental prioritization…Negative homology-search results require sensitivity validationNegative homology-search results require sens…Ontology and Category-Schema Dependence of Biological ConclusionsOntology and Category-Schema Dependence of Bi…Research-Attention Inequality and Functional DarknessResearch-Attention Inequality and Functional…Sequence-space depth predicts functional annotation richnessSequence-space depth predicts functional anno…Validating Functional Markers Before Ecological InferenceValidating Functional Markers Before Ecologic…Functional Dark Matter and Annotation ResolutionFunctional Dark Matterand Annotation ResolutionGene Essentiality Across Conditions and PredictorsGene Essentiality Across Conditions and Predi…Perturbation-Collection Coverage BiasPerturbation-Collection Coverage BiasTransposon Callability Bias in Essentiality InferenceTransposon Callability Bias in Essentiality I…Unequal evidence callability can make ecological contrasts untestableUnequal evidence callability can make ecologi…Uneven Experimental Condition Coverage Biases Fitness-Based Gene PrioritizationUneven Experimental Condition Coverage Biases…Why transposon fitness and complete-knockout essentiality disagreeWhy transposon fitness and complete-knockout…Gene Essentiality and Perturbation-Assay ValidityGene Essentiality andPerturbation-Assay ValidityCofitness Network Architecture, Organism Specificity, and Shared DispensabilityCofitness Network Architecture, Organism Spec…Condition-Dependent Gene Fitness Trade-OffsCondition-Dependent Gene Fitness Trade-OffsCondition-space dimensionality separates general sensitivity from substrate-specific requirementsCondition-space dimensionality separates gene…Condition-Specific Mutant FitnessCondition-Specific Mutant FitnessFitness-Matched Null Models for Functional EnrichmentFitness-Matched Null Models for Functional En…Fitness-Module Discovery Depends on Thresholds and Decomposition ConstraintsFitness-Module Discovery Depends on Threshold…Multi-gene fitness modules predict pangenome co-inheritance better than pairwise linksMulti-gene fitness modules predict pangenome…Ortholog-transferred fitness phenotypes are constrained by organism-specific network architectureOrtholog-transferred fitness phenotypes are c…Outer-membrane lipid homeostasis after lipid A lossOuter-membrane lipid homeostasis after lipid…Physically Dispersed Genes Can Form Tightly Coupled Metabolic SystemsPhysically Dispersed Genes Can Form Tightly C…Separating Shared Stress Responses from Stressor-Specific Fitness RequirementsSeparating Shared Stress Responses from Stres…Gene Fitness Landscapes and Cofitness ModulesGene Fitness Landscapesand Cofitness ModulesCalibrating Conservation Metrics for Unknown Bacterial GenesCalibrating Conservation Metrics for Unknown…Decoupling between pangenome conservation and fitness costDecoupling between pangenome conservation and…Evolutionary loss of costly, non-conserved genesEvolutionary loss of costly, non-conserved ge…Laboratory Fitness as an Imperfect Proxy for Natural SelectionLaboratory Fitness as an Imperfect Proxy for…Testing whether laboratory fitness phenotypes predict environmental gene distributionsTesting whether laboratory fitness phenotypes…The Core-Genome Burden ParadoxThe Core-Genome Burden ParadoxLaboratory Fitness Versus Natural Selection and Gene ConservationLaboratory FitnessVersus Natural Selection and…Cultivation and collection bias constrain ecological genomic inferenceCultivation and collection bias constrain eco…Habitat Enrichment of Lanthanide Methylotrophy Does Not Track Rare-Earth-Rich EnvironmentsHabitat Enrichment of Lanthanide Methylotroph…Lanthanide-Chelator Machinery Is Far Narrower Than Lanthanide-Dependent Dehydrogenase DistributionLanthanide-Chelator Machinery Is Far Narrower…lanthanide-dependent-methanol-dehydrogenase-predominancelanthanide-dependent-methanol-dehydrogenase-p…Lanthanide-Dependent MethylotrophyLanthanide-DependentMethylotrophyEC-Less Reactions Are a Distinct Annotation-Resolution BarrierEC-Less Reactions Are a Distinct Annotation-R…Gapfilled Models Can Make Their Own Validation CircularGapfilled Models Can Make Their Own Validatio…Metabolic evidence is condition-dependent across assays and databasesMetabolic evidence is condition-dependent acr…Metabolic Model Gapfilling and Prediction ReliabilityMetabolic Model Gapfilling and Prediction Rel…Pathway-completeness predictions gain support from matched growth phenotypesPathway-completeness predictions gain support…Pathway-Level Evidence Does Not Map Directly to Reaction-Level Gene AssignmentsPathway-Level Evidence Does Not Map Directly…Metabolic Models and Pathway-Level EvidenceMetabolic Models andPathway-Level EvidenceActive-Learning Selection of Next Experiments from Model Error and UncertaintyActive-Learning Selection of Next Experiments…Biosynthetic Prototrophy, Auxotrophy, and Nutrient DependenceBiosynthetic Prototrophy, Auxotrophy, and Nut…Community Metabolic Interdependence and Black Queen PredictionsCommunity Metabolic Interdependence and Black…Cultured genomes do not necessarily capture extreme biosynthetic self-sufficiencyCultured genomes do not necessarily capture e…Environmental occurrence does not establish compound catabolismEnvironmental occurrence does not establish c…Genomic Capability Is More Predictable Than Continuous Growth KineticsGenomic Capability Is More Predictable Than C…habitat-structured-community-metabolic-potentialhabitat-structured-community-metabolic-potent…Organism-Dark Compounds: Compounds Not Linked to a Degrading Organism in Queried ResourcesOrganism-Dark Compounds: Compounds Not Linked…Polyhydroxybutyrate pathway ecology, genome size, and horizontal transferPolyhydroxybutyrate pathway ecology, genome s…Respiratory-chain dependence tracks reducing-equivalent load rather than substrate identityRespiratory-chain dependence tracks reducing-…Species-level utilization claims require sample-size-aware strain consensusSpecies-level utilization claims require samp…Utilization capacities are phylogenetically concentrated and specialist-dominatedUtilization capacities are phylogenetically c…Metabolic Traits, Auxotrophy, and Community DependenceMetabolic Traits,Auxotrophy, and Community Dep…Chromosomal and Integrative Routes of Horizontal Gene TransferChromosomal and Integrative Routes of Horizon…Conserved Within-Species Functions Can Coexist with Between-Species Functional DivergenceConserved Within-Species Functions Can Coexis…Horizontal Gene Transfer as a Driver of Bacterial Gene NoveltyHorizontal Gene Transfer as a Driver of Bacte…Metabolic and Sampling Determinants of Pangenome OpennessMetabolic and Sampling Determinants of Pangen…Pangenome Core Boundaries and Clade-Size BiasPangenome Core Boundaries and Clade-Size BiasPangenome Integration Across Identifier SystemsPangenome Integration Across Identifier Syste…Phylogenetic acquisition depth and ecological distribution of gene functionsPhylogenetic acquisition depth and ecological…Phylogenetic Confounding of Pangenome AssociationsPhylogenetic Confounding of Pangenome Associa…Two-Speed Bacterial Genomes Separate Conserved Metabolism from Accessory InnovationTwo-Speed Bacterial Genomes Separate Conserve…Pangenome Structure and Genome EvolutionPangenome Structure andGenome EvolutionDefense-system syndromes and prophage-associated anti-phage arms racesDefense-system syndromes and prophage-associa…Environmental structuring of the bacterial resistomeEnvironmental structuring of the bacterial re…Fitness costs and conditional benefits of antimicrobial-resistance genesFitness costs and conditional benefits of ant…Limits of Composite Resistance Scores for Mechanistic InferenceLimits of Composite Resistance Scores for Mec…Metal cross-resistance across bacterial fitness landscapesMetal cross-resistance across bacterial fitne…Resistance-Island Co-inheritance and Mechanistic LinkageResistance-Island Co-inheritance and Mechanis…Scale-Dependent Mobile-Element Associations and Mobilization InferenceScale-Dependent Mobile-Element Associations a…Resistance, Defense Systems, and Mobile ElementsResistance, DefenseSystems, and Mobile ElementsClassifier database compatibility limits cross-study taxonomic quantificationClassifier database compatibility limits cros…Confirmatory Nulls and Exploratory Signals in Ecological Association TestingConfirmatory Nulls and Exploratory Signals in…Coverage and Study Bias in Microbial Phenotype DatabasesCoverage and Study Bias in Microbial Phenotyp…Eukaryotic and Plastid DNA Admixture in Prokaryotic MetagenomesEukaryotic and Plastid DNA Admixture in Proka…Feature Attribution Is Not Gene-Level Evidence When Genomic Features Are CorrelatedFeature Attribution Is Not Gene-Level Evidenc…Genomic under-representation limits inference about microbial functional potentialGenomic under-representation limits inference…null-results-under-limited-statistical-resolutionnull-results-under-limited-statistical-resolu…Pooled sequencing runs complicate the statistical unit and metadata assignmentPooled sequencing runs complicate the statist…Sampling Depth and Downsampling EffectsSampling Depth and Downsampling EffectsSelection-on-outcome leakage in microbiome and genomic inferenceSelection-on-outcome leakage in microbiome an…Spatial Sampling Effort and Geographic Hotspot ConfoundingSpatial Sampling Effort and Geographic Hotspo…Study and batch confounding can reverse environmental generalizationStudy and batch confounding can reverse envir…Taxonomic Resolution Controls Detectable Functional AssociationsTaxonomic Resolution Controls Detectable Func…Sampling Coverage and Statistical ConfoundingSampling Coverage andStatistical ConfoundingContaminant Gradients Select Subsurface Community CompositionContaminant Gradients Select Subsurface Commu…Ecological memory preserves community differences across changing environmentsEcological memory preserves community differe…Hydrogeological depth and flow structure subsurface microbial communitiesHydrogeological depth and flow structure subs…long-term-soil-warming-microbial-responselong-term-soil-warming-microbial-responsesoil-horizon-response-heterogeneitysoil-horizon-response-heterogeneitySubsurface Bacillota_B specialization and genome expansionSubsurface Bacillota_B specialization and gen…Subsurface and Soil Community EcologySubsurface and SoilCommunity EcologyBiosynthetic Gene Cluster Catalogs Explain Only Some Pathobiont AssociationsBiosynthetic Gene Cluster Catalogs Explain On…Cheap Proxies Do Not Yet Substitute for Metagenomic Community-State AssignmentCheap Proxies Do Not Yet Substitute for Metag…compositional-robustness-of-differential-abundance-callscompositional-robustness-of-differential-abun…Cross-Cohort Portability of Microbiome Classifiers and MetabolomicsCross-Cohort Portability of Microbiome Classi…Decomposing Species-Level Disease Association into Carriage, Within-Carrier Function, and Strain ContentDecomposing Species-Level Disease Association…Designing Protective Microbial Consortia Requires Joint Optimization of Inhibition, Coverage, Safety, and EngraftabilityDesigning Protective Microbial Consortia Requ…ecological-cost-of-microbiome-target-depletionecological-cost-of-microbiome-target-depletiongut-microbiome-ecotypes-as-patient-stratagut-microbiome-ecotypes-as-patient-strataIron and Heme Acquisition as a Convergent Pathobiont SignatureIron and Heme Acquisition as a Convergent Pat…Laboratory Reference Strains May Not Represent the Populations They Are Used to ModelLaboratory Reference Strains May Not Represen…metabolite-class-signatures-of-gut-inflammationmetabolite-class-signatures-of-gut-inflammati…species-cooccurrence-modules-as-intervention-unitsspecies-cooccurrence-modules-as-intervention-…Translating Phage Host-Range Evidence into Patient-Specific TherapyTranslating Phage Host-Range Evidence into Pa…Translational Microbiome and Phage TherapeuticsTranslational Microbiomeand Phage Therapeutics
A concept the topic gathers, sized by how linked it isA concept no topic claims, on a dashed tether498 wikilinks cross between topics, summed into one line per pairHover a concept for its own links, a topic for everything leaving it.

Topics

What each hub covers, and how much evidence stands behind it.

TopicWhat it coversConceptsReportsConflictsEntities
Data Infrastructure, Provenance, and Research Practice

Covers how data in the KBase Data Lakehouse is owned, named, joined and ingested. Several projects audit the platform itself.

820125
Distributed Computation and Analysis Execution

Covers where queries run on the Spark SQL cluster and how results reach a single Python driver. It also lists the failures that stop work, some of which raise no error.

9103
Ecotypes and Environmental Gene-Content Differentiation

Asks whether environment shapes which accessory genes bacteria carry. One broad test covers 172 species, and many targeted tests ask where any such signal sits.

717125
Functional Dark Matter and Annotation Resolution

Separates genes that lack functional annotation from genes that lack connected publications. A gene without text-mined papers may still carry curated knowledge.

92096
Gene Essentiality and Perturbation-Assay Validity

Treats direct perturbation and measured growth as the strongest evidence of essentiality, treats conservation, annotation and modeling as predictors, and tests the measurements themselves.

621145
Gene Fitness Landscapes and Cofitness Modules

Groups genes by how disrupting them changes growth across many conditions. Cofitness measures how similar two genes’ fitness profiles are across conditions, and a fitness module is a group of genes with coordinated fitness patterns across experiments.

1122105
Laboratory Fitness Versus Natural Selection and Gene Conservation

Asks whether a gene’s laboratory growth effect explains whether a species keeps or loses it in nature. Several projects link genome-wide mutant fitness data from the Fitness Browser, measured by random barcode transposon sequencing (RB-TnSeq), to conservation across the pangenome, the full set of gene clusters across a species’ genomes.

617127
Lanthanide-Dependent Methylotrophy

Follows the use of rare-earth elements as cofactors for methanol oxidation by the xoxF methanol dehydrogenase. The calcium-dependent mxaF form contrasts with it.

5105
Metabolic Models and Pathway-Level Evidence

Asks how far genome-derived metabolic predictions can be trusted. It covers genome-scale models run with flux balance analysis (FBA), a constraint-based method that predicts feasible metabolic fluxes and growth, and pathway-completeness calls from GapMind.

61297
Metabolic Traits, Auxotrophy, and Community Dependence

Reads pathway gaps in genomes as possible auxotrophies, meaning dependence on an externally supplied nutrient, and asks whether shared metabolites let community members lose costly functions. The corpus pairs GapMind, a predictor of pathway completeness, with measured gene-fitness data.

121585
Pangenome Structure and Genome Evolution

Splits a species’ gene clusters into a core, the conserved component, and auxiliary genes that vary between genomes. Projects set the core threshold in different ways.

926196
Resistance, Defense Systems, and Mobile Elements

Brings together antimicrobial-resistance genes, metal tolerance and anti-phage defense with the mobile genetic elements that can move these functions between genomes.

7201410
Sampling Coverage and Statistical Confounding

Asks when an apparent microbial pattern reflects biology and when it reflects which samples were collected or how the analysis was built.

1421146
Subsurface and Soil Community Ecology

Weighs five candidate drivers of community structure in groundwater, sediments, clay formations and layered soils.

6808
Translational Microbiome and Phage Therapeutics

Asks which organism should be removed or added in which patient, and at what cost to the rest of the community. A Crohn’s disease gut project carries the argument end to end.

13417