Specific named things: organisms, genes and pathways, compounds, methods, and datasets. Entities that only one project cites do not appear here.
Collection
Entities
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- Entities
- 185
- Kinds
- 6 kinds
185 items under this folder.
Organisms
46 pages, most linked first
Escherichia coliEscherichia coli reference strain with fitness, pangenome, and disease-ecology evidencePseudomonas aeruginosaCystic-fibrosis pathogen and intensively studied Pseudomonas model.Acinetobacter baylyi ADP1Acinetobacter baylyi ADP1 genome, fitness, metabolism, and respiratory wiringRhodanobacterENIGMA genus associated with denitrification and environmental partitioningDesulfovibrio vulgaris HildenboroughAnaerobic sulfate-reducing bacterium studied for metal fitness and gene function.Klebsiella pneumoniaeAMR-variable bacterial pathogen with extensive accessory resistancePseudomonas FW300-N2E3ENIGMA groundwater Pseudomonas isolate linked across the KBase Data Lakehouse fitness and metabolite resourcesBacillota_B lineages compared across deep-clay and soil habitatsBacillota_B lineages compared across deep-clay and soil habitatsMycobacteriaceaeMycobacteriaceae, a bacterial family linked to mycolic-acid innovation and PHB enrichmentPseudomonas fluorescensPseudomonas fluorescens utilization phenotypes and carbon-ecology contextStaphylococcus aureusOrganism with predominantly accessory AMR and clinical-associated genomic variationBacteroidotaBacteroidota is a bacterial phylum with diverse ecological and functional profiles.Methanococcus maripaludisArchaeal methanogen represented by Fitness Browser and SNIPE analysesclostridium-scindensHuman 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.SphingomonasEnvironmental bacterial genus associated with Oak Ridge and plant-associated ecologyCaulobacter crescentusModel alphaproteobacterium studied for envelope and lipid A-loss adaptationMycobacterium tuberculosisTuberculosis pathogen with accessory AMR and extensive literature coverage.Pseudomonas stutzeri RCH2Pseudomonas stutzeri RCH2 strain and its fitness–pangenome outlier profileSalmonella entericaHost-associated species with extensive accessory AMR and metabolic ecotype structureStreptococcus pneumoniaeClinical-dominant pathogen with a highly accessory AMR repertoireBacteroides thetaiotaomicronBacteroidetes organism with low gapfilling resolution and distinctive co-inheritance patternsPseudomonadotaBacterial phylum with high xoxF and PHB pathway prevalenceAzospirillum brasilenseModel bacterium used in metabolic, fitness, and ecology studiesbacillus-subtilisBacillus subtilis 168, the Gram-positive model bacterium proposed in the corpus as a priority genetic-library addition and used as a prophage validation species.GeobacterGeobacter 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.Klebsiella michiganensisKlebsiella michiganensis, an organism with high annotation-gap resolution and latent capability.MarinobacterMarinobacter, a bacterial genus studied through annotation and fitness analyses.Shewanella oneidensisShewanella oneidensis MR1, a model organism for fitness and pathway analysis.Alistipes onderdonkiiAlistipes 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.Barnesiella intestinihominisBarnesiella intestinihominis is a gut commensal bacterium that ties with Alistipes onderdonkii for the most inferred metabolic ecotypes in the BERIL pathway-capability analysis.Klebsiella oxytocaKlebsiella oxytoca studied for co-fitness, pangenome co-inheritance, and essential dark genesMethylobacterium extorquensOrganism associated with lanmodulin and plant-microbiome phylogenetic coverage gapsPseudomonas putidaPseudomonas putida evidence spans co-fitness, metabolism, and ecological carbon useRalstoniaRalstonia 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.Synechococcus elongatusSynechococcus 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.AcidobacteriaAcidobacteria is a bacterial phylum with warming and methylotrophy-associated genomic evidence.lactiplantibacillus-plantarumPlant- 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.Neisseria gonorrhoeaeNeisseria gonorrhoeae, the organism whose initial analysis generated the predictions later tested across species in the COG analysis project.Sinorhizobium melilotiRhizobial model organism used in fitness, pathway, and pangenome analyses.Pseudomonas syringae B728aPseudomonas syringae B728a in co-fitness and pangenome analysesblautia-wexleraeHuman gut bacterial species listed among the discovery digest's trustworthy Crohn's-enriched E3 candidates but dropped from that set by a stricter E3-restricted recheck.DesulfosporosinusDesulfosporosinus is a spore-forming, sulfate-reducing Bacillota_B genus that recurs in deep-clay subsurface genome cohorts from Mont Terri and Beyelii Yar.GeothrixGeothrix is an iron-reducing bacterial genus that the cited literature reports, alongside Geobacter, among the dominant rock-attached taxa in Mont Terri Opalinus clay.PatescibacteriaPatescibacteria (the Candidate Phyla Radiation superphylum) appear in the corpus as a literature contrast for small-genome streamlining and as a shallow-enriched phylum in ENIGMA SSO subsurface amplicon data.Prevotella copriHuman gut commensal that defines the E2 "Prevotella copri enterotype" — a near-exclusively healthy, largely non-Western ecotype absent from a UC Davis clinical cohort — and a named marker species for proposed qPCR ecotype panels.ralstonia-solanacearumRalstonia solanacearum is one of the six species directly matched between the Fitness Browser and BacDive, and in a plant-microbiome ecotype analysis its subclade × plant-host association passed Benjamini–Hochberg FDR but not across-species Bonferroni correction.
Methods
42 pages, most linked first
Transposon SequencingTransposon sequencing for gene essentiality and condition-specific fitnessBenjamini–Hochberg FDRMultiple-testing correction controlling false discovery rates across microbial ecology analysesBaktaBacterial genome annotation method used for AMR and functional discovery.AMRFinderPlusAMRFinderPlus annotates antimicrobial- and metal-resistance genes.Flux Balance AnalysisMetabolic-modeling method that predicts fluxes and growth from stoichiometric constraintsInterProScanDomain and functional annotation method for gene clusters and proteins16S Amplicon SequencingMicrobial-community profiling method using 16S rRNA ampliconsMann-Whitney U TestStatistical method for rank-based comparisons of cofitness and pathway completenessIndependent component analysis of fitness modulesIndependent component analysis for discovering bacterial fitness modulesMetaPhlAn3MetaPhlAn3 taxonomic profiling method and cross-cohort microbiome namespaceFisher's exact testExact test for categorical enrichment, depletion, and associationCRISPRi-based transcriptional knockdown for testing essential dark genesCRISPRi method for testing essential and functionally dark genesPERMANOVAPermutational multivariate analysis of variance for multivariate composition testskruskal-wallis-testThe 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.LinDALinDA, 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.Principal component analysisDimensionality-reduction method for detecting ecosystem-associated pathway structureDIAMONDDIAMOND sequence-comparison method for fitness, pangenome, and annotation linkingPhylogenetic Generalized Least SquaresPhylogeny-aware regression for testing trait associationsCorrected multi-heme cytochrome detector using PFAM and CXXCH signalsMethod for detecting multi-heme cytochrome signals with PFAM and CXXCH evidenceMantel testDistance-matrix correlation method used for ecological and genomic comparisonsSHAPSHAP explains feature contributions in predictive models.UMAPUMAP is a nonlinear method for visualizing structure in genome embeddings.Average Nucleotide IdentityGenome-comparison method for estimating relatedness through nucleotide identity.Bonferroni correctionBonferroni 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.kaijuKaiju, 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.KMeans clusteringPartitioning method used to identify gene-content and metabolic ecotypesKraken2Prokaryote-restricted classifier evaluated for eukaryotic read detection.MMseqs2Sequence-search and clustering method used for protein-family and TerL lineage analysisXGBoostXGBoost method for predicting genome-based metal toleranceBidirectional Best-Hit OrthologyOrthology-inference method based on reciprocal best-hit gene relationshipsCentrifugeTaxonomic classifier with genus-level ambiguity in this NMDC deploymentCheckMCheckM 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.DBSCANDensity-based clustering method for identifying embedding and ecotype clustersgeNomadgeNomad is a mobile-genetic-element prediction tool that BERIL projects used for mobilome detection or named as a dedicated alternative for prophage identification.humann3HUMAnN3, 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.Distance-based redundancy analysisMultivariate method for relating distance-based functional profiles to explanatory variablesGene knockoutComplete-gene deletion method for testing essentiality and growth defectsGroupKFoldGrouped cross-validation method for testing generalization across studies.Partial correlationMethod for measuring associations while controlling for confounding variablesProteomicsProtein-expression measurement used to interpret essentiality and respiratory-chain wiringcohens-dCohen's d, the standardized mean-difference effect size, and how BERIL projects used and qualified it in genome-completeness and functional-atlas comparisons.procrustes-analysisProcrustes analysis is an ordination-alignment method used in BERIL projects to test whether community or functional configurations correspond to physical layouts or to each other.
Datasets
39 pages, most linked first
KBase Fitness BrowserKBase Data Lakehouse dataset of comparative microbial mutant-growth fitness measurementsKBase KE PangenomeKBase Data Lakehouse pangenome dataset linking genomes, gene clusters, annotations, and phenotypesGenome Taxonomy DatabaseGTDB is a versioned genome-taxonomy and pangenome dataset for microbial analysis.GapMindDataset for assessing metabolic pathway completeness across genomes and communitiesBacDiveBacterial strain database linking phenotypes and isolation metadata to genome analyseseggNOGCross-project synthesis of eggNOG orthology, annotation coverage, and interpretation limits.Metal Fitness AtlasGenome-derived resource and cross-species atlas of bacterial metal-fitness and tolerance.KEGGDataset for genes, pathways, and functional annotationsENIGMA CORALENIGMA CORAL is an Oak Ridge field-sample dataset for geochemistry and microbial communities.AlphaEarthEnvironmental embedding dataset for ecological context in microbial genomescuratedMetagenomicDataCross-cohort microbiome dataset used for ecotype and IBD analysesKEScience AlphaFoldStructural-protein dataset connecting AlphaFold models, MSA depth, and fitness data.ModelSEEDMetabolic reconstruction, reaction, and compound resource used in the KBase Data Lakehouse workflows.PfamProtein-family domain database used for gene annotation and functional interpretationWeb of MicrobesExometabolomics database linking microbial compounds to organism observationsKEScience PaperBLASTKBase Data Lakehouse dataset linking protein sequences, genes, annotations, and literature.PhageFoundryDataset of phage, mobile-element, and strain-susceptibility recordsMGnifyMetagenomic dataset supporting global and soil functional ecology analysesSSOGroundwater and field-occurrence dataset used in ENIGMA subsurface ecology studies.UniProtProtein sequence dataset used for cross-dataset identification and annotation.Acinetobacter baylyi ADP1 single-gene deletion collection (de Berardinis et al. 2008)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.COG Functional CategoriesCOG-based functional categories for comparing microbial gene content and ecologyNCBI Environment MetadataGenome-associated environmental metadata used for habitat classification and ecological analysisNMDC ARKinArkin-derived NMDC dataset with environmental and multi-omics productsProtein Data BankThe Protein Data Bank (PDB), the collection of experimental macromolecular structures available in the KBase Data Lakehouse and used by PaperBLAST, with its query pitfalls.Canonical NMDC biosample metadata resourceCanonical NMDC biosample metadata resource and its provenance boundariesMetaCycMetaCyc 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.National Ecological Observatory NetworkNational Ecological Observatory Network (NEON), a dataset distinct from NMDC.NMDC analysis-results resourceNMDC analysis-results dataset and its provenance-aware access boundaryPROTECT Genome DepotPathogen-genome data collection supporting PROTECT and KBase Data Lakehouse analysesCARD (Comprehensive Antibiotic Resistance Database)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.Microbial AtlasGlobal environmental 16S dataset for habitat and genomic-representation analysisSEEDSEED is a functional annotation and pathway-membership resource.SILVA rRNA databaseSILVA is a ribosomal RNA reference sequence database that BERIL amplicon projects used for 16S rRNA taxonomy assignment.Swiss-ProtReviewed protein-sequence dataset used for homology and integrated annotation evidence.ENIGMA Genome DepotDataset linking ENIGMA isolates, genomes, annotations, and utilization phenotypesGene Ontology functional annotation resourceGene Ontology annotations and their provenance in the KBase Data Lakehouse and NMDC holdingsPROTECT GoldPROTECT Gold is a curated data collection of isolate, assay, growth-kinetic, patient-metagenomic and pairwise-interaction tables used in cystic fibrosis formulation-design analyses.unirefUniRef protein clusters at three redundancy levels (UniRef100, UniRef90, UniRef50) as held in the KBase Data Lakehouse, with snapshot counts, dataset variants and query caveats.
Genes and pathways
20 pages, most linked first
PQQ BiosynthesisPQQ biosynthesis pathway and its condition-specific, ecological, and pangenome evidenceSNIPE defense systemMobile SNIPE phage-defense system with PF13250 and PF13455 domainsBeta-ketoadipate pathwayAromatic degradation pathway converting quinate-derived intermediates to TCA-cycle inputsComplex IRespiratory Complex I links NADH flux to condition-specific fitness in ADP1bile-acid-7alpha-dehydroxylationGut-microbial bai-operon bile-acid transformation whose active taxa, metabolite signature, and ecological cost shape IBD phage-cocktail design.CRISPR-CasCRISPR-Cas microbial defense-system gene category and anti-phage defense systemdissimilatory-sulfate-reductionThe 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.Entner-Doudorff PathwayGlucose-associated pathway supporting condition-specific metabolism in ADP1Glyoxylate ShuntAcetate-associated pathway supporting growth through central metabolismCOG0443COG0443 is a pan-bacterial ortholog group that the functional dark matter analyses rank among the most broadly conserved yet functionally uncharacterized gene families.COG0468COG0468 is a pan-bacterial ortholog group that ranks first among functionally uncharacterized ('dark') gene families by the conservation × ignorance importance score.Quinate and Protocatechuate Degradation PathwayAromatic pathway converting quinate and protocatechuate to TCA-cycle intermediates[NiFe]-hydrogenase[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.wood-ljungdahl-pathwayThe 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.ManXYZMannose/glucosamine PTS transporter linked to SNIPE phage defensepcacpcaC (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.Tryptophan biosynthesisTryptophan biosynthesis pathway with AMR and FW300-N2E3 fitness evidenceType IV Secretion SystemType IV secretion system markers and machinery involved in microbial transfer.Bacterial flagellar motility and assemblyBacterial flagellar motility and assembly functions enriched in AMR networksCOG0491COG0491 is a COG ortholog group found across nearly all bacterial phyla and ranked among the top functionally unknown gene families in the BERIL dark-matter analyses.
Compounds
35 pages, most linked first
NickelNickel, a metal linked to broad and condition-specific microbial stressCopperCopper evidence spans metal fitness, cross-resistance, and soil functional genomics.AcetateCarbon-source substrate linked to demanding growth and respiratory-chain requirements.ArabinosePentose proposed as a selective prebiotic for two commensalsCobaltCobalt and its conserved, environment-dependent microbial fitness responsesFucoseFucose, 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.QuinateQuinate is an aromatic carbon source with distinctive Complex I dependence in ADP1.rhamnoseRhamnose, 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.UraniumUranium’s ecological associations and metal-specific fitness determinantsXyloseXylose is a proposed selective prebiotic substrate for commensals over Pseudomonas aeruginosa.ZincZinc, a metal linked to shared stress, cross-resistance, and environmental gene shifts.ArginineArginine evidence across fitness, utilization, pathway, and community datasetsChromiumMetal associated with fitness specificity and soil functional-gene shiftsGlucoseCarbon source associated with ADP1's Entner–Doudoroff metabolism and respiratory redundancy.Iron (Fe)Iron (Fe), a metal condition associated with conserved fitness responses.LactateLactate links condition-specific respiration with microbial metabolite production.TyrosineTyrosine, an amino acid whose community biosynthesis completeness in NMDC metagenomes was an outlier both in Black Queen Hypothesis tests and in ecosystem-type differentiation.UreaNitrogenous compound used as a demanding ADP1 growth conditionGlycineGlycine, an amino acid and strongly ecosystem-differentiated biosynthesis pathwayLeucineAmino acid linked to community biosynthesis and accessory pathway variationArsenicArsenic and its microbial resistance and soil-gene associationsCadmiumCadmium, a metal linked to specific and environmental stress responsesGluconateGluconate 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.IsoleucineIsoleucine 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.MercuryMercury, a metal assessed in fitness and soil functional-genomics studiesMolybdenumMolybdenum (Mo), an essential metal with conserved stress-associated fitness determinants.nitrateNitrate (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.sorbitolSorbitol, 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.TryptophanAromatic amino acid linked to microbial metabolism and ipdC distributionValineA branched-chain amino acid with cross-database pathway evidence.Aluminum (Al)Aluminum and its condition-specific bacterial fitness responsesLysineLysine, an amino acid linked to pathway completeness and utilization evidenceManganeseEssential metal associated with strongly core-enriched and partly metal-specific fitness determinants.SeleniumSelenium, a metal assessed for microbial fitness and stress specificity.TungstenEssential metal associated with conserved and metal-specific fitness effects.
Other entities
3 pages, most linked first
Oak Ridge Field Research CenterOak Ridge groundwater research site and ENIGMA field-study locationNational Microbiome Data Collaborative authority and data ecosystemNational Microbiome Data Collaborative dataset ecosystem and provenance authorityMont Terri Opalinus borehole and rock-porewater sampling siteMont Terri site for deep-clay borehole and rock-porewater sampling.