José Pablo Dundore‐Arias

California State University--Monterey Bay

Affiliations

Department Of Biology And Chemistry

NoneJosé Pablo Dundore‐arias is currently serving as a Biology And Chemistry faculty at California State University--Monterey Bay.

Honors

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Experiences

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Education

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José Pablo Dundore‐Arias

California State University--Monterey Bay

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microbiology microbial ecology microbiome environmental microbiology infectious diseases applied microbiology environmental science sustainable agriculture metagenomics plant science metatranscriptomics microbial diversity phenomics soil microbiology public health bacteria microbial consortium clinical microbiology plant diversity climate change sustainability science scientific data sustainable development plant physiology integrative plant biology plant biotechnology organization studies soil biology pest science horticulture research food microbiology insect science laboratory investigation dysbiosis synthetic plant biology experimental plant biology sustainable future public participation research culture network topology biological networks community structure continuous integration microbial systematics agricultural sciences food contaminants pathogen transmission foodborne illness microbial contamination crop rotation sustainable food systems biological samples microbiome samples microbiome metadata standards plant systems science biological systems community-driven metadata standards soilborne streptomyces resistance phenotypes nutrient use carbon amendments understanding organization network structure indigenous soil microbiomes functional capacities host-associated microbiome studies technical reporting

Notable Scholarly Works

Notable Federal Grants

Collaborators

Stimulating New Ways of Thinking in Agricultural Microbiome Research: A Community-Based Interactive Thinkathon Workshop. Phytobiomes Journal (2026)

microbiomegut microbeslaboratory investigationthinking skillscommunity engagementmetagenomicslearning sciencesenvironmental microbiologyapplied microbiologymicrobial ecologyresearch policyeducational strategyeducationglobal healthcommunity-engaged researchmicrobial consortiummicrobiology

Microbiome Data Management in Action Workshop: Atlanta, Ga, USA, June 12–13, 2024. Environmental Microbiome (2025)

Julia M KelliherMashael AljumaahSarah R BordensteinJ Rodney BristerPatrick S G ChainJose Pablo Dundore-AriasJoanne B EmersonVanessa Moreira C FernandesRoberto FloresAntonio GonzalezZoe A HansenEneida L HatcherScott A JacksonChristina A KelloggRamana MadupuCassandra Maria Luz MillerChloe MirzayiAhmed M MoustafaChristopher MungallAaron OliverNonia ParienteJennifer Pett-RidgeSydne RecordLinta RejiAnna-Louise ReysenbachVirginia I RichLorna RichardsonLynn M SchrimlReed S ShabmanMaria A SierraMatthew B SullivanPunithavathi SundaramurthyKatherine M ThibaultLuke R ThompsonScott TigheEthell VereenEmiley A Eloe-Fadrosh

microbiomeenvironmental science

Streams Guidelines: Standards for Technical Reporting in Environmental and Host-Associated Microbiome Studies. Nature Microbiology (2025)

microbiomemicrobial diversitytechnical reportingapplied microbiologyenvironmental microbiologymicrobial ecologyhost-associated microbiome studiesinfectious diseasesstreams guidelinesmicrobiologymetatranscriptomics

Geospatial Analysis of California Strawberry Fields Reveals Regional Differences in Crop Rotation Patterns and the Potential for Lengthened Rotations at Current Levels of Production. Frontiers in Sustainable Food Systems (2024)

Gerardo RamosPolly GoldmanJason SharrettGabriel O. SacherKayla K. PennermanChristine Jade Dilla-ErmitaJose H. JaimeMary E. SteeleShashika S. HewavitharanaGerald J. HolmesHannah WaterhouseJosé Pablo Dundore-AriasPeter Henry

sustainable agriculturecrop rotationgeographycrop rotation patternsgeospatial analysislengthened rotationssustainable food systems

More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes. Annual Review of Phytopathology (2023)

J.P. Dundore-AriasM. Michalska-SmithM. MillicanL.L. Kinkel

microbiomenetwork structureorganization studiessystems biologycommunity structuremicrobial ecologybiological networksnetwork topologynetwork sciencemicroorganismsinfectious diseasesunderstanding organizationnetwork analysismicrobiology

Predictive Ecology and Management of Phyllosphere Microbial Communities Through Cross-Scale Synthesis. Phytobiomes Journal (2023)

David W. ArmitageMorgan E. CarterRobin A. ChoudhuryMitja N. P. Remus-EmsermannCindy E. MorrisJohan H. LeveauLinda L. KinkelJosé Pablo Dundore-Arias

phenomicsmicrobial ecologypredictive ecologyphyllosphere microbial communitiescross-scale synthesisecology

Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science. mSystems (2022)

Kathryn C. Milligan-McClellanJosé Pablo Dundore-AriasJonathan L. KlassenAshley ShadeLinda L. KinkelBenjamin E. Wolfe

public healthmicrobiomecontinuous integrationinclusive scienceintegrating theory

Removing Systemic Barriers to Equity, Diversity, and Inclusion: Report of the 2019 Plant Science Research Network Workshop “Inclusivity in the Plant Sciences”. Plant Direct (2022)

Natalie A. HenkhausWolfgang BuschAngela ChenAdán Colón‐CarmonaMaya CothranNicolas DiazJose Pablo Dundore‐AriasMichael GonzalesDenita HadziabdicRebecca A. HayesGustavo C. MacIntoshAli NaBlessing Nyamasoka‐MagonziwaDianne PaterF. Christopher Peritore‐GalveTara Phelps‐DurrKerry RouhierDelanie B. SicklerJohn H. StarnesQuentin R. TylerEvelyn Valdez‐WardMiguel E. Vega‐SánchezRon R. WalcottJoy K. WardSarah E. WyattFelipe ZapataAsh T. ZemenickDavid B. Stern

diversity (business)plant diversityplant sciencesystemic barriersecology

Correction for Vangay Et Al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-on Activities”. mSystems (2021)

Pajau VangayJosephine BurginAnjanette JohnstonKristen L. BeckDaniel C. BerriosKai BlumbergShane CanonPatrick ChainJohn-Marc ChandoniaDanielle ChristiansonSylvain V. CostesJoan DamerowWilliam D. DuncanJose Pablo Dundore-AriasKjiersten FagnanJonathan M. GalazkaSean M. GibbonsDavid HaysJudson HerveyBin HuBonnie L. HurwitzPankaj JaiswalMarcin P. JoachimiakLinda KinkelJoshua LadauStanton L. MartinLee Ann McCueKayd MillerNigel MounceyChris MungallEvangelos PafilisT. B. K. ReddyLorna RichardsonSimon RouxLynn M. SchrimlJustin P. ShafferJagadish Chandrabose SundaramurthiLuke R. ThompsonRuth E. TimmeJie ZhengElisha M. Wood-CharlsonEmiley A. Eloe-Fadrosh

microbiomemicrobial diversityjose pablometagenomicsclinical microbiologyenvironmental microbiologyapplied microbiologymicrobial ecologyvolume 6infectious diseasesaffiliation linemicrobiologymetatranscriptomicsmicrobial systematics

Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-on Activities. mSystems (2021)

microbiomemicrobiome metadata standardsmicrobial diversitymetagenomicsapplied microbiologyenvironmental microbiologymicrobial ecologyscientific datamicrobiome samplesbiological samplesdysbiosisinfectious diseasesbacteriamicrobial consortiummicrobiologymetatranscriptomics