DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes

Julian Damashek; Cody S. Sheik; Caitlin Petro; Christian F. Reeder; Subhadeep Chowdhury; Benjamin J. Kramer; Stephen E. DeVilbiss; Juan J. Pierella Karlusich; Jane C. Marks; Patricia M. Valdespino-Castillo; Paula C. Furey; Megan E. Berberich; Amy M. Marcarelli; J. Thad Scott; Robinson W. Fulweiler

doi:10.1128/mra.00897-25

DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes

Julian Damashek
, Cody S. Sheik
, Caitlin Petro
, Christian F. Reeder
, Subhadeep Chowdhury
, Benjamin J. Kramer
, Stephen E. DeVilbiss
, Juan J. Pierella Karlusich
, Jane C. Marks
, Patricia M. Valdespino-Castillo
, Paula C. Furey
, Megan E. Berberich
, Amy M. Marcarelli
, J. Thad Scott
, Robinson W. Fulweiler

Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

Microbial nitrogen fixation (diazotrophy) is a critical ecological process. We curated DiazoTIME (Diazotroph Taxonomic Identity and MEtabolism), a comprehensive database of diazotroph genomes including taxonomic annotation and metabolic prediction. DiazoTIME is unique among databases for classifying diazotrophs because it resolves both taxonomy and metabolic functionality.

Original language	English (US)
Journal	Microbiology Resource Announcements
Volume	14
Issue number	11
DOIs	https://doi.org/10.1128/mra.00897-25
State	Published - Nov 2025

Keywords

biogeochemistry
diazotrophs
genomics
metabolism
microbial ecology
nitrogen cycle enzymes
nitrogen fixation

ASJC Scopus subject areas

Molecular Biology
Immunology and Microbiology (miscellaneous)
Genetics

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10.1128/mra.00897-25

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Damashek, J., Sheik, C. S., Petro, C., Reeder, C. F., Chowdhury, S., Kramer, B. J., DeVilbiss, S. E., Pierella Karlusich, J. J., Marks, J. C., Valdespino-Castillo, P. M., Furey, P. C., Berberich, M. E., Marcarelli, A. M., Scott, J. T., & Fulweiler, R. W. (2025). DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes. Microbiology Resource Announcements, 14(11). https://doi.org/10.1128/mra.00897-25

Damashek, J, Sheik, CS, Petro, C, Reeder, CF, Chowdhury, S, Kramer, BJ, DeVilbiss, SE, Pierella Karlusich, JJ, Marks, JC, Valdespino-Castillo, PM, Furey, PC, Berberich, ME, Marcarelli, AM, Scott, JT & Fulweiler, RW 2025, 'DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes', Microbiology Resource Announcements, vol. 14, no. 11. https://doi.org/10.1128/mra.00897-25

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abstract = "Microbial nitrogen fixation (diazotrophy) is a critical ecological process. We curated DiazoTIME (Diazotroph Taxonomic Identity and MEtabolism), a comprehensive database of diazotroph genomes including taxonomic annotation and metabolic prediction. DiazoTIME is unique among databases for classifying diazotrophs because it resolves both taxonomy and metabolic functionality.",

keywords = "biogeochemistry, diazotrophs, genomics, metabolism, microbial ecology, nitrogen cycle enzymes, nitrogen fixation",

author = "Julian Damashek and Sheik, \{Cody S.\} and Caitlin Petro and Reeder, \{Christian F.\} and Subhadeep Chowdhury and Kramer, \{Benjamin J.\} and DeVilbiss, \{Stephen E.\} and \{Pierella Karlusich\}, \{Juan J.\} and Marks, \{Jane C.\} and Valdespino-Castillo, \{Patricia M.\} and Furey, \{Paula C.\} and Berberich, \{Megan E.\} and Marcarelli, \{Amy M.\} and Scott, \{J. Thad\} and Fulweiler, \{Robinson W.\}",

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month = nov,

doi = "10.1128/mra.00897-25",

language = "English (US)",

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journal = "Microbiology Resource Announcements",

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AU - Damashek, Julian

AU - Sheik, Cody S.

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AU - Reeder, Christian F.

AU - Chowdhury, Subhadeep

AU - Kramer, Benjamin J.

AU - DeVilbiss, Stephen E.

AU - Pierella Karlusich, Juan J.

AU - Marks, Jane C.

AU - Valdespino-Castillo, Patricia M.

AU - Furey, Paula C.

AU - Berberich, Megan E.

AU - Marcarelli, Amy M.

AU - Scott, J. Thad

AU - Fulweiler, Robinson W.

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AB - Microbial nitrogen fixation (diazotrophy) is a critical ecological process. We curated DiazoTIME (Diazotroph Taxonomic Identity and MEtabolism), a comprehensive database of diazotroph genomes including taxonomic annotation and metabolic prediction. DiazoTIME is unique among databases for classifying diazotrophs because it resolves both taxonomy and metabolic functionality.

KW - biogeochemistry

KW - diazotrophs

KW - genomics

KW - metabolism

KW - microbial ecology

KW - nitrogen cycle enzymes

KW - nitrogen fixation

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UR - https://www.scopus.com/pages/publications/105021669418#tab=citedBy

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JF - Microbiology Resource Announcements

IS - 11

ER -

DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes

Abstract

Keywords

ASJC Scopus subject areas

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