Work

Listed below are links to the work I’ve contributed to in various industry settings and a list of my academic publications. You can find a full listing of publications that are indexed on my Google Scholar Profile. For all publications I’ve made a concerted effort to provide links to open access versions of the article or preprint, the underlying code, and data repositories. If you have trouble accessing a paper, dataset, or code, please don’t hesitate to contact me!

Microcosm Foods

Microcosm Foods was a residency project funded by the Astera Institute with the goal of producing public datasets and publishing results through non-journal formats. We primarily released all of our datasets through Zenodo with CC0 open-access licenses, all computational workflows available on GitHub through MIT licenses, and deposited raw sequencing data on NCBI. Below are preprints that I contributed to while at Microcosm Foods and links to our open datasets.

Preprints

Enabling predictive modeling of molecular connections between fermented foods and human inflammation through a paired dataset of cell-based models and multi-omics approaches. preprint McDaniel EA, Schertler M., Edillor C., Dutton RJ. bioRxiv. 2026. DOI:10.64898/2026.09.22.753573

Leveraging publicly available datasets and machine learning approaches for predicting the health benefits of fermented foods. preprint McDaniel EA, Edillor C., Schertler M., Dutton RJ. bioRxiv. 2026. DOI:10.64898/2026.03.05.709865

Open Datasets and Collaborations

Explore Microcosm Foods Datasets on Zenodo such as curated genomes, annotations, and peptide bioactivity predictions using machine learning classifications.

Interactively explore a curated set of microbial genomes from fermented foods on KBase, a free platform for curating, analyzing, and sharing genomes.

Interactively explore functional annotations for a subset of bacterial genomes from fermented foods on Tatta Bio’s SeqHub platform, and read about our partnership here.

Arcadia Science

Arcadia Science is reimagining scientific publishing and does not publish work in traditional peer-reviewed journals. You can check out their work at research.arcadiascience.com.

Pubs

See pubs that I specifically contributed to here, with a select few pubs listed below that I led:

Authors are listed in alphabetical order and not by pub contribution

Discovering shared protein structure signatures connected to polyphosphate accumulation in diverse bacteria. pub code data Avasthi P, Celebi FM, McDaniel EA. 2023. DOI: 10.57844/arcadia-ac10-23e7

Quickly processing and profiling microbial community sequencing data with a Nextflow workflow for metagenomics. pub workflow Dutton RJ, McDaniel EA. 2023. DOI: 10.57844/arcadia-7etp-pj24

Creating reproducible workflows for complex computational pipelines. pub Celebi FM, McDaniel EA, Reiter T. 2023. DOI: 10.57844/arcadia-cc5j-a519

Workflows and Packages

Arcadia-Science/metagenomics Nextflow workflow for handling metagenomics processing including QC, assembly, mapping stats, and preliminary taxonomy classifications for Illumina and Oxford Nanopore reads.

Arcadia-Science/reads2genome Nextflow workflow for assembling single-organism sequencing projects from Illumina, Nanopore, or PacBio technologies. Includes read QC, assembly, mapping stats, and interactive HTML reports.

arcadiathemeR R package for creating publication-quality figures that adhere to the company’s internal style guide.

Academic Publications

# Denotes equal contribution.

17. Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism. preprint publication Friedline S., McDaniel E.A., Scarborough M., Waring K., Lin V.S., Malmstrom R.R., Goudeau D., Chrisler W., Dueholm M.K.D., Gorham L.J., Kombala C.J., Griggs L.D., Olson H.M., Lehmann S.B., Munoz N., Trejo J., Tolic N., Pasa-Tolic L., Williams S.M., Lipton M., Hallam S.J., Ziels R.M. Nature Microbiology. Oct. 2025. DOI: 10.1038/s41564-025-02146-w

16. Sulfate Reduction Drives Elevated Methylmercury Formation in the Water Column of a Eutrophic Freshwater Lake. publication. Peterson B.D., Janssen S.E., Poulin B.A., Ogorek J.M., White A.M., McDaniel E.A., Marick R.A., Armstrong G.J., Scheel N.D., Tate M.T., Krabbenhoft D.P., McMahon K.D. Environmental Science and Technology. Mar. 2025. DOI: 10.1021/acs.est.4c12759.

15. Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium. publication code data McDaniel E.A, Scarborough M., Mulat D.G., Lin X., Sampara P.S., Olson H.M., Young R.P., Eder E.K., Attah I.K., Markillie L.M., Hoyt D.W., Lipton M.S., Hallam S.J., Ziels R.M. ISMEJ. Oct. 2023. DOI: 10.1038/s41396-023-01542-6.

14. Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria. preprint publication #Tran P.Q., #Bachand S.C., #Hotvedt J.C., Kieft K, McDaniel E.A., McMahon K.D., Anantharaman K. mSystems. June 2023. DOI: 10.1138/msystems.00201-23.

13. Environmental predictors of electroactive bacterioplankton in small boreal lakes. preprint publication Olmsted C.N., Ort R., Tran P.Q., McDaniel E.A., Robert E.E., Bond D.R., He S., McMahon K.D. Environmental Microbiology. Dec. 2022. DOI: 10.1111/1462-2920.16314.

12. TbasCO: Trait-Based Comparative ’Omics Identifies Ecosystem-Level and Niche-Differentiating Adaptations in an Engineered Microbiome. preprint publication software code BioProject data #McDaniel E.A., #van Steenbrugge, J.J.M, Noguera D.R., McMahon K.D., Raaijmakers J.M., Medema M.H., Oyserman B.O. ISME Communications. Nov 2022. DOI: 10.1038/s43705-022-00189-2

11. Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities. preprint code Abigail supplementary data R1 supplementary data Abigail BioProject R1 BioProject McDaniel E.A., Moya-Flores F., Mendez D., Weathersby C., Oyserman B.O., Flowers J., He S., Petriglieri F., Singleton C.M., Nielsen P.H., McMahon K.D. bioRxiv. October 2022. DOI: 10.1101/2022.10.01.510452

10. Expanded diversity of tfdA harboring bacteria across the natural and built environment. preprint data #White A.M., #Gonzalez Vasquez A., McDaniel E.A., Peterson B.D., Koch P.L, Remucal C.K., McMahon K.D. bioRxiv. September 2022. DOI: 10.1101/2022.09.28.509959

9. Re-evaluation of the phylogenetic diversity and global distribution of the lineage Candidatus Accumulibacter. preprint publication Petriglieri F., Singleton C.M., Kondrotaite Z., Dueholm M.S., McDaniel E.A., McMahon K.D., Nielsen P.H. mSystems. April 2022. DOI: 10.1128/msystems.00016-22.

8. Prospects for Multi-omics in the Microbial Ecology of Water Engineering. preprint publication McDaniel E.A., Wahl S.A., Ishii S., Pinto A., Ziels R., Nielsen P.H., McMahon K.D., Williams R.B.H. Water Research. Oct. 2021. DOI: 10.1016/j.waterres.2021.117608

7. Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics. preprint publication code BioProject data #McDaniel E.A., #Moya-Flores F., Keene Beach N., Camejo P.Y., Oyserman B.O., Kizaric M., Khor E.H., Noguera D.R., McMahon K.D. mSystems. July 2021, 6 (4) e00474-21; DOI: 10.1128/mSystems.00474-21

6. Genome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient Removal. publication code BioProject data McDaniel E.A., Wever R., Oyserman B.O., Noguera D.R., McMahon K.D. Microbiology Resource Announcements. May 2021, 10 (18) e00244-21; DOI: 10.1128/MRA.00244-21

5. Community-led, integrated, reproducible multi-omics with anvi’o. publication Eren A.M., Kiefl E., Shaiber A., Veseli I., Miller S.E., Schecter M.S., Fink I., Pan J.N., Yousef M., Fogarty E.C., Trigodet F., Watson A.R., Esen O.C., Moore R.M., Clayssen Q., Lee M.D., Kivenson V., Graham E.D., Merrill B.D., Karkman A., Blankenberg D., Eppley J.M., Sjoden A., Scott J.J., Vazquez-Campos X., McKay L.J, McDaniel E.A., Stevens S.L.R., Anderson R., Fuessel J., Fernandez-Guerra A., Maignien L., Delmont T.O., Willis A.D. Nature Microbiology (Commentary). Jan. 2021, 6, 3-6. DOI: 10.1038/s41564-020-00834-3.

4. Mercury methylation genes identified across diverse anaerobic microbial guilds in a eutrophic sulfate-enriched lake. preprint publication data Peterson B.D., McDaniel E.A., Schmidt A.G., Lepak R.F., Tran P.Q., Marick R.A., Ogorek J.M., DeWild J.F., Krabbenhoft D.P., McMahon K.D. Environmental Science and Technology. Nov. 2020, 54 (24), 15840-15851; DOI: 10.1021/acs.est.0c05435

3. Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms. preprint publication code data McDaniel E.A., Peterson B., Stevens S.L.R., Tran P.Q., Anantharaman K., McMahon K.D. mSystems. Aug 2020, 5 (4) e00299-20; DOI: 10.1128/mSystems.00299-20

2. metabolisHMM: Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways. preprint software McDaniel E.A., Anantharaman, K., McMahon K.D. bioRxiv. Dec. 2019, DOI: 10.1101/2019.12.20.884627.

1. Independent Mechanisms for Acquired Salt Tolerance versus Growth Resumption Induced by Mild Ethanol Pretreatment in Saccharomyces cerevisiae. preprint publication McDaniel E.A., Stuecker T.N., Veluvolu M., Gasch A.P., Lewis J.A. mSphere. Editors Pick. Nov 2018, 3 (6) e0057418; DOI: 10.1128/mSphere.00574-18