Jeremiah "Jake" Minich, PhD

Education

Postdoc: Salk
PhD Marine Biology, Scripps Institution of Oceanography University of California San Diego
MS Molecular Biology, San Diego State University
BS: Biochemistry, Point Loma Nazarene University

Courses Taught

Undergraduate Biology Courses

Graduate Catalog

• BIO 3300 Experimental Metagenomics 
• BIO 5312 Introduction to Multiomics Experimentation and Analysis

Biography

Jake was born and raised in a rural part of central Pennsylvania (Appalachia; US). He received a BS in biochemistry and minor in Spanish from Point Loma Nazarene University in San Diego, US, and an MS in molecular biology from San Diego State University. After his masters studies, Minich lived and did research in Malawi, Africa, as a Fulbright scholar. Upon return, he completed a PhD in marine biology at Scripps Institution of Oceanography in the labs of Rob Knight and Eric Allen, where he studied the microbial ecology of mucosal sites in wild and farmed fish. Minich received the prestigious NSF Postdoctoral Research Fellowship in Biology, investigating host–microbe interactions in over 100 species of marine fish using a combination of microbial sequencing, comparative genomics of fish, and fish physiology in Todd Michael’s lab at Salk. As a NOMIS Fellow at the Salk, he investigated the role of the gut microbiome in infant malnutrition. He developed a new long-read metagenomic sequencing approach where he discovered genetic associations of bacteria with childhood undernutrition including stunting.

Research Interests

Malnutrition impacts over 149 million children worldwide and is the result of a combination of inadequate diet, micronutrient deficiencies, enteric dysfunction, gut inflammation and microbiome disruption. The Minich lab is motivated to 

• Investigate the role of the child GI microbiome and diet on childhood undernutrition including stunting and environmental enteric dysfunction.
• Evaluate how the consumption of animal source protein and particularly fish influences human gut health
• Improve aquaculture (fish farming) production, sustainability, and nutritional value, while improving human health outcomes

To address these research questions, the lab is pioneering novel high-throughput, long-read sequencing approaches to measure and compare microbiomes

Selected Publications

* co-first author

^ undergraduate or high school students

• JJ Minich, N Allsing, MO Din, MJ Tisza, K Maleta, D McDonald, N Hartwick, A Mamerto, C Brennan, L Hansen, J Shaffer, ER Murray, T Duong, R Knight, K Stephenson, MJ Manary, and TP Michael. Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition. Cell. 2025 (accepted)
• JJ Minich and TP Michael.A review of using duckweed (Lemnaaceae) in fish feeds. Reviews in Aquaculture. 2024
• JJ Minich* and ML Moore*, NA Allsing, A Aylward, ER Murray, L Tran^, and TP Michael. Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation. Communications Biology. 2023.
• JJ Minich, A Harer, J Vechinski^, BW Frable, ZR Skelton, E Kunselman^, MA Shane, DS Perry, A Gonzalez, D McDonald, R Knight, TP Michael, and EA Allen. Host biology, ecology, and the environment influence microbial biomass and diversity in 101 marine fish species. Nature Communications. 2022.
• JJ Minich, B Nowak, A Elizur, R Knight, S Fielder, and EE Allen. Impacts of the marine hatchery built environment, water, and feed on mucosal microbiome colonization across ontogeny in yellowtail kingfish, Seriola lalandi. Frontiers in marine science. 2021.
• JJ Minich, F Ali, C Marotz, P Belda-Ferre, L Chiang, JP Shaffer, CS Carpenter, D McDonald, J Gilbert, SM Allard, EE Allen, R Knight, DA Sweeney, AD Swafford. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome. 2021.
• JJ Minich, C Power, M Melanson^, R Knight, C Webber, K Rought, NJ Bott, B Nowak, EE Allen. The Southern bluefin tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment. Frontiers in microbiology. 2020.
• JJ Minich, S Petrus, JD Michael^, TP Michael, R Knight, EE Allen. Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish,Scomber japonicus.
• JJ Minich, GD Poore, K Jantawongsri, C Johnston, K Bowie, J Bowman, R Knight, B Nowak,  EE Allen. Microbial ecology of Atlantic Salmon (Salmo salar) hatcheries: impacts of the built environment on fish mucosal microbiota. Applied Environmental Microbiology. 2020.
• JJ Minich, JG Sanders, A Amir, G Humphrey, JA Gilbert, R Knight. Quantifying and understanding well-to-well contamination in microbiome research. mSystems. 2019.
• R Eisenhofer, JJ Minich, C Marotz, A Cooper, R Knight, LS Weyrich. Contamination in low microbial biomass microbiome studies: issues and recommendations. Trends in Microbiology. 2019.
• JJ Minich, G Humphrey, RAS Benitez, JG Sanders, A Swafford, EE Allen, R Knight. High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity. mSystems. 2018.
• JJ Minich, Q Zhu, Z Xu, A Amir, M Ngochera, M Simwaka^, EE Allen, H Zidana, R Knight. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). 2018.
• JJ Minich, Q Zhu, S Janssen, R Hendrickson, A Amir, R Vetter, J Hyde, MM Doty, K Stillwell, J Benardini, JH Kim, EE Allen, K Venkateswaran, R Knight. KatharoSeq enables high-throughput microbiome analysis from low-biomass samples. mSystems.  2018.
• JJ Minich, MM Morris, M Brown, M Doane, MS Edwards, TP Michael, EA Dinsdale. Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption.

See: https://scholar.google.com/citations?user=A0w36gMAAAAJ&hl=en&oi=ao for full publication list