Michael J. Shreve, PhD, E.I.T.

Pennsylvania, USA (remote/hybrid)
Email: shrevemj@hyphamind.ai
Phone: (814) 730-0272
Links: Founder Page · ORCID · LinkedIn

This standalone site copy is synchronized to the canonical Markdown CV in the HyphaMindTM repo and published here as a direct reading surface.

Summary

Environmental engineering PhD (Penn State, 2018; NSF Graduate Research Fellow) specializing in complex environmental and bioprocess systems, microbial ecology, wastewater intelligence, and reproducible scientific evaluation for AI-assisted workflows. Experience spans campus-scale wastewater surveillance, multi-factor anaerobic digestion programs with endpoint multi-omics, full-scale IFAS contaminant removal studies, and applied fungal/biological transformation of emerging contaminants, including PFAS-relevant contexts. Strengths include scientific fidelity, uncertainty-aware reasoning, and clear technical communication that holds up under review.

Current work extends that foundation into provenance-bearing workflow systems for science and public-interest settings. Through founding and stewarding HyphaMindTM, I have gained hands-on experience in proof-coupled workflow design, local-first AI orchestration, runtime governance for bounded automation, and research infrastructure that preserves continuity, receipts, and recovery across people, tools, and time.

Core strengths

• Wastewater systems, environmental surveillance, and wastewater-based epidemiology (WBE)
• Anaerobic digestion and fermentation systems; mixed consortia; continuous reactor operations; stability troubleshooting
• Microbial ecology; multi-omics integration (genomics, transcriptomics, proteomics) in engineered systems
• Occurrence and fate of organic contaminants; environmental chemistry and transformation pathways, including endocrine disruptors and PFAS-relevant compounds
• Experimental design (multi-factor matrices), QA/QC, data integrity, and uncertainty handling in real-world datasets
• Scientific writing, peer review, and cross-functional collaboration across bench, field, and decision workflows
• AI-facing problem framing: testable reasoning tasks, rubric design, evaluation, and tool-use workflows optimized for reproducible inference
• Proof-coupled workflow design, local-first AI orchestration, provenance-bearing exports, and replay/recovery discipline
• Python for research scripting, analysis automation, and reproducibility (Git/CLI-first)

Current systems and AI practice

• Translate narrative intent into bounded, testable workflow tranches that can be executed locally, validated against explicit constraints, and resumed without losing continuity.
• Couple model-assisted generation to receipts, traces, replayable artifacts, and recovery paths so workflow acceleration compounds into stronger rails rather than higher entropy.
• Design bounded automation for scientific and public-interest contexts where provenance, legibility, uncertainty, and reviewability matter as much as speed.
• Build reviewer-ready artifacts from messy evidence: explicit assumptions, uncertainty bounds, traceable inputs/outputs, and reproducible runs that survive handoff.

Experience

HyphaMindTM Labs — Founder & Research Lead | 2024-Present

• Build consent-first, provenance-forward research workflows translating environmental science practice into auditable, evaluable AI-assisted systems.
• Design proof-coupled workflow architecture for bounded automation, with explicit attention to continuity across people, tools, and time.
• Turn natural-language intent into executable, validated work tranches using local-first model orchestration, runtime constraints, receipt preservation, and recovery paths.
• Convert messy real-world evidence into reviewer-ready artifacts: explicit assumptions, uncertainty bounds, traceable inputs/outputs, and reproducible runs.
• Develop lightweight patterns for signed/traceable exports, reusable analysis templates, and governed handoff surfaces that support verification, reuse, and downstream review.

Allonnia, LLC — Research Scientist (Environmental Microbiology) | 2023-2024

• Conducted applied R&D on biological transformation of PFAS-relevant compounds, including anaerobic consortium enrichment and characterization workflows.
• Partnered on aerobic fungal transformation investigations; contributed methods and defensible interpretation under analytical uncertainty.
• Maintained and curated a fungal cryobank; supported comparative genomics investigations aligned to experimental outcomes.
• Improved lab throughput and reliability via workflow optimization, documentation, and EH&S-aligned practices.

Penn State University — Postdoctoral Researcher (DOE-funded, multi-year anaerobic digestion program) | 2019-2023

• Designed and implemented a multi-factor reactor program testing 18 condition sets for anaerobic conversion of switchgrass, including discovery of an unexpected basic-range optimum and high-methane-fraction biogas.
• Built, operated, and optimized continuous anaerobic reactor platforms across replicated pH, temperature, and retention-time matrices with long-horizon stability requirements.
• Integrated process performance with endpoint multi-omics (genomics, transcriptomics, proteomics) to interpret system behavior under environmental forcing.
• Strengthened operational continuity via data-integrity workflows, handoff documentation, equipment calibration, lab renovation coordination, and mentorship of undergraduate staff.
• Contributed to IP generation from bioconversion results (see Patents & patent applications).

Penn State — Wastewater Surveillance Scientist (campus-scale COVID-19 WBE operational response) | 2019-2021

• Supported field sampling and defensible interpretation under real-time public health constraints.
• Contributed to analytical method development (virus concentration, isolation, extraction, and qPCR quantification) and led targeted near-building sampling to improve spatial resolution in the sewer network.
• Inferred population-level trends from noisy wastewater signals while accounting for confounders and system dynamics; communicated uncertainty clearly to cross-disciplinary stakeholders.

Penn State University — Graduate Researcher / NSF Graduate Research Fellow (Environmental Engineering) | 2011-2018

• Conducted doctoral research on trace organic contaminant occurrence, fate, and removal in wastewater treatment systems; dissertation on TrOCs and microbial diversity in IFAS systems.
• Led full-scale IFAS investigations across six municipal facilities, linking treatment performance, biofilm vs. suspended-growth ecology, and contaminant removal.
• Planned and executed marker-gene community surveys spanning bacterial, archaeal, and fungal diversity in attached vs. suspended phases; identified core communities and growth-phase effects.
• Designed bench-scale fungal bioreactors demonstrating white-rot fungal growth in wastewater matrices and reductions in estrogenic activity for endocrine-disruptor mixtures.
• Improved estrogenic-activity measurement approaches by adapting commercially available nuclear receptor screening bioassays for wastewater applications.
• Supported funded research execution and proposal development through proof-of-concept experiments and rigorous documentation.

Selected technical outcomes & project highlights

• HyphaMindTM systems building: Designed and stewarded proof-coupled, locally orchestrated workflow systems that translate narrative intent into bounded, validated, replayable work with receipts, traces, and recovery paths.
• Operational wastewater surveillance (COVID-19): Supported Penn State’s COVID-19 monitoring response via wastewater surveillance; contributed to method development (concentration, extraction, qPCR workflow context) and led targeted field sampling to increase resolution within the sewer network by sampling near buildings.
• Anaerobic digestion / fermentation of switchgrass: Designed and executed a large-scale fermentation experiment comparing a combinatorial matrix of 18 condition sets for anaerobic conversion of switchgrass; identified an unexpected optimal pH in the basic range and high-purity methane outcomes; work resulted in two filed patent applications.
• Microbial ecology in full-scale IFAS systems: Planned and implemented a marker-gene survey spanning bacterial, fungal, and archaeal communities across attached vs. suspended growth phases in full-scale IFAS wastewater treatment systems; characterized growth-phase effects and identified core fungal/bacterial communities across multiple plants.
• Fungal biocatalysis in wastewater matrices: Designed and implemented bench-scale fungal bioreactors demonstrating growth of Trametes versicolor in carbon-amended domestic wastewater and significant reductions in estrogenic activity for a spiked mixture of common endocrine-disrupting compounds.
• Estrogenic-activity measurement for wastewater: Developed a modified procedure using commercially available nuclear receptor screening bioassays to quantify estrogenic activity in domestic wastewater, supporting more approachable monitoring workflows.
• Renewable/green polymer synthesis (early research): Synthesized polymers from renewable precursors while minimizing pre-treatment, catalyst loading, and solvent consumption.

Education

PhD, Environmental Engineering — Penn State University (2018)
Dissertation: Trace organic contaminants and microbial diversity in integrated fixed-film activated sludge wastewater treatment systems.

BS, Environmental Systems Engineering (Honors) — Penn State University (2010)
Honors thesis: Alginate encapsulation of Phanerochaete chrysosporium for fungal biocatalysis of endocrine disrupting compounds in wastewater.
Top Graduate, College of Earth and Mineral Sciences (highest distinction).

Certification

Engineer-in-Training (E.I.T.) — License No. ET016163

Selected publications

Peer-reviewed journal articles

• Jones, M.J., Ibrahim, R., Clark, S., Brooks, Y.M., Preisendanz, H.E., Richard, T.L., Read, A.F., Robinson, C.J., Noorali, S., Shreve, M.J., Dennington, N.L., Silverman, J.D., Van Oost, C., & McGraw, E.A. (2025). Wastewater surveillance of SARS-CoV-2 and influenza in a dynamic university community: understanding how wastewater measurements correspond to reported cases. Science of The Total Environment, 1000, 180377. DOI: 10.1016/j.scitotenv.2025.180377
• Hayden, K.R., Jones, M., Elkin, K.R., Shreve, M.J., Clees II, W.I., Clark, S., Mashtare, M.L., Veith, T.L., Elliott, H.A., Watson, J.E., Silverman, J., Richard, T.L., Read, A.F., & Preisendanz, H.E. (2022). Impacts of the COVID-19 pandemic on pharmaceuticals in wastewater treated for beneficial reuse: Two case studies in central Pennsylvania. Journal of Environmental Quality, 51(5), 1066-1082. DOI: 10.1002/jeq2.20398
• Shreve, M.J., & Brennan, R.A. (2019). Trace organic contaminant removal in six full-scale integrated fixed-film activated sludge (IFAS) systems treating municipal wastewater. Water Research, 151, 318-331. DOI: 10.1016/j.watres.2018.12.042
• Calicioglu, O., Shreve, M.J., Richard, T.L., & Brennan, R.A. (2018). Effect of pH and temperature on microbial community structure and carboxylic acid yield during the acidogenic digestion of duckweed. Biotechnology for Biofuels, 11, 275. DOI: 10.1186/s13068-018-1278-6
• Shreve, M.J., Brockman, A., Hartleb, M., Prebihalo, S., Dorman, F.L., & Brennan, R.A. (2016). The white-rot fungus Trametes versicolor reduces the estrogenic activity of a mixture of emerging contaminants in wastewater treatment plant effluent. International Biodeterioration & Biodegradation, 109, 132-140. DOI: 10.1016/j.ibiod.2016.01.018
• Mathers, R.T., Shreve, M.J., Meyler, E., Damodaran, K., Iwig, D.F., & Kelley, D.J. (2011). Synthesis and polymerization of renewable 1,3-cyclohexadiene using metathesis, isomerization, and cascade reactions with late-metal catalysts. Macromolecular Rapid Communications, 32, 1338-1342.

Trade / practitioner publication

• Shreve, M.J., & Brennan, R.A. (2017). Trametes versicolor (Turkey Tail) removes 17beta-estradiol from wastewater effluent. Mushroom News, 65(2), 6-11.

Conference proceedings

• Calicioglu, O., Shreve, M.J., Urban, N.L., Richard, T.L., & Brennan, R.A. (2018). Enhancing carboxylic acid yields from duckweed by acidogenic digestion. European Biomass Conference and Exhibition (EUBCE) Proceedings, 953-956. DOI: 10.5071/26thEUBCE2018-3BO.7.3

Manuscripts in preparation

• Shreve, M.J., Carper, D., Chirania, P., Giannone, R., Hettick, B., Regan, J.M., & Richard, T.L. Multi-omics analysis of the solubilization of senescent switchgrass by anaerobic mixed cultures. In preparation (target: Applied and Environmental Microbiology).
• Shreve, M.J., & Brennan, R.A. Fungal diversity of biofilm and suspended growth in six full-scale IFAS domestic wastewater treatment plants. In preparation (target: Applied and Environmental Microbiology).
• Hirl, K., Shreve, M.J., Bharadwaj, A., Regan, J.M., & Richard, T.L. Elevated pH enhances the solubilization of senescent switchgrass by anaerobic mixed cultures, yielding high titers of acetate and high-methane-fraction biogas. In preparation (target: Bioresource Technology).

Patents & patent applications

• Regan, J.M.; Hirl, K.; Shreve, M.J.; Bharadwaj, A.; Richard, T.L. (2025). “Systems and Methods for the Production of Biogases from a Lignocellulosic Feedstock.” U.S. Patent Application Publication US 2025/0002951 A1 (Pub. No. 20250002951), published Jan 2, 2025.
• Regan, J.M.; Hirl, K.; Shreve, M.J.; Bharadwaj, A.; Richard, T.L. (2024). “Method for the Production of High Purity Biogases from a Lignocellulosic Feedstock.” U.S. Patent Application Publication US 2024/0368636 A1 (Pub. No. 20240368636), published Nov 7, 2024.

Selected talks & presentations

• 2022 — “The science behind anaerobic digestion.” Digester Systems Webinar (Penn State), oral presentation (March 30).
• 2018 — “What’s new in QIIME 2?” Microbiome Center Weekly Meeting (Penn State), oral presentation (March 30).
• 2017 — “Removal of trace organic contaminants and estrogenic activity in six full-scale IFAS wastewater treatment plants.” 254th American Chemical Society (ACS) National Meeting (Washington, DC), oral presentation (Aug 22).
• 2017 — “Fungal populations in IFAS biofilms in the context of trace organic contaminant removal.” Pennsylvania Water Environment Association (PennTec 2017) (Pocono Manor, PA), oral presentation (Student Research Award recipient) (June 6).
• 2017 — “Contaminants in the environment: wastewater as a conduit for trace organic contaminants.” Science Café (State College, PA), oral presentation (Feb 22).
• 2015 — “Removal of emerging contaminants and estrogenic activity by a white-rot fungus grown in wastewater treatment plant effluent.” College of Engineering Research Symposium (Penn State), oral presentation (1st Place - Logoa Ray Monkowski Award) (Apr 2).

Recognition and leadership

Fellowships & major academic honors

• National Science Foundation (NSF) Graduate Research Fellowship (GRFP) (awarded May 2012)
• Cecil M. Pepperman Memorial Graduate Fellowship, Dept. of Civil & Environmental Engineering, Penn State (Jan 2011)
• Top Graduate, College of Earth and Mineral Sciences, Penn State (Dec 2010)
• Evan Pugh Scholar Award (top 0.5% of class), Penn State (2009-2010)
• Trustee / Centennial scholarships (Penn State; 2008-2011)
• Alpha Sigma Lambda Honor Society (adult learners) (May 2008)

Research & presentation awards

• 1st Place Poster, Microbiome Center Networking Event (Oct 2017)
• Student Research Award, Pennsylvania Water Environment Association Technical Conference (Mar 2017)
• 1st Place Paper Presentation, College of Engineering Research Symposium, Penn State (Apr 2016)
• Student Research Award, PA Water Environment Association Technical Conference (Mar 2016)
• 1st Place Paper Presentation, College of Engineering Research Symposium, Penn State (Apr 2015)
• 2nd Place Poster, American Water Works Association (AWWA) PA Section Annual Conference (Apr 2015)
• 3rd Place Oral Presentation, Environmental Chemistry Student Symposium (Apr 2015)
• Student Research Award, PA Water Environment Association Technical Conference (Mar 2015)
• Young Professional of the Month, AWWA (Jul 2013)
• 1st Place Poster, AWWA PA Section Annual Conference (Apr 2013)
• Best Overall Poster Presentation, Environmental Chemistry Student Symposium (May 2012)
• Best Oral Presentation + Student Research Award, PA Water Environment Association Technical Conference (May 2012)
• Student Research Award, PA Water Environment Association Technical Conference (Jun 2011)

Leadership

• President, Student Association for Environmental Science & Engineering (SAESE), Penn State (May 2015 - May 2016)
• Vice President, SAESE, Penn State (Jul 2013 - May 2015)

Teaching, mentoring, and professional service

Teaching

• CE 476: Solid and Hazardous Wastes (Penn State) — independently taught a five-lecture module on fate and transport of hazardous waste in the subsurface; created and updated course materials and assessments; held office hours; incorporated student feedback into course refinement.

Mentoring

• Mentored NSF-REU undergraduates; developed protocols and training materials for safe, repeatable lab practice.
• Trained students in fungal culture and maintenance, estrogenic-activity bioassays, and bioreactor design and construction.
• Tutored college and high-school students in mathematics (one-on-one).

Peer review & conference service

• Journal reviewer: Fungal Biology
• Student reviewer: College of Engineering Research Symposium (2017-2018)
• Co-chair, “Trace Organic Contaminants (TrOCs) in Aquatic Systems: Advancements in Monitoring & Remediation,” Research Symposium, ACS 254th National Meeting, Washington, D.C. (Aug 2017)
• Co-chair / organizing committee, 16th Annual Environmental Chemistry & Microbiology Student Symposium (ECMSS), Penn State (2013)

Funded proposal support

• Contributed proof-of-concept experimental data and assisted proposal preparation for: “Enzymatic Biocatalysis of Endocrine Disrupting Chemicals in Wastewater: A Sustainable Technology for Emerging Contaminants,” NSF Award No. CBET-1236730 ($308,000; PI: Rachel Brennan; 2012-2015).

International field experience

• Nyeri, Kenya — Biogas generator installation & youth education (May 2010): designed and installed a biogas generator at a youth center; delivered instruction on operation and maintenance; supported market surveys for small-scale rural biogas adoption.
• Roatán, Honduras — Water quality assessment for estuary restoration design (Oct 2014): conducted an initial water-quality assessment of an estuary impacted by domestic wastewater; generated baseline information to support restoration design work.

Tools

Python · Git · CLI workflows · data QA/QC · experimental design · continuous reactor ops · qPCR workflow familiarity · omics integration (analysis/interpretation) · scientific writing and review