About

Matthias Hess, Ph.D., is a Professor and Hellman Fellow at the UC Davis Department of Animal Science. He holds a B.A. in Microbial Ecology & Botany, an M.S. in Microbiology & Limnology from the University of Konstanz, and a Ph.D. in Microbiology & Biotechnology from Hamburg University of Technology. His research focuses on animal health and microbiology, particularly the microbiome of ruminants, aiming to understand microbe-microbe and microbe-host interactions to promote animal well-being. Additionally, he investigates microbial communities in agricultural systems to develop strategies for reducing greenhouse gas emissions, such as N₂O and CO₂, from ruminants, manure, and soils. His work also explores natural products derived from microorganisms, utilizing cultivation-independent approaches like metagenomics and metatranscriptomics to discover antimicrobial compounds and enzymes. Dr. Hess has contributed to understanding anaerobic fungi during ruminal degradation of plant fiber and has been recognized with awards including the 2021 Faculty Award for Outstanding Mentorship and the 2016 Hellman Fellowship.

Research topics

• Biology
• Genetics
• Computational biology
• Computer Science
• Evolutionary biology
• Food science
• Animal science
• Ecology
• Biochemistry
• Astronomy
• Bioinformatics
• Agronomy
• Biotechnology
• Environmental science
• Chemistry
• Physics
• Data science
• World Wide Web
• Library science

Selected publications

• A Comparison of Three Artificial Rumen Systems for Rumen Microbiome Modeling

  Fermentation · 2023 · 23 citations

  Senior authorCorresponding
  • Biology
  • Animal science
  • Food science

  The rumen contains a complex mixture of microbes, crucial for the animal’s ability to degrade feed. Some of the feed-derived carbon is released as methane, a potent greenhouse gas, into the atmosphere. There is growing interest in reducing the loss of feed-derived carbon, making it available to the animal and improving animal productivity. Artificial rumen systems (ARSs) have been widely used to evaluate novel feed additives in terms of their ability to reduce methane production in the rumen and their effect on the rumen microbiome function prior to conducting resource-intensive animal trials. While the value of ARSs is widely acknowledged, it remains unclear which of these in vitro systems simulate the natural system most accurately. Here, we evaluated three different ARSs and compared them to in vivo rumen metrics. The results showed that all systems were capable of maintaining stable pH, redox potential, and temperature over time. The batch-style ARS simulated the rumen over 48 h. The semi-continuous ARS mimicked the volatile fatty acid profile and microbiota of the in vivo rumen for up to 120 h. Similarly, all ARSs maintained the prokaryotic and eukaryotic rumen populations over the duration of the study, with the semi-continuous ARS maintaining the natural rumen microbiome more accurately and for up to 120 h. In sum, our results suggest that three of the widely used ARSs simulate the rumen ecosystem adequately for many short-term rumen microbiome studies, with the more advanced semi-continuous ARS being more accurate when rumen simulation is extended to over 48 h.

  PublisherOA PDFDOI

• Unraveling the functional dark matter through global metagenomics

  Nature · 2023 · 193 citations

  • Computational biology
  • Evolutionary biology
  • Biology

  . Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

  PublisherOA PDFDOI

• Comparison of three artificial rumen systems for rumen microbiome modeling

  Research Square (Research Square) · 2022 · 1 citations

  Senior authorCorresponding
  • Biology
  • Food science
  • Animal science

  Abstract Background The rumen contains a complex mixture of microbes, which are crucial for ruminant health and feed fermentation. During the fermentation process some of the feed-derived carbon becomes carbon dioxide and methane, which are released into the atmosphere where they act as greenhouse gases and contribute to climate change. There is growing interest in reducing the loss of feed-derived carbon and making it available to the animal, improving animal productivity, while also reducing the carbon footprint of the ruminant industry. To this end, artificial rumen systems (ARS) have been used for evaluating novel feed additives for their effect on the rumen microbiome and rumen function prior to conducting resource intensive animal trials. Whereas ARS are capable of predicting the response of the rumen and its microbiome, it is unclear how accurately different in vitro systems simulate the natural system and how results compare between the artificial systems that are being employed. Here we evaluated physical, chemical and microbiome metrics of three ARS over five days and compared them to those metrics in the in vivo rumen. Results Over a 48 hrs sampling period, the batch style platform (Ankom) was able to replicate pH, volatile fatty acid profile, and bacterial and fungal microbiome of the in vivo rumen, but its accuracy of mimicking in vivo metrics dropped significantly beyond 48 hrs. In contrast, the semi-continuous RUSITEC models, RUSITEC PP and RUSITEC prime, were able to mimic the volatile fatty acid profile and microbiota of the in vivo rumen for up to 120 hrs of rumen simulation. Comparison of gas production across vessel types demonstrated that the semi-continuous RUSITEC platforms display less variability among vessel replicates and time compared to the Ankom system. Conclusions In this study, we found that three widely used ARS were able to simulate the rumen ecosystem adequately for the first 48 hrs, with predictions from the more advanced semi-continuous ARS being more accurate when simulations extended over 48 hrs. Findings of this study will help to select the appropriate in vitro system for evaluating the response of the complex rumen microbiome to feed additives. Further work is necessary to improve the capabilities of these platforms and to standardize the methodology for large-scale application.

  PublisherOA PDFDOI

• Expansion of the global RNA virome reveals diverse clades of bacteriophages

  Cell · 2022 · 294 citations

  • Biology
  • Genetics
  • Evolutionary biology
  PublisherOA PDFDOI

• Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

  Nature Communications · 2021 · 225 citations

  • Biology
  • Ecology
  • Chemistry

  Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

  DOI

• Author Correction: A genomic catalog of Earth’s microbiomes

  Nature Biotechnology · 2021 · 19 citations

  • Computer Science
  • Computational biology
  • Biology

  A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.

  PublisherOA PDFDOI

• Publisher Correction: A genomic catalog of Earth’s microbiomes

  Nature Biotechnology · 2020 · 26 citations

  • Computer Science
  • Computational biology
  • Biology

  An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  PublisherOA PDFDOI

• A genomic catalog of Earth’s microbiomes

  Nature Biotechnology · 2020 · 963 citations

  • Biology
  • Evolutionary biology
  • Ecology

  The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

  PublisherOA PDFDOI

• Methane Reduction Potential of Two Pacific Coast Macroalgae During in vitro Ruminant Fermentation

  Frontiers in Marine Science · 2020 · 45 citations

  Senior authorCorresponding
  • Environmental science
  • Agronomy
  • Biology

  With increasing interest in feed-based methane mitigation strategies and regional legal directives aimed at methane production from the agricultural sector, identifying local sources of biological feed additives will be critical for rendering these strategies affordable. In a recent study, the red alga Asparagopsis taxiformis harvested offshore Australia was identified as highly effective for reducing methane production from enteric fermentation. Due to potential difference in methane-reduction potential and the financial burden associated with transporting the harvested seaweed over long distances, we examined locally sourced red seaweed A. taxiformis and brown seaweed Zonaria farlowii for their ability to mitigate methane production when added to feed widely used in the Californian dairy industry. At a dose rate of 5% dry matter (DM), California-sourced A. taxiformis and Z. farlowii reduced methane production by up to 74% (p ≤ 0.05) and 11% (p ≤ 0.05) during in vitro rumen fermentation respectively. No effect on CO2 production was observed for either seaweed. The measured decrease in methane production induced by A. taxiformis and Z. farlowii amendment, suggest that these local macroalgae are indeed promising candidates for biotic methane mitigation strategies in California, the largest milk producing state in the US. To determine their real potential as methane mitigating feed supplements in the dairy industry, their effect in vivo will need to be investigated.

  PublisherOA PDFDOI

Frequent coauthors

• Bernard Henrissat

  Centre National de la Recherche Scientifique

  96 shared

• Vincent Lombard

  Architecture et Fonction des Macromolécules Biologiques

  91 shared

• Douglas Baxter

  Environmental Molecular Sciences Laboratory

  88 shared

• Ananth Kalyanaraman

  76 shared

• Roderick I. Mackie

  University of Illinois Urbana-Champaign

  75 shared

• Trent R. Northen

  Joint BioEnergy Institute

  64 shared

• Richard W. Castenholz

  University of Oregon

  62 shared

• Stephen R. Lindemann

  Purdue University West Lafayette

  61 shared

Labs

• Hess LabPI

Awards & honors

• Faculty Award for Outstanding Mentorship; University Honors…
• Hellman Fellowship; University of California, Davis, CA (201…
• Wiley Research Fellowship; Department of Energy Environmenta…