Johl J, Yuna Park P and Hess M.; Growing Healthier Chickens by Feeding Their Gut Microbes Frontiers for Young Minds; doi: 10.3389/frym.2022.727426.

Hu R, Weaver ME, Day LA, Marquez JM, Aronson HS, Meier DAO, Romero P, Halim F, Maxwell AD, Costa KN, Deutschbauer AM, Price MN, Hess M, Roy KS, Radanielson A, Coates JD, Tsesmetzis N, Carlson HK. Hypophosphite is a naturally-occurring selective inhibitor of syntrophic methanogenesis. bioRxiv. 2026. doi:10.64898/2026.03.11.711166.

Zhang P, Roque B, Romero P, Shapiro N, Eloe-Fadrosh E, Kebreab E, Diamond S, Hess M. Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria. Microbiome. 2025. doi:10.1186/s40168-025-02251-2.

Torosian N, Covington JK, Cook AM, Nou NO, Palmer M, Mewalal R, Harmon-Smith M, Blaby IK, Cheng JF, Hess M and Hedlund BP. Characterization of the thermophilic xylanase Fsa02490Xyn from the hyperthermophile Fervidibacter sacchari belonging to glycoside hydrolase family 10. FEBS OpenBio. 2025. doi:10.1002/2211-5463.70072.

Hug LA, Hatzenpichler R, Moraru C., Soares AR, Meyer F, Heyder A, Hess M (as part of The Data Reuse Consortium), Probst AJ. A roadmap for equitable reuse of public microbiome data. Nat Microbiol. 2025. doi:1038/s41564-025-02116-2.

Kelly L, Pressman E, Ramirez-Agudelo J, Chernavsky H, Alvarez-Hess P, Jaques S, Hess M, Kebreab E. The effect of Rumin8 Investigational Veterinary Product – a bromoform based feed additive – on enteric methane emissions, animal production parameters, and the rumen environment in feedlot cattle. Translational Animal Science. 2025. doi:10.1093/tas/txaf028.

Nou N, Covington JK, Lai D, Mayali X, Cale O. Seymour CO, Johnston J, Jiao J, Buesseker S, Mosier D, Alise R. Muok AR, Torosian N, Allison M. Cook AM, Briegel A, Woyke T, Eloe-Fadrosh E, Shapiro N, Scott G. Bryan SG, Sleezer S, Hess M, Carlson R, Zhu S, Liu F, Sun X, Gao B, Mewala R, Harmon-Smith M, Blaby IK, Chen J, Weber P, Li W, Dekas A, Pett-Ridge J, Dodsworth JA, Palmer M, Hedlund BP. Genome-guided isolation and ecophysiology of polysaccharide-degrading Fervidibacter sacchari and universal polysaccharide metabolism in the Armatimonadota. Nature Communications. 2024. doi:10.1038/s41467-024-53784-3.

Ladau J, Brodie EL, Falco N, Bansal I, Hoffman EB, Joachimiak MP, Mora AM, Walker AM,  Wainwright HM, Wu Y, Pavicic M, Jacobson D, Hess M, Brown JB, Abuabara K. Estimating geographic variation of infection fatality ratios during epidemics.  Infectious Disease Modeling. 2024. doi:10.1016/j.idm.2024.02.009.

Merk K, Link KG, Guy RD & Hess M; Sensitivity analysis of a mechanistic model of rumen fermentation and methane production by rumen microbiota in the presence of Asparagopsis taxiformis. BioXriv. doi:10.1101/2023.11.30.569127.

Shaw CA, Park Y, Gonzalez M, Duong RA, Pandey PK, Brooke CG, Hess, M. A Comparison of Three Artificial Rumen Systems for Rumen Microbiome Modeling. Fermentation. 2023. doi:10.3390/fermentation9110953.

Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad AP, Roux S, Call L, Ivanova NI, Chen IM, Paez-Espino D, Karatzas E, Hess M (as member of the Novel Metagenome Protein Families Consortium), Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A & Kyrpides N; Unraveling the functional dark matter through global metagenomics. Nature. 2023. doi:10.1038/s41586-023-06583-7.

Shaw C, Hess M, Weimer BC; Microbial-Derived Tryptophan Metabolites and Their Role in Neurological Disease: Anthranilic Acid and Anthranilic Acid Derivatives; Microorganisms. 2023.doi:10.3390/microorganisms11071825

Mohamad-Fauzi N, Shaw C, Foutouhi SH, Hess M, Kong N, Kol A, Storey DB, Desai PT, Shah J, Borjesson D, Murray JD and Weimer BC. Salmonella Enhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells. Frontiers in Cell and Developmental Biology. 2023. doi: 10.3389/fcell.2023.1077350.

Shaw C., Hess M., Weimer B. Two-Component Systems Regulate Bacterial Virulence in Response to the Host Gastrointestinal Environment and Metabolic Cue. Virulence. 2022. doi: 10.1080/21505594.2022.2127196

Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Allen LZ, Paez-Espino D, Bryant DA, Devaki Bhaya D, Hess M (as member of the RNA Virus Discovery Consortium), Krupovic M, Valerian V. Dolja VV, Kyrpides NC, Koonin EV, Gophna U. A five-fold expansion of the global RNA virome reveals new groups of RNA phages. Cell. 2022. doi: 10.1016/j.cell.2022.08.023.

Oyama L, Olleik H, Teixeira AC, Guidini M, Pickup J, Hui B, Vidal N, Cookson A, Vallin H, Wilkinson T, Bazzolli D, Richards J, Wootton M, Mikut R, Hilpert K,  Maresca M, Perrier J, Hess M, Mantovani H, Fernandez-Fuentes N, Creevey C, and Huws S. In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus. npj Biofilms and Microbiomes. 2022. doi: 10.1038/s41522-022-00320-0.

Nalla K, Kumar N, Dhillon HS, Kanade SR, Rokana N, Hess M, and Puniya AK. Impact of Probiotics on Dairy Production Efficiency. Frontiers in Systems Microbiology. 2022. doi:10.3389/fmicb.2022.805963.

Ladau J, Abuabara K, Walker AM, Joachimiak MP, Bansal I, Wu Y, Hoffman EB, Kuo C, Falco N, Streich J, van der Lan MJ, Wainwright HM, Brodie EL, Hess M, Jacobson DA, and Brown JB. The impact of environmental mycobiomes on geographic variation in COVID-19 mortality. medRxiv. doi:10.1101/2021.12.14.2126754.

Shaw CA, Brooke CG, Avalos A, Blow M, Shapiro N, Woyke T, and Hess M. Epigenetic Regulation of Nostoc punctiforme ATCC 29133 in Response to Nitrogen Availability. Journal of Student Research. 2021. doi: 10.47611/jsr.v10i3.1267.

Kieft K, Zhou Z, Anderson RE, Buchan A, Campbell BJ, Hallam S, Hess M, Sullivan MB, Walsh DA, Roux S, Anantharaman K. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nature Communication. 2021. doi:10.1038/s41467-021-23698-5.

Roux S, Paul BG, Bagby SC, Allen MA, Attwood G, Cavicchioli R, Chistoserdova L, Hallam SJ, Hernandez ME, Hess M, Liu W, O’Malley MA, Peng X, Rich VI, Saleska S, and Eloe-Fadrosh EA. Ecology and molecular targets of hypermutation in the global microbiome. Nature Communication. 2021. doi:10.1038/s41467-021-23402-7.

Vijn S, Compart DP, Dutta N, Foukis A, Hess M, Hristov AN, Kalscheur K, Kebreab E, Nuzhdin S, Price NN, Sun Y, Tricarico JM, Turzillo A, Weisbjerg M, Yarish C. & Kurt T. Key Considerations for the Use of Seaweed to Reduce Enteric Methane Emissions from Cattle. Frontiers in Veterinary Science. 2020. doi:10.3389/fvets.2020.597430.

Shaw C, Brooke CG, Connolly MP, Garcia JA, Harmon-Smith M, Shapiro N, Hawley E, Barton M, Tringe SG, Glavina del Rio T, Culley DE, Castenholtz RE & Hess M. Phototrophic co-cultures from extreme environments: community structure and potential value for fundamental and applied research. Frontiers in Microbiology. 2020. doi:10.3389/fmicb.2020.572131.

Hess M, Paul SS, Puniya AK, van der Giezen M, Shaw C, Edwards JE, Fliegerova KO. Anaerobic fungi: past, present and future. Frontiers in Microbiology. 2020. doi:10.3389/fmicb.2020.584893.

Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe S, Visel A, Hess M (as “IMG/M Data Consortium” member), Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA. A Genomic Catalogue of Earth’s Microbiomes. Nature Biotech. 2020. doi:10.1038/s41587-020-0718-6.

Hagen LH, Brooke CG, Shaw C, Norbeck AD, Piao H, Arntzen MØ, Brewer H, Copeland A, Isern N, Shukla A, Roux S, Lombard V, Henrissat B, O’Malley MA, Grigoriev IV, Tringe S, Mackie R, Pasa-Tolic L, Pope PB, Hess M. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. ISMEJ. 2020. doi:10.1038/s41396-020-00769-x.

Brooke C, Roque BM, Shaw C, Najafi N, Gonzalez M, Pfefferlen A, DeAnda V, Ginsburg DW, Harden MC, Nuzhdin SV, Salwen J, Kebreab E & Hess M. Methane Reduction Potential of Two Pacific Coast Macroalgae During in-vitro Ruminant Fermentation. Frontiers in Marine Science. 2020. doi: 10.3389/fmars.2020.00561.

Cabral L, Noronha MF, Pereira de Sousa ST, Júnior GVL, Richter L, Fostier AH, Andreote FD, Hess M and de Oliveira VM. The metagenomic landscape of xenobiotics biodegradation in mangrove sediments. Ecotoxicology and Environmental Safety. 2019; 179. doi:10.1016/j.ecoenv.2019.04.044.

Zengler K, Hofmockel K, Baliga N, Behie S, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas, Venturelli OS, Wallenstein M, Shank EA, Northen TR. EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nature Methods. 2019. doi:10.1038/s41592-019-0465-0.

Brooke CG, Najafi N, Dykier KC, Hess M. Prevotella copri, a potential indicator for high feed efficiency in western steers. Animal Science Journal. 2019. doi:10.1111/asj.13197.

Chang C, Brooke C, Piao H, Mack J, Babnigg G, Joachimiak A, Hess M. A 2.08 Å resolution structure of HLB5, a novel cellulase from the anaerobic gut bacterium Parabacteroides johnsonii DSM 18315. Protein Science. 2019. doi:10.1002/pro.3582.

Roque BM, Brooke CG, Ladau J, Polley T, Marsh L, Najafi N, Pandey P, Singh L, Kinley R, Salwen JK, Eloe-Fadrosh E, Kebreab E, Hess M. Effect of the macroalgae Asparagopsis taxiformis on methane production and the rumen microbiome assemblage. Animal Microbiome. 2019; 1:3. doi:10.1186/s42523-019-0004-4.

Huws SA, Creevey C, Oyama LB, Mizrahi I, Denman SE, Popova M, Munoz-tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan S, Yanez-Ruiz DR, Belanche A, Guan LL, Gruninger RJ, McAllister T, Newbold J, Roehe R, Dewhurst RJ, TSnelling TJ, Watson M, Suen G, Hart E, Kingston-Smith A, Scollan N, Do Prado RM, Pilau E, Mantovani HC, Attwood GT, JEdwards JE, McEwan N, Morrison S, Mayorga O, Elliott C, D Morgavi DP. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future. Frontiers in Microbiology. 2018. doi: 10.3389/fmicb.2018.02161.

Lai E, Hess M, and Mitloehner F. Profiling of the microbiome associated with nitrogen removal during vermifiltration of wastewater from a commercial dairy. Frontiers in Microbiology. 2018. doi:10.3389/fmicb.2018.01964.

Cabral L, Pereira de Sousa ST, Júnior GVL, Hawley E, Andreote FD, Hess M, and de Oliveira VM. Microbial functional responses to long-term anthropogenic impact in mangrove soils. Ecotoxicology and Environmental Safety. 2018;160:231. doi: 10.1016/j.ecoenv.2018.04.050.

Sieber C, Probst A, Sharrar A, Thomas B, Hess M, Tringe S, and Banfield J. Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy. Nature Microbiology. 2018. doi:10.1038/s41564-018-0171-1.

Schulze-Makuch D, Wagner D, Kounaves SP, Mangelsdorf K,  Devine KG, de Vera JP, Schmitt-Kopplin P, Grossart HP, Parro V, Kaupenjohann M, Galy A, Schneider B, Airo A, Frösler J, Davila AF, Arens FL, Cáceres L, Cornejo FS, Carrizo D, Dartnell L, DiRuggiero J, Flury M, Ganzert L, Gessner MO, Grathwohl P, Guan L, Heinz J, Hess M, Keppler F, Maus D, McKay CP, Meckenstock RU, Montgomery W, Oberlin EA, Probst AJ, Sáenz JS, Sattler T, Schirmack J, Sephton MA, Schloter M, Uhl J, Valenzuela B, Vestergaard G, Wörmer L and Zamorano P., Transitory microbial habitat in the hyperarid Atacama Desert. PNAS. 2018. doi: 10.1073/pnas.1714341115.

Naas A, Solden LM, Norbeck AD, Brewer H, Hagen L. Heggenes I, McHardy AC, Mackie RI, Pasa-Tolic L, Arntzen MØ, Eijsink VGH; Nicole Koropatkin N, Hess M, Wrighton KC, Pope PB., “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the Type IX secretion system. Microbiome. 2018; 6:44. doi: 10.1186/s40168-018-0421-8.

Oyama L, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Privé F, Vallin HE, Wilkinson TJ, Golyshin PN, Golyshina OV, Mikut R, Hilpert K, Richards J, Wootton M, Edwards JE, Maresca M, Perrier J, Lundy FT, Luo Y, Zhou M, Hess M, Mantovani HC, Creevey CJ, Huws SA., The rumen microbiome: an underexplored resource for novel antimicrobial discovery. npj Biofilms & Microbiomes. 2017;3. doi:10.1038/s41522-017-0042-1.

Oyama LB, Crochet J, Edwards JE, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Hilpert K, Golyshin PN, Golyshin OV, Privé F, Hess M, Mantovani HC, Creevey JC, Sharon A Huws SA., Buwchitin: an antimicrobial peptide with therapeutic potential against Enterococcus faecalis infection. Frontiers in Chemistry. 2017;7.  doi:10.3389/fchem.2017.00051.

Moraes LE, Blow MJ, Hawely ER, Piao H, Kuo R, Chiniquy J, Shapiro N, Woyke T, Fadel JG, Hess M., Resequencing and Annotation of the Nostoc punctiforme ATTC 29133 Genome: Facilitating Biofuel and High-Value Chemical Production. AMB Express. 2017;7:42. doi: 10.1186/s13568-017-0338-9.

Cabral L, Lacerda Júnior GV, Pereira de Sousa ST, Franco Dias AC, Cadete LL, Andreote FD, Hess M, de Oliveira VM. Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities. Environmental Pollution. 2016. Epub 11 June 2016.

Piao H, Hawley E, Kopf S, DeScenzo R, Sealock S, Henick-Kling T, Hess M., Insights into the bacterial community and its temporal succession during the fermentation of wine grapes. Frontiers in Microbiology. 2015;6:809. doi: 10.3389/fmicb.2015.00809. eCollection 2015.

Boundy-Mills K, Hess M, Bennett AR, Ryan M, Kang S, Nobles D, Eisen JA, Inderbitzin P, Sitepu IR, Torok T, Brown DR, Cho J, Wertz JE, Mukherjee S, Cady SL, McCluskey K., The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections. Applied Environmental Microbiology. 2015;81(17):5671-4. doi: 10.1128/AEM.01176-15.

Cantor M, Nordberg H, Smirnova T, Hess M, Tringe SG, Dubchak I., Elviz – exploration of metagenome assemblies with an interactive visualization tool.BMC Bioinformatics. 2015. doi: 10.1186/s12859-015-0566-4.

Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, Del Rio TG, Pati A, Jansson JR, Gilbert JA, Tringe SG, Lorenson TD, Hess M., Metagenomes from two microbial consortia associated with Santa Barbara seep oil. Marine Genomics. 2014. doi: 10.1016/j.margen.2014.06.003.

Piao H, Lachman M, Malfatti S, Sczyrba A, Knierim B, Auer M, Tringe SG, Mackie RI, Yeoman CJ and Hess M., Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling. Frontiers in Microbiology. 2014; 5:307. doi: 10.3389/fmicb.2014.00307.

Piao H, Froula J, Du C, Kim TW, Hawley ER, Bauer S, Wang Z, Ivanova N, Clark DS, Klenk HP and Hess M., Identification of novel biomass-degrading enzymes from genomic dark matter: populating genomic sequence space with functional annotation. Biotechnology & Bioengineering. 2014; 111(8):1550-65. doi: 10.1002/bit.25250.

Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK and Gilbert JA. The microbial nitrogen cycling potential in marine sediments is impacted by polyaromatic hydrocarbon pollution. Frontiers in Microbiology. 2014; 5:108. doi:10.3389/fmicb.2014.00108.

Hawley ER and Hess M., Metagenome Sequencing of the Prokaryotic Microbiota of the Hypersaline and Meromictic Soap Lake, Washington. Genome Announcements. 2014; 2(1):e01212-13.

Hawley ER, Schackwitz W and Hess M., Metagenomic Sequencing of Two Salton Sea Microbiomes. Genome Announcements. 2014; 2(1):e1208-13.

Hawley ER, Piao H, Scott NM, Malfatti N, Pagani I, Huntemann M, Chen A, Glavina del Rio T, Foster B, Copeland A, Jansson J, Pati A, Tringe S, Gilbert JA, Lorenson TD and Hess M., Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Standards in Genomic Sciences. 2014; 9(3).

Piao H, Markillie LM, Culley DE, Mackie RI and Hess M., Improved method for isolation of microbial RNA from biofuel feedstock for metatranscriptomics. Advances in Microbiology. 2013; 3(1):101-107. doi:10.4236/aim.2013.31016.

Kim TW, Chokhawala HA,Hess M, Dana CM, Baer Z, Sczyrba A, Rubin EM, Blanch HW and Clark DS., High-throughout In vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery. Angewandte Chemie International Edition. 2011; 50(47):11215-18.

Hess M, Sczyrba S, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, and Rubin EM., Massive-Scale Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen. Science. 2011; 331(6016):463-7.

Warnecke F and Hess M., A perspective: Metatranscriptomics as a tool for the discovery of novel biocatalysts. Journal of Biotechnology. 2009; 142(1):91-5. Epub 2009 Apr 9.

Hess M.,Thermoacidophilic proteins for biofuel production. Trends in Microbiology. 2008; 16(9):414-9.

Hess M, Katzer M and Antranikian G., Extremely thermostable esterases from the thermoacidophilic euryarchaeon Picrophilus torridus. Extremophiles. 2008; 12(3):351-64.

Hess M and Antranikian G., Archaeal alcohol dehydrogenase active at increased temperatures and in the presence of organic solvents. Applied Microbiology and Biotechnology. 2008; 77(5):1003-13.

Dock C, Hess M and Antranikian G., A thermoactive glucoamylase with biotechnological relevance from the thermoacidophilic Euryarchaeon Thermoplasma acidophilum. Applied Microbiology and Biotechnology. 2008; 78(1):105-14. Epub 2007 Dec 15.

Daly MJ, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Venkateswaran A,Hess M, Omelchenko MV, Kostandarithes HM, Makarova KS, Wackett LP, Fredrickson JK and Ghosal D., Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science. 2004; 306(5698):1025-8. Epub 2004 Sep 30.