2022
- *P. Ostrowski, *S.L. La Rosa, B.J. Kunath, A. Robertson, G. Pereira, L.H. Hagen, N. Varghese, T. Yao, G. Flint, S. McDonald, D. Buttner, N.A. Pudlo, M.K. Schnizlein, V.B. Young, H. Brumer, T. Schmidt, N. Terrapon, V. Lombard, B. Henrissat, B. Hamaker, E.A Eloe-Fadrosh, A. Tripathi, P.B. Pope, E.C. Martens (2022). Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nature Microbiology. doi.org/10.1038/s41564-022-01093-0
- L. La Rosa, M.P. Ostrowski, A.V.P. de Leon, L.S. McKee, J. Larsbrink, V.G. H. Eijsink, E.C. Lowe, E.C. Martens, P.B. Pope (2022). Glycan processing in gut microbiomes. Current Opinions in Microbiology. https://doi.org/10.1016/j.mib.2022.102143
- D. Prelman, M. Martinez-Alvaro, S. Morais, I. Altshuler, L.H. Hagen, E. Jami, R. Roehe, *P.B. Pope, *I. Mizrahi (2022).Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development. * equal contributions.Annu. Rev. Anim. Biosci. doi: 10.1146/annurev-animal-013020-020412
2021
- Van Den Bossche, M.Ø. Arntzen, D. Becher, D. Benndorf, C. Henry, P. Jagtap, N. Jehmlich, C. Juste, B.J. Kunath, B. Mesuere, T. Muth, P.B. Pope, J. Seifert, A. Tanca, S. Uzzau, J. Armengaud, R. Hettich (2021). The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome 9; 243.
- K.R. Jonassen, L.H. Hagen, S.H.W. Vick, M.Ø. Arntzen, Vincent G. H. Eijsink, Å. Frostegård, P. Lycus, L. Molstad, P.B. Pope, L.R. Bakken (2021). Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions. ISME J. doi: 10.1038/s41396-021-01101-x
- F. Xie, W. Jin, H. Si, Y. Yuan, Y. Tao, J. Liu, X. Wang, C. Yang, Q. Li, X. Yan, L. Lin, Q. Jiang, L. Zhang, C. Guo, C. Greening, R. Heller, L. Guan, P.B. Pope, Z. Tan, G. Li, W. Zhu, W. Wang, M. Wang, Q. Qiu, Z. Li, S. Mao (2021). An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. Microbiome 9; 137
- L.S. McKee, S.L. La Rosa, B. Westereng, V.G.H. Eijsink, P.B. Pope, J. Larsbrink (2021). Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature. Environ. Microbiol. Rep. https://doi.org/10.1111/1758-2229.12980
- L.J. Lindstad, G. Lo, S. Leivers, L. Michalak, Z. Lu, G.V. Pereira, Å.K. Rørh, E.C. Martens, L.S. McKee, S.H. Duncan, B. Westereng, P.B. Pope, S.L. La Rosa (2021). Human gut Faecalibacterium prausnitzii deploy a highly efficient conserved system to cross-feed on β-mannan-derived oligosaccharides. mBio 12; e03628-20
- S. Mehta, M. Crane, E. Leith, B. Batut, S. Hiltemann, M.Ø. Arntzen, P.B. Pope, B.J. Kunath, F. Delogu, R. Sajulga, P. Kumar, J.E. Johnson, T.J. Griffin, P.D. Jagtap. ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Research 10; 103
- K. Jameson, G. Mathiesen, P.B. Pope, B. Westereng, S.L. La Rosa (2021). Biochemical characterization of two cellobiose 2-epimerases and application for efficient production of lactulose and epilactose. Curr Res Biotechnol. doi.org/10.1016/j.crbiot.2021.02.003
- M.A. Strand, Y. Jin, S.R. Sandve, P.B. Pope, T.R. Hvidsten (2021). Trans-kingdom network analysis provides insight into host-microbiome interactions in Atlantic salmon. Comput Struct Biotechnol J. doi: 10.1016/j.csbj.2021.01.038
2020
- L. Michalak, J.C. Gaby, L. Lagos, S.L. La Rosa, T.R. Hvidsten, C. Tétard-Jones, W.G.T. Willats, N. Terrapon, V. Lombard, B. Henrissat, J. Dröge, M.Ø. Arntzen, L.H. Hagen, M. Øverland, P.B. Pope*, B. Westereng* (2020). Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut. *equal contributions. Nature Communications. 11; 5773
- Nayfach, S. Roux, R. Seshadri, D. Udwary, N. Varghese, F. Schulz, D. Wu, D. Paez-Espino, I-M. Chen, M. Huntemann, K. Palaniappan, J. Ladau, S. Mukherjee, T.B.K. Reddy, T. Nielsen, E. Kirton, J.P. Faria, J.N. Edirisinghe, C.S. Henry, S.P. Jungbluth, D. Chivian, P. Dehal, E.M. Wood-Charlson, A.P. Arkin, S.Tringe, A.Visel, IMG/M Data Consortium, T. Woyke, N.J. Mouncey, N.N. Ivanova, N.C. Kyrpides, E.A. Eloe-Fadrosh (2020). A Genomic Catalogue of Earth’s Microbiomes. Nature Biotech. doi: 10.1038/s41587-020-0718-6
- F. Delogu, B.J. Kunath, P.N. Evans, M.Ø. Arntzen, T.R. Hvidsten, P.B. Pope (2020). Integration of absolute multi-omics reveals translational and metabolic interplay in mixed-kingdom microbiomes. Nature Communications. doi.org/10.1038/s41467-020-18543-0
- L.H. Hagen, C.G. Brooke, C. Shaw, I. Brand-Thomas, A.D. Norbeck, H. Piao, M.Ø. Arntzen, H. Brewer, A. Copeland, N. Isern, A. Shukla, V. Lombard, B. Henrissat, M. O’Malley, I. Grigoriev, S.G. Tringe, R.I. Mackie, L. Pasa-Tolic, P.B. Pope, M. Hess (2020). Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. ISME J. doi.org/10.1038/s41396-020-00769-x
- S. Mazurkewich, R. Helland, A.K. MacKenzie, V.G.H. Eijsink, P.B. Pope, G. Brändén, J. Larsbrink (2020). Structural analysis of the enzymes from the Chitin Utilization Locus of Flavobacterium johnsoniae. Sci. Rep. 10; 13775
- M. Shaffer, M.A. Borton, B.B. McGivern, L.M. Solden, A.A. Zayed, S.L. La Rosa, P. Liu, J. Rodriguez-Ramos, A.B. Narrowe, B. Bolduc, R.A. Daly, G. Smith, D. Vik, P.B. Pope, M.B. Sullivan, S. Roux, K.C. Wrighton (2020). Distilling microbial metabolism to automate the curation of microbiome function. Nucl. Acids Res. doi: 10.1093/nar/gkaa621
- T.O. Andersen, L.H. Hagen, M.Ø. Arntzen, P.B. Pope (2020). Rumen metaproteomics: Closer to linking rumen microbial activities to animal productivity traits. Methods. https://doi.org/10.1016/j.ymeth.2020.07.011
- M. Kujawska, S.L. La Rosa, P.B. Pope, L. Hoyles, A. McCartney, L.J. Hall (2020). Succession of Bifidobacterium longum strains in response to the changing early life nutritional environment reveals specific adaptations to distinct dietary substrates. iScience. 23; 101368
- A. Gilbert, E. Townsend, K.S. Crew, T. Hitch, J. Friedersdorff, C.J. Creevey, P.B. Pope, D. Ouwerkerk, E. Jameson (2020). Rumen virus populations: technological advances enhancing current understanding. Front. Microbiol. 11; 450
2019
- G. Minniti, S.R. Sandve, S. Linden, P.B. Pope, M.Ø. Arntzen, G. Vaaje-Kolstad (2019). The farmed Atlantic salmon (Salmo salar) skin-mucus proteome and its nutrient potential for the resident bacterial community. Genes. 10; e515
- B.J. Kunath, G. Minniti, M. Skaugen, L.H. Hagen, G. Vaaje-Kolstad, V.G.H. Eijsink, P.B. Pope, M.Ø. Arntzen (2019). Metaproteomics: Sample Preparation and Methodological Considerations. Adv Exp Med Biol. 1073:187-215
- A. Salgado-Flores, A.T. Tveit, A.D. Wright, P.B. Pope, M.A. Sundset (2019). Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway. PLoS One. 14:e0213503
- S. Leanti La Rosa, M.L. Leth, L. Michalak, M.E. Hansen, M.Ø. Arntzen, P.B. Pope, E.C. Martens, M.A. Hachem, B. Westereng (2019). The Human Gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans. Nature Communications. 10:905.
- S. Leanti La Rosa, V. Kachrimanidou, F. Buffetto, P.B. Pope, N. Pudlo, E.C. Martens, R. Rastall, G. Gibson, B. Westereng (2019). Wood-derived Dietary Fibers Promote Beneficial Human Gut Microbiota. mSphere. 4: e00554-18
2018
- B.J. Kunath, F. Delogu, M.Ø. Arntzen, V.G.H. Eijsink, T.R. Hvidsten, P.B. Pope (2018) From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus. ISME J. 13: 603-617.
- N. Liu, H. Li, M.G. Chevrette, L. Zhang, L. Cao, H. Zhou, X. Zhou, Z. Zhou, P.B. Pope, C.R. Currie, Y. Huang and Q. Wang (2018). Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood feeding higher termite. ISME J. 13: 104-117.
- M. Taillefer, M.Ø. Arntzen, B. Henrissat, P.B. Pope, J. Larsbrink (2018). Proteomic dissection of the cellulolytic machineries used by soil dwelling Bacteroidetes. mSystems. doi: 10.1128/mSystems.00240-18
- L.M. Solden, A.E. Naas, S. Roux, R.A. Daly, W.B. Collins, C.D. Nicora, S.O. Purvine, J. Schuckel, B. Jorgensen, W.G.T. Willats, D.E. Spalinger, M.S. Lipton,M.B. Sullivan, P.B. Pope, K.C. Wrighton (2018). Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem. Nature Microbiology. doi: 10.1038/s41564-018-0225-4
- J.B. Emerson, S. Roux, J.R. Brum, B. Bolduc, B.J. Woodcroft, H.B. Jang, C.M. Singleton, L.M. Solden, A.E. Naas, J.A. Boyd, S.B. Hodgkins, R.M. Wilson, G.Trubl, C. Li, S. Frolking, P.B. Pope, K.C. Wrighton, P.M. Crill, J.P. Chanton, S.R. Saleska, G.W. Tyson, V.I. Rich, M.B. Sullivan (2018). Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology. doi: 10.1038/s41564-018-0190-y.
- M.S. Jensen, L. Fredriksen, A.K. MacKenzie, P.B. Pope, I. Leiros, P. Chylenski, A.K. Williamson, T. Christopeit, H. Østby, G. Vaaje-Kolstad, V.G.H. Eijsink (2018). Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome. PLoS One. 13; e0197862
- A.E. Naas, L.M. Solden, A.D. Norbeck, H. Brewer, L. H. Hagen, I. M. Heggenes, A.C. McHardy, R.I. Mackie, L. Paša-Tolić, M.Ø. Arntzen, V.G.H. Eijsink, N.M. Koropatkin, M. Hess, K.C. Wrighton, P.B. Pope (2018). "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the Type IX secretion system. Microbiome. DOI: 10.1186/s40168-018-0421-8
- K. Rudi, I.L. Angell, P.B. Pope, J.O. Vik, S.R. Sandve, L.G. Snipen (2017). A stable core gut microbiota across fresh-to salt water transition for farmed Atlantic salmon. Appl. Environ. Microb. doi: 10.1128/AEM.01974-17
2017
- G. Minniti, L.H. Hagen, D. Porcellato, S.M. Jørgensen, *P.B. Pope, *G. Vaaje-Kolstad (2017). The skin-mucus microbial community of farmed Atlantic salmon (Salmo salar). Front. Microbiol. doi: 10.3389/fmicb.2017.02043 * equal contributions.
- M.Ø. Arntzen, A. Várnai, R.I. Mackie, V.G.H. Eijsink, P.B. Pope (2017). Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of Carbohydrate-Active Enzymes with versatile polysaccharide-degrading capacity. Environ Microbiol. 19; 2701-2714.
- B.J. Kunath, A. Bremges, A. Weimann, A.C. McHardy, P.B. Pope (2017). Metagenomics and CAZyme Discovery. Methods Mol Biol. 1588;255-277
- J. Larsbrink, T.R. Tuveng, P.B. Pope, V. Bulone, V.G.H. Eijsink, H. Brumer, L.S. McKee (2017). Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis. Data in Brief. 11; 484-490.
- J. Larsbrink, T.R. Tuveng, P.B. Pope, V. Bulone, V.G.H. Eijsink, H. Brumer, L.S. McKee (2017). Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis. J Proteomics. 156; 63-74.
- D. Paez-Espino, I.-M.A. Chen, K. Palaniappan, A. Ratner, K. Chu, E. Szeto, M. Pillay, J. Huang, V.M. Markowitz, T. Nielsen, M. Huntemann, T.B.K. Reddy, G.A. Pavlopoulos, M.B. Sullivan, B.J. Campbell, F. Chen, K. McMahon, S.J. Hallam, V. Denef, R. Cavicchioli, S.M. Caffrey, W.R. Streit, J. Webster, K.M. Handley, G.H. Salekdeh, N. Tsesmetzis, J.C. Setubal, P.B. Pope, W-T. Liu, A.R. Rivers, N.N. Ivanova, N.C. Kyrpides (2017). IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucl. Acids Res.45(D1); D457-D465.
2016
- A. Weimann, K, Mooren, J.A. Frank, P.B. Pope, A. Bremges, A.C. McHardy (2016). From genomes to phenotypes: Traitar, the microbial trait analyzer. mSystems 1; 00101-16.
- J. Larsbrink, Y. Zhu, S.S. Kharade, K.J. Kwiatkowski, V.G.H. Eijsink, N.M. Koropatkin, M.J. McBride, P.B. Pope (2016). A Polysaccharide Utilization Locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Biotechnol. Biofuels. 9; 260.
- L.H. Hagen, J.A. Frank, M. Zamanzadeh, V.G.H. Eijsink, P.B. Pope, S.J. Horn, M.Ø. Arntzen (2016). Quantitative metaproteomics highlight the metabolic contributions of uncultured phylotypes in a thermophilic anaerobic digester. Appl. Environ. Microb. 83; e01955-16.
- Ö.C. Umu, C. Bäuerl, M. Oostindjer, P.B. Pope, P.E. Hernández, G. Pérez-Martínez, D.B. Diep (2016). The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health. PLoS One 11;e0164036.
- J.A. Frank, M.Ø. Arntzen, L. Sun, L.H. Hagen, A.C. McHardy, S.J. Horn, V.G.H. Eijsink, A. Schnürer, P.B. Pope (2016). Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome. mSystems 1; e00092-16
- A. Salgado-Flores, M. Bockwoldt, L.H. Hagen, P.B. Pope, M.A. Sundset (2016). A first insight into the fecal microbiota of the high Arctic muskoxen (Ovibos moschatus). Microbial Genomics doi: 10.1099/mgen.0.00006
- A. Salgado-Flores, L.H. Hagen, S.L. Ishaq, M. Zamanzadeh, A.D. Wright, P.B. Pope, M.A. Sundset (2016). Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions. PLoS One 11; e0155213.
- J.A. Frank, Y. Pan, A. Tooming-Klunderud, V.G.H. Eijsink, A.C. McHardy, A.J. Nederbragt, P.B. Pope (2016). Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Sci. Rep. 6; 25373.
2015
- G. Henderson, F. Cox, S. Ganesh, A. Jonker, W. Young, Global Rumen Census Collaborators, and P. H. Janssen (2015). Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 5; p14567.
- L. Sun, P.B. Pope, V.G.H. Eijsink, A. Schnürer (2015). Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure. Microb Biotechnol. 8; p815.
- A.E. Naas, A.K. MacKenzie, B. Dalhus, V.G.H. Eijsink, P.B. Pope (2015). Structural features of a Bacteroidetes-affiliated cellulase linked to a polysaccharide utilization locus. Sci. Rep. 5; p11666.
- L.H. Hagen, V. Vivekanand, P.B. Pope, V.G.H. Eijsink, S.J. Horn (2015). The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture. Appl. Microb Biotechnol. 99; p5749.
- Ö.C.O. Umu, J.A. Frank, J.U. Fangel, M. Oostindjer, C. Souza da Silva, E.J. Bolhuis, G. Bosch, W.G.T. Willats, *P.B. Pope and *D.B. Diep (2015). Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations. Microbiome 3; p16. * equal contributions.
- A.K. Mackenzie, A.E. Naas, J. Mravec, S. Kracun, J. Schückel, J.U. Fangel, J.W. Agger, W.G.T. Willats, V.G.H. Eijsink, P.B. Pope (2015). A Polysaccharide utilisation locus from an uncultured Bacteroidetes phylotype infers ecological adaptation and substrate versatility. Appl. Environ. Microb. 81; p187.
2014
- S. Konietzny, P.B. Pope, A. Weimann, A.C. McHardy (2014). Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders Biotechnol. Biofuels 7; p124.
- L.H. Hagen, V. Vivekanand, R. Linjordet, P.B. Pope, V.G.H. Eijsink, S.J. Horn (2014). Microbial community structure and dynamics during co-digestion of whey permeate and cow manure in CSTR systems Bioresour Technol. 171: p350.
- A.E. Naas, A.K. Mackenzie, J. Mravec, J. Schückel, W.G.T. Willats, V.G.H. Eijsink, P.B. Pope (2014). Do rumen Bacteroidetes utilize an alternative mechanism for cellulose degradation? mBio 5; e01401-14.
- Y. Zhou, P.B. Pope, et al. (2014). Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community Sci. Rep. 4; p5288.
- C.P. Rosewarne, P.B. Pope, J.L. Cheung and M. Morrison (2014). Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum BacteroidetesJ. Ind. Microbiol. Biot. 41(3); p601.
- E. Avershina, O. Storrø, T. Øyen, R. Johnsen, P.B. Pope and K. Rudi (2014). Major fecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children FEMS Microbiol Ecol. 87(1); p280.
2013
- Ö.C.O. Umu, M. Oostindjer, P.B. Pope, B. Svihus, B. Egelandsdal, I.F. Nes and D.B. Diep (2013). Potential applications of gut microbiota to control human physiology. Antonie van Leeuwenhoek 104(5); p609.
- K.E. Præsteng, P.B. Pope, R.I. Mackie, I.K.O. Cann, S.D. Mathiesen, A.S. Blix, L.P. Folkow, V.G.H. Eijsink and M.A. Sundset (2013). Probiotic dosing of a highly fibrolytic Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer Microbiol Ecol. 66(4); p840.
- P.B. Pope, V. Vivekanand, V.G.H Eijsink and S.J. Horn (2013). Microbial Community Structure in a Biogas Digester Utilizing the Marine Energy Crop Saccharinalatissima3Biotech 3(5); p407.
- A. Weimann, Y. Trukhina, P.B. Pope, S.G.A. Konietzny and A.C. McHardy (2013). De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes. Biotechnol. Biofuels 6 (1); p24.
2012
- C.R. Kleiveland, L.T.O. Hult, K. Kuczkowska, M. Jacobsen, T. Lea and P.B. Pope (2012). Draft Genome Sequence of the Methane Oxidizing Bacterium Methylococcus capsulatus(Texas). J. Bacteriol. 194(23); p6626.
- A.K. Mackenzie, P.B. Pope, H.L. Pedersen, R.Gupta, M. Morrison, W.G.T. Willats and V.G.H. Eijsink (2012). Two SusD-like proteins encoded within a Polysaccharide Utilization Locus of an uncultured ruminant Bacteroidetes phylotype bind strongly to cellulose. Appl. Environ. Microb. 78(16); p5935.
- P.B. Pope, A.K. Mackenzie, I. Gregor, W. Smith, M.A. Sundset, A.C. McHardy, M. Morrison and V.G.H. Eijsink (2012). Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS ONE 7(6); p38571.
2011
- P.B. Pope, W. Smith, S.E. Denman, S.G. Tringe, K. Barry, P. Hugenholtz, C.S. McSweeney, A.C. McHardy and M. Morrison (2011). Isolation and cultivation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 333(7); p646.
- K.Patil, P. Haider, P.B. Pope, P.J. Turnbaugh, M. Morrison, T. Scheffer, and A.C. McHardy (2011). Taxonomic metagenome sequence assignment with structured output models. Nat. Methods. 8(3); p191.
- C.P. Rosewarne, P.B. Pope, S.E. Denman, C.S. McSweeney, P. OCuiv and M. Morrison (2011). High-yield and phylogenetically robust methods of DNA recovery for metagenomic analysis of the microbial biofilms adherent to plant biomass in the herbivore gut. Microb. Ecol. 61(2); p448.
- P.B. Pope, M. Totsika, D. Aguirre de Carcer, M. A. Schembri and M. Morrison (2011). Muramidases found in the foregut microbiome of the Tammar wallaby can direct cell-aggregation and biofilm formation. ISME J. 5(2); p341.
2010
2009
2008