The MEMO group applies interdisciplinary approaches to study the microbiomes inhabiting digestive systems, including important production animals (cows, pigs and salmon), wild herbivores (moose, reindeer), environmental sediments as well as us! We also on occasion delve into commercial biogas reactors that recycle municipal waste in Scandinavia.
Key MEMO research interests are using multi-omic tools to deconvolute the intimate genetic and physiological relationship between the host animal, its environment and its microbiome. We combine analytical metadata, biochemistry and growth experiments with metabolic reconstructions of population genomes to visualize flow of metabolites in complex microbiomes, and have used temporal meta-omics and co-expression network analysis to interpret synergistic interactions between fiber-degrading and methanogenic microbial populations. We are now seeking to expand these approaches to envelop additional “molecular layers” from the animal holobiont (i.e. host transcriptome and proteome), a concept otherwise known as “holo-omics”.
MEMO is structured as a focus group and our MEMO members are formally integrated accross several faculties and research groups at NMBU, including the Nutrition group and CIGENE at BIOVIT. In addition, MEMO members work in concert at KBM with the PEP group to faciliate the coupling of high-resolution omics with in-depth biochemistry, and the BIAS group for bioinformatics. We are funded by the European Research Council (ERC Starting Grant), The Research Council of Norway (FRIMEDBIO and HAVBRUK), The BlueBio Co-fund (ERA-Net), The European Commission (Horizon 2020) and the Novo Nordisk Foundation(NNF).
If you are interested in our pubs, pre-prints or projects, check out the links above and follow us on twitter!
- *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
- 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
- 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
- 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
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- P.B. Pope, S.E. Denman, M. Jones, S.G. Tringe, K. Barry, S.A. Malfatti, A.C. McHardy, J-F. Cheng, P. Hugenholtz, C.S. McSweeney, and M. Morrison (2010). Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different to other herbivores. Proc. Natl. Acad. Sci. USA 107 (33); p14793.
- M. Morrison, P.B. Pope, S. Denman and C. McSweeney (2009). Plant biomass degradation by gut microbiomes: More of the same or something new? Curr Opin Biotechnol. 20 (3); p358.
Our research activities are best summarized by the currently active projects that are listed in the following table.
More detail concerning specific projects (SuPA[cow], ImprovAFish, SeaCow, Back to basics and Multi‐omic informatics) are outlined below.
021-2026 D. Morgavi (P.B. Pope: WP Leader). Horizon 2020. “HoloRuminant” Understanding microbiomes of the ruminant holobiont. NMBU funding: 620,560 EUR. 2021-2025 A. Alberti (P.B. Pope: WP Leader). Horizon 2020. “3D-omics” Three-dimensional holo’omic landscapes to unveil host-microbiota interactions shaping animal production NMBU funding: 978,933 EUR 2020-2023 M.Ø. Arntzen (WPL), L.H. Hagen, P.B. Pope. Horizon 2020. "PRODIGIO": Developing early-warning systems for improved microalgae PROduction and anaerobic DIGestIOn". Funding: €483,625 2020-2025 M.Ø. Arntzen. PI. Novo Nordisk Foundation. "DENITRO": Oxidative Polysaccharide Conversion in Anoxia by Denitrifying Organisms Funding: €1,340,000 2020-2024 L.H. Hagen. PI. The Research Council of Norway - FriPro Young Talent. SeaCow: Promoting 'efficient, low emitting' cows through nutritional manipulation of the rumen microbiome. Funding: €800,000 2020-2023 P.B. Pope. Coordinator. BlueBio CoFund (ERA-Net). “ImprovAFish” Improving aquaculture sustainability by modulating the feed-microbiome-host axis in Fish. Funding: €1,940,000 2020-2024 P.B. Pope. PI. Novo Nordisk Foundation “SuPA[cow]”: Sustainable production of animals by optimizing the feed-microbiome-host axis. Funding: €1,340,000 2019-2022 P.B. Pope. PI. NMBU. “BoGAS”: The effect of Bovine host genetics on microbiota and methane GAS emissions. Funding: €308,768 2019-2022 M. Øverland (Partner P.B. Pope). The Research Council of Norway. Project title: Trained immunity and nutritional programming for resilient salmon. Funding: € 1,030,800 2018-2020 M.Ø. Arntzen. Norwegian Centennial Chair (NOCC) Seed grant – Norway-Minnesota, USA collaboration: “Multi‐omic informatics for characterizing microbiomes and their role in health, disease and environment”. Funding: €135,000 2018-2020 T.R. Hvidsten, S.R. Sandve, P.B. Pope. NMBU. Project title: “MetaNorSE”: Meta-omic interpretation of Norwegian Salmon gastrointestinal Ecosystems. Funding: € 208,588 2016-2020 P.B. Pope. PI. The Research Council of Norway. Project title: “Back to basics”: simplifying microbial communities to decrypt complex interactions. Funding: €1,030,800
- The MEMO group is part of a new EU H2020 project aiming to better understand microbiomes of the ruminant holobiont. See HERE
- The MEMO group is part of a new EU H2020 project aiming to improve animal production: Unraveling the animal-microbe interplay at the microscale. See HERE
- As we all adapt with COVID life and online conferences, we will try and paste links from our recent attempts of "home-office keynotes".
- A summary of our recent efforts to use animal dietary trials, carbohydrate analytics, multi-omics and biochemistry to visualize and improve our understanding of microbiota-direct fibre and gut digestion: See HERE
- We were recently co-authored an article in Scientific American "The Suprising Complexity of Nurturing a Healthy Gut". This was part of a "pilot" with Nature Publishing Group to trial the use of a new service that offers popular science articles derived from recent NPG papers.
- We are part of a successful H2020 application called "PRODIGIO": Developing early-warning systems for improved microalgae PROduction and anaerobic DIGestIOn. Magnus Arntzen and Live Hagen will use our omic capabilites to explore process monitoring and failure in bioreactors
- Magnus Arntzen has been awarded an ~13.5 mNOK Emerging Investigator Fellowship from the Novo Nordisk Fonden. Project title: DENITRO: Oxidative Polysaccharide Conversion in Anoxia by Denitrifying Organisms
- Magnus Arntzen has published a new blog post looking at using Galaxy to integrate multi-omic datasets. See HERE
- Live Hagen has been awarded an 8 mNOK Young Research Talent Researcher project from NFR! "SeaCow: Promoting efficient, low emitting cows through manipulation of the rumen microbiome". Bessy gonna eat seaweed!
- ImprovAFish is funded! Our ~19.5 mNOK BlueBio CoFund (ERA-Net) project: “Improving aquaculture sustainability by modulating the feed-microbiome-host axis in Fish”
- We have just been awarded a new grant! A 5yr, ~13.5 mNOK Ascending Investigator Fellowship from the Novo Nordisk Fonden, called: SuPA[cow]: Sustainable production of animals by optimizing the feed-microbiome-host axis
- Sabina's mSphere paper is highlighted in an American Society for Microbiology press release
- Our AGa story in Microbiome features as part of the "Washington's Week in Science" newsletter
- "Bakterier og virus hjelper elgen å fordøye kvist og bark" Read the Forskning.no article here
- Nature Microbiology "Behind the paper": Uncovering microbial interactions with a network of scientist
- Sabina Leanti La Rosa took out the best poster prize at the 2018 ROWETT-INRA Conference!
- "Newly discovered bacteria can break down biomass" Read the Phys.orgarticle here or the Renewable Energy Magazine article here
WHAT WHO WHERE STATUS "Designer fiber" for the precise manipulation of animal gut microbiomes. Sabina Microbiome Interactions in Health and Disease conference, 24-26 October 2022, Wellcome Genome Campus, Hinxton (UK) Invited Talk. Integrating multi-omics and enzymology to untangle systems for typical and atypical glycan deconstruction in gut microbiomes Sabina CBM14 (Carbohydrate Bioengineering Meeting). September 25th-28th 2022, Norefjell (Norway). Invited Talk. Decrypting the mechanism for xanthan gum processing by human gut bacteria through multi-omics and enzymology. Sabina CIGENE seminar series. April 6th 2022, Ås (Norway) Invited Talk. Reconstructing complex microbiomes in the “-Ome” era Phil 1st Norwegian Symposium on Proteomics and Biological Mass Spectrometry May 5th 2022 Invited Talk. Digital optimization of the feed-microbiome-host nexus. Phil Australian Microbial Ecology Conference Nov. 7-9, 2022, Melbourne, Australia Invited Talk. Digital optimization of the feed-microbiome-host nexus. Phil FASEB Microbial Glycobiology Conference. Jun. 12-16, 2022, Lisbon, Portugal. Invited Talk. Digital optimization of the feed-microbiome-host nexus. Phil Applied Hologenomics Conference. Sep. 13-15, 2022, Bilbao, Spain Invited Talk. Digital optimization of the feed-microbiome-host nexus. Phil Congress on Gastrointestinal Function. Apr. 11-13, 2022, Chicago, USA Invited Talk. Genome-centric metaproteomics reveals metabolic influence of the ciliate Entodinium caudatum within the rumen microbiome Thea Congress on Gastrointestinal Function. Apr. 11-13, 2022, Chicago, USA Talk Transkingdom network analysis across the host-microbiome nexus in the bovine rumen reveals associations to host fitness. Ianina ISME, Lausanne, Switzerland, 14-19 August 2022 Submitted abstract Holo-omics and host-microbiome interactions in the herbivore rumen Carl ISME, Lausanne, Switzerland, 14-19 August 2022 Submitted abstract The Salmon Microbial Genome Atlas (SMGA) enables novel insights into bacteria-fish interactions via functional mapping Arturo ISME, Lausanne, Switzerland, 14-19 August 2022 Submitted abstract Feed-microbiome host interactions in Atlantic salmon over time Shashank ISME, Lausanne, Switzerland, 14-19 August 2022 Submitted abstract Disentangling microbial changes upon organic loading rate disturbances in anaerobic reactors Juline ISME, Lausanne, Switzerland, 14-19 August 2022 Submitted abstract Genome-centric metaproteomics reveals metabolic influence of the ciliate Entodinium caudatum within the rumen microbiome Thea ISME, Lausanne, Switzerland, 14-19 August 2022 Submitted abstract Polysaccharide-degrading potential of microbiomes in agricultural field denitrification beds Valerie ISME, Lausanne, Switzerland, 14-19 August 2022 Submitted abstract Microbial indicators of process failure upon organic loading rates disturbances Juline 17th World Congress on Anaerobic Digestion: Biogas+Beyond, USA Submitted abstract Disentangling microbial changes upon organic loading rate disturbances in anaerobic reactors Juline 4th International Conference on Biogas Microbiology, Portugal Submitted abstract
- T.O. Andersen, I. Altshuler, A.V.P. de Leon, J. Walter, E. McGovern, K. Keog, C. Martin, L. Bernard, H. Fougère, D.P. Morgavi, J.L. Firkins, Z. Yu, T.R. Hvidsten, S.M. Waters, M. Popova, M.Ø. Arntzen, L.H. Hagen, P.B. Pope (2022). The metabolic influence of the core ciliate Entodinium caudatum within the rumen microbiome. https://doi.org/10.1101/2022.06.22.497163
- *M.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, ^B. Pope, ^E.C. Martens (2021). The Food Additive Xanthan Gum Drives Adaptation of the Human Gut Microbiota. doi: https://doi.org/10.1101/2021.06.02.446819
- H.R. Jonassen, L.H. Hagen, S.H.W. Vick, S.H.W. Vick, M.Ø. Arntzen, V.G.H. Eijsink, Å. Frostegård, P. Lycus, l. Molstad, P.B. Pope, L.R. Bakken (2021). Bacteria in biogas digestates for reduced climate forcing. bioRxiv https://doi.org/10.1101/2020.11.16.384990
- A.E. Naas, P.B. Pope (2019). A mechanistic overview of ruminal fibre digestion. PeerJ Preprints 7:e27831v1 https://doi.org/10.7287/peerj.preprints.27831v1
BIO326: Genome Sequencing: tools and analysis
Using the latest technologies and computational strategies, this course will explore the different approaches used to recover and reconstruct genome sequences from various biological sources including prokaryotic and eukaryotic cells, as well as complex microbial communities (i.e. microbiomes).
More information can be found HERE.
BIN420: Bioinformatics for functional meta-omics
This course includes an array of contrasting tools to decrypt microbial communities, including those that assess community structure (metagenomics, predictive genome-reconstruction) and function (metatranscriptomics, metaproteomics). More information can be found via the NMBU and NORBIS websites
HFX407 Emissions and Microbiota: a path to sustainable animal production
Qualify the students to conduct, evaluate and discuss experiments and concepts in (animal nutrition) research related to feed digestion by microbial fermentation and emissions of methane, carbon dioxide and ammonia. More information can be here.
Genome Science Msc Program
The Genome Science study combines the disciplines of genetics, genome biology, genome technologies, statistics and bioinformatics. More information can be found here.
We have multiple project investigating sustainable production of animals by optimizing the feed-microbiome-host-axis
Background: Human population growth is driving a rise in animal production for food, which necessitates more efficient and sustainable practices. One promising route to achieve this, is to unravel the connection between the feed animals eat, their bodily function and the microbes in their gut, not only to optimize nutrition but also to reduce negative impacts such as the emission of greenhouse gases (methane). Our new strategy to collectively study the animal, its diet and all its microbes as one unit (the holobiont), is known as holo-omics. This strategy, enabled by recent biotechnological developments, can improve our understanding of how animals digest their feed and sustain their growth. These projects combines novel methane-inhibiting feed ingredients, animal experiments and holo-omics to jointly analyze animals, their feed and their microbes. The outcome will be optimization of feeding strategies tailored to specific types of animals, to ultimately improve their growth and production whilst reducing their carbon footprint.
Methods: You will learn how to study complex microbiomes, handle next-generation sequecing data and operate state of the art analytical equipment.
Some key biological and societal questions your MEMO Msc project can answer:
• How do microbes assist nutrition and control methane emissions in cows?
• How do microbiomes control natural cycles that effect our climate?
• How do gut microbes enable us to digest food and maintain our health?
• How do gut microbes support their host animal/fish?
• How can we use microbiomes to recycle waste and create green energy?
List of speakers
Date Speaker Room 12.01 Ronja Aksnes 26.01 Phil Aksnes 09.02 Valerie Aksnes 23.02 Lindah Aksnes 09.03 Sabina Aksnes 23.03 Carl Aksnes 30.03 Magnus Aksnes 06.04 Easter Aksnes 13.04 Arturo Aksnes 27.04 New postdoc Aksnes 11.05 New phd Aksnes 25.05 Alessandra Aksnes 08.06 Shashank Aksnes 22.06 Thea Aksnes
Date Speaker Room 06.10 Alessandra MU166 20.10 Shashank Aksnes 03.11 Thea&Carl - special edition 45 min Aksnes 17.11 Juline MU166 01.12 Live Aksnes 15.12 Christmas lunch Vitenparken
Sorry, nothing at the moment
- Francesco Delogu (PhD) ---> Postdoc in the Wilmes Lab
- J. Chris Gaby (Postdoc) ---> USDA Agricultural Research Service
- Benoit J. Kunath (PhD) ---> Postdoc in the Wilmes Lab
- Johan Larsbrink (Postdoc) ---> Assistant Professor Chalmers University
- Jeremy A. Frank (Postdoc) ---> Software engineer, Cloudbeds
- Adrian E. Naas (Postdoc) ---> Head Engineer, Univ. of South-Eastern Norway
- Thea Os Andersen (Msc - KBM)
- Tina Johannessen (Msc - BIOVIT)
- Alexsander Lysberg (Msc - BIOVIT)
- Katrine Sømliøy Eikanger (Msc - KBM - PEP)
- Sander Johnsen (Msc - BIOVIT)