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Items: 49

1.

Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway.

Salgado-Flores A, Tveit AT, Wright AD, Pope PB, Sundset MA.

PLoS One. 2019 Mar 11;14(3):e0213503. doi: 10.1371/journal.pone.0213503. eCollection 2019.

2.

The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans.

La Rosa SL, Leth ML, Michalak L, Hansen ME, Pudlo NA, Glowacki R, Pereira G, Workman CT, Arntzen MØ, Pope PB, Martens EC, Hachem MA, Westereng B.

Nat Commun. 2019 Feb 22;10(1):905. doi: 10.1038/s41467-019-08812-y.

3.

Wood-Derived Dietary Fibers Promote Beneficial Human Gut Microbiota.

La Rosa SL, Kachrimanidou V, Buffetto F, Pope PB, Pudlo NA, Martens EC, Rastall RA, Gibson GR, Westereng B.

mSphere. 2019 Jan 23;4(1). pii: e00554-18. doi: 10.1128/mSphere.00554-18.

4.

Proteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling Bacteroidetes.

Taillefer M, Arntzen MØ, Henrissat B, Pope PB, Larsbrink J.

mSystems. 2018 Nov 20;3(6). pii: e00240-18. doi: 10.1128/mSystems.00240-18. eCollection 2018 Nov-Dec.

5.

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.

Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, Purvine SO, Hoyt DW, Schückel J, Jørgensen B, Willats W, Spalinger DE, Firkins JL, Lipton MS, Sullivan MB, Pope PB, Wrighton KC.

Nat Microbiol. 2018 Nov;3(11):1274-1284. doi: 10.1038/s41564-018-0225-4. Epub 2018 Oct 24.

PMID:
30356154
6.

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus.

Kunath BJ, Delogu F, Naas AE, Arntzen MØ, Eijsink VGH, Henrissat B, Hvidsten TR, Pope PB.

ISME J. 2019 Mar;13(3):603-617. doi: 10.1038/s41396-018-0290-y. Epub 2018 Oct 12.

PMID:
30315317
7.

Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite.

Liu N, Li H, Chevrette MG, Zhang L, Cao L, Zhou H, Zhou X, Zhou Z, Pope PB, Currie CR, Huang Y, Wang Q.

ISME J. 2019 Jan;13(1):104-117. doi: 10.1038/s41396-018-0255-1. Epub 2018 Aug 16.

8.

Host-linked soil viral ecology along a permafrost thaw gradient.

Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, Singleton CM, Solden LM, Naas AE, Boyd JA, Hodgkins SB, Wilson RM, Trubl G, Li C, Frolking S, Pope PB, Wrighton KC, Crill PM, Chanton JP, Saleska SR, Tyson GW, Rich VI, Sullivan MB.

Nat Microbiol. 2018 Aug;3(8):870-880. doi: 10.1038/s41564-018-0190-y. Epub 2018 Jul 16.

PMID:
30013236
9.

Discovery and characterization of a thermostable two-domain GH6 endoglucanase from a compost metagenome.

Jensen MS, Fredriksen L, MacKenzie AK, Pope PB, Leiros I, Chylenski P, Williamson AK, Christopeit T, Østby H, Vaaje-Kolstad G, Eijsink VGH.

PLoS One. 2018 May 24;13(5):e0197862. doi: 10.1371/journal.pone.0197862. eCollection 2018.

10.

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.

Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB.

Microbiome. 2018 Mar 1;6(1):44. doi: 10.1186/s40168-018-0421-8.

11.

The Skin-Mucus Microbial Community of Farmed Atlantic Salmon (Salmo salar).

Minniti G, Hagen LH, Porcellato D, Jørgensen SM, Pope PB, Vaaje-Kolstad G.

Front Microbiol. 2017 Oct 20;8:2043. doi: 10.3389/fmicb.2017.02043. eCollection 2017.

12.

Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon.

Rudi K, Angell IL, Pope PB, Vik JO, Sandve SR, Snipen LG.

Appl Environ Microbiol. 2018 Jan 2;84(2). pii: e01974-17. doi: 10.1128/AEM.01974-17. Print 2018 Jan 15.

13.

Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity.

Arntzen MØ, Várnai A, Mackie RI, Eijsink VGH, Pope PB.

Environ Microbiol. 2017 Jul;19(7):2701-2714. doi: 10.1111/1462-2920.13770. Epub 2017 May 29.

PMID:
28447389
14.

Metagenomics and CAZyme Discovery.

Kunath BJ, Bremges A, Weimann A, McHardy AC, Pope PB.

Methods Mol Biol. 2017;1588:255-277. doi: 10.1007/978-1-4939-6899-2_20.

PMID:
28417375
15.

First insight into the faecal microbiota of the high Arctic muskoxen (Ovibos moschatus).

Salgado-Flores A, Bockwoldt M, Hagen LH, Pope PB, Sundset MA.

Microb Genom. 2016 Jul 29;2(7):e000066. doi: 10.1099/mgen.0.000066. eCollection 2016 Jul.

16.

Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis.

Larsbrink J, Tuveng TR, Pope PB, Bulone V, Eijsink VG, Brumer H, McKee LS.

Data Brief. 2017 Feb 17;11:484-490. doi: 10.1016/j.dib.2017.02.032. eCollection 2017 Apr.

17.

Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis.

Larsbrink J, Tuveng TR, Pope PB, Bulone V, Eijsink VG, Brumer H, McKee LS.

J Proteomics. 2017 Mar 6;156:63-74. doi: 10.1016/j.jprot.2017.01.003. Epub 2017 Jan 6.

PMID:
28069559
18.

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.

Weimann A, Mooren K, Frank J, Pope PB, Bremges A, McHardy AC.

mSystems. 2016 Dec 27;1(6). pii: e00101-16. doi: 10.1128/mSystems.00101-16. eCollection 2016 Nov-Dec.

19.

A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin.

Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VG, Koropatkin NM, McBride MJ, Pope PB.

Biotechnol Biofuels. 2016 Nov 28;9:260. eCollection 2016.

20.

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.

Frank JA, Arntzen MØ, Sun L, Hagen LH, McHardy AC, Horn SJ, Eijsink VG, Schnürer A, Pope PB.

mSystems. 2016 Sep 13;1(5). pii: e00092-16. eCollection 2016 Sep-Oct.

21.

Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester.

Hagen LH, Frank JA, Zamanzadeh M, Eijsink VG, Pope PB, Horn SJ, Arntzen MØ.

Appl Environ Microbiol. 2016 Dec 30;83(2). pii: e01955-16. doi: 10.1128/AEM.01955-16. Print 2017 Jan 15.

22.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

23.

The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health.

Umu ÖC, Bäuerl C, Oostindjer M, Pope PB, Hernández PE, Pérez-Martínez G, Diep DB.

PLoS One. 2016 Oct 3;11(10):e0164036. doi: 10.1371/journal.pone.0164036. eCollection 2016.

24.

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions.

Salgado-Flores A, Hagen LH, Ishaq SL, Zamanzadeh M, Wright AD, Pope PB, Sundset MA.

PLoS One. 2016 May 9;11(5):e0155213. doi: 10.1371/journal.pone.0155213. eCollection 2016.

25.

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.

Frank JA, Pan Y, Tooming-Klunderud A, Eijsink VG, McHardy AC, Nederbragt AJ, Pope PB.

Sci Rep. 2016 May 9;6:25373. doi: 10.1038/srep25373.

26.

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure.

Sun L, Pope PB, Eijsink VG, Schnürer A.

Microb Biotechnol. 2015 Sep;8(5):815-27. doi: 10.1111/1751-7915.12298. Epub 2015 Jul 8.

27.

Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus.

Naas AE, MacKenzie AK, Dalhus B, Eijsink VG, Pope PB.

Sci Rep. 2015 Jul 2;5:11666. doi: 10.1038/srep11666.

28.

The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture.

Hagen LH, Vivekanand V, Pope PB, Eijsink VG, Horn SJ.

Appl Microbiol Biotechnol. 2015 Jul;99(13):5749-61. doi: 10.1007/s00253-015-6623-0. Epub 2015 May 7.

PMID:
25947246
29.

Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations.

Umu ÖC, Frank JA, Fangel JU, Oostindjer M, da Silva CS, Bolhuis EJ, Bosch G, Willats WG, Pope PB, Diep DB.

Microbiome. 2015 Apr 16;3:16. doi: 10.1186/s40168-015-0078-5. eCollection 2015.

30.

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders.

Konietzny SG, Pope PB, Weimann A, McHardy AC.

Biotechnol Biofuels. 2014 Sep 9;7(1):124. doi: 10.1186/s13068-014-0124-8. eCollection 2014.

31.

A polysaccharide utilization locus from an uncultured bacteroidetes phylotype suggests ecological adaptation and substrate versatility.

Mackenzie AK, Naas AE, Kracun SK, Schückel J, Fangel JU, Agger JW, Willats WG, Eijsink VG, Pope PB.

Appl Environ Microbiol. 2015 Jan;81(1):187-95. doi: 10.1128/AEM.02858-14. Epub 2014 Oct 17.

32.

Microbial community structure and dynamics during co-digestion of whey permeate and cow manure in continuous stirred tank reactor systems.

Hagen LH, Vivekanand V, Linjordet R, Pope PB, Eijsink VG, Horn SJ.

Bioresour Technol. 2014 Nov;171:350-9. doi: 10.1016/j.biortech.2014.08.095. Epub 2014 Aug 30.

PMID:
25222739
33.

Do rumen Bacteroidetes utilize an alternative mechanism for cellulose degradation?

Naas AE, Mackenzie AK, Mravec J, Schückel J, Willats WG, Eijsink VG, Pope PB.

MBio. 2014 Aug 5;5(4):e01401-14. doi: 10.1128/mBio.01401-14.

34.

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community.

Zhou Y, Pope PB, Li S, Wen B, Tan F, Cheng S, Chen J, Yang J, Liu F, Lei X, Su Q, Zhou C, Zhao J, Dong X, Jin T, Zhou X, Yang S, Zhang G, Yang H, Wang J, Yang R, Eijsink VG, Wang J.

Sci Rep. 2014 Jun 13;4:5288. doi: 10.1038/srep05288.

35.

Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes.

Rosewarne CP, Pope PB, Cheung JL, Morrison M.

J Ind Microbiol Biotechnol. 2014 Mar;41(3):601-6. doi: 10.1007/s10295-013-1395-y. Epub 2014 Jan 22.

PMID:
24448980
36.

Potential applications of gut microbiota to control human physiology.

Umu OC, Oostindjer M, Pope PB, Svihus B, Egelandsdal B, Nes IF, Diep DB.

Antonie Van Leeuwenhoek. 2013 Nov;104(5):609-18. doi: 10.1007/s10482-013-0008-0. Epub 2013 Aug 23. Review.

PMID:
23975514
37.

Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer.

Præsteng KE, Pope PB, Cann IK, Mackie RI, Mathiesen SD, Folkow LP, Eijsink VG, Sundset MA.

Microb Ecol. 2013 Nov;66(4):840-9.

PMID:
23959114
38.

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes.

Weimann A, Trukhina Y, Pope PB, Konietzny SG, McHardy AC.

Biotechnol Biofuels. 2013 Feb 15;6(1):24. doi: 10.1186/1754-6834-6-24.

39.

Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima.

Pope PB, Vivekanand V, Eijsink VG, Horn SJ.

3 Biotech. 2013 Oct;3(5):407-414. doi: 10.1007/s13205-012-0097-x. Epub 2012 Oct 25.

40.

Draft genome sequence of the methane-oxidizing bacterium Methylococcus capsulatus (Texas).

Kleiveland CR, Hult LT, Kuczkowska K, Jacobsen M, Lea T, Pope PB.

J Bacteriol. 2012 Dec;194(23):6626. doi: 10.1128/JB.01656-12.

41.

Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci.

Pope PB, Mackenzie AK, Gregor I, Smith W, Sundset MA, McHardy AC, Morrison M, Eijsink VG.

PLoS One. 2012;7(6):e38571. doi: 10.1371/journal.pone.0038571. Epub 2012 Jun 6. Erratum in: PLoS One. 2014;9(7):e104612.

42.

Two SusD-like proteins encoded within a polysaccharide utilization locus of an uncultured ruminant Bacteroidetes phylotype bind strongly to cellulose.

Mackenzie AK, Pope PB, Pedersen HL, Gupta R, Morrison M, Willats WG, Eijsink VG.

Appl Environ Microbiol. 2012 Aug;78(16):5935-7. doi: 10.1128/AEM.01164-12. Epub 2012 Jun 8.

43.

Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies.

Pope PB, Smith W, Denman SE, Tringe SG, Barry K, Hugenholtz P, McSweeney CS, McHardy AC, Morrison M.

Science. 2011 Jul 29;333(6042):646-8. doi: 10.1126/science.1205760. Epub 2011 Jun 30.

44.

Taxonomic metagenome sequence assignment with structured output models.

Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, McHardy AC.

Nat Methods. 2011 Mar;8(3):191-2. doi: 10.1038/nmeth0311-191. No abstract available.

45.

High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut.

Rosewarne CP, Pope PB, Denman SE, McSweeney CS, O'Cuiv P, Morrison M.

Microb Ecol. 2011 Feb;61(2):448-54. doi: 10.1007/s00248-010-9745-z. Epub 2010 Sep 14.

PMID:
20838785
46.

Muramidases found in the foregut microbiome of the Tammar wallaby can direct cell aggregation and biofilm formation.

Pope PB, Totsika M, Aguirre de Carcer D, Schembri MA, Morrison M.

ISME J. 2011 Feb;5(2):341-50. doi: 10.1038/ismej.2010.116. Epub 2010 Jul 29.

47.

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.

Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, McHardy AC, Cheng JF, Hugenholtz P, McSweeney CS, Morrison M.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14793-8. doi: 10.1073/pnas.1005297107. Epub 2010 Jul 28.

48.

Plant biomass degradation by gut microbiomes: more of the same or something new?

Morrison M, Pope PB, Denman SE, McSweeney CS.

Curr Opin Biotechnol. 2009 Jun;20(3):358-63. doi: 10.1016/j.copbio.2009.05.004. Epub 2009 Jun 8. Review.

PMID:
19515552
49.

Metagenomic analysis of a freshwater toxic cyanobacteria bloom.

Pope PB, Patel BK.

FEMS Microbiol Ecol. 2008 Apr;64(1):9-27. doi: 10.1111/j.1574-6941.2008.00448.x. Epub 2008 Mar 4.

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