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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Myer PR, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL.

Genome Biol. 2019 Aug 2;20(1):153. doi: 10.1186/s13059-019-1760-x.


Valorisation of the invasive species, Prosopis juliflora, using the carboxylate platform to produce volatile fatty acids.

Njokweni SG, Weimer PJ, Warburg L, Botes M, van Zyl WH.

Bioresour Technol. 2019 Sep;288:121602. doi: 10.1016/j.biortech.2019.121602. Epub 2019 Jun 5.


A global analysis of gene expression in Fibrobacter succinogenes S85 grown on cellulose and soluble sugars at different growth rates.

Neumann AP, Weimer PJ, Suen G.

Biotechnol Biofuels. 2018 Oct 27;11:295. doi: 10.1186/s13068-018-1290-x. eCollection 2018.


Diet Influences Early Microbiota Development in Dairy Calves without Long-Term Impacts on Milk Production.

Dill-McFarland KA, Weimer PJ, Breaker JD, Suen G.

Appl Environ Microbiol. 2019 Jan 9;85(2). pii: e02141-18. doi: 10.1128/AEM.02141-18. Print 2019 Jan 15.


Camelina Seed Supplementation at Two Dietary Fat Levels Change Ruminal Bacterial Community Composition in a Dual-Flow Continuous Culture System.

Dai X, Weimer PJ, Dill-McFarland KA, Brandao VLN, Suen G, Faciola AP.

Front Microbiol. 2017 Nov 3;8:2147. doi: 10.3389/fmicb.2017.02147. eCollection 2017.


Symposium review: Host-rumen microbe interactions may be leveraged to improve the productivity of dairy cows.

Bickhart DM, Weimer PJ.

J Dairy Sci. 2018 Aug;101(8):7680-7689. doi: 10.3168/jds.2017-13328. Epub 2017 Nov 6. Review.


Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows.

Weimer PJ, Cox MS, Vieira de Paula T, Lin M, Hall MB, Suen G.

J Dairy Sci. 2017 Sep;100(9):7165-7182. doi: 10.3168/jds.2017-12746. Epub 2017 Jul 6.


Fermentation of model hemicelluloses by Prevotella strains and Butyrivibrio fibrisolvens in pure culture and in ruminal enrichment cultures.

Emerson EL, Weimer PJ.

Appl Microbiol Biotechnol. 2017 May;101(10):4269-4278. doi: 10.1007/s00253-017-8150-7. Epub 2017 Feb 8.


In vitro ruminal fermentation of treated alfalfa silage using ruminal inocula from high and low feed-efficient lactating cows.

Contreras-Govea FE, Muck RE, Weimer PJ, Hymes-Fecht UC.

J Appl Microbiol. 2016 Aug;121(2):333-40. doi: 10.1111/jam.13103.


Erratum to: Impacts of ruminal microorganisms on the production of fuels: how can we intercede from the outside?

Weimer PJ, Kohn RA.

Appl Microbiol Biotechnol. 2016 Apr;100(8):3399. doi: 10.1007/s00253-016-7411-1. No abstract available.


Impacts of ruminal microorganisms on the production of fuels: how can we intercede from the outside?

Weimer PJ, Kohn RA.

Appl Microbiol Biotechnol. 2016 Apr;100(8):3389-98. doi: 10.1007/s00253-016-7358-2. Epub 2016 Feb 16. Review. Erratum in: Appl Microbiol Biotechnol. 2016 Apr;100(8):3399.


Divergent utilization patterns of grass fructan, inulin, and other nonfiber carbohydrates by ruminal microbes.

Hall MB, Weimer PJ.

J Dairy Sci. 2016 Jan;99(1):245-57. doi: 10.3168/jds.2015-10417. Epub 2015 Nov 18.


Effects of ruminal dosing of Holstein cows with Megasphaera elsdenii on milk fat production, ruminal chemistry, and bacterial strain persistence.

Weimer PJ, Da Silva Cabral L, Cacite F.

J Dairy Sci. 2015 Nov;98(11):8078-92. doi: 10.3168/jds.2015-9721. Epub 2015 Aug 20.


Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths.

Dill-McFarland KA, Weimer PJ, Pauli JN, Peery MZ, Suen G.

Environ Microbiol. 2016 May;18(5):1391-402. doi: 10.1111/1462-2920.13022. Epub 2015 Sep 10.


Redox mediators modify end product distribution in biomass fermentations by mixed ruminal microbes in vitro.

Nerdahl MA, Weimer PJ.

AMB Express. 2015 Dec;5(1):130. doi: 10.1186/s13568-015-0130-7. Epub 2015 Aug 4.


Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency.

Jewell KA, McCormick CA, Odt CL, Weimer PJ, Suen G.

Appl Environ Microbiol. 2015 Jul;81(14):4697-710. doi: 10.1128/AEM.00720-15. Epub 2015 May 1.


Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations.

Weimer PJ.

Front Microbiol. 2015 Apr 10;6:296. doi: 10.3389/fmicb.2015.00296. eCollection 2015. Review.


Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay.

Mohammed R, Brink GE, Stevenson DM, Neumann AP, Beauchemin KA, Suen G, Weimer PJ.

Front Microbiol. 2014 Dec 9;5:689. doi: 10.3389/fmicb.2014.00689. eCollection 2014.


Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis.

Christopherson MR, Dawson JA, Stevenson DM, Cunningham AC, Bramhacharya S, Weimer PJ, Kendziorski C, Suen G.

BMC Genomics. 2014 Dec 4;15:1066. doi: 10.1186/1471-2164-15-1066.


Production of medium-chain volatile fatty acids by mixed ruminal microorganisms is enhanced by ethanol in co-culture with Clostridium kluyveri.

Weimer PJ, Nerdahl M, Brandl DJ.

Bioresour Technol. 2015 Jan;175:97-101. doi: 10.1016/j.biortech.2014.10.054. Epub 2014 Oct 18.


Improving ethanol production from alfalfa stems via ambient-temperature acid pretreatment and washing.

Zhou S, Weimer PJ, Hatfield RD, Runge TM, Digman M.

Bioresour Technol. 2014 Oct;170:286-292. doi: 10.1016/j.biortech.2014.08.002. Epub 2014 Aug 9.


A syndrome of mutualism reinforces the lifestyle of a sloth.

Pauli JN, Mendoza JE, Steffan SA, Carey CC, Weimer PJ, Peery MZ.

Proc Biol Sci. 2014 Jan 22;281(1778):20133006. doi: 10.1098/rspb.2013.3006. Print 2014 Mar 7.


Unique interrelationships between fiber composition, water-soluble carbohydrates, and in vitro gas production for fall-grown oat forages.

Coblentz WK, Nellis SE, Hoffman PC, Hall MB, Weimer PJ, Esser NM, Bertram MG.

J Dairy Sci. 2013;96(11):7195-7209. doi: 10.3168/jds.2013-6889. Epub 2013 Sep 5.


Changes in rumen bacterial community composition in steers in response to dietary nitrate.

Lin M, Guo W, Meng Q, Stevenson DM, Weimer PJ, Schaefer DM.

Appl Microbiol Biotechnol. 2013 Oct;97(19):8719-27. doi: 10.1007/s00253-013-5143-z. Epub 2013 Aug 18.


Fermentation of alfalfa wet-fractionation liquids to volatile fatty acids by Streptococcus bovis and Megasphaera elsdenii.

Weimer PJ, Digman MF.

Bioresour Technol. 2013 Aug;142:88-94. doi: 10.1016/j.biortech.2013.05.016. Epub 2013 May 14.


In vitro degradation and fermentation of three dietary fiber sources by human colonic bacteria.

Bliss DZ, Weimer PJ, Jung HJ, Savik K.

J Agric Food Chem. 2013 May 15;61(19):4614-21. doi: 10.1021/jf3054017. Epub 2013 May 3.


Quantitative analysis of growth and volatile fatty acid production by the anaerobic ruminal bacterium Megasphaera elsdenii T81.

Weimer PJ, Moen GN.

Appl Microbiol Biotechnol. 2013 May;97(9):4075-81. doi: 10.1007/s00253-012-4645-4. Epub 2012 Dec 28.


Individual animal variability in ruminal bacterial communities and ruminal acidosis in primiparous Holstein cows during the periparturient period.

Mohammed R, Stevenson DM, Weimer PJ, Penner GB, Beauchemin KA.

J Dairy Sci. 2012 Nov;95(11):6716-30. doi: 10.3168/jds.2012-5772. Epub 2012 Sep 12.


Changes in ruminal bacterial community composition following feeding of alfalfa ensiled with a lactic acid bacterial inoculant.

Mohammed R, Stevenson DM, Beauchemin KA, Muck RE, Weimer PJ.

J Dairy Sci. 2012 Jan;95(1):328-39. doi: 10.3168/jds.2011-4492.


Isolation, characterization, and quantification of Clostridium kluyveri from the bovine rumen.

Weimer PJ, Stevenson DM.

Appl Microbiol Biotechnol. 2012 Apr;94(2):461-6. doi: 10.1007/s00253-011-3751-z. Epub 2011 Dec 9.


Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7.

Suen G, Stevenson DM, Bruce DC, Chertkov O, Copeland A, Cheng JF, Detter C, Detter JC, Goodwin LA, Han CS, Hauser LJ, Ivanova NN, Kyrpides NC, Land ML, Lapidus A, Lucas S, Ovchinnikova G, Pitluck S, Tapia R, Woyke T, Boyum J, Mead D, Weimer PJ.

J Bacteriol. 2011 Oct;193(19):5574-5. doi: 10.1128/JB.05621-11.


The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist.

Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J, Deneke J, Drinkwater C, Ivanova NN, Mikhailova N, Chertkov O, Goodwin LA, Currie CR, Mead D, Brumm PJ.

PLoS One. 2011 Apr 19;6(4):e18814. doi: 10.1371/journal.pone.0018814.


End product yields from the extraruminal fermentation of various polysaccharide, protein and nucleic acid components of biofuels feedstocks.

Weimer PJ.

Bioresour Technol. 2011 Feb;102(3):3254-9. doi: 10.1016/j.biortech.2010.11.050. Epub 2010 Dec 8.


Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents.

Weimer PJ, Stevenson DM, Mantovani HC, Man SL.

J Dairy Sci. 2010 Dec;93(12):5902-12. doi: 10.3168/jds.2010-3500.


An insect herbivore microbiome with high plant biomass-degrading capacity.

Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR.

PLoS Genet. 2010 Sep 23;6(9):e1001129. doi: 10.1371/journal.pgen.1001129.


Optimizing on-farm pretreatment of perennial grasses for fuel ethanol production.

Digman MF, Shinners KJ, Casler MD, Dien BS, Hatfield RD, Jung HJ, Muck RE, Weimer PJ.

Bioresour Technol. 2010 Jul;101(14):5305-14. doi: 10.1016/j.biortech.2010.02.014. Epub 2010 Mar 3.


Comparative study of SPORL and dilute-acid pretreatments of spruce for cellulosic ethanol production.

Shuai L, Yang Q, Zhu JY, Lu FC, Weimer PJ, Ralph J, Pan XJ.

Bioresour Technol. 2010 May;101(9):3106-14. doi: 10.1016/j.biortech.2009.12.044. Epub 2010 Jan 12.


pH dynamics and bacterial community composition in the rumen of lactating dairy cows.

Palmonari A, Stevenson DM, Mertens DR, Cruywagen CW, Weimer PJ.

J Dairy Sci. 2010 Jan;93(1):279-87. doi: 10.3168/jds.2009-2207.


Shifts in bacterial community composition in the rumen of lactating dairy cows under milk fat-depressing conditions.

Weimer PJ, Stevenson DM, Mertens DR.

J Dairy Sci. 2010 Jan;93(1):265-78. doi: 10.3168/jds.2009-2206.


Plant species composition and biofuel yields of conservation grasslands.

Adler PR, Sanderson MA, Weimer PJ, Vogel KP.

Ecol Appl. 2009 Dec;19(8):2202-9.


Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants.

Pinto-Tomás AA, Anderson MA, Suen G, Stevenson DM, Chu FS, Cleland WW, Weimer PJ, Currie CR.

Science. 2009 Nov 20;326(5956):1120-3. doi: 10.1126/science.1173036.


ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle.

Welkie DG, Stevenson DM, Weimer PJ.

Anaerobe. 2010 Apr;16(2):94-100. doi: 10.1016/j.anaerobe.2009.07.002. Epub 2009 Jul 15.


Lessons from the cow: what the ruminant animal can teach us about consolidated bioprocessing of cellulosic biomass.

Weimer PJ, Russell JB, Muck RE.

Bioresour Technol. 2009 Nov;100(21):5323-31. doi: 10.1016/j.biortech.2009.04.075. Epub 2009 Jun 26. Review.


Forage quality and composition measurements as predictors of ethanol yield from maize (Zea mays L.) stover.

Lorenz AJ, Anex RP, Isci A, Coors JG, de Leon N, Weimer PJ.

Biotechnol Biofuels. 2009 Mar 9;2(1):5. doi: 10.1186/1754-6834-2-5.


Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen.

Russell JB, Muck RE, Weimer PJ.

FEMS Microbiol Ecol. 2009 Feb;67(2):183-97. doi: 10.1111/j.1574-6941.2008.00633.x. Review.


Effect of monensin feeding and withdrawal on populations of individual bacterial species in the rumen of lactating dairy cows fed high-starch rations.

Weimer PJ, Stevenson DM, Mertens DR, Thomas EE.

Appl Microbiol Biotechnol. 2008 Aug;80(1):135-45. doi: 10.1007/s00253-008-1528-9. Epub 2008 Jun 6.


Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR.

Stevenson DM, Weimer PJ.

Appl Microbiol Biotechnol. 2007 May;75(1):165-74. Epub 2007 Jan 18. Erratum in: Appl Microbiol Biotechnol. 2009 Jul;83(5):987-8.


Studies of the extracellular glycocalyx of the anaerobic cellulolytic bacterium Ruminococcus albus 7.

Weimer PJ, Price NP, Kroukamp O, Joubert LM, Wolfaardt GM, Van Zyl WH.

Appl Environ Microbiol. 2006 Dec;72(12):7559-66. Epub 2006 Oct 6.

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