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Items: 1 to 50 of 104

1.

"Candidatus Nitrosotenuis aquarius," an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter.

Sauder LA, Engel K, Lo CC, Chain P, Neufeld JD.

Appl Environ Microbiol. 2018 Sep 17;84(19). pii: e01430-18. doi: 10.1128/AEM.01430-18. Print 2018 Oct 1.

PMID:
29959256
2.

Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia.

Ross AA, Müller KM, Weese JS, Neufeld JD.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):E5786-E5795. doi: 10.1073/pnas.1801302115. Epub 2018 Jun 5.

3.

Development of a microbial test suite and data integration method for assessing microbial health of contaminated soil.

Kvas S, Rahn J, Engel K, Neufeld JD, Villeneuve PJ, Trevors JT, Lee H, Scroggins RP, Beaudette LA.

J Microbiol Methods. 2017 Dec;143:66-77. doi: 10.1016/j.mimet.2017.10.004. Epub 2017 Oct 17.

PMID:
29050881
4.

The Skin Microbiome of Cohabiting Couples.

Ross AA, Doxey AC, Neufeld JD.

mSystems. 2017 Jul 20;2(4). pii: e00043-17. doi: 10.1128/mSystems.00043-17. eCollection 2017 Jul-Aug.

5.

Anaerobic oxidation of methane coupled with extracellular electron transfer to electrodes.

Gao Y, Lee J, Neufeld JD, Park J, Rittmann BE, Lee HS.

Sci Rep. 2017 Jul 11;7(1):5099. doi: 10.1038/s41598-017-05180-9.

6.

Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity.

Hall MW, Singh N, Ng KF, Lam DK, Goldberg MB, Tenenbaum HC, Neufeld JD, G Beiko R, Senadheera DB.

NPJ Biofilms Microbiomes. 2017 Jan 26;3:2. doi: 10.1038/s41522-016-0011-0. eCollection 2017.

7.

Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors.

Duguma D, Hall MW, Smartt CT, Neufeld JD.

Microb Ecol. 2017 Nov;74(4):979-989. doi: 10.1007/s00248-017-0988-9. Epub 2017 May 11.

PMID:
28492989
8.

Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry.

Schiff SL, Tsuji JM, Wu L, Venkiteswaran JJ, Molot LA, Elgood RJ, Paterson MJ, Neufeld JD.

Sci Rep. 2017 Apr 27;7:46708. doi: 10.1038/srep46708.

9.

Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences.

Cheng J, Romantsov T, Engel K, Doxey AC, Rose DR, Neufeld JD, Charles TC.

PLoS One. 2017 Mar 8;12(3):e0172545. doi: 10.1371/journal.pone.0172545. eCollection 2017.

10.

Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice.

De Palma G, Lynch MD, Lu J, Dang VT, Deng Y, Jury J, Umeh G, Miranda PM, Pigrau Pastor M, Sidani S, Pinto-Sanchez MI, Philip V, McLean PG, Hagelsieb MG, Surette MG, Bergonzelli GE, Verdu EF, Britz-McKibbin P, Neufeld JD, Collins SM, Bercik P.

Sci Transl Med. 2017 Mar 1;9(379). pii: eaaf6397. doi: 10.1126/scitranslmed.aaf6397.

PMID:
28251905
11.

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.

Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD.

ISME J. 2017 May;11(5):1142-1157. doi: 10.1038/ismej.2016.192. Epub 2017 Feb 14.

12.

Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses.

Duguma D, Hall MW, Smartt CT, Neufeld JD.

mSphere. 2017 Feb 1;2(1). pii: e00387-16. doi: 10.1128/mSphere.00387-16. eCollection 2017 Jan-Feb.

13.

SSUnique: Detecting Sequence Novelty in Microbiome Surveys.

Lynch MD, Neufeld JD.

mSystems. 2016 Dec 20;1(6). pii: e00133-16. doi: 10.1128/mSystems.00133-16. eCollection 2016 Nov-Dec.

14.

Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity.

Coyotzi S, Doxey AC, Clark ID, Lapen DR, Van Cappellen P, Neufeld JD.

Environ Microbiol. 2017 Mar;19(3):1189-1208. doi: 10.1111/1462-2920.13643. Epub 2017 Feb 1.

PMID:
27943515
15.

Biogeography of soil Thaumarchaeota in relation to soil depth and land usage.

Lu X, Seuradge BJ, Neufeld JD.

FEMS Microbiol Ecol. 2017 Feb;93(2). pii: fiw246. doi: 10.1093/femsec/fiw246. Epub 2016 Dec 8.

PMID:
27940645
16.

Depth-dependent influence of different land-use systems on bacterial biogeography.

Seuradge BJ, Oelbermann M, Neufeld JD.

FEMS Microbiol Ecol. 2017 Feb;93(2). pii: fiw239. doi: 10.1093/femsec/fiw239. Epub 2016 Dec 2.

PMID:
27915285
17.

DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.

Jameson E, Taubert M, Coyotzi S, Chen Y, Eyice Ö, Schäfer H, Murrell JC, Neufeld JD, Dumont MG.

Methods Mol Biol. 2017;1539:57-74.

PMID:
27900684
18.

Migrating SSU rRNA gene surveys to the metagenomics era.

Neufeld JD.

Environ Microbiol Rep. 2017 Feb;9(1):23-24. doi: 10.1111/1758-2229.12493. Epub 2016 Dec 6. No abstract available.

PMID:
27775868
19.

Direct-geneFISH: tuning up microscopic and molecular methodologies for targeted cell visualization.

Neufeld JD.

Environ Microbiol. 2017 Jan;19(1):3-4. doi: 10.1111/1462-2920.13480. Epub 2016 Aug 25. No abstract available.

PMID:
27486074
20.

Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria.

Sauder LA, Ross AA, Neufeld JD.

FEMS Microbiol Lett. 2016 Apr;363(7). pii: fnw052. doi: 10.1093/femsle/fnw052. Epub 2016 Mar 4.

PMID:
26946536
21.

Targeted metagenomics of active microbial populations with stable-isotope probing.

Coyotzi S, Pratscher J, Murrell JC, Neufeld JD.

Curr Opin Biotechnol. 2016 Oct;41:1-8. doi: 10.1016/j.copbio.2016.02.017. Epub 2016 Mar 3. Review.

PMID:
26946369
22.

Back to the Future of Soil Metagenomics.

Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LF, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P.

Front Microbiol. 2016 Feb 10;7:73. doi: 10.3389/fmicb.2016.00073. eCollection 2016. No abstract available.

23.

Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies.

Taubert M, Grob C, Howat AM, Burns OJ, Chen Y, Neufeld JD, Murrell JC.

Methods Mol Biol. 2016;1399:235-55. doi: 10.1007/978-1-4939-3369-3_14.

PMID:
26791507
24.

Microbial biogeography of a university campus.

Ross AA, Neufeld JD.

Microbiome. 2015 Dec 1;3:66. doi: 10.1186/s40168-015-0135-0.

25.

Current and future resources for functional metagenomics.

Lam KN, Cheng J, Engel K, Neufeld JD, Charles TC.

Front Microbiol. 2015 Oct 29;6:1196. doi: 10.3389/fmicb.2015.01196. eCollection 2015.

26.

MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes.

Petrenko P, Lobb B, Kurtz DA, Neufeld JD, Doxey AC.

BMC Biol. 2015 Nov 5;13:92. doi: 10.1186/s12915-015-0195-4.

27.

Microbial dynamics and properties of aerobic granules developed in a laboratory-scale sequencing batch reactor with an intermediate filamentous bulking stage.

Aqeel H, Basuvaraj M, Hall M, Neufeld JD, Liss SN.

Appl Microbiol Biotechnol. 2016 Jan;100(1):447-60. doi: 10.1007/s00253-015-6981-7. Epub 2015 Sep 22.

PMID:
26394861
28.

State Policies Influence Medicare Telemedicine Utilization.

Neufeld JD, Doarn CR, Aly R.

Telemed J E Health. 2016 Jan;22(1):70-4. doi: 10.1089/tmj.2015.0044. Epub 2015 Jul 28.

PMID:
26218148
29.

Developmental succession of the microbiome of Culex mosquitoes.

Duguma D, Hall MW, Rugman-Jones P, Stouthamer R, Terenius O, Neufeld JD, Walton WE.

BMC Microbiol. 2015 Jul 24;15:140. doi: 10.1186/s12866-015-0475-8.

30.

Telemedicine Spending by Medicare: A Snapshot from 2012.

Neufeld JD, Doarn CR.

Telemed J E Health. 2015 Aug;21(8):686-93. doi: 10.1089/tmj.2014.0185. Epub 2015 Apr 3.

PMID:
25839672
31.

Ecology and exploration of the rare biosphere.

Lynch MD, Neufeld JD.

Nat Rev Microbiol. 2015 Apr;13(4):217-29. doi: 10.1038/nrmicro3400. Epub 2015 Mar 2. Review.

PMID:
25730701
32.

Life in a World without Microbes.

Gilbert JA, Neufeld JD.

PLoS Biol. 2014 Dec 16;12(12):e1002020. doi: 10.1371/journal.pbio.1002020. eCollection 2014 Dec. No abstract available.

33.

Phylogenetic identification of methanogens assimilating acetate-derived carbon in dairy and swine manures.

Barret M, Gagnon N, Morissette B, Kalmokoff ML, Topp E, Brooks SP, Matias F, Neufeld JD, Talbot G.

Syst Appl Microbiol. 2015 Feb;38(1):56-66. doi: 10.1016/j.syapm.2014.11.006. Epub 2014 Nov 29.

PMID:
25511087
34.

Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

Bagchi S, Vlaeminck SE, Sauder LA, Mosquera M, Neufeld JD, Boon N.

PLoS One. 2014 Dec 5;9(12):e113515. doi: 10.1371/journal.pone.0113515. eCollection 2014.

35.

Vegetation-associated impacts on arctic tundra bacterial and microeukaryotic communities.

Shi Y, Xiang X, Shen C, Chu H, Neufeld JD, Walker VK, Grogan P.

Appl Environ Microbiol. 2015 Jan;81(2):492-501. doi: 10.1128/AEM.03229-14. Epub 2014 Oct 31.

36.

Opinion: Conservation and stewardship of the human microbiome.

O'Doherty KC, Neufeld JD, Brinkman FS, Gardner H, Guttman DS, Beiko RG.

Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14312-3. doi: 10.1073/pnas.1413200111. No abstract available.

37.

Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators.

Galimanas V, Hall MW, Singh N, Lynch MD, Goldberg M, Tenenbaum H, Cvitkovitch DG, Neufeld JD, Senadheera DB.

Microbiome. 2014 Aug 26;2:32. doi: 10.1186/2049-2618-2-32. eCollection 2014.

38.

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria.

Sonthiphand P, Hall MW, Neufeld JD.

Front Microbiol. 2014 Aug 6;5:399. doi: 10.3389/fmicb.2014.00399. eCollection 2014.

39.

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production.

Doxey AC, Kurtz DA, Lynch MD, Sauder LA, Neufeld JD.

ISME J. 2015 Feb;9(2):461-71. doi: 10.1038/ismej.2014.142. Epub 2014 Aug 15.

40.

Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

Verastegui Y, Cheng J, Engel K, Kolczynski D, Mortimer S, Lavigne J, Montalibet J, Romantsov T, Hall M, McConkey BJ, Rose DR, Tomashek JJ, Scott BR, Charles TC, Neufeld JD.

MBio. 2014 Jul 15;5(4):e01157-14. doi: 10.1128/mBio.01157-14.

41.

Evaluating bias of illumina-based bacterial 16S rRNA gene profiles.

Kennedy K, Hall MW, Lynch MD, Moreno-Hagelsieb G, Neufeld JD.

Appl Environ Microbiol. 2014 Sep;80(18):5717-22. doi: 10.1128/AEM.01451-14. Epub 2014 Jul 7.

42.

Recovering glycoside hydrolase genes from active tundra cellulolytic bacteria.

Pinnell LJ, Dunford E, Ronan P, Hausner M, Neufeld JD.

Can J Microbiol. 2014 Jul;60(7):469-76. doi: 10.1139/cjm-2014-0193. Epub 2014 Jun 11.

PMID:
24983351
43.

Norwegian deep-water coral reefs: cultivation and molecular analysis of planktonic microbial communities.

Jensen S, Lynch MD, Ray JL, Neufeld JD, Hovland M.

Environ Microbiol. 2015 Oct;17(10):3597-609. doi: 10.1111/1462-2920.12531. Epub 2014 Jul 7.

PMID:
24911121
44.

Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries.

Lam KN, Hall MW, Engel K, Vey G, Cheng J, Neufeld JD, Charles TC.

PLoS One. 2014 Jun 9;9(6):e98968. doi: 10.1371/journal.pone.0098968. eCollection 2014.

45.

Telemental health evaluations enhance access and efficiency in a critical access hospital emergency department.

Southard EP, Neufeld JD, Laws S.

Telemed J E Health. 2014 Jul;20(7):664-8. doi: 10.1089/tmj.2013.0257. Epub 2014 May 8.

PMID:
24811858
46.

Versatile broad-host-range cosmids for construction of high quality metagenomic libraries.

Cheng J, Pinnell L, Engel K, Neufeld JD, Charles TC.

J Microbiol Methods. 2014 Apr;99:27-34. doi: 10.1016/j.mimet.2014.01.015. Epub 2014 Feb 1.

PMID:
24495694
47.

Biokinetic and molecular studies of methanogens in phased anaerobic digestion systems.

Zamanzadeh M, Parker WJ, Verastegui Y, Neufeld JD.

Bioresour Technol. 2013 Dec;149:318-26. doi: 10.1016/j.biortech.2013.09.058. Epub 2013 Sep 21.

PMID:
24125797
48.

Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm.

Bartram AK, Jiang X, Lynch MD, Masella AP, Nicol GW, Dushoff J, Neufeld JD.

FEMS Microbiol Ecol. 2014 Feb;87(2):403-15. doi: 10.1111/1574-6941.12231. Epub 2013 Oct 25.

49.

Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada.

Sonthiphand P, Cejudo E, Schiff SL, Neufeld JD.

Appl Environ Microbiol. 2013 Dec;79(23):7454-65. doi: 10.1128/AEM.02202-13. Epub 2013 Sep 20.

50.

Bacterial communities associated with culex mosquito larvae and two emergent aquatic plants of bioremediation importance.

Duguma D, Rugman-Jones P, Kaufman MG, Hall MW, Neufeld JD, Stouthamer R, Walton WE.

PLoS One. 2013 Aug 15;8(8):e72522. doi: 10.1371/journal.pone.0072522. eCollection 2013.

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