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Items: 44

1.

A census-based estimate of Earth's bacterial and archaeal diversity.

Louca S, Mazel F, Doebeli M, Parfrey LW.

PLoS Biol. 2019 Feb 4;17(2):e3000106. doi: 10.1371/journal.pbio.3000106. eCollection 2019 Feb.

2.

Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?

Mazel F, Davis KM, Loudon A, Kwong WK, Groussin M, Parfrey LW.

mSystems. 2018 Oct 23;3(5). pii: e00097-18. doi: 10.1128/mSystems.00097-18. eCollection 2018 Sep-Oct.

3.

Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera.

Lin JD, Lemay MA, Parfrey LW.

Front Microbiol. 2018 Aug 20;9:1914. doi: 10.3389/fmicb.2018.01914. eCollection 2018.

4.

Bacterial diversification through geological time.

Louca S, Shih PM, Pennell MW, Fischer WW, Parfrey LW, Doebeli M.

Nat Ecol Evol. 2018 Sep;2(9):1458-1467. doi: 10.1038/s41559-018-0625-0. Epub 2018 Jul 30.

PMID:
30061564
5.

Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns.

Nieves-Ramírez ME, Partida-Rodríguez O, Laforest-Lapointe I, Reynolds LA, Brown EM, Valdez-Salazar A, Morán-Silva P, Rojas-Velázquez L, Morien E, Parfrey LW, Jin M, Walter J, Torres J, Arrieta MC, Ximénez-García C, Finlay BB.

mSystems. 2018 Jun 26;3(3). pii: e00007-18. doi: 10.1128/mSystems.00007-18. eCollection 2018 May-Jun.

6.

Evaluating rodent experimental models for studies of Blastocystis ST1.

Růžková J, Květoňová D, Jirků M, Lhotská Z, Stensvold CR, Parfrey LW, Jirků Pomajbíková K.

Exp Parasitol. 2018 Aug;191:55-61. doi: 10.1016/j.exppara.2018.06.009. Epub 2018 Jun 28.

PMID:
29959915
7.

The benign helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system.

Jirků Pomajbíková K, Jirků M, Levá J, Sobotková K, Morien E, Parfrey LW.

Parasitology. 2018 Sep;145(10):1324-1335. doi: 10.1017/S0031182018000896. Epub 2018 Jun 18.

PMID:
29909781
8.

Introduction: The host-associated microbiome: Pattern, process and function.

Parfrey LW, Moreau CS, Russell JA.

Mol Ecol. 2018 Apr;27(8):1749-1765. doi: 10.1111/mec.14706. No abstract available.

PMID:
29727917
9.

Function and functional redundancy in microbial systems.

Louca S, Polz MF, Mazel F, Albright MBN, Huber JA, O'Connor MI, Ackermann M, Hahn AS, Srivastava DS, Crowe SA, Doebeli M, Parfrey LW.

Nat Ecol Evol. 2018 Jun;2(6):936-943. doi: 10.1038/s41559-018-0519-1. Epub 2018 Apr 16. Review.

PMID:
29662222
10.

Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae.

Chen MY, Parfrey LW.

Mol Ecol. 2018 Apr;27(8):1966-1979. doi: 10.1111/mec.14548. Epub 2018 Apr 10.

PMID:
29524281
11.

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem.

Louca S, Doebeli M, Parfrey LW.

Microbiome. 2018 Feb 26;6(1):41. doi: 10.1186/s40168-018-0420-9.

12.

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting.

Arrieta MC, Arévalo A, Stiemsma L, Dimitriu P, Chico ME, Loor S, Vaca M, Boutin RCT, Morien E, Jin M, Turvey SE, Walter J, Parfrey LW, Cooper PJ, Finlay B.

J Allergy Clin Immunol. 2018 Aug;142(2):424-434.e10. doi: 10.1016/j.jaci.2017.08.041. Epub 2017 Dec 11.

13.

High taxonomic variability despite stable functional structure across microbial communities.

Louca S, Jacques SMS, Pires APF, Leal JS, Srivastava DS, Parfrey LW, Farjalla VF, Doebeli M.

Nat Ecol Evol. 2016 Dec 5;1(1):15. doi: 10.1038/s41559-016-0015.

PMID:
28812567
14.

UniEuk: Time to Speak a Common Language in Protistology!

Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C.

J Eukaryot Microbiol. 2017 May;64(3):407-411. doi: 10.1111/jeu.12414. Epub 2017 Apr 21. Review.

15.

Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment.

Avena CV, Parfrey LW, Leff JW, Archer HM, Frick WF, Langwig KE, Kilpatrick AM, Powers KE, Foster JT, McKenzie VJ.

Front Microbiol. 2016 Nov 17;7:1753. eCollection 2016.

16.

Decoupling function and taxonomy in the global ocean microbiome.

Louca S, Parfrey LW, Doebeli M.

Science. 2016 Sep 16;353(6305):1272-7. doi: 10.1126/science.aaf4507.

17.

Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin.

Loudon AH, Venkataraman A, Van Treuren W, Woodhams DC, Parfrey LW, McKenzie VJ, Knight R, Schmidt TM, Harris RN.

Front Microbiol. 2016 Mar 16;7:333. doi: 10.3389/fmicb.2016.00333. eCollection 2016.

18.

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water.

Korajkic A, Parfrey LW, McMinn BR, Baeza YV, VanTeuren W, Knight R, Shanks OC.

Water Res. 2015 Feb 1;69:30-39. doi: 10.1016/j.watres.2014.11.003. Epub 2014 Nov 13.

PMID:
25463929
19.

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.

Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R.

Front Microbiol. 2014 Jun 19;5:298. doi: 10.3389/fmicb.2014.00298. eCollection 2014.

20.

Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus).

Loudon AH, Woodhams DC, Parfrey LW, Archer H, Knight R, McKenzie V, Harris RN.

ISME J. 2014 Apr;8(4):830-40. doi: 10.1038/ismej.2013.200. Epub 2013 Dec 12.

21.

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO.

Nucleic Acids Res. 2014 Jan;42(Database issue):D643-8. doi: 10.1093/nar/gkt1209. Epub 2013 Nov 28.

22.

The amphibian skin-associated microbiome across species, space and life history stages.

Kueneman JG, Parfrey LW, Woodhams DC, Archer HM, Knight R, McKenzie VJ.

Mol Ecol. 2014 Mar;23(6):1238-50. doi: 10.1111/mec.12510. Epub 2013 Oct 31.

PMID:
24171949
23.

Meeting report: fungal its workshop (october 2012).

Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE.

Stand Genomic Sci. 2013 Apr 15;8(1):118-23. doi: 10.4056/sigs.3737409. eCollection 2013 Apr 15.

24.

Multicellularity arose several times in the evolution of eukaryotes (response to DOI 10.1002/bies.201100187).

Parfrey LW, Lahr DJ.

Bioessays. 2013 Apr;35(4):339-47. doi: 10.1002/bies.201200143. Epub 2013 Jan 11.

PMID:
23315654
25.

Global biogeography of highly diverse protistan communities in soil.

Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, Fierer N.

ISME J. 2013 Mar;7(3):652-9. doi: 10.1038/ismej.2012.147. Epub 2012 Dec 13.

26.

The revised classification of eukaryotes.

Adl SM, Simpson AG, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Le Gall L, Lynn DH, McManus H, Mitchell EA, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Schoch CL, Smirnov A, Spiegel FW.

J Eukaryot Microbiol. 2012 Sep;59(5):429-93. doi: 10.1111/j.1550-7408.2012.00644.x. Erratum in: J Eukaryot Microbiol. 2013 May-Jun;60(3):321. Shadwick, Lora [corrected to Shadwick, Laura].

27.

Defining the human microbiome.

Ursell LK, Metcalf JL, Parfrey LW, Knight R.

Nutr Rev. 2012 Aug;70 Suppl 1:S38-44. doi: 10.1111/j.1753-4887.2012.00493.x. Review.

28.

Spatial and temporal variability of the human microbiota.

Parfrey LW, Knight R.

Clin Microbiol Infect. 2012 Jul;18 Suppl 4:8-11. doi: 10.1111/j.1469-0691.2012.03861.x. Review.

29.

The impact of the gut microbiota on human health: an integrative view.

Clemente JC, Ursell LK, Parfrey LW, Knight R.

Cell. 2012 Mar 16;148(6):1258-70. doi: 10.1016/j.cell.2012.01.035. Review.

30.

Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life.

Katz LA, Grant JR, Parfrey LW, Burleigh JG.

Syst Biol. 2012 Jul;61(4):653-60. doi: 10.1093/sysbio/sys026. Epub 2012 Feb 14.

31.

Experimental and analytical tools for studying the human microbiome.

Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R.

Nat Rev Genet. 2011 Dec 16;13(1):47-58. doi: 10.1038/nrg3129. Review.

32.

Human-associated microbial signatures: examining their predictive value.

Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R.

Cell Host Microbe. 2011 Oct 20;10(4):292-6. doi: 10.1016/j.chom.2011.09.003.

33.

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.

Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R.

Trends Microbiol. 2011 Oct;19(10):472-82. doi: 10.1016/j.tim.2011.07.006. Epub 2011 Aug 25. Review.

34.

Estimating the timing of early eukaryotic diversification with multigene molecular clocks.

Parfrey LW, Lahr DJ, Knoll AH, Katz LA.

Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13624-9. doi: 10.1073/pnas.1110633108. Epub 2011 Aug 2.

35.

Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions.

Parfrey LW, Walters WA, Knight R.

Front Microbiol. 2011 Jul 11;2:153. doi: 10.3389/fmicb.2011.00153. eCollection 2011.

36.

Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes.

Katz LA, Grant J, Parfrey LW, Gant A, O'Kelly CJ, Anderson OR, Molestina RE, Nerad T.

Protist. 2011 Nov;162(5):762-73. doi: 10.1016/j.protis.2011.05.002. Epub 2011 Jul 1.

PMID:
21723191
37.

The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms.

Lahr DJ, Parfrey LW, Mitchell EA, Katz LA, Lara E.

Proc Biol Sci. 2011 Jul 22;278(1715):2081-90. doi: 10.1098/rspb.2011.0289. Epub 2011 Mar 23. Review.

38.

Genome dynamics are influenced by food source in Allogromia laticollaris strain CSH (Foraminifera).

Parfrey LW, Katz LA.

Genome Biol Evol. 2010;2:678-85. doi: 10.1093/gbe/evq051. Epub 2010 Aug 13.

39.

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.

Parfrey LW, Grant J, Tekle YI, Lasek-Nesselquist E, Morrison HG, Sogin ML, Patterson DJ, Katz LA.

Syst Biol. 2010 Oct;59(5):518-33. doi: 10.1093/sysbio/syq037. Epub 2010 Jul 23.

40.
41.

The dynamic nature of eukaryotic genomes.

Parfrey LW, Lahr DJ, Katz LA.

Mol Biol Evol. 2008 Apr;25(4):787-94. doi: 10.1093/molbev/msn032. Epub 2008 Feb 6.

42.

Evaluating support for the current classification of eukaryotic diversity.

Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ, Katz LA.

PLoS Genet. 2006 Dec;2(12):e220. Epub 2006 Nov 13.

43.

Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae.

Yarragudi A, Parfrey LW, Morse RH.

Nucleic Acids Res. 2007;35(1):193-202. Epub 2006 Dec 7.

44.

Phylogeny and ultrastructure of Miliammina fusca: evidence for secondary loss of calcification in a Miliolid Foraminifer.

Habura A, Goldstein ST, Parfrey LW, Bowser SS.

J Eukaryot Microbiol. 2006 May-Jun;53(3):204-10.

PMID:
16677344

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