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Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes.

Wang Y, Youssef NH, Couger MB, Hanafy RA, Elshahed MS, Stajich JE.

mSystems. 2019 Aug 27;4(4). pii: e00247-19. doi: 10.1128/mSystems.00247-19.


Novel LC-MS/MS method for analysis of metformin and canagliflozin in human plasma: application to a pharmacokinetic study.

Mohamed D, Elshahed MS, Nasr T, Aboutaleb N, Zakaria O.

BMC Chem. 2019 Jul 9;13(1):82. doi: 10.1186/s13065-019-0597-4. eCollection 2019 Dec.


Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage.

Murphy CL, Youssef NH, Hanafy RA, Couger MB, Stajich JE, Wang Y, Baker K, Dagar SS, Griffith GW, Farag IF, Callaghan TM, Elshahed MS.

Appl Environ Microbiol. 2019 Jul 18;85(15). pii: e00988-19. doi: 10.1128/AEM.00988-19. Print 2019 Aug 1.


Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics.

Youssef NH, Farag IF, Hahn CR, Premathilake H, Fry E, Hart M, Huffaker K, Bird E, Hambright J, Hoff WD, Elshahed MS.

Syst Appl Microbiol. 2019 Jan;42(1):85-93. doi: 10.1016/j.syapm.2018.11.002. Epub 2018 Nov 15.


The Nile River Microbiome Reveals a Remarkably Stable Community Between Wet and Dry Seasons, and Sampling Sites, in a Large Urban Metropolis (Cairo, Egypt).

Eraqi WA, ElRakaiby MT, Megahed SA, Yousef NH, Elshahed MS, Yassin AS.

OMICS. 2018 Aug;22(8):553-564. doi: 10.1089/omi.2018.0090.


Novel contribution to the simultaneous monitoring of pramipexole dihydrochloride monohydrate and levodopa as co-administered drugs in human plasma utilizing UPLC-MS/MS.

Mohamed D, Hegazy MA, Elshahed MS, Toubar SS, Helmy MI.

Eur J Mass Spectrom (Chichester). 2018 Oct;24(5):397-407. doi: 10.1177/1469066718788800. Epub 2018 Jul 17.


Feramyces austinii, gen. nov., sp. nov., an anaerobic gut fungus from rumen and fecal samples of wild Barbary sheep and fallow deer.

Hanafy RA, Elshahed MS, Youssef NH.

Mycologia. 2018 May-Jun;110(3):513-525. doi: 10.1080/00275514.2018.1466610. Epub 2018 Jul 3.


Anaeromyces contortus, sp. nov., a new anaerobic gut fungal species (Neocallimastigomycota) isolated from the feces of cow and goat.

Hanafy RA, Johnson B, Elshahed MS, Youssef NH.

Mycologia. 2018 May-Jun;110(3):502-512. doi: 10.1080/00275514.2018.1465773. Epub 2018 Jun 26.


Liquid chromatography-tandem MS/MS method for simultaneous quantification of paracetamol, chlorzoxazone and aceclofenac in human plasma: An application to a clinical pharmacokinetic study.

Mohamed D, Hegazy MA, Elshahed MS, Toubar SS, Helmy MI.

Biomed Chromatogr. 2018 Jul;32(7):e4232. doi: 10.1002/bmc.4232. Epub 2018 Apr 19.


Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A.

Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger MB, Elshahed MS, Youssef NH.

PeerJ. 2018 Jan 30;6:e4276. doi: 10.7717/peerj.4276. eCollection 2018.


Pecoramyces ruminantium, gen. nov., sp. nov., an anaerobic gut fungus from the feces of cattle and sheep.

Hanafy RA, Elshahed MS, Liggenstoffer AS, Griffith GW, Youssef NH.

Mycologia. 2017;109(2):231-243. doi: 10.1080/00275514.2017.1317190. Epub 2017 Apr 18.


Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA).

Morrison JM, Baker KD, Zamor RM, Nikolai S, Elshahed MS, Youssef NH.

PLoS One. 2017 May 11;12(5):e0177488. doi: 10.1371/journal.pone.0177488. eCollection 2017.


Utilizing Anaerobic Fungi for Two-stage Sugar Extraction and Biofuel Production from Lignocellulosic Biomass.

Ranganathan A, Smith OP, Youssef NH, Struchtemeyer CG, Atiyeh HK, Elshahed MS.

Front Microbiol. 2017 Apr 11;8:635. doi: 10.3389/fmicb.2017.00635. eCollection 2017.


Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3).

Farag IF, Youssef NH, Elshahed MS.

Appl Environ Microbiol. 2017 May 1;83(10). pii: e00521-17. doi: 10.1128/AEM.00521-17. Print 2017 May 15.


Microbial communities mediating algal detritus turnover under anaerobic conditions.

Morrison JM, Murphy CL, Baker K, Zamor RM, Nikolai SJ, Wilder S, Elshahed MS, Youssef NH.

PeerJ. 2017 Jan 10;5:e2803. doi: 10.7717/peerj.2803. eCollection 2017.


A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A.

Morrison JM, Elshahed MS, Youssef N.

PeerJ. 2016 Aug 3;4:e2289. doi: 10.7717/peerj.2289. eCollection 2016.


A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates.

Calkins S, Elledge NC, Hanafy RA, Elshahed MS, Youssef N.

J Microbiol Methods. 2016 Aug;127:206-213. doi: 10.1016/j.mimet.2016.05.019. Epub 2016 Jun 8.


Draft Genome of the Arthrobacter sp. Strain Edens01.

Couger MB, Hanafy RA, Edens C, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Dec 17;3(6). pii: e01475-15. doi: 10.1128/genomeA.01475-15.


The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens.

Couger MB, Hanafy RA, Mitacek RM, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Dec 10;3(6). pii: e01450-15. doi: 10.1128/genomeA.01450-15.


Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A.

Couger MB, Youssef NH, Struchtemeyer CG, Liggenstoffer AS, Elshahed MS.

Biotechnol Biofuels. 2015 Dec 8;8:208. doi: 10.1186/s13068-015-0390-0. eCollection 2015.


Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism.

Spain AM, Elshahed MS, Najar FZ, Krumholz LR.

PeerJ. 2015 Sep 22;3:e1259. doi: 10.7717/peerj.1259. eCollection 2015.


Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01.

Couger MB, Hurlbut A, Murphy CL, Budd C, French DP, Hoff WD, Elshahed MS, Youssef NH.

Genome Announc. 2015 Sep 17;3(5). pii: e01071-15. doi: 10.1128/genomeA.01071-15.


Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA).

Coveley S, Elshahed MS, Youssef NH.

PeerJ. 2015 Aug 20;3:e1182. doi: 10.7717/peerj.1182. eCollection 2015.


Assessing the global phylum level diversity within the bacterial domain: A review.

Youssef NH, Couger MB, McCully AL, Criado AE, Elshahed MS.

J Adv Res. 2015 May;6(3):269-82. doi: 10.1016/j.jare.2014.10.005. Epub 2014 Nov 4. Review.


In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3).

Youssef NH, Farag IF, Rinke C, Hallam SJ, Woyke T, Elshahed MS.

PLoS One. 2015 Jun 3;10(6):e0127499. doi: 10.1371/journal.pone.0127499. eCollection 2015.


Patterns and determinants of halophilic archaea (class halobacteria) diversity in tunisian endorheic salt lakes and sebkhet systems.

Najjari A, Elshahed MS, Cherif A, Youssef NH.

Appl Environ Microbiol. 2015 Jul;81(13):4432-41. doi: 10.1128/AEM.01097-15. Epub 2015 Apr 24.


Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure.

Struchtemeyer CG, Ranganathan A, Couger MB, Liggenstoffer AS, Youssef NH, Elshahed MS.

Sci Rep. 2014 Nov 4;4:6892. doi: 10.1038/srep06892.


Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'.

Youssef NH, Rinke C, Stepanauskas R, Farag I, Woyke T, Elshahed MS.

ISME J. 2015 Feb;9(2):447-60. doi: 10.1038/ismej.2014.141. Epub 2014 Aug 1.


Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential.

Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef N, Dagar SS, Fliegerova K, Griffith GW, Forster R, Tsang A, McAllister T, Elshahed MS.

FEMS Microbiol Ecol. 2014 Oct;90(1):1-17. doi: 10.1111/1574-6941.12383. Epub 2014 Aug 11. Review.


Evaluating the utility of hydrothermolysis pretreatment approaches in enhancing lignocellulosic biomass degradation by the anaerobic fungus Orpinomyces sp. strain C1A.

Liggenstoffer AS, Youssef NH, Wilkins MR, Elshahed MS.

J Microbiol Methods. 2014 Sep;104:43-8. doi: 10.1016/j.mimet.2014.06.010. Epub 2014 Jun 24.


Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8).

Farag IF, Davis JP, Youssef NH, Elshahed MS.

PLoS One. 2014 Mar 17;9(3):e92139. doi: 10.1371/journal.pone.0092139. eCollection 2014.


Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales.

Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, Hoff WD, Elshahed MS.

ISME J. 2014 Mar;8(3):636-49. doi: 10.1038/ismej.2013.165. Epub 2013 Sep 19.


The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader.

Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA, Najar FZ, Atiyeh HK, Wilkins MR, Elshahed MS.

Appl Environ Microbiol. 2013 Aug;79(15):4620-34. doi: 10.1128/AEM.00821-13. Epub 2013 May 24.


Capillary electrophoretic determination of antimigraine formulations containing caffeine, ergotamine, paracetamol and domperidone or metoclopramide.

Sultan MA, Maher HM, Alzoman NZ, Alshehri MM, Rizk MS, Elshahed MS, Olah IV.

J Chromatogr Sci. 2013 Jul;51(6):502-10. doi: 10.1093/chromsci/bms175. Epub 2012 Nov 23.


Bacterial communities associated with production facilities of two newly drilled thermogenic natural gas wells in the Barnett Shale (Texas, USA).

Davis JP, Struchtemeyer CG, Elshahed MS.

Microb Ecol. 2012 Nov;64(4):942-54. doi: 10.1007/s00248-012-0073-3. Epub 2012 May 24.


Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone Spring, Oklahoma), revealed using a combined pyrosequencing-sanger approach.

Youssef N, Steidley BL, Elshahed MS.

Appl Environ Microbiol. 2012 Apr;78(8):2677-88. doi: 10.1128/AEM.00002-12. Epub 2012 Feb 3.


Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats.

Youssef NH, Ashlock-Savage KN, Elshahed MS.

Appl Environ Microbiol. 2012 Mar;78(5):1332-44. doi: 10.1128/AEM.07420-11. Epub 2011 Dec 16.


Bacterial communities associated with hydraulic fracturing fluids in thermogenic natural gas wells in North Central Texas, USA.

Struchtemeyer CG, Elshahed MS.

FEMS Microbiol Ecol. 2012 Jul;81(1):13-25. doi: 10.1111/j.1574-6941.2011.01196.x. Epub 2011 Nov 1.


Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

Youssef NH, Blainey PC, Quake SR, Elshahed MS.

Appl Environ Microbiol. 2011 Nov;77(21):7804-14. doi: 10.1128/AEM.06059-11. Epub 2011 Sep 9.


Influence of the drilling mud formulation process on the bacterial communities in thermogenic natural gas wells of the Barnett Shale.

Struchtemeyer CG, Davis JP, Elshahed MS.

Appl Environ Microbiol. 2011 Jul;77(14):4744-53. doi: 10.1128/AEM.00233-11. Epub 2011 May 20.


Effect of warming and drought on grassland microbial communities.

Sheik CS, Beasley WH, Elshahed MS, Zhou X, Luo Y, Krumholz LR.

ISME J. 2011 Oct;5(10):1692-700. doi: 10.1038/ismej.2011.32. Epub 2011 Mar 31.


Insights into chemotaxonomic composition and carbon cycling of phototrophic communities in an artesian sulfur-rich spring (Zodletone, Oklahoma, USA), a possible analog for ancient microbial mat systems.

B├╝hring SI, Sievert SM, Jonkers HM, Ertefai T, Elshahed MS, Krumholz LR, Hinrichs KU.

Geobiology. 2011 Mar;9(2):166-79. doi: 10.1111/j.1472-4669.2010.00268.x. Epub 2011 Jan 19.


Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): the role of the rare biosphere.

Youssef NH, Couger MB, Elshahed MS.

PLoS One. 2010 Aug 26;5(8):e12414. doi: 10.1371/journal.pone.0012414.


Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores.

Liggenstoffer AS, Youssef NH, Couger MB, Elshahed MS.

ISME J. 2010 Oct;4(10):1225-35. doi: 10.1038/ismej.2010.49. Epub 2010 Apr 22.


Biodegradation of low-molecular-weight alkanes under mesophilic, sulfate-reducing conditions: metabolic intermediates and community patterns.

Savage KN, Krumholz LR, Gieg LM, Parisi VA, Suflita JM, Allen J, Philp RP, Elshahed MS.

FEMS Microbiol Ecol. 2010 Jun;72(3):485-95. doi: 10.1111/j.1574-6941.2010.00866.x. Epub 2010 Mar 19.


Bacterial diversity in Amblyomma americanum (Acari: Ixodidae) with a focus on members of the genus Rickettsia.

Heise SR, Elshahed MS, Little SE.

J Med Entomol. 2010 Mar;47(2):258-68.


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