Publications


ResearchGate

Google Scholar

 Publications                  

Undergraduate students

 

 

Journal Manuscripts (*Corresponding author, Undergraduate authors are underlined)

Submitted manuscripts

JM Morrison, K Baker, R Zamor, S Nikolai, MS Elshahed, NH Youssef*. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). (Under Review)

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed. Anaerobic fungi as a novel platform for sugar extraction and biofuel production from lignocellulosic biomass. (Under Review).

RA Hanafy, MS Elshahed, AS Liggenstoffer, GW Griffith, NH Youssef*. Pecoramyces ruminatum, gen. nov, sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. (Under Review).

IF Farag, NH Youssef, and MS Elshahed. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). (Under Review) 

Manuscripts in Press

JM Morrison, CL Murphy, KD Baker, R Zamor, S Nikolai, S Wilder, MS Elshahed, NH Youssef* 2017. Microbial communities mediating algal detritus turnover under anaerobic conditions. Peer J. (In Press)

Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Kusel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MGA, Youssef NH, Zhang X, Wei Z, Hol WHG. 2017. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J (In Press)

Published manuscripts

2016

JM Morrison, MS Elshahed, and NH Youssef* 2016. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci. Rep. 6:29217.

JM Morrison, MS Elshahed, and NH Youssef* 2016. A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A. Peer J. 4:e2289 

S. Calkins, NC Elledge, RA Hanafy, MS Elshahed, NH Youssef 2016. A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates. J. Microbiol. Methods. 127: 206-213.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. Genomics Data 9: 154–159.

Hanafy RA, Couger MB, Baker K, Murphy C, O’kane SD, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Micrococcus luteus strain O’kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. Genomics Data 9: 148–153.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential, Genomics Data 10: 54-60.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. Genomics Data 10: 63-68.

Calkins SS, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. Genomics Data, 10: 91-96.

Calkins SS, Youssef NH*. 2016. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in theAnaerobic Fungus Orpinomyces sp. C1A. PLoS One 11: e0163553.

Moore J, Yang R, Wheeler K, Youssef NH*. 2016. Sequencing the microbial world one bug at a time. Research Reports from Life Science Freshmen Research Scholars 2.

S Dalvi, NH Youssef, BZ Fathepure. 2016. Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment. Extremophiles 20: 311-321.

2015

MB Couger, A Hurlbut, CL Murphy, C Budd, DP French, WD Hoff, MS Elshahed, and NH Youssef. Draft Genome Sequence of the Environmental Isolate Chryseobacterium sp. Hurlbut01. Genome Announc. 3:e01071-15.

S Coveley, MS Elshahed, and NH Youssef 2015. Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA). PeerJ 3:e1182.

Youssef NH, Farag I, Rinke C, Hallam SJ , Woyke T, and Elshahed MS. Exploring the metabolic potential and niche specialization of candidate phylum “Latescibacteria” (WS3) using single-cell genomics. PLoS ONE. 10:e0127499. 

Najjari, A, Elshahed MS, Cherif A, and Youssef NH. Patterns and determinants of diversity and community structure of Halophilic Archaea (Class Halobacteria) in Tunisian endorheic salt lakes and sebkhet systems. Appl. Environ. Microbiol. 81: 4432-4441. 

Youssef NH, Couger MB, McCully AL , Criado AEG, and Elshahed MS . Assessing the global phylum level diversity within the bacterial domain: A review. J. Adv. Res. 3:269-282.

Youssef NH, Rinke C, Stepanauskas R, Farag I, Woyke T, and Elshahed MS. 2015. Insights into the metabolism, lifestyle, and putative evolutionary history of the novel archaeal phylum Diapherotrites. The ISME J 9:447-460.

2013-2014

Liggenstoffer AS, Youssef NH, Wilkins MR, and Elshahed MS, Evaluating the utility of hydrothermolysis pretreatment approaches in enhancing lignocellulosic biomass degradation by the anaerobic fungus Orpinomyces sp. Strain C1A. J. Microbiol. Meth., 2014. 104:43-48.

Struchtemeyer CG, Ranganathan A, Couger MB, Liggenstoffer AS, Youssef NH, Elshahed MS, Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure. Sci. Rep., 2014. 4:4682. DOI: 10.1038/srep06892.

Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef NH, Dagar SS, et al., Anaerobic fungi (phylum neocallimastigomycota): Advances in understanding of their taxonomy, life cycle, ecology, role, and biotechnological potential. FEMS Microbiol. Ecol., 2014. 90:1-17.

Farag IH, Davis JP, Youssef NH, and Elshahed MS, Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8). PLoS ONE, 2014. 9:e92139.

Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, Hoff WD, et al., Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the halobacteriales. The ISME J., 2013. 8:636-649.

Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA, Najar FZ, et al., Genome of the anaerobic fungus Orpinomyces sp. C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl. Environ. Microbiol., 2013. 79:4620-4634.

Youssef NH, Simpson DR, McInerney, MJ, Duncan KE. In-situ lipopeptide biosurfactant production by Bacillus strains correlates with improved oil recovery in two oil wells approaching their economic limit of production. Int. Biodet. Biodeg., 2013. 81:127-132.

2011-2012

Youssef NH, Savage-Ashlock KN, and Elshahed M, Phylogenetic diversities and community structure of members of the extremely halophilic archaea (order halobacteriales) in multiple saline sediment habitats. Appl. Environ.Microbiol., 2012. 78:1332-1344.

Youssef NH, Steidley BL, and Elshahed MS, Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone Spring, Oklahoma), revealed using a combined pyrosequencing-sanger approach. Appl. Environ. Microbiol., 2012. 78: p. 2677-2688.

Youssef NH, Blainey PC, Quake SR, and Elshahed MS, Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone spring, Oklahoma). Appl. Environ. Microbiol., 2011. 77:7804-7814.

Youssef NH, Wofford NQ, and McInerney MJ, Importance of the Long-Chain Fatty Acid Beta-Hydroxylating Cytochrome P450 Enzyme YbdT for Lipopeptide Biosynthesis in Bacillus subtilis Strain OKB105. Int. J. Mol. Sci., 2011. 12:1767-1786.

2009-2010

Youssef NH, Couger MB, and Elshahed MS, Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone spring, OK, USA): The role of the rare biosphere. PLoS ONE, 2010. 5:e12414

Liggenstoffer AS, Youssef NH, Couger MB, and Elshahed MS, Phylogenetic diversity and community structure of anaerobic fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. The ISME J., 2010. 4:1225–1235.

Youssef NH, Sheik CS, Krumholz LR, Najar FZ, Roe BA, and Elshahed MS, Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol, 2009. 75:5227-36.

Davis JP, Youssef NH, Elshahed MS, Assessment of the Diversity, Abundance, and Ecological Distribution of Members of Candidate Division SR1 Reveals a High Level of Phylogenetic Diversity but Limited Morphotypic Diversity. Appl Environ Microbiol, 2009. 75:4139-4148.

Youssef NH, and Elshahed MS, Diversity rankings among bacterial lineages in soil. The ISME J., 2009. 3:305-310.

2007-2008

Youssef NH and Elshahed MS, Species richness in soil bacterial communities: A proposed approach to overcome sample size bias. J. Microbiol. Meth., 2008. 75: p. 86-91.

Elshahed MS, Youssef NH, Spain AM, Sheik C, Najar FZ, Sukharnikov LO, Roe BA, Davis JP, Schloss PD, Bailey VL, Krumholz LR, Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere. Appl Environ Microbiol, 2008. 74:5422-5428.

Nguyen TT, Youssef NH, McInerney MJ, Sabatini DA, Rhamnolipid biosurfactant mixtures for environmental remediation. Water Res., 2008. 42:1735-1743.

Elshahed MS, Youssef NH, Luo QW, Najar FZ, Roe BA, Sisk TM, Bühring SI, Hinrichs K-U, Krumholz LR, Phylogenetic and metabolic diversity of Planctomycetes from anaerobic, sulfide-and sulfur-rich Zodletone Spring, Oklahoma. Appl Environ Microbiol, 2007. 73:4707-4716.

Youssef NH, Nguyen TT, Sabatini DA, McInerney MJ, Basis for formulating biosurfactant mixtures to achieve ultra low interfacial tension values against hydrocarbons. J. Ind. Microbiol. Biotechnol., 2007. 34:497-507.

Youssef NH, DR Simpson, KE Duncan, MJ McInerney, M Folmsbee, T Fincher, RM Knapp, In situ biosurfactant production by Bacillus strains injected into a limestone petroleum reservoir. Appl Environ Microbiol, 2007. 73:1239-1247.

2006 and before

Youssef NH, Duncan KE, McInerney MJ. Importance of 3-hydroxy fatty acid composition of lipopeptides for biosurfactant activity. Appl Environ Microbiol, 2005. 71:7690-7695.

Youssef NH, Duncan KE, Nagle DP, Savage KN, Knapp RM, McInerney MJ, Comparison of methods to detect biosurfactant production by diverse microorganisms. J. Microbiol. Meth., 2004. 56:339-347.

Book Chapters

Youssef NH, Elshahed MS, and McInerney MJ, Microbial processes in oil fields: Culprits, problems, and opportunities, in Advances in applied microbiology, Allen I. Laskin S S and Geoffrey M G, Editors. 2009, Academic Press. p. 141-251.

Youssef NH and Elshahed MS, Novelty and uniqueness patterns of rare members of the soil biosphere, in Handbook of molecular microbial ecology ii: Metagenomics in different habitats., Bruijn F d, Editor. 2011, Wiley/Blackwell Publishing CO

Youssef NH and Elshahed MS, The phylum planctomycetes, in The prokaryotes, 4th edition, Roesenberg E, Stackebrant E, Thompson F, DeLong E F, and Lory S, Editors. 2014, Springer, New York: New York, NY.

B. Journal Manuscripts (*Corresponding author, Undergraduate authors are underlined)

1. Submitted manuscripts

JM Morrison, K Baker, R Zamor, S Nikolai, MS Elshahed, NH Youssef*. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). (Under Review)

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed. Anaerobic fungi as a novel platform for sugar extraction and biofuel production from lignocellulosic biomass. (Under Review).

RA Hanafy, MS Elshahed, AS Liggenstoffer, GW Griffith, NH Youssef*. Pecoramyces ruminatum, gen. nov, sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. (Under Review).

IF Farag, NH Youssef, and MS Elshahed. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). (Under Review) 

2. Manuscripts in Press

JM Morrison, CL Murphy, KD Baker, R Zamor, S Nikolai, S Wilder, MS Elshahed, NH Youssef* 2017. Microbial communities mediating algal detritus turnover under anaerobic conditions. Peer J. (In Press)

Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Kusel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MGA, Youssef NH, Zhang X, Wei Z, Hol WHG. 2017. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J (In Press)

3. Published manuscripts

2016

JM Morrison, MS Elshahed, and NH Youssef* 2016. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci. Rep. 6:29217.

JM Morrison, MS Elshahed, and NH Youssef* 2016. A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A. Peer J. 4:e2289 

S. Calkins, NC Elledge, RA Hanafy, MS Elshahed, NH Youssef 2016. A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates. J. Microbiol. Methods. 127: 206-213.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. Genomics Data 9: 154–159.

Hanafy RA, Couger MB, Baker K, Murphy C, O’kane SD, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Micrococcus luteus strain O’kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. Genomics Data 9: 148–153.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential, Genomics Data 10: 54-60.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. Genomics Data 10: 63-68.

Calkins SS, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. Genomics Data, 10: 91-96.

Calkins SS, Youssef NH*. 2016. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in theAnaerobic Fungus Orpinomyces sp. C1A. PLoS One 11: e0163553.

Moore J, Yang R, Wheeler K, Youssef NH*. 2016. Sequencing the microbial world one bug at a time. Research Reports from Life Science Freshmen Research Scholars 2.

S Dalvi, NH Youssef, BZ Fathepure. 2016. Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment. Extremophiles 20: 311-321.

JM Morrison, K Baker, R Zamor, S Nikolai, MS Elshahed, NH Youssef*. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). (Under Review)

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed. Anaerobic fungi as a novel platform for sugar extraction and biofuel production from lignocellulosic biomass. (Under Review).

RA Hanafy, MS Elshahed, AS Liggenstoffer, GW Griffith, NH Youssef*. Pecoramyces ruminatum, gen. nov, sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. (Under Review).

IF Farag, NH Youssef, and MS Elshahed. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). (Under Review) 

B. Journal Manuscripts (*Corresponding author, Undergraduate authors are underlined)

1. Submitted manuscripts

JM Morrison, K Baker, R Zamor, S Nikolai, MS Elshahed, NH Youssef*. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). (Under Review)

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed. Anaerobic fungi as a novel platform for sugar extraction and biofuel production from lignocellulosic biomass. (Under Review).

RA Hanafy, MS Elshahed, AS Liggenstoffer, GW Griffith, NH Youssef*. Pecoramyces ruminatum, gen. nov, sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. (Under Review).

IF Farag, NH Youssef, and MS Elshahed. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). (Under Review) 

2. Manuscripts in Press

JM Morrison, CL Murphy, KD Baker, R Zamor, S Nikolai, S Wilder, MS Elshahed, NH Youssef* 2017. Microbial communities mediating algal detritus turnover under anaerobic conditions. Peer J. (In Press)

Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Kusel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MGA, Youssef NH, Zhang X, Wei Z, Hol WHG. 2017. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J (In Press)

3. Published manuscripts

2016

JM Morrison, MS Elshahed, and NH Youssef* 2016. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci. Rep. 6:29217.

JM Morrison, MS Elshahed, and NH Youssef* 2016. A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A. Peer J. 4:e2289 

S. Calkins, NC Elledge, RA Hanafy, MS Elshahed, NH Youssef 2016. A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates. J. Microbiol. Methods. 127: 206-213.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. Genomics Data 9: 154–159.

Hanafy RA, Couger MB, Baker K, Murphy C, O’kane SD, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Micrococcus luteus strain O’kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. Genomics Data 9: 148–153.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential, Genomics Data 10: 54-60.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. Genomics Data 10: 63-68.

Calkins SS, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. Genomics Data, 10: 91-96.

Calkins SS, Youssef NH*. 2016. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in theAnaerobic Fungus Orpinomyces sp. C1A. PLoS One 11: e0163553.

Moore J, Yang R, Wheeler K, Youssef NH*. 2016. Sequencing the microbial world one bug at a time. Research Reports from Life Science Freshmen Research Scholars 2.

S Dalvi, NH Youssef, BZ Fathepure. 2016. Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment. Extremophiles 20: 311-321.

B. Journal Manuscripts (*Corresponding author, Undergraduate authors are underlined)

1. Submitted manuscripts

JM Morrison, K Baker, R Zamor, S Nikolai, MS Elshahed, NH Youssef*. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). (Under Review)

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed. Anaerobic fungi as a novel platform for sugar extraction and biofuel production from lignocellulosic biomass. (Under Review).

RA Hanafy, MS Elshahed, AS Liggenstoffer, GW Griffith, NH Youssef*. Pecoramyces ruminatum, gen. nov, sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. (Under Review).

IF Farag, NH Youssef, and MS Elshahed. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). (Under Review) 

2. Manuscripts in Press

JM Morrison, CL Murphy, KD Baker, R Zamor, S Nikolai, S Wilder, MS Elshahed, NH Youssef* 2017. Microbial communities mediating algal detritus turnover under anaerobic conditions. Peer J. (In Press)

Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Kusel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MGA, Youssef NH, Zhang X, Wei Z, Hol WHG. 2017. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J (In Press)

3. Published manuscripts

2016

JM Morrison, MS Elshahed, and NH Youssef* 2016. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci. Rep. 6:29217.

JM Morrison, MS Elshahed, and NH Youssef* 2016. A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A. Peer J. 4:e2289 

S. Calkins, NC Elledge, RA Hanafy, MS Elshahed, NH Youssef 2016. A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates. J. Microbiol. Methods. 127: 206-213.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. Genomics Data 9: 154–159.

Hanafy RA, Couger MB, Baker K, Murphy C, O’kane SD, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Micrococcus luteus strain O’kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. Genomics Data 9: 148–153.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential, Genomics Data 10: 54-60.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. Genomics Data 10: 63-68.

Calkins SS, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. Genomics Data, 10: 91-96.

Calkins SS, Youssef NH*. 2016. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in theAnaerobic Fungus Orpinomyces sp. C1A. PLoS One 11: e0163553.

Moore J, Yang R, Wheeler K, Youssef NH*. 2016. Sequencing the microbial world one bug at a time. Research Reports from Life Science Freshmen Research Scholars 2.

S Dalvi, NH Youssef, BZ Fathepure. 2016. Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment. Extremophiles 20: 311-321.

B. Journal Manuscripts (*Corresponding author, Undergraduate authors are underlined)

1. Submitted manuscripts

JM Morrison, K Baker, R Zamor, S Nikolai, MS Elshahed, NH Youssef*. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). (Under Review)

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed. Anaerobic fungi as a novel platform for sugar extraction and biofuel production from lignocellulosic biomass. (Under Review).

RA Hanafy, MS Elshahed, AS Liggenstoffer, GW Griffith, NH Youssef*. Pecoramyces ruminatum, gen. nov, sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. (Under Review).

IF Farag, NH Youssef, and MS Elshahed. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). (Under Review) 

2. Manuscripts in Press

JM Morrison, CL Murphy, KD Baker, R Zamor, S Nikolai, S Wilder, MS Elshahed, NH Youssef* 2017. Microbial communities mediating algal detritus turnover under anaerobic conditions. Peer J. (In Press)

Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Kusel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MGA, Youssef NH, Zhang X, Wei Z, Hol WHG. 2017. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J (In Press)

3. Published manuscripts

2016

JM Morrison, MS Elshahed, and NH Youssef* 2016. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci. Rep. 6:29217.

JM Morrison, MS Elshahed, and NH Youssef* 2016. A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A. Peer J. 4:e2289 

S. Calkins, NC Elledge, RA Hanafy, MS Elshahed, NH Youssef 2016. A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates. J. Microbiol. Methods. 127: 206-213.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. Genomics Data 9: 154–159.

Hanafy RA, Couger MB, Baker K, Murphy C, O’kane SD, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Micrococcus luteus strain O’kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. Genomics Data 9: 148–153.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential, Genomics Data 10: 54-60.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. Genomics Data 10: 63-68.

Calkins SS, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. Genomics Data, 10: 91-96.

Calkins SS, Youssef NH*. 2016. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in theAnaerobic Fungus Orpinomyces sp. C1A. PLoS One 11: e0163553.

Moore J, Yang R, Wheeler K, Youssef NH*. 2016. Sequencing the microbial world one bug at a time. Research Reports from Life Science Freshmen Research Scholars 2.

S Dalvi, NH Youssef, BZ Fathepure. 2016. Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment. Extremophiles 20: 311-321.

Journal Manuscripts (*Corresponding author, Undergraduate authors are underlined)

Submitted manuscripts

JM Morrison, K Baker, R Zamor, S Nikolai, MS Elshahed, NH Youssef*. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). (Under Review)

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed. Anaerobic fungi as a novel platform for sugar extraction and biofuel production from lignocellulosic biomass. (Under Review).

RA Hanafy, MS Elshahed, AS Liggenstoffer, GW Griffith, NH Youssef*. Pecoramyces ruminatum, gen. nov, sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. (Under Review).

IF Farag, NH Youssef, and MS Elshahed. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). (Under Review) 

Manuscripts in Press

JM Morrison, CL Murphy, KD Baker, R Zamor, S Nikolai, S Wilder, MS Elshahed, NH Youssef* 2017. Microbial communities mediating algal detritus turnover under anaerobic conditions. Peer J. (In Press)

Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Kusel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MGA, Youssef NH, Zhang X, Wei Z, Hol WHG. 2017. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J (In Press)

Published manuscripts

2016

JM Morrison, MS Elshahed, and NH Youssef* 2016. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci. Rep. 6:29217.

JM Morrison, MS Elshahed, and NH Youssef* 2016. A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A. Peer J. 4:e2289 

S. Calkins, NC Elledge, RA Hanafy, MS Elshahed, NH Youssef 2016. A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates. J. Microbiol. Methods. 127: 206-213.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. Genomics Data 9: 154–159.

Hanafy RA, Couger MB, Baker K, Murphy C, O’kane SD, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Micrococcus luteus strain O’kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. Genomics Data 9: 148–153.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential, Genomics Data 10: 54-60.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. Genomics Data 10: 63-68.

Calkins SS, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. Genomics Data, 10: 91-96.

Calkins SS, Youssef NH*. 2016. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in theAnaerobic Fungus Orpinomyces sp. C1A. PLoS One 11: e0163553.

Moore J, Yang R, Wheeler K, Youssef NH*. 2016. Sequencing the microbial world one bug at a time. Research Reports from Life Science Freshmen Research Scholars 2.

S Dalvi, NH Youssef, BZ Fathepure. 2016. Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment. Extremophiles 20: 311-321.

Journal Manuscripts (*Corresponding author, Undergraduate authors are underlined)

Submitted manuscripts

JM Morrison, K Baker, R Zamor, S Nikolai, MS Elshahed, NH Youssef*. Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA). (Under Review)

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed. Anaerobic fungi as a novel platform for sugar extraction and biofuel production from lignocellulosic biomass. (Under Review).

RA Hanafy, MS Elshahed, AS Liggenstoffer, GW Griffith, NH Youssef*. Pecoramyces ruminatum, gen. nov, sp. nov., an anaerobic gut fungus from the feces of cattle and sheep. (Under Review).

IF Farag, NH Youssef, and MS Elshahed. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). (Under Review) 

Manuscripts in Press

JM Morrison, CL Murphy, KD Baker, R Zamor, S Nikolai, S Wilder, MS Elshahed, NH Youssef* 2017. Microbial communities mediating algal detritus turnover under anaerobic conditions. Peer J. (In Press)

Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Kusel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MGA, Youssef NH, Zhang X, Wei Z, Hol WHG. 2017. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J (In Press)

Published manuscripts

2016

JM Morrison, MS Elshahed, and NH Youssef* 2016. Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass. Sci. Rep. 6:29217.

JM Morrison, MS Elshahed, and NH Youssef* 2016. A multifunctional GH39 glycoside hydrolase from the anaerobic gut fungus Orpinomyces sp. strain C1A. Peer J. 4:e2289 

S. Calkins, NC Elledge, RA Hanafy, MS Elshahed, NH Youssef 2016. A fast and reliable procedure for spore collection from anaerobic fungi: Application for RNA uptake and long-term storage of isolates. J. Microbiol. Methods. 127: 206-213.

Miller NT, Fuller D, Couger MB, Bagazinski M, Boyne P, Devor RC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. Genomics Data 9: 154–159.

Hanafy RA, Couger MB, Baker K, Murphy C, O’kane SD, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Micrococcus luteus strain O’kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. Genomics Data 9: 148–153.

Avramov AP, Couger MB, Hartley EL, Land C, Wellendorf R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential, Genomics Data 10: 54-60.

Moghadam F, Couger MB, Russ B, Ramsey R, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. Genomics Data 10: 63-68.

Calkins SS, Couger MB, Jackson C, Zandler J, Hudgins GC, Hanafy RA, Budd C, French DP, Hoff WD, Youssef NH*. 2016. Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. Genomics Data, 10: 91-96.

Calkins SS, Youssef NH*. 2016. Insights into the Utility of the Focal Adhesion Scaffolding Proteins in theAnaerobic Fungus Orpinomyces sp. C1A. PLoS One 11: e0163553.

Moore J, Yang R, Wheeler K, Youssef NH*. 2016. Sequencing the microbial world one bug at a time. Research Reports from Life Science Freshmen Research Scholars 2.

S Dalvi, NH Youssef, BZ Fathepure. 2016. Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment. Extremophiles 20: 311-321.