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Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, F. Schulz et al. A Genomic Catalogue of Earth’s Microbiomes (Under Review).

J Beam , E Becraft, J Brown, F Schulz, J Jarett, O Bezuidt, N Poulton, K Clark, P Dunfield, N Ravin, J Spear, B Hedlund, K Kormas, S Sievert, MS Elshahed, H Barton, M Stott, J Eisen, D Moser, T Onstott, T Woyke, R Stepanauskas. Patescibacteria and DPANN may precede the evolution of respiration (Under Review)

A Yadav, J. Vilcaez, IF Farag, B. Johnson, K. Mueller, NH Youssef, and MS Elshahed*. Candidatus Mcinerneyibacterium aminivorans gen. nov., sp. nov., the first representative of the candidate phylum Mcinerneyibacteriota phyl. nov. recovered from a high temperature, high salinity tertiary oil reservoir in north central Oklahoma, USA (In revision).

V Dollhofer, D Young, S Seppälä, C Hooker, N Youssef, S M Podmirseg, M Nagler, M Reilly, Y Li, K Fliegerová, Y Cheng, G W Griffith, MS Elshahed, K V Solomon, M A O’Malley, M K Theodorou. 2019. The biotechnological potential of anaerobic gut fungi. The Mycota (In Press).

CL Murphy, NH Youssef, S. Hartson, and MS Elshahed*. The extraradical proteins of Rhizophagus irregularis: a shotgun proteomics approach. Fungal Biol. (In Press).

RA Hanafy, VB Lanjekar, PK Dhakephalkar, TM Callaghan, SS Dagar, GW Griffith, MS Elshahed, and NH Youssef. 2019. Seven new Neocallimastigomycota genera from wild, zoo-housed, and domesticated herbivores greatly expand the taxonomic diversity of the phylum. Mycologia (In Press).


Wang, NH Youssef, MB Couger, R. Hanafy, MS Elshahed, and J. Stajich. Comparative genomics and divergence time estimation of the anaerobic fungi in herbivorous mammals. mSystems 4:e00247-19.

CL Murphy, NH Youssef, RA Hanafy, MB Couger, J Stajich, Y Wang, K Baker, SS Dagar, GY Griffith, IF Farag, TM Callaghan, and MS Elshahed*. Horizontal Gene Transfer forged the evolution of anaerobic gut fungi into a phylogenetically distinct gut-dwelling fungal lineage. Appl. Environ. Microbiol. 85:e00988-19.

NH Youssef, IF Farag, S Rudy, A Mulliner, K Walker, F Caldwell, M Miller, WD Hoff, and MS Elshahed. The Wood-Ljungdahl pathway as a key driver of metabolic versatility in Candidate phylum Bipolaricaulota (Acetothermia, OP1). Env. Microbiol. Rep. 11:538-547.

O. Arends, B. Seymor, B. Benko, MS Elshahed, L Yakoweshen, S Ganguly-Mink. An ounce of prevention is worth a pound of biofilm mitigation. SPE-193598-MS

NH Youssef, IF Farag, CR Hahn, J Jarrett, E Becraft, E Eloe-Fadrosh, J Lightfoot, A Bourgeois, T Cole, S Ferrante, M Truelock, W Marsh, M Jamaleddine, S Ricketts, R Simpson, A McFadden, W Hoff, NV Ravin, S Sievert, R Stepanauskas, T Woyke, and MS Elshahed. Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities. Appl. Environ. Microbiol. 85: e00110-19.

NH Youssef, IF Farag, CR Hahn, H Premathilake, E Fry, M Hart, K Huffaker, E Bird, J Hambright, WD Hoff, and MS Elshahed. Candidatus Krumholzibacterium zodletonensis, the first representative of the candidate phylum Krumholzbacterota, recovered from an anoxic sulfidic spring using genome resolved metagenomics. Syst. Appl. Microbiol. 42:85-93.


WA Eraqi, MT ElRakaiby, SA Megahed, NH Yousef, MS Elshahed and AS Yassin. The Nile river microbiome reveals a remarkably stable community between wet and dry seasons, and sampling sites, in a large urban metropolis. (Cairo, Egypt). Omics 22:553-564.

Vilcaez, J York, NH Youssef, and MS Elshahed. Stimulation of methanogenic crude oil biodegradation in depleted oil reservoirs. Fuel. 232:581-590.

RA Hanafy, MS Elshahed, B. Johnson, and NH Youssef. Anaeromyces contortus sp. nov., a new anaerobic gut fungal species (Neocallimastigomycota) isolated from the feces of cow and goat. Mycologia. 110:502-512

RA Hanafy, MS Elshahed, and NH Youssef. Feramyces austinii, gen. nov, sp. nov., an anaerobic gut fungus from rumen and fecal samples of wild Barbary sheep and fallow deer. Mycologia 110:513-525

SS Calkins, NC Elledge, SM Marek, MB Couger, K Meuller, MS Elshahed, and NH Youssef 2018. Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Peer J. 6:e4276


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). PLOS ONE 12: e0177488.

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. Mycologia 109:231-243.

IF Farag, NH Youssef, and MS Elshahed*. Global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3). Appl. Environ. Microbiol. 83:e00521.

A Ranganathan, OP Smith, NH Youssef, CG Struchtemeyer, HK Atiyeh, and MS Elshahed*. Utilizing Anaerobic Fungi for Two-stage Sugar Extraction and Biofuel Production from Lignocellulosic Biomass. Frontiers in Microbiol. 8:635.

JM Morrison, CL Murphy, K Baker, R Zamor, S Nikolai, S Wilder, MS Elshahed, NH Youssef 2017. Microbial communities mediating algal detritus turnover under anaerobic conditions. Peer J 5:e2803.


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

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.


MB Couger, NH Youssef, CG Struchtemeyer, AS Liggenstoffer, and MS Elshahed* 2015. Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A. Biotechnol. Biofuels. 8:208.

MB Couger, R Hanafy, C Edens, C Budd, DP French, WD Hoff, MS Elshahed, and NH Youssef 2015. Draft genome of the Arthrobacter sp. strain Edens01 contains a range of genes relevant to bioremediation. Genome Announc. 3:e01475-15.

MB Couger, R Hanafy, RM Mitacek, C Budd, DP French, WD Hoff, MS Elshahed, and NH Youssef 2015. The draft Genome of the Xanthomonas species strain Mitacek01 expands the pangenome of a genus of plant pathogens. Genome Announc. 3:e01450-15.

Spain AM, MS Elshahed, FZ Najar, and LR Krumholz 2015. Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism. PeerJ 3:e1259.

Couger MB, 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.

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

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

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

Struchtemeyer CG, MB Couger, A. Ranganathan, AS Liggenstoffer, NH Youssef, and MS Elshahed. Survival of the anaerobic fungus Orpinomyces sp. strain C1A after prolonged air exposure. Scientific Rep. 4:6892.

Gruninger RJ, AK Puniya, TM Callaghan, JE. Edwards, NH Youssef, SS Dagar, K Fliegerova, GW Griffith, R Forster, A Tsang, T McAllister, and MS. Elshahed. Anaerobic Fungi (Phylum Neocallimastigomycota): Advances in understanding of their taxonomy, life cycle, ecology, role, and biotechnological potential. FEMS Microbiol. Ecol. 90:1-17.

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

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

Youssef NH, KN Savage-Ashlock, AL McCully, B Luedtke, EI Shaw, WD Hoff, and MS Elshahed. 2014. Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales. The ISME. J. 8:636-649.

CG Struchtemeyer, NH Youssef, and MS Elshahed. Protocols for investigating the microbiology of drilling fluids, hydraulic fracturing fluids, and formations in unconventional natural gas reservoirs. In “Hydrocarbon and Lipid Microbiology Protocols”. Springer Protocols Series. Springer-Verlag Berlin Heidelburg.

NH Youssef and MS Elshahed. The phylum Planctomycetes in E. Roesenberg, E. Stackebrant, F. Thompson, E. F. DeLong, and S. Lory. The Prokaryotes 4th edition. Springer, New York: New York.

Youssef NH, MB Couger, CG Struchtemeyer, AS Liggenstoffer, RA Prade, FZ Najar, HK Atiyeh, MR Wilkins, and MS Elshahed. Genome of the anaerobic fungus Orpinomyces sp. C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl. Environ. Microbiol. 79:4620-4634.

Davis JP, Struchtemeyer CG, and MS Elshahed. Bacterial communities associated with production facilities of two newly drilled thermogenic natural gas wells in the Barnett shale (Texas, USA). Micr. Ecol. 64:942-954.

Struchtemeyer CG, and MS Elshahed. Bacterial communities associated with hydraulic fracturing fluids in thermogenic natural gas wells in North Central Texas, USA. FEMS Microbiol Ecol. 81:13-25.

Struchtemeyer CG, M Morrison, and MS Elshahed. A critical assessment of the efficacy of biocides used during the hydraulic fracturing process in shale natural gas wells. Int. J. Biodeg. Bioremed. 71:15-21.

Schoch CL, KA Seifert, S Huhndorf, V Robert, JL Spouge, CA Levesque, W Chen; et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. USA 109:6241-6246.

Youssef NH, B Steidley, and MS Elshahed. Novel high-rank phylogenetic diversities within a sulfur spring (Zodletone spring, Oklahoma, USA) revealed using a combined pyrosequencing/Sanger approach. Appl. Environ. Microbiol. 78: 2677-2688.

Youssef NH, KN Savage-Ashlock, and MS Elshahed. Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats. Applied Environmental Microbiology. Appl. Environ. Microbiol. 78: 1332-1344.

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

Sheik CS, WH Beasley, MS Elshahed, X Zhou, Y Luo, and LR Krumholz. Effect of warming and drought on grassland microbial communities. The ISME Journal 5:1692-1700.

Struchtemeyer CG, JP Davis, MS Elshahed. Influence of the Drilling Mud Formulation Process on the Bacterial Communities in Thermogenic Natural Gas Wells of the Barnett Shale Appl. Environ. Microbiol. 77: 4744-4753.

Bühring SI, SM Sievert, HM Jonkers, T Ertefai, MS Elshahed, LR Krumholz, and K-U Hinrichs. Insights into the chemotaxonomic composition and carbon cycling in phototrophic microbial mats in an artesian sulfur-rich spring (Zodletone, Oklahoma, USA), a possible analogue for ancient microbial mat systems. Geobiology 9:166-179.

MS Elshahed and NH Youssef. Novelty and uniqueness patterns of rare members of the soil biosphere In F. de Bruijn (editor) Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. Wiley/Blackwell Publishing CO.

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

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

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

Elshahed. Biodegradation of low molecular weight alkanes under mesophilic, sulfate-reducing conditions: evidence, metabolic intermediates, and community patterns. FEMS Microbiol. Ecol. 72:485-495.

MS Elshahed* 2010 Microbiological aspects of biofuel production: current status and future directions. J. Adv. Res. 1:103-111.

SR Heise, MS Elshahed, and SE Little. Bacterial diversity in Amblyomma americanum with a focus on members of the genus Rickettsia. J. Med. Entymol. 47: 258-268.

Youssef NH, C Sheik, LR Krumholz, FZ Najar, BA Roe, and MS Elshahed. A Comparative study of species richness estimates obtained using near complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl. Environ. Microbiol. 75: 5227-5236.

Davis JP, NH Youssef, and MS Elshahed. Assessment of the diversity, abundance, and ecological distribution of candidate division SR1 reveals a high phylogenetic, but a limited morphotypic diversity. Appl. Environ. Microbiol. 75: 4139-4148.

Spain, AM, LR Krumholz, and MS Elshahed. Abundance, composition, diversity, and novelty of soil Proteobacteria. The ISME J. 3: 992-1000.

Youssef NH, MS Elshahed, and MJ McInerney. Microbially-mediated processes in oil fields: culprits, problems, and opportunities. Adv. Appl. Microbiol. 66:141-251.

Youssef NH, and MS Elshahed. Diversity rankings among bacterial lineages in soil. The ISME J. 3: 305-313.

Elshahed MS, NH Youssef, AM Spain, C. Sheik, FZ Najar, LO Sukharnikov, BA Roe, JP Davis, PD Schloss, VL Bailey, and LR Krumholz. Novelty and uniqueness patterns within rare members of the soil biosphere. Appl. Environ. Microbiol. 74: 5422-5428.

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

Savage KN, LR Krumholz, A Oren, and MS Elshahed. Halosarcina pallida gen. nov., sp. nov., a halophilic archaeon isolated from Zodletone spring in southwestern Oklahoma. Int. J. Syst. Evol. Microbiol. 58: 856-860.

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

Spain AM, AD Peacock, J Istook, MS Elshahed, FZ Najar, BA Roe, DC White, and LR Krumholz. Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate- and uranium-contaminated aquifer. Appl. Environ. Microbiol. 73:4892-4904.

Savage KN, LR Krumholz, A Oren and MS Elshahed. Haladaptatus paucihalophilus gen. nov., sp. nov., a halophilic archaeon isolated from a low-salt, high-sulfide spring. Int. J. Syst. Evol. Microbiol. 57:19-24.


Elshahed MS, FZ Najar, M Aycock, C Qu, BA Roe, and LR Krumholz 2005. Metagenomic analysis of the microbial community at Zodletone spring: Insights into the genome of novel Candidate division OD1. Appl. Environ. Microbiol. 71: 7958-7962.

Luo Q, LR Krumholz, FZ Najar, BA Roe, AD Peacock, DC White, and MS Elshahed. Diversity of the microeukaryotic community in sulfide-rich Zodletone spring. 71:6175-6184.

Struchtemeyer CG, MS Elshahed, KE Duncan, and MJ McInerney. Evidence for Acetoclastic Methanogenesis in the Presence of Sulfate in a Gas Condensate-Contaminated Aquifer. Appl. Environ. Microbiol. 71:5348-5355.

Elshahed MS, KN Savage, A Ventosa, M Carmen-Gutierrez, A Oren, and LR Krumholz. Haloferax sulfurifontissp. nov., a halophilic archaeon isolated from a sulfide and sulfur-rich spring. Int. J. Syst. Evol. Microbiol. 54:2275-2279.

Senko JM, BS Campbell, JR Henricksen, MS Elshahed, TA Dewers, and LR Krumholz. Barite deposition mediated by phototrophic sulfide oxidizing bacteria. Geochem. Cosmochem. Acta. 68:773-780.

Elshahed MS, FZ Najar, BA Roe, A Oren, TA Dewers, and LR Krumholz. Survey of archaeal diversity reveals abundance of halophilic Archaea in a low-salt, anaerobic sulfur spring. Appl. Environ. Microbiol. 70:2230-2239.

Elshahed MS, JM Senko, FZ Najar, SM Kenton, BA Roe, TA Dewers, JR Spear, and LR Krumholz.Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. Appl. Environ. Microbiol. 69:5609-5621.

Elshahed MS, and MJ McInerney 2001.Benzoate fermentation by the anaerobic bacterium Syntrophus aciditrophicus in absence of hydrogen-utilizing microorganisms. Appl. Environ. Microbiol. 67:5520-5525.

Elshahed MS, VK Bhupathiraju, NQ Wofford, MA Nanny, and MJ McInerney 2001. Metabolism of benzoate, cyclohex-1-ene carboxylate and cyclohexane carboxylate by Syntrophus aciditrophicus strain SB in syntrophic association with H2-using microorganisms. Appl. Environ. Microbiol. 67:1728-1738.

Elshahed MS, and MJ McInerney 2001. Is interspecies hydrogen transfer needed for toluene degradation under sulfate-reducing conditions? FEMS Microbiol. Ecol. 35:163-169.

Elshahed MS, LM Gieg, MJ McInerney, and JM Suflita 2001. Signature metabolites attesting to the in situ attenuation of alkylbenzenes in anaerobic environments. Environ. Sci. and Technol. 35:682-689.