Publications and other media from the Martens Lab

Preprints available in BioArchive (note: these are submitted for peer review, but have not undergone full peer-review evaluation)

Glowacki RWP, Pudlo NA, Tuncil Y, Luis AS, Terekhov AI, Hamaker BR, Martens EC. 2019. A genetically adaptable strategy for ribose scavenging in a human gut symbiont plays a diet-dependent role in colon colonization. Submitted March 2019.

Porter NT, Hryckowian AJ, Merrill BD, Gardner JO, Singh S, Sonnenburg JL, and Martens EC. 2019. Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron. Submitted 15 January 2019.

Slides and recent presentations

2019 ASM Microbe, San Francisco, CA

Purdue University, Celebration of Science Keynote, April 2019 (click link for slides), video at:

Bibliography 2019 (click citation to download PDF)

Briliūtė J, Urbanowicz PA, Luis AS, Baslé A, Paterson N, Rebello O, Hendel J, Ndeh DA, Lowe EC, Martens EC, Spencer DIR, Bolam DN, Crouch LI. 2019. Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci. Nature Microbiology 2019 doi: 10.1038/s41564-019-0466-x.

Caruso R, Mathes T, Martens EC, Kamada N, Nusrat A, Inohara N, Núñez G. 2019. A specific gene-microbe interaction drives the development of Crohn's disease-like colitis in mice. Science Immunology 4(34). pii: eaaw4341.

La Rosa SL, Leth ML, Michalak L, Hansen ME, Pudlo NA, Glowacki R, Pereira G, Workman CT, Arntzen MØ, Pope PB, Martens EC, Hachem MA, Westereng B. 2019. The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans. Nature Communications 10(1): 905.

Wegorzewska MM, Glowacki RWP, Hsieh SA, Donermeyer DL, Hickey CA, Horvath SC, Martens EC, Stappenbeck TS, Allen PM. 2019. Diet modulates colonic T cell responses by regulating the expression of a Bacteroides thetaiotaomicron antigen. Science Immunology 4(32). pii: eaau9079.

La Rosa SL, Kachrimanidou V, Buffetto F, Pope PB, Pudlo NA, Martens EC, Rastall RA, Gibson GR, Westereng B. 2019. Wood-Derived Dietary Fibers Promote Beneficial Human Gut Microbiota. mSphere :pii: e00554-18.

Bibliography 2018 (click citation to download PDF)

Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, Lucas SK, Beura LK, Thompson EA, Till LM, Batres R, Paw B, Pergament SL, Saenyakul P, Xiong M, Kim AD, Kim G, Masopust D, Martens EC, Angkurawaranon C, McGready R, Kashyap PC, Culhane-Pera KA, Knights D. 2018. US Immigration Westernizes the Human Gut Microbiome. Cell 175:962-972

Luis AS, Martens EC. 2018. Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes. Current Opinion in Chemical Biology 47:126-133

Porter NT, Luis AS, Martens EC. 2018. Microbe of the month: Bacteroides thetaiotaomicron. Trends Microbiology pii: S0966-842X(18)30177

Martens EC, Neumann M, Desai MS. 2018. Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier. Nature Reviews Microbiology doi: 10.1038/s41579-018-0036

Mendis M, Martens EC, Simsek S. 2018. How fine structural differences of xylooligosaccharides and arabinoxylooligosaccharides regulate differential growth of Bacteroides species. Journal of Agricultural and Food Chemistry 66:8398-8405.

Lam KN, Martens EC, Charles TC. 2018. Developing a Bacteroides system for function-based screening of DNA from the human gut microbiome. mSystems 3: pii: e00195-17.

Pluvinage B, Grondin JM, Amundsen C, Klassen L, Moote PE, Xiao Y, Thomas D, Pudlo NA, Anele A, Martens EC, Inglis GD, Uwiera RER, Boraston AB, Abbott DW. 2018. Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont. Nature Communications. 9:1043.

Foley MH, Martens EC, Koropatkin NM. 2018. SusE facilitates starch uptake independent of starch binding in B. thetaiotaomicron. Molecular Microbiology 108:551-566.

Luis AS, Briggs J, Zhang X, Farnell B, Ndeh D, Labourel A, Baslé A, Cartmell A, Terrapon N, Stott K, Lowe EC, McLean R, Shearer K, Schückel J, Venditto I, Ralet MC, Henrissat B, Martens EC, Mosimann SC, Abbott DW, Gilbert HJ. 2018. Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. 2018. Nature Microbiology 3:210-219

Media 2018 (click for link)

Martens quote in New York Times Carl Zimmer article

Bibliography 2017 (click citation to download PDF)

Tamura K, Hemsworth GR, Déjean G, Rogers TE, Pudlo NA, Urs K, Jain N, Davies GJ, Martens EC, Brumer H. 2017. Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides. Cell Reports 21:417-430

Tuncil YE, Xiao Y, Porter NT, Reuhs BL, Martens EC, Hamaker BR. 2017. Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence. MBio 8: pii: e01068-1

Porter NT, Canales P, Peterson DA, Martens EC. 2017. A Subset of Polysaccharide Capsules in the Human Symbiont Bacteroides thetaiotaomicron Promote Increased Competitive Fitness in the Mouse Gut. Cell Host & Microbe 22:494-506

Koropatkin NM, Martens EC. 2017. Meds Modify Microbiome, Mediating Their Effects. Cell Metabolism 26:456-457.

Porter NT, Martens EC. 2017. The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology. Annual Review of Microbiology 71:349-369

Seregin SS, Golovchenko N, Schaf B, Chen J, Pudlo NA, Mitchell J, Baxter NT, Zhao L, Schloss PD, Martens EC, Eaton KA, Chen GY. 2017. NLRP6 Protects Il10-/- Mice from Colitis by Limiting Colonization of Akkermansia muciniphila. Cell Reports 19:733-745

Kim YG, Sakamoto K, Seo SU, Pickard JM, Gillilland MG 3rd, Pudlo NA, Hoostal M, Li X, Wang TD, Feehley T, Stefka AT, Schmidt TM, Martens EC, Fukuda S, Inohara N, Nagler CR, Núñez G. 2017. Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens. Science 356:315-319

Ndeh D, Rogowski A, Cartmell A, Luis AS, Baslé A, Gray J, Venditto I, Briggs J, Zhang X, Labourel A, Terrapon N, Buffetto F, Nepogodiev S, Xiao Y, Field RA, Zhu Y, O'Neil MA, Urbanowicz BR, York WS, Davies GJ, Abbott DW, Ralet MC, Martens EC, Henrissat B, Gilbert HJ. 2017. Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature 544:65-70

Bågenholm V, Reddy SK, Bouraoui H, Morrill J, Kulcinskaja E, Bahr CM, Aurelius O, Rogers T, Xiao Y, Logan DT, Martens EC, Koropatkin NM, Stålbrand H. 2017. Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus: enzyme synergy and crystal structure of a beta-mannanase. Journal of Biological Chemistry 292:229-243

Media 2016 (click for link)

University of Michigan press release: Desai et al. dietary fiber study

Martens interview at 2016 Probiota Americas Conference-Chicago

Bibliography 2016 (click citation to download PDF)

Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Núñez G, Martens EC. 2016. A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell 167:1339-1353

Tauzin AS, Laville E, Xiao Y, Nouaille S, Le Bourgeois P, Heux S, Portais JC, Monsan P, Martens EC, Potocki-Veronese G, Bordes F. 2016. Functional characterization of a gene locus from an uncultured gut Bacteroides conferring xylo-oligosaccharides utilization to Escherichia coli. Molecular Microbiology 102:579-592

Wu J, Zhu J, Yin H, Liu X, An M, Pudlo NA, Martens EC, Chen GY, Lubman DM. 2016. Development of an Integrated Pipeline for Profiling Microbial Proteins from Mouse Fecal Samples by LC-MS/MS. Journal of Proteome Research 15:3635-3642

Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Chambon C, Yeoman CJ, Berg Miller ME, Fields CJ, Martens EC, Terrapon N, Henrissat B, White BA, Mosoni P. 2016. Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics 17:326

Moraïs S, Cockburn DW, Ben-David Y, Koropatkin NM, Martens EC, Duncan SH, Flint HJ, Mizrahi I, Bayer EA. 2016. Lysozyme activity of the Ruminococcus champanellensis cellulosome. Environmental Microbiology 18:5112-5122

Reddy SK, Bågenholm V, Pudlo NA, Bouraoui H, Koropatkin NM, Martens EC, Stålbrand H. 2016. A β-mannan utilization locus in Bacteroides ovatus involves a GH36 α-galactosidase active on galactomannans. FEBS Letters 590:2106-18

Porter NT, Martens EC. 2016. Love Thy Neighbor: Sharing and Cooperativity in the Gut Microbiota. Cell Host & Microbe 19:745-6

Martens EC. 2016. Microbiome: Fibre for the future. Nature 529:158-9

Bibliography 2015 (click citation to download PDF)

Pudlo NA, Urs K, Kumar SS, German JB, Mills DA, Martens EC. 2015. Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans. MBio 6:e01282-15

Abbott DW, Martens EC, Gilbert HJ, Cuskin F, Lowe EC. 2015. Coevolution of yeast mannan digestion: Convergence of the civilized human diet, distal gut microbiome, and host immunity. Gut Microbes 6:334-9

Hutkins RW, Krumbeck JA, Bindels LB, Cani PD, Fahey G Jr, Goh YJ, Hamaker B, Martens EC, Mills DA, Rastal RA, Vaughan E, Sanders ME. 2015. Prebiotics: why definitions matter. Current Opinion Biotechnology 37:1-7

Kovatcheva-Datchary P, Nilsson, Akrami, Lee, De Vadder, Arora, Hallen, Martens EC, Björck I, Bäckhed F. 2015. Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella. Cell Metabolism 22:971-82

Moraïs S, Ben David Y, Bensoussan L, Duncan SH, Koropatkin NM, Martens EC, Flint HJ, Bayer EA. 2016. Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition. Environmental Microbiology 18:542-56

Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Baslé A, Morland C, Day AM, Zheng H, Rogers TE, Thompson P, Hawkins AR, Yadav MP, Henrissat B, Martens EC, Dupree P, Gilbert HJ, Bolam DN. 2015. Glycan complexity dictates microbial resource allocation in the large intestine. Nature Communications 6:7481

Hickey CA, Kuhn KA, Donermeyer DL, Porter NT, Jin C, Cameron EA, Jung H, Kaiko GE, Wegorzewska M, Malvin NP, Glowacki RW, Hansson GC, Allen PM, Martens EC, Stappenbeck TS. 2015. Colitogenic Bacteroides thetaiotaomicron Antigens Access Host Immune Cells in a Sulfatase-Dependent Manner via Outer Membrane Vesicles. Cell Host & Microbe 17:672-80

Ben David Y, Dassa B, Borovok I, Lamed R, Koropatkin NM, Martens EC, White BA, Bernalier-Donadille A, Duncan SH, Flint HJ, Bayer EA, Moraïs S. 2015. Ruminococcal cellulosome systems from rumen to human. Environmental Microbiology 17:3407-26

Lammerts van Bueren A, Saraf A, Martens EC, Dijkhuizen L. 2015. Differential Metabolism of Exopolysaccharides from Probiotic Lactobacilli by the Human Gut Symbiont Bacteroides thetaiotaomicron. Applied Environmental Microbiology 81:3973-83

Cuskin F, Lowe EC, Temple MJ, Zhu Y, Cameron E, Pudlo NA, Porter NT, Urs K, Thompson AJ, Cartmell A, Rogowski A, Hamilton BS, Chen R, Tolbert TJ, Piens K, Bracke D, Vervecken W, Hakki Z, Speciale G, Munōz-Munōz JL, Day A, Peña MJ, McLean R, Suits MD, Boraston AB, Atherly T, Ziemer CJ, Williams SJ, Davies GJ, Abbott DW, Martens EC, Gilbert HJ. 2015. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature 517:165-169

Bibliography 2014 (click citation to download PDF)

Karunatilaka KS, Cameron EA, Martens EC, Koropatkin NM, Biteen JS. 2014. Superresolution imaging captures carbohydrate utilization dynamics in human gut symbionts. MBio 5:e02172

Martens EC, Sonnenburg JL, Relman DA. 2014. Editorial overview: insights into molecular mechanisms of microbiota. Journal of Molecular Biology 426:3827-9

Cameron EA, Kwiatkowski KJ, Lee BH, Hamaker BR, Koropatkin NM, Martens EC. 2014. Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis. MBio 5:e01441-14

Martens EC, Kelly AG, Tauzin AS, Brumer H. 2014. The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes. Journal of Molecular Biology 426:3851-65

Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, Klinter S, Pudlo NA, Urs K, Koropatkin NM, Creagh AL, Haynes CA, Kelly AG, Cederholm SN, Davies GJ, Martens EC, Brumer H. 2014. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature 506:498-502

TerAvest MA, He Z, Rosenbaum MA, Martens EC, Cotta MA, Gordon JI, Angenent LT. 2014. Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats. Biotechnology and Bioengineering 111:165-73

Bibliography 2013 (click citation to download PDF)

McNulty NP, Wu M, Erickson AR, Pan C, Erickson BK, Martens EC, Pudlo NA, Muegge BD, Henrissat B, Hettich RL, Gordon JI. 2013. Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome. PLoS Biology 11:e1001637

Engel K, Ashby D, Brady SF, Cowan DA, Doemer J, Edwards EA, Fiebig K, Martens EC, McCormac D, Mead DA, Miyazaki K, Moreno-Hagelsieb G, O'Gara F, Reid A, Rose DR, Simonet P, Sjöling S, Smalla K, Streit WR, Tedman-Jones J, Valla S, Wellington EM, Wu CC, Liles MR, Neufeld JD, Sessitsch A, Charles TC. 2013. Meeting report: 1st international functional metagenomics workshop May 7-8, 2012, St. Jacobs, Ontario, Canada. Standards in Genomic Science 8:106-11

Rogers TE, Pudlo NA, Koropatkin NM, Bell JS, Moya Balasch M, Jasker K, Martens EC. 2013. Dynamic responses of Bacteroides thetaiotaomicron during growth on glycan mixtures. Molecular Microbiology 88:876-90

Bibliography 2012 (click citation to download PDF)

Hehemann JH, Kelly AG, Pudlo NA, Martens EC, Boraston AB. 2012. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proceedings of the National Academy of Sciences USA 109:19786-91

Cameron EA, Maynard MA, Smith CJ, Smith TJ, Koropatkin NM, Martens EC. 2012. Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism. Journal of Biological Chemistry 287:34614-25

Kamada N, Kim YG, Sham HP, Vallance BA, Puente JL, Martens EC, Núñez G. 2012. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336:1325-9

Koropatkin NM, Cameron EA, Martens EC. 2012. How glycan metabolism shapes the human gut microbiota. Nature Review Microbiology 10:323-35

Bibliography 2011 (click citation to download PDF)

Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, Abbott DW, Henrissat B, Gilbert HJ, Bolam DN, Gordon JI. 2011. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biology 9:e1001221

Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Léon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Médigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair H. 2011. The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PLoS One 6:e27909

Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, Lebrilla CB, Weimer BC, Mills DA, German JB, Sonnenburg JL. 2011. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host & Microbe 10:507-14

Benjdia A, Martens EC, Gordon JI, Berteau O. 2011. Sulfatases and a radical S-adenosyl-L-methionine (AdoMet) enzyme are key for mucosal foraging and fitness of the prominent human gut symbiont, Bacteroides thetaiotaomicron. Journal of Biological Chemistry 286:25973-82

Bibliography 2009 (click citation to download PDF)

McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, Staroscik AM, Hoover TR, Cheng YQ, Stein JL. 2009. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Applied Environmental Microbiology 75:6864-75

Martens EC, Koropatkin NM, Smith TJ, Gordon JI. 2009. Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. Journal of Biological Chemistry 284:24673-7

Martens EC, Roth R, Heuser JE, Gordon JI. 2009. Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont. Journal of Biological Chemistry 284:18445-57

Koropatkin N, Martens EC, Gordon JI, Smith TJ. 2009. Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Biochemistry 48:1532-42

Bibliography 2008 (click to download PDF)

Martens EC, Chiang HC, Gordon JI. 2008. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host & Microbe 4:447-57

Koropatkin NM, Martens EC, Gordon JI, Smith TJ. 2008. Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16:1105-15

Bibliography 2007 (click to download PDF)

Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI. 2007. Evolution of symbiotic bacteria in the distal human intestine.  PLoS Biology 5:e156

Cowles KN, Cowles CE, Richards GR, Martens EC, Goodrich-Blair H. 2007. The global regulator Lrp contributes to mutualism, pathogenesis and phenotypic variation in the bacterium Xenorhabdus nematophila. Cellular Microbiology 9:1311-23

Bibliography 2006 (click to download PDF)

Bjursell MK, Martens EC, Gordon JI. 2006. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. Journal of Biological Chemistry 281:36269-79

Bibliography 2005 (click to download PDF)

Martens EC, Goodrich-Blair H. 2005. The Steinernema carpocapsae intestinal vesicle contains a subcellular structure with which Xenorhabdus nematophila associates during colonization initiation. Cellular Microbiology 7:1723-35

Martens EC, Russell FM, Goodrich-Blair H. 2005. Analysis of Xenorhabdus nematophila metabolic mutants yields insight into stages of Steinernema carpocapsae nematode intestinal colonization. Molecular Microbiology 58:28-45

Bibliography 2003 (click to download PDF)

Martens EC, Gawronski-Salerno J, Vokal DL, Pellitteri MC, Menard ML, Goodrich-Blair H. 2003. Xenorhabdus nematophila requires an intact iscRSUA-hscBA-fdx operon to colonize Steinernema carpocapsae nematodes. Journal of Bacteriology 185:3678-82

Martens EC, Heungens K, Goodrich-Blair H. 2003. Early colonization events in the mutualistic association between Steinernema carpocapsae nematodes and Xenorhabdus nematophila bacteria. Journal of Bacteriology 185:3147-54