Research Output

2020
Open Access

Dynamic shifts within volatile fatty acid–degrading microbial communities indicate process imbalance in anaerobic digesters

Mathai, P. P., Nicholes, M. S., Venkiteshwaran, K., Brown, C. M., Morris, R. L., Zitomer, D. H. & Maki, J. S., May 1 2020, In : Applied Microbiology and Biotechnology. 104, 10, p. 4563-4575 13 p.

Research output: Contribution to journalArticle

Evidence for auxiliary anaerobic metabolism in obligately aerobic Zetaproteobacteria

Jain, A. & Gralnick, J. A., Apr 1 2020, In : ISME Journal. 14, 4, p. 1057-1062 6 p.

Research output: Contribution to journalArticle

Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria

Shaw, D. R., Ali, M., Katuri, K. P., Gralnick, J. A., Reimann, J., Mesman, R., van Niftrik, L., Jetten, M. S. M. & Saikaly, P. E., Dec 1 2020, In : Nature communications. 11, 1, 2058.

Research output: Contribution to journalArticle

Open Access

In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display

Newton, M. S., Cabezas-Perusse, Y., Tong, C. L. & Seelig, B., Feb 21 2020, In : ACS Synthetic Biology. 9, 2, p. 181-190 10 p.

Research output: Contribution to journalReview article

Resistance of South American opossums to vWF-binding venom C-type lectins

Drabeck, D. H., Rucavado, A., Hingst-Zaher, E., Cruz, Y. P., Dean, A. M. & Jansa, S. A., Apr 30 2020, In : Toxicon. 178, p. 92-99 8 p.

Research output: Contribution to journalArticle

Role of wastewater treatment plants on environmental abundance of Antimicrobial Resistance Genes in Chilean rivers

Bueno, I., Verdugo, C., Jimenez-Lopez, O., Alvarez, P. P., Gonzalez-Rocha, G., Lima, C. A., Travis, D. A., Wass, B., Zhang, Q., Ishii, S. & Singer, R. S., Jan 2020, In : International Journal of Hygiene and Environmental Health. 223, 1, p. 56-64 9 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Sex bias in gut microbiome transmission in newly paired marmosets (Callithrix jacchus)

Zhu, L., Clayton, J. B., Suhr Van Haute, M. J., Yang, Q., Hassenstab, H. R., Mustoe, A. C., Knights, D., Benson, A. K. & French, J. A., Apr 2020, In : mSystems. 5, 2, e00910-19.

Research output: Contribution to journalArticle

Open Access

Synthetic Biology: What's in It for Electrical Engineers-

Hajimorad, M. & Gralnick, J. A., Mar 1 2020, In : IEEE Potentials. 39, 2, p. 9-14 6 p., 9027156.

Research output: Contribution to journalArticle

Water and sediment act as reservoirs for microbial taxa associated with invasive dreissenid mussels

Mathai, P. P., Magnone, P., Dunn, H. M. & Sadowsky, M. J., Feb 10 2020, In : Science of the Total Environment. 703, 134915.

Research output: Contribution to journalArticle

2019

Adaptive Landscapes in the Age of Synthetic Biology

Yi, X. & Dean, A. M., May 1 2019, In : Molecular biology and evolution. 36, 5, p. 890-907 18 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Algae as a green technology for heavy metals removal from various wastewater

Salama, E. S., Roh, H. S., Dev, S., Khan, M. A., Abou-Shanab, R. A. I., Chang, S. W. & Jeon, B. H., May 1 2019, In : World Journal of Microbiology and Biotechnology. 35, 5, 75.

Research output: Contribution to journalReview article

2 Scopus citations

A microfluidic platform for the simultaneous quantification of methanogen populations in anaerobic digestion processes

Mathai, P. P., Dunn, H. M., Venkiteshwaran, K., Zitomer, D. H., Maki, J. S., Ishii, S. & Sadowsky, M. J., May 2019, In : Environmental microbiology. 21, 5, p. 1798-1808 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides

Corts, A. D., Thomason, L. C., Gill, R. T. & Gralnick, J. A., Dec 1 2019, In : Scientific Reports. 9, 1, 39.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study

Muñiz Pedrogo, D. A., Chen, J., Hillmann, B., Jeraldo, P., Al-Ghalith, G., Taneja, V., Davis, J. M., Knights, D., Nelson, H., Faubion, W. A., Raffals, L. & Kashyap, P. C., Apr 11 2019, In : Inflammatory bowel diseases. 25, 5, p. 902-913 12 p.

Research output: Contribution to journalArticle

4 Scopus citations

Antibiotic-induced Disruption of Intestinal Microbiota Contributes to Failure of Vertical Sleeve Gastrectomy

Jahansouz, C., Staley, C., Kizy, S., Xu, H., Hertzel, A. V., Coryell, J., Singroy, S., Hamilton, M., DuRand, M., Bernlohr, D. A., Sadowsky, M. J., Khoruts, A. & Ikramuddin, S., Jun 1 2019, In : Annals of surgery. 269, 6, p. 1092-1100 9 p.

Research output: Contribution to journalArticle

Antibiotic resistance genes in freshwater trout farms in a watershed in Chile

Bueno, I., Travis, D., Gonzalez-Rocha, G., Alvarez, J., Lima, C., Benitez, C. G., Phelps, N. B. D., Wass, B., Johnson, T. J., Zhang, Q., Ishii, S. & Singer, R. S., Jan 1 2019, In : Journal of Environmental Quality. 48, 5, p. 1462-1471 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

Antibiotics and host-tailored probiotics similarly modulate effects on the developing avian microbiome, mycobiome, and host gene expression

Ward, T. L., Weber, B. P., Mendoza, K. M., Danzeisen, J. L., Llop, K., Lang, K., Clayton, J. B., Grace, E., Brannon, J., Radovic, I., Beauclaire, M., Heisel, T. J., Knights, D., Cardona, C., Kogut, M., Johnson, C., Noll, S. L., Arsenault, R., Reed, K. M. & Johnson, T. J., Jan 1 2019, In : mBio. 10, 5, e02171-19.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

A pilot study of fecal bile acid and microbiota profiles in inflammatory bowel disease and primary sclerosing cholangitis

Vaughn, B. P., Kaiser, T., Staley, C. M., Hamilton, M. J., Reich, J., Graiziger, C., Singroy, S., Kabage, A. J., Sadowsky, M. J. & Khoruts, A., Jan 1 2019, In : Clinical and Experimental Gastroenterology. 12, p. 9-19 11 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations
2 Scopus citations

Association of dietary patterns with the gut microbiota in older, community-dwelling men

Shikany, J. M., Demmer, R. T., Johnson, A. J., Fino, N. F., Meyer, K., Ensrud, K. E., Lane, N. E., Orwoll, E. S., Kado, D. M., Zmuda, J. M. & Langsetmo, L., Oct 1 2019, In : American Journal of Clinical Nutrition. 110, 4, p. 1003-1014 12 p.

Research output: Contribution to journalArticle

6 Scopus citations

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Nature Biotechnology, (2019), 37, 8, (852-857), 10.1038/s41587-019-0209-9)

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K. & 92 others, Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R. & Caporaso, J. G., Sep 1 2019, In : Nature biotechnology. 37, 9, 1 p.

Research output: Contribution to journalComment/debate

Open Access
2 Scopus citations

Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus)

Clayton, J. B., Shields-Cutler, R. R., Hoops, S. L., Al-Ghalith, G. A., Sha, J. C. M., Johnson, T. J. & Knights, D., Oct 1 2019, In : American journal of primatology. 81, 10-11, e22977.

Research output: Contribution to journalArticle

Biological Conversion of Amino Acids to Higher Alcohols

El-Dalatony, M. M., Saha, S., Govindwar, S. P., Abou-Shanab, R. A. I. & Jeon, B. H., Aug 2019, In : Trends in biotechnology. 37, 8, p. 855-869 15 p.

Research output: Contribution to journalReview article

5 Scopus citations

Biosynthesis and chemical diversity of β-lactone natural products

Robinson, S. L., Christenson, J. K. & Wackett, L. P., Mar 2019, In : Natural Product Reports. 36, 3, p. 458-475 18 p.

Research output: Contribution to journalReview article

17 Scopus citations

Characterization of Campylobacter jejuni, Campylobacter upsaliensis, and a novel Campylobacter sp. in a captive non-human primate zoological collection

Clayton, J. B., Danzeisen, J. L., Johnson, T. J., Trent, A. M., Hayer, S. S., Murphy, T., Wuenschmann, A., Elder, M., Shen, Z., Mannion, A., Bryant, E., Knights, D. & Fox, J. G., Apr 2019, In : Journal of Medical Primatology. 48, 2, p. 114-122 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

Combined effects of sulfamethazine and sulfamethoxazole on a freshwater microalga, Scenedesmus obliquus: toxicity, biodegradation, and metabolic fate

Xiong, J. Q., Kim, S. J., Kurade, M. B., Govindwar, S., Abou-Shanab, R. A. I., Kim, J. R., Roh, H. S., Khan, M. A. & Jeon, B. H., May 15 2019, In : Journal of Hazardous Materials. p. 138-146 9 p.

Research output: Contribution to journalArticle

23 Scopus citations

Comparative decay of sewage-associated marker genes in beach water and sediment in a subtropical region

Ahmed, W., Zhang, Q., Kozak, S., Beale, D., Gyawali, P., Sadowsky, M. J. & Simpson, S., Feb 1 2019, In : Water Research. 149, p. 511-521 11 p.

Research output: Contribution to journalArticle

11 Scopus citations

Compositional and temporal stability of fecal taxon libraries for use with SourceTracker in sub-tropical catchments

O'Dea, C., Zhang, Q., Staley, C., Masters, N., Kuballa, A., Fisher, P., Veal, C., Stratton, H., Sadowsky, M. J., Ahmed, W. & Katouli, M., Nov 15 2019, In : Water Research. 165, 114967.

Research output: Contribution to journalArticle

Cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis

Shi, K., Cho, S., Aukema, K. G., Lee, T., Bera, A. K., Seffernick, J. L., Wackett, L. P. & Aihara, H., Jun 2019, In : PloS one. 14, 6, e0216979.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

Johnson, A. J., Personalized Microbiome Class Students & Shmagel, A. K., Jun 12 2019, In : Cell Host and Microbe. 25, 6, p. 789-802.e5

Research output: Contribution to journalArticle

Open Access
37 Scopus citations

Development of a synthetic cumate-inducible gene expression system for Bacillus

Seo, S. O. & Schmidt-Dannert, C., Jan 1 2019, In : Applied Microbiology and Biotechnology. 103, 1, p. 303-313 11 p.

Research output: Contribution to journalArticle

2 Scopus citations

Dietary factors in sulfur metabolism and pathogenesis of ulcerative colitis

Teigen, L. M., Geng, Z., Sadowsky, M. J., Vaughn, B. P., Hamilton, M. J. & Khoruts, A., Apr 2019, In : Nutrients. 11, 4, 931.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

Durable long-term bacterial engraftment following encapsulated fecal microbiota transplantation to treat clostridium difficile infection

Staley, C., Kaiser, T., Vaughn, B. P., Graiziger, C., Hamilton, M. J., Kabage, A. J., Khoruts, A. & Sadowsky, M. J., Jul 1 2019, In : mBio. 10, 4, e01586-19.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia

Rashidi, A., Kaiser, T., Shields-Cutler, R. R., Graiziger, C., Holtan, S. G., Rehman, T. U., Wasko, J., Weisdorf, D. J., Dunny, G. M., Khoruts, A. & Staley, C. M., Dec 1 2019, In : Scientific reports. 9, 1, 6083.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Early E. Casseliflavus gut colonization and outcomes of allogeneic hematopoietic cell transplantation

Rashidi, A., Ebadi, M., Shields-Cutler, R. R., Kruziki, K., Manias, D. A., Barnes, A. M. T., DeFor, T. E., Ferrieri, P., Young, J. A. H., Knights, D., Blazar, B. R., Weisdorf, D. J. & Dunny, G. M., Jan 1 2019, In : PloS one. 14, 8, e0220850.

Research output: Contribution to journalArticle

Open Access

Efficient and Precise Genome Editing in Shewanella with Recombineering and CRISPR/Cas9-Mediated Counter-Selection

Corts, A. D., Thomason, L. C., Gill, R. T. & Gralnick, J. A., Aug 16 2019, In : ACS Synthetic Biology. 8, 8, p. 1877-1889 13 p.

Research output: Contribution to journalArticle

Engineering Streptomyces peucetius for Doxorubicin and Daunorubicin Biosynthesis

Shrestha, B., Pokhrel, A. R., Darsandhari, S., Parajuli, P., Sohng, J. K. & Pandey, R. P., 2019, Engineering Streptomyces peucetius for Doxorubicin and Daunorubicin Biosynthesis. Springer Nature, p. 191-209 19 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Genetic Code Evolution Investigated through the Synthesis and Characterisation of Proteins from Reduced-Alphabet Libraries

Newton, M. S., Morrone, D. J., Lee, K. H. & Seelig, B., Mar 15 2019, In : ChemBioChem. 20, 6, p. 846-856 11 p.

Research output: Contribution to journalArticle

2 Scopus citations

Genetic effects on the commensal microbiota in inflammatory bowel disease patients

Aschard, H., Laville, V., Tchetgen, E. T., Knights, D., Imhann, F., Seksik, P., Zaitlen, N., Silverberg, M. S., Cosnes, J., Weersma, R. K., Xavier, R., Beaugerie, L., Skurnik, D. & Sokol, H., Mar 2019, In : PLoS genetics. 15, 3, e1008018.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Impact of long-term grazing exclusion on soil microbial community composition and nutrient availability

Wang, Z., Zhang, Q., Staley, C., Gao, H., Ishii, S., Wei, X., Liu, J., Cheng, J., Hao, M. & Sadowsky, M. J., Feb 1 2019, In : Biology and Fertility of Soils. 55, 2, p. 121-134 14 p.

Research output: Contribution to journalArticle

7 Scopus citations

Inexpensive microbial dipstick diagnostic for nitrate in water

Aukema, K. G. & Wackett, L. P., Feb 2019, In : Environmental Science: Water Research and Technology. 5, 2, p. 406-416 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

Influence of Library Composition on SourceTracker Predictions for Community-Based Microbial Source Tracking

Brown, C. M., Mathai, P. P., Loesekann, T., Staley, C. & Sadowsky, M. J., Jan 2 2019, In : Environmental Science and Technology. 53, 1, p. 60-68 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Influence of short-term changes in dietary sulfur on the relative abundances of intestinal sulfate-reducing bacteria

Dostal Webster, A., Staley, C. M., Hamilton, M. J., Huang, M., Fryxell, K., Erickson, R., Kabage, A. J., Sadowsky, M. J. & Khoruts, A., Jul 4 2019, In : Gut microbes. 10, 4, p. 447-457 11 p.

Research output: Contribution to journalArticle

2 Scopus citations

In situ imaging of the bacterial flagellar motor disassembly and assembly processes

Kaplan, M., Subramanian, P., Ghosal, D., Oikonomou, C. M., Pirbadian, S., Starwalt-Lee, R., Mageswaran, S. K., Ortega, D. R., Gralnick, J. A., El-Naggar, M. Y. & Jensen, G. J., Jul 15 2019, In : EMBO Journal. 38, 14, e100957.

Research output: Contribution to journalArticle

3 Scopus citations

Mechanism of a Standalone β-Lactone Synthetase: New Continuous Assay for a Widespread ANL Superfamily Enzyme

Robinson, S. L., Christenson, J. K., Richman, J. E., Jenkins, D. J., Neres, J., Fonseca, D. R., Aldrich, C. & Wackett, L. P., Jul 1 2019, In : ChemBioChem. 20, 13, p. 1701-1711 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

Mechanisms of toxicity by and resistance to ferrous iron in anaerobic systems

Bennett, B. D. & Gralnick, J. A., Aug 20 2019, In : Free Radical Biology and Medicine. 140, p. 167-171 5 p.

Research output: Contribution to journalReview article

Open Access

Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela upwelling system

Zoss, R., Medina Ferrer, F., Flood, B. E., Jones, D. S., Louw, D. C. & Bailey, J., Jan 2019, In : Geobiology. 17, 1, p. 76-90 15 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Microbiome learning Repo (ML Repo): A public repository of microbiome regression and classification tasks

Vangay, P., Hillmann, B. M. & Knights, D., Jan 1 2019, In : GigaScience. 8, 5

Research output: Contribution to journalArticle

Open Access

Microfluidic dielectrophoresis illuminates the relationship between microbial cell envelope polarizability and electrochemical activity

Wang, Q., Jones, A. A. D., Gralnick, J. A., Lin, L. & Buie, C. R., Jan 1 2019, In : Historia da Historiografia. 11, 28, eaat5664.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations