The publications below reflect work from clients that have successfully employed microbiome research in their work. We invite you to explore this research and see how the microbiome can impact your own scientific efforts.

Human Health and Disease

  1. DADA2: High-resolution sample inference from Illumina amplicon data. Callahan, B et al. Nat Meth. 2016. doi:10.1038/nmeth.3869
  2. Intestinal epithelial TLR4 signaling affects epithelial function, colonic microbiota and promotes risk for transmissible colitis. Dheer, R et al. Infect and Immun. 2016. doi: 10.1128/IAI.01374-15
  3. Dietary Isomers of Sialyllactose Increase Ganglioside Sialic Acid Concentrations in the Corpus Callosum and Cerebellum and Modulate the Colonic Microbiota of Formula-Fed Piglets. Jacobi, et al. 2015. J Nutr doi: 10.3945/jn.115.220152.
  4. Microbiota studies in the bile duct strongly suggest a role for Helicobacter pylori in extra hepatic cholangiocarcinoma. Aviles-Jimenez, F et al. Clin Microbio and Infect. 2015; Oct 20. doi: 10.1016/j.cmi.2015.10.008
  5. Gut Microbiota in Multiple Sclerosis: Possible Influence of Immunomodulators. Cantarel, BL, et al. J Investig Med. 2015;63 No 5. Epub
  6. An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile. Miezeiewski, M et al. ISME J. 2015 February 9. 321-332.
  7. Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression. Rogier EW, et al PNAS 2014. cgi/doi/10.1073/pnas.1315792111.
  8. The Microbial Community of Cystic Fibrosis Airway Is Disrupted in Early Life. Renwick J, et al. PLOS One. December 19, 2014. DOI: 10.1371/journal.pone.0109798
  9. Microbial Dysbiosis Is Associated with Human Breast Cancer. Xuan, C et al. PLOS One. Jan 8, 2014. DOI: 10.1371/journal.pone.0083844
  10. Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer. Aviles-Jimenez, F et al. Scientific Reports 4. February 26, 2014. DOI: 10.1038/srep04202.
  11. A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis. Rivas NM, et al. J Allergy Clin Immunol. 2013 Jan;131(1):201-12.
  12. Changes in Abundance of Oral Microbiota Associated with Oral Cancer. Schmidt, BL, et al. PLOS One. June 2, 2014. DOI: 10.1371/journal.pone.0098741.
  13. Exercise Attenuates PCB-induced Changes in Mouse Gut. Choi JJ, et al. Environ Health Perspect 121:725–730 (2013).
  14. Gastrointestinal Microbiome Signatures Of Pediatric Patients With Irritable Bowel Syndrome. Saulnier DM, et al. Gastroenterology. 2011 Nov;141(5):1782-91.
  15. PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity. Nelson TA, et al., Neurogastroenterol Motil. 2011 Feb;23(2):169-77, e41-2. doi: 10.1111/j.1365-2982.2010.01637.x. Epub 2010 Dec 3.
  16. Structure of the human gastric bacterial community in relation to Helicobacter pylori status. Maldonado-Contreras A, et al. ISME J. 2011Apr 5(4):574-9.
  17. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. Huang YJ, et al; National Heart, Lung, and Blood Institute's Asthma Clinical Research Network. J Allergy Clin Immunol. 2011 Feb;127(2):372-381.e1-3. Epub 2010 Dec 30.
  18. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. Huang YJ et al. OMICS. 2010 Feb;14(1):9-59.
  19. Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. Cox MJ et al. PLoS One. 2010 Jan 18;5(1):e8745.


  1. Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean. Kellogg, CA et al. PLOS One. October 7, 2014. DOI: 10.1371/journal.pone.0108767.
  2. Bacterial profiling of White Plague Disease in a comparative coral species framework. Roder C, et al. ISME J (2014) 8, 31-39.
  3. Deciphering the Bacterial Microbiome of Citrus Plants in Response to 'Candidatus Liberibacter asiaticus'-Infection and Antibiotic Treatments. Zhang, M et al. PLOS ONe. November 8, 2013. DOI: 10.1371/journal.pone.0076331
  4. Intercontinental Dispersal of Bacteria and Archaea by Transpacific Winds. Smith, DJ, et al. Appl Envir Microbiol. Feb 2013(79):4; 1134-1139.
  5. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. He Z, et al. ISME J. 2012. Feb;6(2):259-72.
  6. Bacterial Diversity of Terrestrial Crystalline Volcanic Rocks, Iceland. Kelly LC, et al. Microb Ecol. 2011 May 17. [Epub ahead of print]
  7. Characterization of Airborne Bacteria at an Underground Subway Station. Dybwad M, et al. Environ Microbiol. 2012 Mar; 78(6): 1917-1929.
  8. Characterization of trapped lignin-degrading microbes in tropical forest soil. Deangelis KM, et al. PLoS One. 2011 Apr 29;6(4):e19306.
  9. Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria. Mendes R, et al. Science. 2011 May 5. [Epub ahead of print]
  10. Investigation of Microbial Populations in the Extremely Metal-Contaminated Coeur d'Alene River Sediments.Rastogi G, Barua S, Sani RK, Peyton BM. Microb Ecol. 2011 Feb 18. [Epub ahead of print]
  11. PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa.Weinert N, et al. FEMS Microbiol Ecol. 2011 Mar;75(3):497-506. doi: 10.1111/j.1574-6941.2010.01025.x. Epub 2011 Jan 11.
  12. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Hazen TC, et al. Science. 2010 Oct 8;330(6001):204-8. Epub 2010 Aug 24.
  13. Selective progressive response of soil microbial community to wild oat roots. DeAngelis KM, et al. The ISME Journal (2009) 3, 168–178.