Human Health and Disease

  1. Restructuring of the Gut Microbiome by Intermittent Fasting Prevents Retinopathy and Prolongs Survival in db/db Mice. Beli, E et al. Diabetes 2018 Apr; db180158.
  2. DADA2: High-resolution sample inference from Illumina amplicon data. Callahan, B et al. Nat Meth. 2016. doi:10.1038/nmeth.3869
  3. 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
  4. 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.
  5. 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
  6. Gut Microbiota in Multiple Sclerosis: Possible Influence of Immunomodulators. Cantarel, BL, et al. J Investig Med. 2015;63 No 5. Epub
  7. 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.
  8. 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.
  9. 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
  10. Microbial Dysbiosis Is Associated with Human Breast Cancer. Xuan, C et al. PLOS One. Jan 8, 2014. DOI: 10.1371/journal.pone.0083844
  11. 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.
  12. 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.
  13. 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.
  14. Exercise Attenuates PCB-induced Changes in Mouse Gut. Choi JJ, et al. Environ Health Perspect 121:725–730 (2013).
  15. Gastrointestinal Microbiome Signatures Of Pediatric Patients With Irritable Bowel Syndrome. Saulnier DM, et al. Gastroenterology. 2011 Nov;141(5):1782-91.
  16. 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.
  17. 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.
  18. 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.
  19. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. Huang YJ et al. OMICS. 2010 Feb;14(1):9-59.
  20. 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.