About the microbiome



Reports on the first-ever study to link the gut microbiome with an eye disease (uveitis, a form of eye inflammation), noting that the microbiome profile of inflammatory bowel disease (IBD) patients with uveitis was distinct from that of IBD patients without uveitis.

Kassam F, Gurry T, Aldarmaki A et al. The role of the gut microbiome in uveitis among patients with inflammatory bowel disease. Presented at American Uveitis Society Fall Meeting. New Orleans, LA, November 12, 2017.

See also: “IBD patients with uveitis show distinct microbiome signature, suggesting gut-eye axis,” Healio Gastroenterology, February 12, 2018.


Discusses how the “mutual and harmonious but intricate” interactions between the gut microbiome, nutrients, and the immune system are essential for brain performance.

Lerner A, Neidhofer S, Matthias T. The gut microbiome feelings of the brain: a perspective for non-microbiologists. Microorganisms 2017;5(4): 66.


Criticizes the dichotomy between “good” bacteria and “bad” bacteria as too simplistic; H. pylori, for example, is positively associated with Alzheimer’s disease but negatively associated with multiple sclerosis.

Park AM, Omura S, Fujita M et al. Helicobacter pylori and gut microbiota in multiple sclerosis versus Alzheimer’s disease: 10 pitfalls of microbiome studies. Clinical & Experimental Neuroimmunology 2017;8(3): 215-232.


Reports that decreased richness and diversity of the vaginal microbiome is associated with preterm birth in African-American women, who experience disproportionately high rates of preterm birth compared to other racial/ethnic groups.

Stout MJ, Zhou Y, Wylie KM et al. Early pregnancy vaginal microbiome trends and preterm birth. American Journal of Obstetrics & Gynecology 2017;217: 356.e1-356.e18.


Suggests that inflammation associated with age is a strong risk factor for overall mortality in older adults; gut dysbiosis may fuel this inflammation and contribute to immune dysfunction.

Thevaranjan N, Puchta A, Schulz C et al. Age-associated microbial dysbiosis promotes intestinal permeability, systemic inflammation, and macrophage dysfunction. Cell, Host & Microbe 2017;21: 455-466.e4.


Reports that prenatal and early-life exposure to furry pets is associated with higher overall species richness in infants’ gut microbiota, which may confer protection against childhood metabolic and atopic disease.

Tun HM, Konya T, Takaro TK et al. Exposure to household furry pets influences the gut microbiota of infants at 3-4 months following various birth scenarios. Microbiome 2017;5: 40.


Suggests that management of the gut microbiota is showing promise as a means of preventing or alleviating symptoms of neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases.

Westfall S, Lomis N, Kahouli I et al. Microbiome, probiotics and neurodegenerative diseases: deciphering the gut brain axis. Cellular and Molecular Life Sciences 2017;74(20): 3759-3787.




Reports on an international research team’s findings about gut health from the isolated Yanomami people in Venezuela and hypothesizes that Westernization significantly affects human microbiome diversity.
Clemente JC, Pehrsson EC, Blaser MJ et al. The microbiome of uncontacted Amerindians. Science Advances 2015;1(3): e1500183.

See also, “Great gut extinction: has modern life destroyed our health?” BBC News, May 3, 2015.


Reports on Yale University researchers’ efforts to figure out how healthy people maintain gut health in the face of environmental challenges.

Cullen TW, Schofield WB, Barry NA et al. Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation. Science 2015;347(6218): 170-175.

See also, “How the body maintains a healthy balance of ‘friendly’ gut bacteria,” Huffington Post, Jan. 15, 2015.


Summarizes work by Johns Hopkins researchers, who are studying gut bacteria and immune system interactions in relation to colon cancer, tuberculosis, and intestinal diseases.

Fields H. The gut: where bacteria and immune system meet. Johns Hopkins Medicine, Nov. 2015.

See also, Perez-Muñoz ME, Bergstrom K, Peng V et al. “Discordance between changes in the gut microbiota and pathogenicity in a mouse model of spontaneous colitis.” Gut Microbes 2014;5: 286-295.


Reports on the first large-scale analysis of intra-species genetic variation in the gut’s resident microorganisms, which highlights the complex relationship between our gut’s bacterial composition and gut function.

Greenblum S, Carr R, Borenstein E. Extensive strain-level copy number variation across human gut microbiome species. Cell 2015;160(4): 583-594.

See also, “Among gut microbes, strains, not just species, matter,” EurekAlert!, Jan. 29, 2015.


Presents comments by the co-founder of the American Gut Project on the current state of microbiome research.

Interview with Rob Knight, One scientist’s race to help microbes help you, NPR, Jan. 18, 2015.


Reports on a longitudinal study suggesting that a decline in microbial diversity in the gut may signal the onset of type 1 diabetes.

Kostic AD, Gevers D, Siljander H et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell, Host & Microbe 2015;17(2): 260-273.

See also, “Gut microbiota shifts likely precede type 1 diabetes onset,” Healio ITJ, Feb. 5, 2015.


Indicates that whereas the immune system encourages “good” gut bacteria to grow, an altered microbiota fosters inflammatory bowel conditions.

Kubinak JL, Petersen C […] Round JL. MyD88 signaling in T cells directs IgA-mediated control of the microbiota to promote health. Cell, Host & Microbe 2015;17(2): 153-163.

See also, “Immune system promotes digestive health by fostering community of ‘good’ bacteria,” EurekAlert!, Jan. 22, 2015.


Discusses H. pylori infection, which may lessen women’s risk of developing multiple sclerosis by “priming” the immune system early in life.

Pedrini MJF, Seewann A, Bennett KA et al. Helicobacter pylori infection as a protective factor against multiple sclerosis risk in females. Journal of Neurology, Neurosurgery & Psychiatry 2015;86(6): 603-607.

See also, “Gut health linked to lower MS risk in women,” NutraIngredients, Jan. 20, 2015.


Reports on research that has uncovered intriguing links between gut microbes and psoriatic arthritis.

Scher JU, Ubeda C, Artacho A et al. Decreased bacterial diversity characterizes an altered gut microbiota in psoriatic arthritis and resembles dysbiosis of inflammatory bowel disease. Arthritis & Rheumatology 2015;67(1): 128-139.

See also, “Arthritis tied to gut bacteria,” Newsmax Health, Jan. 12, 2015; and “Joint pain, from the gut,” The Atlantic, Jan. 12, 2015.




Discusses the effects of gut microbes on sleep, memory, mood, and cognition, as well as their relationship to life problems such as alcoholism, chronic fatigue syndrome, fibromyalgia, and restless legs syndrome.

Galland L. The gut microbiome and the brain. Journal of Medicinal Food 2014;17(12): 1261-1272.




Describes work by Johns Hopkins researchers, who suspect that changes in the gut microbiome may have something to do with the surge in asthma rates over the last 30 years.

Joyce MH. Asthma’s inner world. Johns Hopkins Public Health, Fall 2013.


Reminds readers that bacteria in the gut communicate with the host’s immune system and participate in metabolic processes that benefit both host and microbe.

Quigley EMM. Gut bacteria in health and disease. Gastroenterology & Hepatology 2013;9: 560-569.


Reports research indicating that intestinal dysbiosis may be linked to the onset of rheumatoid arthritis.

Scher JU, Sczesnak A, Longman RS et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2013;2: e01202.

See also, “Could balancing our gut bacteria be the key to unlocking RA?” Healthline, Jan. 27, 2015.



Suggests that the loss of intestinal barrier function (“leaky gut”) may be a key precondition to developing autoimmune disease.

Fasano A. Leaky gut and autoimmune diseases. Clinical Reviews in Allergy & Immunology 2012;42: 71-78.


Describes new techniques that are allowing researchers to better understand the human microbiome and develop personalized medicine strategies to improve health.

Ursell LK, Metcalf JL, Parfrey LW et al. Defining the human microbiome. Nutrition Reviews 2012;70: S38-S44.



Discusses the Human Microbiome Project (HMP), which is using newly available technologies to map the normal human microbiome for various tissues and identify opportunities to improve health.

NIH HMP Working Group, Peterson J, Garges S et al. The NIH Human Microbiome Project. Genome Research 2009;19: 2317-2323.

See also, “Unlocking the secrets of the microbiome,” The New York Times, Nov. 6, 2017.