What is the science linking the gut microbiome to health?

Over the last decade, research into the gut microbiome and how it affects human health has rapidly expanded. This research has uncovered numerous links between our gut microbiome and physical and mental disorders such as diabetes, obesity, heart disease, inflammatory bowel disease, colon cancer, Parkinson’s, multiple sclerosis, Alzheimer’s, depression and several more.

Read more here (open-source articles that can be accessed freely are denoted by *):

Diabetes

Academic

  • *Brunkwall, L. & Orho-Melander, M. The gut microbiome as a target for prevention and treatment of hyperglycaemia in type 2 diabetes: from current human evidence to future possibilities. Diabetologia 60, 943-951 (2017). Doi: 10.1007/s00125-017-4278-3
  • *Delzenne, N. M., Cani, P. D., Everard, A., Neyrinck, A. M. & Bindels, L. B. Gut microorganisms as promising targets for the management of type 2 diabetes. Diabetologia 58, 2206-2217 (2015). Doi: 10.1007/s00125-015-3712-7
  • *Kostic, A. D. et al. The Dynamics of the Human Infant Gut Microbiome in Development and in Progression towards Type 1 Diabetes. Cell host & microbe 17, 260-273 (2015). Doi: 10.1016/j.chom.2015.01.001
  • Mariño, E. et al. Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes. Nat. Immunol. 18, 552 (2017). Doi: 10.1038/ni.3713
  • *Paun, A., Yau, C. & Danska, J. S. The Influence of the Microbiome on Type 1 Diabetes. The Journal of Immunology 198, 590-595 (2017). Doi: 10.4049/jimmunol.1601519
  • *Zhang, X. et al. Human Gut Microbiota Changes Reveal the Progression of Glucose Intolerance. PLoS One 8, e71108 (2013). Doi: 10.1371/journal.pone.0071108

Science digests/Blogs

  1. https://www.sciencedaily.com/releases/2016/11/161114105642.htm
  2. http://www.the-scientist.com/?articles.view/articleNo/41033/title/Sugar-Substitutes–Gut-Bacteria–and-Glucose-Intolerance/
  3. https://www.sciencedaily.com/releases/2017/05/170530122341.htm
  4. https://www.sciencedaily.com/releases/2017/06/170601124153.htm

Obesity

Academic

  1. *Boulangé, C. L., Neves, A. L., Chilloux, J., Nicholson, J. K. & Dumas, M.-E. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Med. 8, 42 (2016). Doi: 10.1186/s13073-016-0303-2
  2. *Dao, M. C. et al. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut 65, 426-436 (2016). Doi: 10.1136/gutjnl-2014-308778
    *Menni, C. et al. Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain. Int. J. Obes. (Lond.) 41, 1099-1105 (2017). Doi: 10.1038/ijo.2017.66
  3. *Parekh, P. J., Balart, L. A. & Johnson, D. A. The Influence of the Gut Microbiome on Obesity, Metabolic Syndrome and Gastrointestinal Disease. Clinical And Translational Gastroenterology 6, e91 (2015). Doi: 10.1038/ctg.2015.16
  4. *Perry, R. J. et al. Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome. Nature 534, 213, (2016). Doi: 10.1038/nature18309
  5. Thaiss, C. A. et al. Persistent microbiome alterations modulate the rate of post-dieting weight regain. Nature 540, 544 (2016). Doi: 10.1038/nature20796

Science digests/Blogs

  1. https://www.sciencedaily.com/releases/2016/06/160608142554.htm
  2. https://theconversation.com/gut-bacteria-play-a-role-in-long-term-weight-gain-74496
  3. https://www.medicalnewstoday.com/articles/319411.php
  4. https://www.sciencedaily.com/releases/2016/11/161129091143.htm
  5. https://www.sciencenews.org/article/gut-fungi-might-be-linked-obesity-and-inflammatory-bowel-disorders
  6. https://www.sciencealert.com/gastric-bypass-surgery-gives-patients-a-new-set-of-helpful-microbes

Heart Disease

Academic

  1. Aron-Wisnewsky, J. & Clément, K. The gut microbiome, diet, and links to cardiometabolic and chronic disorders. Nature Reviews Nephrology 12, 169, (2015). Doi: 10.1038/nrneph.2015.191
  2. Jie, Z. et al. The gut microbiome in atherosclerotic cardiovascular disease. Nature Communications 8, 845 (2017). Doi: 10.1038/nrcardio.2017.120
  3. Jonsson, A. L. & Bäckhed, F. Role of gut microbiota in atherosclerosis. Nature Reviews Cardiology 14, 79 (2016). Doi: 10.1038/nrcardio.2016.183
  4. Marques, F. Z., Mackay, C. R. & Kaye, D. M. Beyond gut feelings: how the gut microbiota regulates blood pressure. Nature Reviews Cardiology (2017). Doi: 10.1038/nrcardio.2017.120
  5. Tang, W. H. W., Kitai, T. & Hazen, S. L. Gut Microbiota in Cardiovascular Health and Disease. Circul. Res. 120, 1183-1196, (2017). Doi: 10.1161/CIRCRESAHA.117.309715
  6. *Yan, Q. et al. Alterations of the Gut Microbiome in Hypertension. Frontiers in Cellular and Infection Microbiology 7, 381 (2017). Doi: 10.3389/fcimb.2017.00381

Science Digests/Blogs

  1. https://www.sciencedaily.com/releases/2017/07/170711093012.htm
  2. https://www.sciencedaily.com/releases/2016/08/160811120408.htm
  3. https://www.sciencedaily.com/releases/2017/11/171115131251.htm
  4. https://www.scientificamerican.com/article/how-bacteria-may-help-regulate-blood-pressure/
  5. https://www.sciencedaily.com/releases/2013/04/130424185211.htm

IBD

Academic

  1. *He, Q. et al. Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients. GigaScience 6, 1-11 (2017). Doi: 10.1093/gigascience/gix050
  2. Machiels, K. et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut 63, 1275-1283 (2014). Doi: 10.1136/gutjnl-2013-304833
  3. *Matsuoka, K. & Kanai, T. The gut microbiota and inflammatory bowel disease. Semin. Immunopathol. 37, 47-55 (2015). Doi: 10.1007/s00281-014-0454-4
  4. Pascal, V. et al. A microbial signature for Crohn’s disease. Gut (2017). Doi: 10.1136/gutjnl-2016-313235
  5. *Zamani, S. et al. Detection of enterotoxigenic Bacteroides fragilis in patients with ulcerative colitis. Gut Pathog. 9, 53 (2017). Doi: 10.1186/s13099-017-0202-0

Science Digests/Blogs

  1. https://www.sciencedaily.com/releases/2017/02/170213131429.htm
  2. https://www.scientificamerican.com/article/gut-fungus-suspected-in-crohn-s-disease/
  3. https://medicalxpress.com/news/2017-05-gut-microbiomes-clues-ibd-treatment.html
  4. https://www.healthline.com/health-news/gut-microbiome-helps-with-ibd-treatments#2

Colon cancer

Academic

  1. Bhutia, Y. D., Ogura, J., Sivaprakasam, S. & Ganapathy, V. Gut Microbiome and Colon Cancer: Role of Bacterial Metabolites and Their Molecular Targets in the Host. Curr. Colorectal Cancer Rep. 13, 111-118 (2017). Doi: 10.1007/s11888-017-0362-9
  2. Bullman, S. et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science (2017). Doi: 10.1126/science.aal5240
  3. *Sun, J. & Kato, I. Gut microbiota, inflammation and colorectal cancer. Genes & Diseases 3, 130-143 (2016). Doi: 10.1016/j.gendis.2016.03.004
  4. *Zackular, J. P., Rogers, M. A. M., Ruffin, M. T. & Schloss, P. D. The Human Gut Microbiome as a Screening Tool for Colorectal Cancer. Cancer Prevention Research 7, 1112 (2014). Doi: 10.1158/1940-6207.CAPR-14-0129
  5. *Zeller, G. et al. Potential of fecal microbiota for early‐stage detection of colorectal cancer. Mol. Syst. Biol. 10 (2014). Doi: 10.15252/msb.20145645

Science Digests/Blogs

  1. https://www.medicalnewstoday.com/articles/320579.php
  2. https://www.medicalnewstoday.com/articles/315465.php
  3. https://theconversation.com/how-our-gut-bacteria-affect-cancer-risk-and-response-to-treatment-75699
  4. https://www.sciencedaily.com/releases/2015/06/150624071026.htm

Central Nervous System diseases

Academic

  1. *Heintz-Buschart, A. et al. The nasal and gut microbiome in Parkinson’s disease and idiopathic rapid eye movement sleep behavior disorder. Mov. Disord. 33, 88-98 (2018). Doi:
  2. 10.1002/mds.27105
  3. *Jangi, S. et al. Alterations of the human gut microbiome in multiple sclerosis. Nature Communications 7, 12015 (2016). Doi: 10.1038/ncomms12015
  4. *Mangalam, A. et al. Human Gut-Derived Commensal Bacteria Suppress CNS Inflammatory and Demyelinating Disease. Cell Reports 20, 1269-1277 (2017). Doi: 10.1016/j.celrep.2017.07.031
  5. Scheperjans, F. et al. Gut microbiota are related to Parkinson’s disease and clinical phenotype. Mov. Disord. 30, 350-358 (2015). Doi: 10.1002/mds.26069
  6. *Sampson, T. R. et al. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease. Cell 167, 1469-1480.e1412 (2016). doi: 10.1016/j.cell.2016.11.018
  7. *Vogt, N. M. et al. Gut microbiome alterations in Alzheimer’s disease. Sci. Rep. 7, 13537 (2017). Doi: 10.1038/s41598-017-13601-y

Science Digests/Blogs

  1. https://www.med.wisc.edu/news-and-events/2017/october/alzheimers-disease-and-altered-gut-bacteria/
  2. http://www.huffingtonpost.com.au/entry/gut-bacteria-alzheimers_us_589e0e09e4b03df370d628be
  3. http://neurosciencenews.com/parkinsons-gut-microbiome-7380/
  4. http://www.sciencemag.org/news/2017/09/gut-microbes-could-help-trigger-multiple-sclerosis
  5. https://www.sciencedaily.com/releases/2017/08/170808150003.htm

Mental health

Academic

  1. *Foster, J. A., Lyte, M., Meyer, E. & Cryan, J. F. Gut Microbiota and Brain Function: An Evolving Field in Neuroscience. Int. J. Neuropsychopharmacol. 19, pyv114-pyv114, (2016). Doi: 10.1093/ijnp/pyv114
  2. *Foster, J. A. & McVey Neufeld, K.-A. Gut–brain axis: how the microbiome influences anxiety and depression. Trends Neurosci. 36, 305-312, (2013). Doi: 10.1016/j.tins.2013.01.005
  3. *Kelly, J. et al. Breaking Down the Barriers: The Gut Microbiome, Intestinal Permeability and Stress-related Psychiatric Disorders. Front. Cell. Neurosci. 9, (2015). Doi: 10.3389/fncel.2015.00392
  4. O’Mahony, S. M., Clarke, G., Borre, Y. E., Dinan, T. G. & Cryan, J. F. Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. Behav. Brain Res. 277, 32-48, (2015). Doi: 10.1016/j.bbr.2014.07.027
  5. *Rogers, G. B. et al. From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways. Mol. Psychiatry 21, 738, (2016). Doi: 10.1038/mp.2016.50

Science Digests/Blogs

  1. https://www.scientificamerican.com/article/mental-health-may-depend-on-creatures-in-the-gut/
  2. https://www.sciencenews.org/article/how-gut-bacteria-may-affect-anxiety
  3. https://www.newscientist.com/article/2095769-gut-bacteria-spotted-eating-brain-chemicals-for-the-first-time/
  4. Linking mental health and the gut microbiome
  5. https://theconversation.com/gut-feeling-how-your-microbiota-affects-your-mood-sleep-and-stress-levels-65107
  6. https://www.sciencedaily.com/releases/2017/03/170308114709.htm

What is the science linking diet, exercise and probiotics to the gut microbiome?

Research is showing that a balanced diet high in fibre and regular exercise can promote a healthy microbiome.

Diet

Academic

  1. David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559, (2013). Doi: 10.1038/nature12820
  2. *Desai, M. S. et al. A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell 167, 1339-1353.e1321, (2016). Doi: 10.1016/j.cell.2016.10.043
  3. *Graf, D. et al. Contribution of diet to the composition of the human gut microbiota. Microb. Ecol. Health Dis. 26, 10.3402/mehd.v3426.26164 (2015). Doi: 10.3402/mehd.v26.26164
  4. *Singh, R. K. et al. Influence of diet on the gut microbiome and implications for human health. J. Transl. Med. 15, 73, (2017). Doi: 10.1186/s12967-017-1175-y
  5. *Xu, Z. & Knight, R. Dietary effects on human gut microbiome diversity. The British Journal of Nutrition 113, S1-S5 (2015). Doi: 10.1017/S0007114514004127

Science Digests/Blogs

Exercise

Academic

  1. Allen, J. M. et al. Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans. Med. Sci. Sports Exerc. Publish Ahead of Print, (9000). Doi: 10.1249/MSS.0000000000001495
  2. *Cerdá, B. et al. Gut Microbiota Modification: Another Piece in the Puzzle of the Benefits of Physical Exercise in Health? Front. Physiol. 7, 51 (2016). Doi: 10.3389/fphys.2016.00051
  3. *Estaki, M. et al. Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions. Microbiome 4, 42 (2016). Doi: 10.1186/s40168-016-0189-7
  4. *Mach, N. & Fuster-Botella, D. Endurance exercise and gut microbiota: A review. Journal of
  5. Sport and Health Science 6, 179-197 (2017). Doi: 10.1016/j.jshs.2016.05.001
  6. *Yang, Y. et al. The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women. Nutrients 9, 792 (2017). Doi: 10.3390/nu9080792

Science Digests/Blogs

  1. https://blogs.illinois.edu/view/6367/586206
  2. https://www.psychologytoday.com/blog/the-athletes-way/201601/exercise-alters-gut-microbes-promote-brain-health
  3. http://www.sciencenewsline.com/news/2017082117580006.html
  4. https://www.sciencedaily.com/releases/2017/05/170504173454.htm

Probiotics

Academic

  1. *Ciorba, M. A. A Gastroenterologist’s Guide to Probiotics. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association 10, 960-968 (2012). Doi: 10.1016/j.cgh.2012.03.024
  2. Hill, D., Ross, R. P., Arendt, E. & Stanton, C. in Yogurt in Health and Disease Prevention 69-85 (Academic Press, 2017). Doi: 10.1016/B978-0-12-805134-4.00004-3
  3. *Sanders, M. E. Probiotics and microbiota composition. BMC Med. 14, 82 (2016). Doi: 10.1186/s12916-016-0629-z
  4. *Sanders, M. E., Benson, A., Lebeer, S., Merenstein, D. J. & Klaenhammer, T. R. Shared mechanisms among probiotic taxa: implications for general probiotic claims. Curr. Opin. Biotechnol. 49, 207-216, (2018). Doi: 10.1016/j.copbio.2017.09.007
  5. *Tu M-Y, Chen H-L, Tung Y-T, Kao C-C, Hu F-C, Chen C-M. Short-Term Effects of Kefir-Fermented Milk Consumption on Bone Mineral Density and Bone Metabolism in a Randomized Clinical Trial of Osteoporotic Patients. PLoS ONE 10(12): e0144231, (2015). Doi: 10.1371/journal.pone.0144231
  6. *Veiga, P. et al. Changes of the human gut microbiome induced by a fermented milk product. Sci. Rep. 4, 6328, (2014). doi: 10.1038/srep06328

Science Digests/Blogs

  1. https://www.sciencedaily.com/releases/2017/03/170308114709.htm
  2. https://blogs.biomedcentral.com/on-medicine/2016/05/10/probiotics-beneficial-effect-
  3. healthy-adults
  4. https://www.sciencedaily.com/releases/2014/09/140911125045.htm
  5. https://www.sciencedaily.com/releases/2012/11/121105114620.htm

What is the science about 16S rRNA gene sequencing compared to full metagenomics?

The advantages of using full metagenomics instead of 16S rRNA gene sequencing to profile the microbiome are clear.

Academic

  1. *Carlos, N., Tang, Y.-W. & Pei, Z. Pearls and pitfalls of genomics-based microbiome analysis. Emerging Microbes &Amp; Infections 1, e45 (2012). Doi: 10.1038/emi.2012.41
  2. *Jovel, J. et al. Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics. Front. Microbiol. 7, 459 (2016). Doi: 10.3389/fmicb.2016.00459
  3. Ranjan, R., Rani, A., Metwally, A., McGee, H. S. & Perkins, D. L. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem. Biophys. Res. Commun. 469, 967-977 (2016). Doi: 10.1016/j.bbrc.2015.12.083

Science Digests/Blogs

  1. http://blog.dnagenotek.com/microbiome/sequencing-the-microbiome-are-you-getting-the-full-story
  2. https://atlasofscience.org/identify-the-bacteria-within-and-on-your-self/
  3. https://www.sciencenews.org/blog/gory-details/here%E2%80%99s-poop-getting-your-gut-microbiome-analyzed

 

*Open-source