Using the Human Gastrointestinal Microbiome to Personalize Nutrition Advice: Are Registered Dietitian Nutritionists Ready for the Opportunities and Challenges?

Published:December 13, 2016DOI:https://doi.org/10.1016/j.jand.2016.10.020
      The Continuing Professional Education (CPE) quiz for this article is available for free to Academy members through the MyCDRGo app (available for iOS and Android devices) and through www.jandonline.org (click on “CPE” in the menu and then “Academy Journal CPE Articles”). Log in with your Academy of Nutrition and Dietetics or Commission on Dietetic Registration username and password, click “Journal Article Quiz” on the next page, then click the “Additional Journal CPE quizzes” button to view a list of available quizzes. Non-members may take CPE quizzes by sending a request to [email protected] There is a fee of $45 per quiz (includes quiz and copy of article) for non-member Journal CPE. CPE quizzes are valid for 1 year after the issue date in which the articles are published.
      Knowledge of the gastrointestinal (GI) microbiome, including its metabolic potential, provides the opportunity for registered dietitian nutritionists (RDNs) to offer more personalized nutrition advice for our clients. The GI microbiome is the entire community of microbes, which includes bacteria that live within the GI tract. In GI conditions, an opportunity may exist to reduce symptom severity by manipulating the bacteria present in the gut. In metabolic conditions, individual features of the microbiome may explain why individuals respond differently to standardized nutritional interventions.
      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribe:

      Subscribe to Journal of the Academy of Nutrition and Dietetics
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • Qin J.
        • Li R.
        • Raes J.
        • et al.
        A human gut microbial gene catalogue established by metagenomic sequencing.
        Nature. 2010; 464: 59-65
        • Rajilic-Stojanovic M.
        • de Vos W.M.
        The first 1000 cultured species of the human gastrointestinal microbiota.
        FEMS Microbiol Rev. 2014; 38: 996-1047
        • Duffy L.C.
        • Raiten D.J.
        • Hubbard V.S.
        • Starke-Reed P.
        Progress and challenges in developing metabolic footprints from diet in human gut microbial cometabolism.
        J Nutr. 2015; 145: 1123S-1130S
        • Lozupone C.A.
        • Stombaugh J.I.
        • Gordon J.I.
        • Jansson J.K.
        • Knight R.
        Diversity, stability and resilience of the human gut microbiota.
        Nature. 2012; 489: 220-230
        • Vermeer C.
        • Jie K.-S.G.
        • Knapen M.H.J.
        Role of vitamin K in bone metabolism.
        Annu Rev Nutr. 1995; 15: 1-21
        • Binder H.J.
        • Mehta P.
        Short-chain fatty acids stimulate active sodium and chloride absorption in vitro in the rat distal colon.
        Gastroenterology. 1989; 96: 989-996
        • Maslowski K.M.
        • Vieira A.T.
        • Ng A.
        • et al.
        Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43.
        Nature. 2009; 461: 1282-1286
      1. Russo I, Luciani A, De Cicco P, Troncone E, Ciacci C. Butyrate attenuates lipopolysaccharide-induced inflammation in intestinal cells and Crohn's mucosa through modulation of antioxidant defense machinery. PLoS One [Electronic Resource]. 2012;7(3):e32841.

        • Suzuki T.
        • Yoshida S.
        • Hara H.
        Physiological concentrations of short-chain fatty acids immediately suppress colonic epithelial permeability.
        Br J Nutr. 2008; 100: 297-305
        • Hurst N.R.
        • Kendig D.M.
        • Murthy K.S.
        • Grider J.R.
        The short chain fatty acids, butyrate and propionate, have differential effects on the motility of the guinea pig colon.
        Neurogastroenterol Motil. 2014; 26: 1586-1596
        • Neuman H.
        • Debelius J.W.
        • Knight R.
        • Koren O.
        Microbial endocrinology: The interplay between the microbiota and the endocrine system.
        FEMS Microbiol Rev. 2015; 39: 509-521
        • De Filippo C.
        • Cavalieri D.
        • Di Paola M.
        • et al.
        Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.
        Proc Natl Acad Sci U S A. 2010; 107: 14691-14696
        • David L.A.
        • Maurice C.F.
        • Carmody R.N.
        • et al.
        Diet rapidly and reproducibly alters the human gut microbiome.
        Nature. 2014; 505: 559-563
        • Clarke S.F.
        • Murphy E.F.
        • O'Sullivan O.
        • et al.
        Exercise and associated dietary extremes impact on gut microbial diversity.
        Gut. 2014; 63: 1913-1920
        • Petersen C.
        • Round J.L.
        Defining dysbiosis and its influence on host immunity and disease.
        Cell Microbiol. 2014; 16: 1024-1033
        • Yatsunenko T.
        • Rey F.E.
        • Manary M.J.
        • et al.
        Human gut microbiome viewed across age and geography.
        Nature. 2012; 486: 222-227
        • Koboziev I.
        • Reinoso Webb C.
        • Furr K.L.
        • Grisham M.B.
        Role of the enteric microbiota in intestinal homeostasis and inflammation.
        Free Radic Biol Med. 2014; 68: 122-133
        • Xu Z.
        • Knight R.
        Dietary effects on human gut microbiome diversity.
        Br J Nutr. 2015; 113 Suppl: S1-S5
        • Hollister E.B.
        • Gao C.
        • Versalovic J.
        Compositional and functional features of the gastrointestinal microbiome and their effects on human health.
        Gastroenterology. 2014; 146: 1449-1458
        • Zoetendal E.G.
        • Raes J.
        • van den Bogert B.
        • et al.
        The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.
        ISME J. 2012; 6: 1415-1426
        • Rangel I.
        • Sundin J.
        • Fuentes S.
        • Repsilber D.
        • de Vos W.M.
        • Brummer R.J.
        The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects.
        Aliment Pharmacol Ther. 2015; 42: 1211-1221
        • Sundin J.
        • Rangel I.
        • Fuentes S.
        • et al.
        Altered faecal and mucosal microbial composition in post-infectious irritable bowel syndrome patients correlates with mucosal lymphocyte phenotypes and psychological distress.
        Aliment Pharmacol Ther. 2015; 41: 342-351
        • Zeevi D.
        • Korem T.
        • Zmora N.
        • et al.
        Personalized nutrition by prediction of glycemic responses.
        Cell. 2015; 163: 1079-1094
        • Malnick S.
        • Melzer E.
        Human microbiome: From the bathroom to the bedside.
        World J Gastrointest Pathophysiol. 2015; 6: 79-85
        • Varankovich N.V.
        • Nickerson M.T.
        • Korber D.R.
        Probiotic-based strategies for therapeutic and prophylactic use against multiple gastrointestinal diseases.
        Front Microbiol. 2015; 6: 685
        • Morgan X.C.
        • Huttenhower C.
        Chapter 12: Human microbiome analysis.
        PLoS Comput Biol. 2012; 8: e1002808
        • Di Bella J.M.
        • Bao Y.
        • Gloor G.B.
        • Burton J.P.
        • Reid G.
        High throughput sequencing methods and analysis for microbiome research.
        J Microbiol Methods. 2013; 95: 401-414
        • Chumpitazi B.P.
        • Hollister E.B.
        • Oezguen N.
        • et al.
        Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome.
        Gut Microbes. 2014; 5: 165-175
        • Chumpitazi B.P.
        • Cope J.L.
        • Hollister E.B.
        • et al.
        Randomised clinical trial: Gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome.
        Aliment Pharmacol Ther. 2015; 42: 418-427
        • McIntosh K.
        • Reed D.E.
        • Schneider T.
        • et al.
        FODMAPs alter symptoms and the metabolome of patients with IBS: A randomised controlled trial [published online ahead of print March 14, 2016].
        Gut. 2016; https://doi.org/10.1136/gutjnl-2015-311339
        • Sayin S.I.
        • Wahlstrom A.
        • Felin J.
        • et al.
        Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist.
        Cell Metab. 2013; 17: 225-235
        • Turnbaugh P.J.
        • Ley R.E.
        • Mahowald M.A.
        • Magrini V.
        • Mardis E.R.
        • Gordon J.I.
        An obesity-associated gut microbiome with increased capacity for energy harvest.
        Nature. 2006; 444: 1027-1031
        • Xu J.
        • Bjursell M.K.
        • Himrod J.
        • et al.
        A genomic view of the human-Bacteroides thetaiotaomicron symbiosis.
        Science. 2003; 299: 2074-2076
        • Krebs J.D.
        • Elley C.R.
        • Parry-Strong A.
        • et al.
        The Diabetes Excess Weight Loss (DEWL) Trial: A randomised controlled trial of high-protein versus high-carbohydrate diets over 2 years in type 2 diabetes.
        Diabetologia. 2012; 55: 905-914
        • Tay J.
        • Luscombe-Marsh N.D.
        • Thompson C.H.
        • et al.
        A very low-carbohydrate, low-saturated fat diet for type 2 diabetes management: A randomized trial.
        Diabetes Care. 2014; 37: 2909-2918
      2. Saslow LR, Kim S, Daubenmier JJ, et al. A randomized pilot trial of a moderate carbohydrate diet compared to a very low carbohydrate diet in overweight or obese individuals with type 2 diabetes mellitus or prediabetes. PLoS One [Electronic Resource]. 2014;9(4):e91027.

        • Hall Kevin D.
        • Bemis T.
        • Brychta R.
        • et al.
        Calorie for calorie, dietary fat restriction results in more body fat loss than carbohydrate restriction in people with obesity.
        Cell Metab. 2015; 22: 427-436
        • Shepherd S.J.
        • Gibson P.R.
        Fructose malabsorption and symptoms of irritable bowel syndrome: Guidelines for effective dietary management.
        J Am Diet Assoc. 2006; 106: 1631-1639
        • Halmos E.P.
        • Power V.A.
        • Shepherd S.J.
        • Gibson P.R.
        • Muir J.G.
        A diet low in FODMAPs reduces symptoms of irritable bowel syndrome.
        Gastroenterology. 2014; 146: 67-75.e5
        • Staudacher H.M.
        • Whelan K.
        • Irving P.M.
        • Lomer M.C.
        Comparison of symptom response following advice for a diet low in fermentable carbohydrates (FODMAPs) versus standard dietary advice in patients with irritable bowel syndrome.
        J Hum Nutr Diet. 2011; 24: 487-495
        • de Roest R.H.
        • Dobbs B.R.
        • Chapman B.A.
        • et al.
        The low FODMAP diet improves gastrointestinal symptoms in patients with irritable bowel syndrome: A prospective study.
        Int J Clin Pract. 2013; 67: 895-903
        • Ong D.K.
        • Mitchell S.B.
        • Barrett J.S.
        • et al.
        Manipulation of dietary short chain carbohydrates alters the pattern of gas production and genesis of symptoms in irritable bowel syndrome.
        J Gastroenterol Hepatol. 2010; 25: 1366-1373
        • Roager H.M.
        • Hansen L.B.S.
        • Bahl M.I.
        • et al.
        Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut.
        Nat Microbiol. 2016; 1: 16093
        • Smolinska S.
        • Jutel M.
        • Crameri R.
        • O'Mahony L.
        Histamine and gut mucosal immune regulation.
        Allergy. 2014; 69: 273-281
        • Fowlkes V.
        • Wilson C.G.
        • Carver W.
        • Goldsmith E.C.
        Mechanical loading promotes mast cell degranulation via RGD-integrin dependent pathways.
        J Biomech. 2013; 46: 788-795
        • Karaki S.
        • Mitsui R.
        • Hayashi H.
        • et al.
        Short-chain fatty acid receptor, GPR43, is expressed by enteroendocrine cells and mucosal mast cells in rat intestine.
        Cell Tissue Res. 2006; 324: 353-360
        • Ribeiro R.A.
        • Vale M.L.
        • Thomazzi S.M.
        • et al.
        Involvement of resident macrophages and mast cells in the writhing nociceptive response induced by zymosan and acetic acid in mice.
        Eur J Pharmacol. 2000; 387: 111-118
        • Chilton S.N.
        • Burton J.P.
        • Reid G.
        Inclusion of fermented foods in food guides around the world.
        Nutrients. 2015; 7: 390-404
        • Verdam F.J.
        • Fuentes S.
        • de Jonge C.
        • et al.
        Human intestinal microbiota composition is associated with local and systemic inflammation in obesity.
        Obesity (Silver Spring). 2013; 21: E607-E615
        • Zhu L.
        • Baker S.S.
        • Gill C.
        • et al.
        Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: A connection between endogenous alcohol and NASH.
        Hepatology. 2013; 57: 601-609
        • Rinella M.E.
        Nonalcoholic fatty liver disease: a systematic review.
        JAMA. 2015; 313: 2263-2273
        • Zhu L.
        • Baker R.D.
        • Baker S.S.
        Gut microbiome and nonalcoholic fatty liver diseases.
        Pediatr Res. 2015; 77: 245-251
        • Tabernero M.
        • Venema K.
        • Maathuis A.J.H.
        • Saura-Calixto F.D.
        Metabolite production during in vitro colonic fermentation of dietary fiber: Analysis and comparison of two European diets.
        J Agric Food Chem. 2011; 59: 8968-8975
        • Neufeld J.D.
        • Vohra J.
        • Dumont M.G.
        • et al.
        DNA stable-isotope probing.
        Nat Protoc. 2007; 2: 860-866
        • Thompson F.E.
        • Subar A.F.
        • Loria C.M.
        • Reedy J.L.
        • Baranowski T.
        Need for technological innovation in dietary assessment.
        J Am Diet Assoc. 2010; 110: 48-51