gastrointestinal tract


Summary: Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).

Top Publications

  1. Kashyap P, Marcobal A, Ursell L, Larauche M, Duboc H, Earle K, et al. Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology. 2013;144:967-77 pubmed publisher
    ..In addition to the direct influence that diet exerts on microbes, changes in microbiota composition and function can alter host functions such as gastrointestinal (GI) transit time, which in turn can further affect the microbiota...
  2. Kovatcheva Datchary P, Arora T. Nutrition, the gut microbiome and the metabolic syndrome. Best Pract Res Clin Gastroenterol. 2013;27:59-72 pubmed publisher
    ..Furthermore, we review the literature on the effects of probiotics and prebiotics on the gut microbiota and host metabolism, focussing primarily on their anti-obesity potential. ..
  3. Forslund K, Sunagawa S, Kultima J, Mende D, Arumugam M, Typas A, et al. Country-specific antibiotic use practices impact the human gut resistome. Genome Res. 2013;23:1163-9 pubmed publisher
    ..The results are robust over time as the antibiotic resistance determinants of individuals persist in the human gut flora for at least a year. ..
  4. Ngwa C, Glöckner V, Abdelmohsen U, Scheuermayer M, Fischer R, Hentschel U, et al. 16S rRNA gene-based identification of Elizabethkingia meningoseptica (Flavobacteriales: Flavobacteriaceae) as a dominant midgut bacterium of the Asian malaria vector Anopheles stephensi (Dipteria: Culicidae) with antimicrobial activities. J Med Entomol. 2013;50:404-14 pubmed
    ..The antimicrobial and antiplasmodial activities of E. meningoseptica may account for its dominance in the midgut of the malaria vector...
  5. Weiss B, Wang J, Maltz M, Wu Y, Aksoy S. Trypanosome infection establishment in the tsetse fly gut is influenced by microbiome-regulated host immune barriers. PLoS Pathog. 2013;9:e1003318 pubmed publisher
    ..Our results document a novel finding, which is the existence of a positive correlation between tsetse's larval microbiome and the integrity of the emerging adult PM gut immune barrier...
  6. Warner D, Dijkstra J, Hendriks W, Pellikaan W. Passage kinetics of 13C-labeled corn silage components through the gastrointestinal tract of dairy cows. J Dairy Sci. 2013;96:5844-58 pubmed publisher
    ..179/h) and (13)CADF (0.128/h). Total mean retention time in the gastrointestinal tract was approximately double for (13)CDM (64.1h) and (13)CADF (77.6h) compared with Cr-NDF (36.4h)...
  7. Dinan T, Stanton C, Cryan J. Psychobiotics: a novel class of psychotropic. Biol Psychiatry. 2013;74:720-6 pubmed publisher
    ..Such benefits may be related to the anti-inflammatory actions of certain psychobiotics and a capacity to reduce hypothalamic-pituitary-adrenal axis activity. Results from large scale placebo-controlled studies are awaited. ..
  8. Vujkovic Cvijin I, Dunham R, Iwai S, Maher M, Albright R, Broadhurst M, et al. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci Transl Med. 2013;5:193ra91 pubmed publisher
    ..This link suggests that gut-resident microbial populations may influence intestinal homeostasis during HIV disease. ..
  9. Smith M, Yatsunenko T, Manary M, Trehan I, Mkakosya R, Cheng J, et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science. 2013;339:548-54 pubmed publisher
    ..These findings implicate the gut microbiome as a causal factor in kwashiorkor...

More Information


  1. Kimura I, Ozawa K, Inoue D, Imamura T, Kimura K, Maeda T, et al. The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43. Nat Commun. 2013;4:1829 pubmed publisher
    ..These findings establish GPR43 as a sensor for excessive dietary energy, thereby controlling body energy utilization while maintaining metabolic homoeostasis...
  2. Broaders E, Gahan C, Marchesi J. Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes. Gut Microbes. 2013;4:271-80 pubmed publisher insight into the distribution of mobile genetic elements (MGEs) and the extent of HGT in the human gastrointestinal tract. In this mini-review, we explore the current knowledge of mobile genetic elements in the gastrointestinal ..
  3. Sommer F, Backhed F. The gut microbiota--masters of host development and physiology. Nat Rev Microbiol. 2013;11:227-38 pubmed publisher
  4. Antharam V, Li E, Ishmael A, Sharma A, Mai V, Rand K, et al. Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol. 2013;51:2884-92 pubmed publisher
    ..difficile infection. Mechanistic studies focusing on the functional roles of these organisms in diarrheal diseases and resistance against C. difficile colonization are warranted. ..
  5. Sengupta R, Altermann E, Anderson R, McNabb W, Moughan P, Roy N. The role of cell surface architecture of lactobacilli in host-microbe interactions in the gastrointestinal tract. Mediators Inflamm. 2013;2013:237921 pubmed publisher
    Lactobacillus species can exert health promoting effects in the gastrointestinal tract (GIT) through many mechanisms, which include pathogen inhibition, maintenance of microbial balance, immunomodulation, and enhancement of the epithelial ..
  6. Kurek K, Łukaszuk B, Piotrowska D, Wiesiołek P, Chabowska A, Zendzian Piotrowska M. Metabolism, physiological role, and clinical implications of sphingolipids in gastrointestinal tract. Biomed Res Int. 2013;2013:908907 pubmed publisher
    ..studies are needed to fully explore the role of sphingolipids in neoplastic and inflammatory diseases in gastrointestinal tract. Pharmacological agents which regulate metabolism of sphingolipids can be potentially used in the ..
  7. Słupecka M, Wolinski J, Prykhodko O, Ochniewicz P, Gruijc D, Fedkiv O, et al. Stimulating effect of pancreatic-like enzymes on the development of the gastrointestinal tract in piglets. J Anim Sci. 2012;90 Suppl 4:311-4 pubmed publisher
    ..components from the milk and eventually from the solid feed relates to the growth and development of gastrointestinal tract (GIT)...
  8. Lozupone C, Li M, Campbell T, Flores S, Linderman D, Gebert M, et al. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe. 2013;14:329-39 pubmed publisher
    ..S. individuals with carbohydrate-rich, protein- and fat-poor diets. By evaluating innate and adaptive immune responses to lysates from bacteria that differ with HIV, we explore the functional drivers of these compositional differences...
  9. Hernández E, Bargiela R, Diez M, Friedrichs A, Pérez Cobas A, Gosalbes M, et al. Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity. Gut Microbes. 2013;4:306-15 pubmed publisher
    The microbiomes in the gastrointestinal tract (GIT) of individuals receiving antibiotics and those in obese subjects undergo compositional shifts, the metabolic effects and linkages of which are not clearly understood...
  10. Barnett Foster D. Modulation of the enterohemorrhagic E. coli virulence program through the human gastrointestinal tract. Virulence. 2013;4:315-23 pubmed publisher
    Enteric pathogens must not only survive passage through the gastrointestinal tract but must also coordinate expression of virulence determinants in response to localized microenvironments with the host...
  11. Dall Aglio C, Zannoni A, Forni M, Bacci M, Ceccarelli P, Boiti C. Orexin system expression in the gastrointestinal tract of pigs. Res Vet Sci. 2013;95:8-14 pubmed publisher
  12. Gao C, Ji C, Zhao L, Zhang J, Ma Q. Phytase transgenic corn in nutrition of laying hens: residual phytase activity and phytate phosphorus content in the gastrointestinal tract. Poult Sci. 2013;92:2923-9 pubmed publisher
    ..The residual activities of transgenic corn-derived and 2 commercial microbial phytases (PA and PB) along the gastrointestinal tract (GIT) of laying hens were compared to evaluate their relative resistance to hydrolysis in the GIT when ..
  13. Wong P, Li M, Chong C, Ng L, Tan C. Aedes (Stegomyia) albopictus (Skuse): a potential vector of Zika virus in Singapore. PLoS Negl Trop Dis. 2013;7:e2348 pubmed publisher
    ..The vulnerability of Singapore to emerging infectious arboviruses has stimulated our interest to determine the competence of local Ae. albopictus to transmit ZIKV...
  14. Karlsson F, Tremaroli V, Nookaew I, Bergstrom G, Behre C, Fagerberg B, et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature. 2013;498:99-103 pubmed publisher
    ..Therefore, metagenomic predictive tools for T2D should be specific for the age and geographical location of the populations studied...
  15. Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, et al. Human gut microbiota changes reveal the progression of glucose intolerance. PLoS ONE. 2013;8:e71108 pubmed publisher
    ..In conclusion, this research provides further evidence of the structural modulation of gut microbiota in the pathogenesis of diabetes. ..
  16. Kamada N, Chen G, Inohara N, Nunez G. Control of pathogens and pathobionts by the gut microbiota. Nat Immunol. 2013;14:685-90 pubmed publisher
    ..Understanding pathogen-commensal interactions may lead to new therapeutic approaches to treating infectious diseases...
  17. Colson P, Fancello L, Gimenez G, Armougom F, Desnues C, Fournous G, et al. Evidence of the megavirome in humans. J Clin Virol. 2013;57:191-200 pubmed publisher
    ..2-0.45-?m range. Concurrently, there has been accumulating evidence supporting the role of Mimivirus, discovered while investigating a pneumonia outbreak using amoebal coculture, as a causative agent in pneumonia...
  18. Goumon S, Brown J, Faucitano L, Bergeron R, Widowski T, Crowe T, et al. Effects of transport duration on maintenance behavior, heart rate and gastrointestinal tract temperature of market-weight pigs in 2 seasons. J Anim Sci. 2013;91:4925-35 pubmed publisher
    ..Four replicates of each transport duration were conducted during each season. Heart rate and gastrointestinal tract temperature (GTT) were monitored from loading to unloading in 16 pigs from 4 selected trailer compartments ..
  19. Gu S, Chen D, Zhang J, Lv X, Wang K, Duan L, et al. Bacterial community mapping of the mouse gastrointestinal tract. PLoS ONE. 2013;8:e74957 pubmed publisher
    ..As far as we can ascertain, ours is the first study to systematically characterize bacterial communities from the GI tracts of C57BL/6 mice. ..
  20. Hodges R, Dartt D. Tear film mucins: front line defenders of the ocular surface; comparison with airway and gastrointestinal tract mucins. Exp Eye Res. 2013;117:62-78 pubmed publisher
    ..this review will be a presentation of the structure of mucins, regulation of mucin production, role of mucins in ocular surface diseases, and the differences in mucin production by the ocular surface, airways and gastrointestinal tract.
  21. Vitetta L, Linnane A, Gobe G. From the gastrointestinal tract (GIT) to the kidneys: live bacterial cultures (probiotics) mediating reductions of uremic toxin levels via free radical signaling. Toxins (Basel). 2013;5:2042-57 pubmed publisher
    ..Until recently, the gastrointestinal tract (GIT) and its associated micro-biometabolome was a neglected factor in chronic disease development...
  22. Kang D, Park J, Ilhan Z, Wallstrom G, Labaer J, Adams J, et al. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS ONE. 2013;8:e68322 pubmed publisher
    ..Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae. ..
  23. Davin R, Manzanilla E, Klasing K, Perez J. Evolution of zinc, iron, and copper concentrations along the gastrointestinal tract of piglets weaned with or without in-feed high doses of zinc oxide compared to unweaned littermates. J Anim Sci. 2012;90 Suppl 4:248-50 pubmed publisher
    ..of solubilized Zn, the relation of Zn with Fe and Cu, and the concentration of these elements in the gastrointestinal tract (GIT) are key data to understanding its mechanism of action and optimize its use...
  24. Wong A, Chaston J, Douglas A. The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis. ISME J. 2013;7:1922-32 pubmed publisher
    ..This is reminiscent of the patterns of bacterial composition in guts of some other animals, including humans. ..
  25. Lee K, Kim S, Kim E, Ha E, You H, Kim B, et al. Bacterial-derived uracil as a modulator of mucosal immunity and gut-microbe homeostasis in Drosophila. Cell. 2013;153:797-811 pubmed publisher
    ..These results reveal that bacteria with distinct abilities to activate uracil-induced gut inflammation, in terms of intensity and duration, act as critical factors that determine homeostasis or pathogenesis in gut-microbe interactions. ..
  26. Duncan S, Flint H. Probiotics and prebiotics and health in ageing populations. Maturitas. 2013;75:44-50 pubmed publisher
    ..Here we review gut microbial changes associated with aging and how diet, prebiotics and probiotics may modulate the gut microbiota to maintain health in the elderly...
  27. Nayduch D, Cho H, Joyner C. Staphylococcus aureus in the house fly: temporospatial fate of bacteria and expression of the antimicrobial peptide defensin. J Med Entomol. 2013;50:171-8 pubmed
    ..The combined effects of excretion, digestion and antimicrobial effectors likely contribute to loss of ingested bacteria. Nonetheless, house flies are relevant vectors for S. aureus up to 2 h PI and environmental reservoirs up to 6 h PI...
  28. Stewart C, Nelson A, Scribbins D, Marrs E, Lanyon C, Perry J, et al. Bacterial and fungal viability in the preterm gut: NEC and sepsis. Arch Dis Child Fetal Neonatal Ed. 2013;98:F298-303 pubmed publisher
    ..We sought to characterise the bacterial and fungal stool flora of preterm neonates and organism viability and evaluate any associations with NEC and sepsis...
  29. Hsiao E, McBride S, Hsien S, Sharon G, Hyde E, McCue T, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013;155:1451-63 pubmed publisher
    ..Taken together, these findings support a gut-microbiome-brain connection in a mouse model of ASD and identify a potential probiotic therapy for GI and particular behavioral symptoms in human neurodevelopmental disorders...
  30. Ridaura V, Faith J, Rey F, Cheng J, Duncan A, Kau A, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341:1241214 pubmed publisher
    ..These findings reveal transmissible, rapid, and modifiable effects of diet-by-microbiota interactions. ..
  31. Crost E, Tailford L, Le Gall G, Fons M, Henrissat B, Juge N. Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent. PLoS ONE. 2013;8:e76341 pubmed publisher
    ..These new findings provide molecular insights into the strain-specificity of R. gnavus adaptation to the gut environment advancing our understanding of the role of gut commensals in health and disease. ..
  32. Joyce S, Macsharry J, Casey P, Kinsella M, Murphy E, Shanahan F, et al. Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. Proc Natl Acad Sci U S A. 2014;111:7421-6 pubmed publisher
    ..Expression of cloned BSH enzymes in the gastrointestinal tract of gnotobiotic or conventionally raised mice significantly altered plasma bile acid signatures and ..
  33. Zhang C, Li S, Yang L, Huang P, Li W, Wang S, et al. Structural modulation of gut microbiota in life-long calorie-restricted mice. Nat Commun. 2013;4:2163 pubmed publisher
  34. Boucias D, Cai Y, Sun Y, Lietze V, Sen R, Raychoudhury R, et al. The hindgut lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition. Mol Ecol. 2013;22:1836-53 pubmed publisher
  35. Morales Jiménez J, Vera Ponce de León A, García Domínguez A, Martinez Romero E, Zúñiga G, Hernandez Rodriguez C. Nitrogen-fixing and uricolytic bacteria associated with the gut of Dendroctonus rhizophagus and Dendroctonus valens (Curculionidae: Scolytinae). Microb Ecol. 2013;66:200-10 pubmed publisher
    ..Our results suggest that the gut bacteria of these bark beetles could contribute to insect N balance...
  36. Kamada N, Seo S, Chen G, Nunez G. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol. 2013;13:321-35 pubmed publisher
    ..Understanding the interaction of the microbiota with pathogens and the host might provide new insights into the pathogenesis of disease, as well as novel avenues for preventing and treating intestinal and systemic disorders...
  37. Rosenthal A, Zhang X, Lucey K, Ottesen E, Trivedi V, Choi H, et al. Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy. Proc Natl Acad Sci U S A. 2013;110:16163-8 pubmed publisher
  38. Sayin S, Wahlström A, Felin J, Jäntti S, Marschall H, Bamberg K, 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;17:225-35 pubmed publisher
    ..These studies suggest that the gut microbiota not only regulates secondary bile acid metabolism but also inhibits bile acid synthesis in the liver by alleviating FXR inhibition in the ileum...
  39. Sasselli V, Boesmans W, Vanden Berghe P, Tissir F, Goffinet A, Pachnis V. Planar cell polarity genes control the connectivity of enteric neurons. J Clin Invest. 2013;123:1763-72 pubmed publisher
  40. Korup S, Rietscher J, Calvignac Spencer S, Trusch F, Hofmann J, Moens U, et al. Identification of a novel human polyomavirus in organs of the gastrointestinal tract. PLoS ONE. 2013;8:e58021 pubmed publisher
    ..These data indicate that the virus naturally infects humans and that primary infection may already occur in childhood...
  41. Everard A, Cani P. Diabetes, obesity and gut microbiota. Best Pract Res Clin Gastroenterol. 2013;27:73-83 pubmed publisher
    ..These data underline the advantage of investigating and changing the gut microbiota as a therapeutic target in the context of obesity and type 2 diabetes...
  42. Yoshimoto S, Loo T, Atarashi K, Kanda H, Sato S, Oyadomari S, et al. Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature. 2013;499:97-101 pubmed publisher
    ..These findings provide valuable new insights into the development of obesity-associated cancer and open up new possibilities for its control. ..
  43. Lee S, Donaldson G, Mikulski Z, Boyajian S, Ley K, Mazmanian S. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature. 2013;501:426-9 pubmed publisher
    ..disease, little is known about the molecular processes used by symbiotic bacteria to stably colonize the gastrointestinal tract. We sought to define how mammals assemble and maintain the Bacteroides, one of the most numerically ..
  44. McCafferty J, Muhlbauer M, Gharaibeh R, Arthur J, Perez Chanona E, Sha W, et al. Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model. ISME J. 2013;7:2116-25 pubmed publisher
  45. Buchon N, Broderick N, Lemaitre B. Gut homeostasis in a microbial world: insights from Drosophila melanogaster. Nat Rev Microbiol. 2013;11:615-26 pubmed publisher
    ..melanogaster gut homeostasis also involves regeneration of the intestine to repair damage associated with infection. Entomopathogenic bacteria have developed common strategies to subvert these defence mechanisms and kill their host. ..
  46. El Kaoutari A, Armougom F, Gordon J, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol. 2013;11:497-504 pubmed publisher
  47. Patten D, Collett A. Exploring the immunomodulatory potential of microbial-associated molecular patterns derived from the enteric bacterial microbiota. Microbiology. 2013;159:1535-44 pubmed publisher
  48. Lee W, Brey P. How microbiomes influence metazoan development: insights from history and Drosophila modeling of gut-microbe interactions. Annu Rev Cell Dev Biol. 2013;29:571-92 pubmed publisher
    ..In this review, we present a historical account, current views, and novel perspectives for future research directions based on the insights gleaned from the Drosophila gut-microbe interaction model. ..
  49. Vannucchi M, Traini C, Manetti M, Ibba Manneschi L, Faussone Pellegrini M. Telocytes express PDGFR? in the human gastrointestinal tract. J Cell Mol Med. 2013;17:1099-108 pubmed publisher
    ..In conclusion, in the human GI tract the TC are PDGFR?-positive and, therefore, might correspond to the FLC. We also hypothesize that in human gut, there are different TC subpopulations probably playing region-specific roles. ..
  50. Demir I, Schafer K, Tieftrunk E, Friess H, Ceyhan G. Neural plasticity in the gastrointestinal tract: chronic inflammation, neurotrophic signals, and hypersensitivity. Acta Neuropathol. 2013;125:491-509 pubmed publisher
    ..It seems that studying the abundant trophic and activating signals which are generated during this neuro-immune-crosstalk represents the key to understand the remarkable neuroplasticity of the GI tract...
  51. Mazzoni M, De Giorgio R, Latorre R, Vallorani C, Bosi P, Trevisi P, et al. Expression and regulation of ?-transducin in the pig gastrointestinal tract. J Cell Mol Med. 2013;17:466-74 pubmed publisher
    ..These findings provide further support to the concept that taste receptors contribute to luminal chemosensing in the GI tract and suggest they are involved in modulation of food intake and GI function induced by feeding and fasting...
  52. Zhao L. The gut microbiota and obesity: from correlation to causality. Nat Rev Microbiol. 2013;11:639-47 pubmed publisher
  53. David L, Maurice C, Carmody R, Gootenberg D, Button J, Wolfe B, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559-63 pubmed publisher
    ..In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. ..