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Concept: Human gastrointestinal tract


We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated >32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing >95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with >99% Good’s coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32-110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.

Concepts: Archaea, Microbiology, Ribosomal RNA, Digestive system, 16S ribosomal RNA, Gastroenterology, Human gastrointestinal tract, Digestion


Lactobacillus fermentum is a normal inhabitant of the human gastrointestinal tract. Here, we report the draft genome sequence of an Indian isolate of the probiotic strain L. fermentum Lf1, isolated from the human gut.

Concepts: Gut flora, Human Genome Project, Microbiology, Digestive system, Human gastrointestinal tract, Lactobacillus, Digestion, Lactobacillus fermentum


The early Cambrian Guanshan biota of eastern Yunnan, China, contains exceptionally preserved animals and algae. Most diverse and abundant are the arthropods, of which there are at least 11 species of trilobites represented by numerous specimens. Many trilobite specimens show soft-body preservation via iron oxide pseudomorphs of pyrite replacement. Here we describe digestive structures from two species of trilobite, Palaeolenus lantenoisi and Redlichia mansuyi. Multiple specimens of both species contain the preserved remains of an expanded stomach region (a “crop”) under the glabella, a structure which has not been observed in trilobites this old, despite numerous examples of trilobite gut traces from other Cambrian Lagerstätten. In addition, at least one specimen of Palaeolenus lantenoisi shows the preservation of an unusual combination of digestive structures: a crop and paired digestive glands along the alimentary tract. This combination of digestive structures has also never been observed in trilobites this old, and is rare in general, with prior evidence of it from one juvenile trilobite specimen from the late Cambrian Orsten fauna of Sweden and possibly one adult trilobite specimen from the Early Ordovician Fezouata Lagerstätte. The variation in the fidelity of preservation of digestive structures within and across different Lagerstätten may be due to variation in the type, quality, and point of digestion of food among specimens in addition to differences in mode of preservation. The presence and combination of these digestive features in the Guanshan trilobites contradicts current models of how the trilobite digestive system was structured and evolved over time. Most notably, the crop is not a derived structure as previously proposed, although it is possible that the relative size of the crop increased over the evolutionary history of the clade.

Concepts: Evolution, Arthropod, Stomach, Human gastrointestinal tract, Digestion, Ordovician, Trilobite, Cambrian


Systems capable of residing for prolonged periods of time in the gastric cavity have transformed our ability to diagnose and treat patients. Gastric resident systems for drug delivery, ideally need to be: ingestible, be able to change shape or swell to ensure prolonged gastric residence, have the mechanical integrity to withstand the forces associated with gastrointestinal motility, be triggerable to address any side effects, and be drug loadable and release drug over a prolonged period of time. Materials that have been primarily utilized for these applications have been largely restricted to thermoplastics and thermosets. Here we describe a novel set of materials, triggerable tough hydrogels, meeting all these requirement, supported by evaluation in a large animal model and ultimately demonstrate the potential of triggerable tough hydrogels to serve as prolonged gastric resident drug depots. Triggerable tough hydrogels may be applied in myriad of applications, including bariatric interventions, drug delivery, and tissue engineering.The use of drug delivery systems for the gastrointestinal tract has been faced with a number of drawbacks related to their prolonged use. Here, the authors develop a drug-loaded hydrogel with high strength to withstand long-term gastrointestinal motility and can be triggered to dissolve on demand.

Concepts: Time, Pharmacology, Digestive system, Animal, Human gastrointestinal tract, Abdomen, Period, Digestion


Saccharomyces boulardii has been successfully used in the prevention and treatment of antimicrobial-associated diarrhoea in humans. We hypothesised that a viable, dried lyophilised preparation of S boulardii would survive in the gastrointestinal tract of horses with antimicrobial-associated enterocolitis, and significantly decrease the duration of diarrhoea. Twenty-one horses, over one year of age, with antimicrobial-associated diarrhoea of up to 72 hours duration, were consecutively randomised in a controlled prospective study. The treatment group received S boulardii (25 g, orally, every 12 hours) until the cessation of clinical signs. S boulardii was successfully cultured in 58.3 per cent of treatment horses on day 3. No statistically significant differences were found in days to return to normal faecal consistency; resolution of watery diarrhoea; return to normal heart rate, respiratory rate and temperature; resolution of leucopaenia; attitude improvement; appetite improvement; and survival at discharge. This is the first study to demonstrate survival of S boulardii in horses with gastrointestinal illness. Further study of the efficacy and safety of S boulardii in horses with antimicrobial-associated diarrhoea in a larger group is warranted.

Concepts: Statistical significance, Sociology, Gastroenterology, Medical signs, Saccharomyces boulardii, Heart rate, Ronald Fisher, Human gastrointestinal tract


In children, caustic ingestion is due to accidents at home and inadequate storage of caustic agents. In emergency, it is useful to remove the soiled clothes, rinse the affected area, and prevent vomiting and feeding. Caustic ingestion (pH<2 or>12) induces burns of the upper gastrointestinal tract requiring esophagogastro-duodenoscopy between H12 and H24. Strong alkalis cause necrosis with liquefaction of the esophagus, penetrating deeply with a high-risk of perforation. Management of these children requires a specialized care center with an intensive care unit, endoscopic equipment, and a surgical team. Esophageal stricture is the main complication; no prophylactic treatment (steroids) is effective. Strictures occur after the 3rd week, and barium swallow should be performed by the end of the 1st month. Stricture are often multiple, long, and tortuous; endoscopic dilatation is difficult with a high-rate of perforation and a low-rate of success. In situ application of mitomycin C or injection of triamcinolone could reduce the recurrence rate of stricture. In recalcitrant or recurrent strictures, it is recommended to perform an esophageal replacement using a colonic interposition or a gastric tube. Endoscopy should also be performed 15-20years after caustic ingestion to screen for early neoplastic lesions. Prevention is very important for avoiding caustic ingestions. Information and education should be given specifically to the parents of toddlers; caustic products should be stored out of reach of children and they should not be kept with food.

Concepts: Carcinoma in situ, Digestive system, Gastroenterology, Human gastrointestinal tract, Digestion, Esophageal cancer, Esophageal stricture, Barium swallow


Blue Rubber Bleb Nevus Syndrome (BRBS) is a rare disease, characterized by multiple vascular malformations in the skin and gastrointestinal tract. Other organs can also be affected, presenting different clinical manifestations such as arthralgia, epistaxis, hemoptysis, hematuria, hemothorax, mild thrombocytopenia, consumptive coagulopathy, and bone deformities, among others. We present a case of BRBS in a nine-year-old boy with the characteristic clinical manifestations of punctated purplish-blue skin lesions that vary in size and gastrointestinal vascular malformations with upper digestive tract bleeding.

Concepts: Digestive system, Skin, Human gastrointestinal tract, Pneumothorax, Digestion, Blue rubber bleb nevus syndrome


The human gastrointestinal tract is immature at birth, yet must adapt to dramatic changes such as oral nutrition and microbial colonization. The confluence of these factors can lead to severe inflammatory disease in premature infants; however, investigating complex environment-host interactions is difficult due to limited access to immature human tissue. Here, we demonstrate that the epithelium of human pluripotent stem cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naïve epithelium. Our findings demonstrate that the immature epithelium is intrinsically capable of establishing a stable host-microbe symbiosis. Microbial colonization leads to complex contact and hypoxia driven responses resulting in increased antimicrobial peptide production, maturation of the mucus layer, and improved barrier function. These studies lay the groundwork for an improved mechanistic understanding of how colonization influences development of the immature human intestine.

Concepts: Bacteria, Digestive system, Intestine, Gastroenterology, Small intestine, Skin, Human gastrointestinal tract, Digestion


The gastrointestinal (GI) tract plays an important role in the absorption of orally administered drugs. However, in some cases the anatomy of the GI tract is changed due to GI surgery, which has the potential of influencing drug bioavailability. In this review, we aim to compile, review, and comment the existing but sometimes fragmented scientific data regarding the impact of GI surgery on the oral bioavailability of drugs. Relevant reports were gathered through the PubMed database from database inception through January 2012. Drugs for which at least one trial or case report suggested a change in oral bioavailability or absorption caused by GI surgery are discussed in detail. Major methodological differences, such as study design, number of subjects and choice of reference group, were observed in the reported studies. Predicting the impact of GI surgery on the oral bioavailability was therefore difficult to perform, even the most sophisticated classification systems could not be used for predicting purposes.

Concepts: Scientific method, Digestive system, Gastroenterology, Human gastrointestinal tract, Change, Pharmacokinetics, Digestion, Bioavailability


The high frequency of complications accompanying endoscopic submucosal dissection (ESD) and its complex processes suggest that the process requires improvement. The objective of the present study was to investigate the feasibility of an innovated splash-needle for ESD.

Concepts: Digestive system, Human gastrointestinal tract, Digestion