loading the gut — 79,000 triangles of real anatomy…

ACT 01 · THE TRACT — a real scan, mouth to rectum

One body's digestive organs from an anatomical scan, each a separate measured surface: the oesophagus, the stomach, the small intestine in its three named parts, the large intestine from the caecum to the rectum, and the three glands that pour into the duodenum — liver, gallbladder, pancreas. In a living adult the whole tube is about 5 metres from mouth to anus; about two-thirds of it is small intestine. Tap anything to name it.

  • FACT Geometry: BodyParts3D 4.0 (one adult male), the same meshes as the /body page's organs.glb. The intestine is split into its named parts by the source's own segment surfaces.
  • FACT In a living adult: mouth to anus ≈ 5 m, small intestine ≈ 3–3.5 m, large intestine ≈ 1.5 m (Helander & Fändriks 2014). Cadaver measurements run longer: muscle tone is gone.
sources
  • BodyParts3D 4.0, © The Database Center for Life Science (DBCLS), CC BY-SA 2.1 Japan — the organs (via organs.glb), the oesophagus, the gallbladder and the intestine's segments.
  • RCSB Protein Data Bank (CC0): 1PSO, Fujinaga M et al. Crystal structure of human pepsin and its complex with pepstatin. Protein Sci 1995;4:960–972. 1SMD, Ramasubbu N et al. Structure of human salivary α-amylase at 1.6 Å resolution. Acta Cryst D 1996;52:435–446.
  • Helander HF, Fändriks L. Surface area of the digestive tract — revisited. Scand J Gastroenterol 2014;49:681–689 — ≈ 32 m², lengths, fold and villus factors.
  • Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 2016;14:e1002533 — 38 trillion bacteria, 30 trillion human cells.
  • Nandhra GK et al. Gastrointestinal transit times in health as determined using ingestible capsule systems: a systematic review. J Clin Med 2023;12:5272 — small bowel 3.3–7 h, colon 15.9–28.9 h, whole gut 23–37.4 h (ranges of study averages).
  • Abell TL et al. Consensus recommendations for gastric emptying scintigraphy. Am J Gastroenterol 2008;103:753–763 — normal: ≤ 10% of a solid meal left at 4 h.
  • Evans DF et al. Measurement of gastrointestinal pH profiles in normal ambulant human subjects. Gut 1988;29:1035–1041 — the pH profile.
  • Dressman JB et al. Upper gastrointestinal (GI) pH in young, healthy men and women. Pharm Res 1990;7:756–761 — fasting and after-meal stomach pH.
  • Berg HC. The rotary motor of bacterial flagella. Annu Rev Biochem 2003;72:19–54; Berg HC, Brown DA. Chemotaxis in Escherichia coli analysed by three-dimensional tracking. Nature 1972;239:500–504; Turner L, Ryu WS, Berg HC. Real-time imaging of fluorescent flagellar filaments. J Bacteriol 2000;182:2793–2801 — ~3.4 filaments per cell, ~7 µm long.
  • Reid SW et al. The maximum number of torque-generating units in the flagellar motor of Escherichia coli is at least 11. PNAS 2006;103:8066–8071. Meister M, Lowe G, Berg HC. The proton flux through the bacterial flagellar motor. Cell 1987;49:643–650.
  • Tenaillon O et al. The population genetics of commensal Escherichia coli. Nat Rev Microbiol 2010;8:207–217 — E. coli's place in the gut.
  • Johansson MEV et al. The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. PNAS 2008;105:15064–15069.
  • Furness JB. The Enteric Nervous System. Blackwell, 2006 — 200–600 million enteric neurons.
  • Berthoud HR, Neuhuber WL. Functional and chemical anatomy of the afferent vagal system. Auton Neurosci 2000;85:1–17.
  • Cummings DE, Overduin J. Gastrointestinal regulation of food intake. J Clin Invest 2007;117:13–23.
  • Gershon MD, Tack J. The serotonin signaling system: from basic understanding to drug development for functional GI disorders. Gastroenterology 2007;132:397–414.
  • Sudo N et al. Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice. J Physiol 2004;558:263–275.
  • Valles-Colomer M et al. The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol 2019;4:623–632.
  • Braak H et al. Idiopathic Parkinson's disease: possible routes by which vulnerable neuronal types may be subject to neuroinvasion by an unknown pathogen. J Neural Transm 2003;110:517–536.
  • Kang DW et al. Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome 2017;5:10.

Geometry: BodyParts3D, © The Database Center for Life Science, licensed CC BY-SA 2.1 Japan; the derived meshes are re-shared under the same licence. Molecules: RCSB Protein Data Bank entries 1PSO and 1SMD (CC0). Cells, microbes and the motor are drawn by this page from the published dimensions.