Digestive System

The work of the mouth

The mouth (oral cavity) is where digestion physically and chemically begins. Teeth break food into smaller pieces (mastication), the tongue manipulates the bolus, and three pairs of salivary glands moisten everything with saliva. Saliva is mostly water, but it also contains amylase (starts starch digestion), lingual lipase (starts fat digestion), lysozyme + IgA (antibacterial), and a buffering bicarbonate.

The mouth is lined by stratified squamous epithelium — same as your skin, but kept moist (non-keratinized) instead of dry. The hard palate and gums are partly keratinized because they take more abrasion; the cheeks and soft palate are non-keratinized.

MICROGRAPH — Oral mucosa

Non-keratinized stratified squamous epithelium with a thin keratinized surface in higher-friction zones — note the rete ridges where epithelium dips down into the lamina propria.

Epiglottis — the swallowing flap

Sitting at the boundary between the oral cavity and the esophagus, the epiglottis is a leaf-shaped flap that flips down over the laryngeal opening when you swallow, sending the bolus toward the esophagus instead of the trachea. Histologically it has a core of elastic cartilage (you can see the dense black-stained elastic fibers between chondrocytes) covered on both surfaces by stratified squamous epithelium that transitions to pseudostratified ciliated columnar on the laryngeal side.

The esophagus — a tube built for the bolus

The esophagus is a 25 cm muscular tube from pharynx to stomach. It does not absorb anything; its only job is to move the bolus from mouth to stomach by peristalsis. So the histology is built around abrasion-resistance and lubrication:

• Stratified squamous lining (same as the mouth — for abrasion).
• Submucosal mucous glands — one of only TWO regions of the gut with submucosal glands (the other is duodenum's Brunner's glands). Their mucus lubricates the bolus.
• Muscularis externa changes along its length: skeletal muscle in the upper third (you can choke yourself voluntarily), mixed in the middle, smooth muscle in the lower third.
• Adventitia on the outside — NOT serosa! The esophagus is OUTSIDE the peritoneal cavity, so it gets a fibrous adventitia instead.

Walking through the esophagus on a slide

MICROGRAPH — Esophagus submucosal mucous gland

A clear cluster of pale, mucus-secreting acini sitting in the submucosa. Submucosal glands are found in only TWO regions of the gut — esophagus (here) and duodenum (Brunner's). The mucus they produce flows through small ducts up onto the luminal surface to lubricate the bolus.

The myenteric (Auerbach) plexus. Between the inner circular and outer longitudinal layers of the muscularis externa runs the myenteric plexus — clusters of parasympathetic ganglia and nerve fibers belonging to the enteric nervous system. The myenteric plexus controls peristalsis: when you swallow, this plexus times the wave of muscle contractions that pushes the bolus down into the stomach. The enteric nervous system has more neurons than the entire spinal cord and can run digestive functions independently of the CNS — it is sometimes called the "second brain."

MICROGRAPH — Esophagus myenteric plexus

Look between the inner circular and outer longitudinal smooth-muscle layers — the small pale clusters of ganglion cells (large, round, with prominent nucleoli) are the myenteric plexus.

MICROGRAPH — Esophagus adventitia

The outermost layer is fibrous connective tissue — adventitia, NOT serosa — because the esophagus runs OUTSIDE the peritoneal cavity. It blends into the surrounding mediastinal CT instead of being wrapped by mesothelium.

Click to reveal — the swallowing pathway

The first place food (and air) crosses paths is the upper aerodigestive tract. Try to name each numbered structure on the diagram below before clicking the blank to reveal the answer.

• 1click to revealNasal cavity
• 2click to revealHard palate
• 3click to revealTeeth
• 4click to revealTongue
• 5click to revealPharynx
• 6click to revealEpiglottis
• 7click to revealEsophagus
• 8click to revealTrachea

Quick self-check

What the stomach actually does

The stomach is a J-shaped sac with three jobs: mechanical mixing (it churns), chemical digestion (HCl + pepsin), and storage (it lets you eat a meal in 15 minutes and digest it over hours). It also kills most swallowed bacteria thanks to its pH of 1.5–2.

The lining changes immediately at the gastroesophageal junction from stratified squamous to simple columnar, and that simple columnar surface dives down into millions of gastric pits. Below each pit, a deeper gastric gland is packed with the cells that do the real work.

Note: the stomach's muscularis externa is unique — it has three layers of smooth muscle (an extra inner oblique layer below the usual circular and longitudinal). This is what lets it churn so vigorously.

Compare cell composition: body region vs. pyloric region

The same simple columnar surface lines the whole stomach, but the cells underneath the pits change as you move from body to pylorus. Use the diagram below to compare the two regions side by side.

MICROGRAPH — Stomach mucosa

Pits, glands, parietal cells (large pink), and chief cells (smaller blue) all visible.

Quick self-check

MICROGRAPH — Jejunum cross-section, low power, H&E

Three levels of surface amplification

To absorb 95% of your day's calories, the small intestine multiplies its surface area roughly 600× over a smooth tube. It does this with three nested levels of folding:

• Plicae circulares — naked-eye circular folds (mucosa + submucosa).
• Villi — finger-like mucosa-only projections (visible at low microscope power).
• Microvilli — the brush border. Only visible by EM, but you can see the fuzzy edge of the apical surface in LM.

Each villus has a central capillary bed (where most absorbed nutrients go into blood) and a single lacteal — a lymphatic capillary that absorbs fats as chylomicrons.

Telling the three subregions aparttwo features do all the work

Duodenum — has Brunner's glands in the SUBMUCOSA (alkaline mucus to neutralize acid chyme from the stomach). The only place in the gut other than esophagus with submucosal glands.

Jejunum — has neither Brunner's nor Peyer's. The "plain" middle subregion. Tallest villi, most plicae circulares.

Ileum — has Peyer's patches: large lymphoid follicles spanning lamina propria AND submucosa. (Bonus stop has more on this.)

Side-by-side: duodenum (Brunner's), jejunum (plain), ileum (Peyer's).

Look at the real tissue

Quick self-check

What the colon actually does

By the time material reaches the cecum, almost all the calories are gone. The large intestine has only TWO jobs left: reabsorb water (turning watery chyme into solid stool) and store the residue until you can find a bathroom. So the histology drops the absorptive bells and whistles:

• FLAT mucosal surface — no villi (the most-missed exam point).
• Deep, straight crypts packed with goblet cells. The mucus they make lubricates feces.
• NO Paneth cells (the colon doesn't need them — it's already a thick microbial environment).
• The outer longitudinal muscle is concentrated into THREE thick bands — the taenia coli. Their tonic contraction creates the pouches called haustra.

The frame of the colonhow it sits in your abdomen

Cecum (with the appendix hanging off) → ascending colon (right side) → hepatic flexure (under the liver) → transverse colon (across the top) → splenic flexure (under the spleen) → descending colon (left side) → sigmoid colon (S-shape) → rectum → anal canal → anus. The colon literally frames the small intestine.

• 1click to revealCecum
• 2click to revealAppendix
• 3click to revealAscending colon
• 4click to revealHepatic flexure
• 5click to revealTransverse colon
• 6click to revealSplenic flexure
• 7click to revealDescending colon
• 8click to revealSigmoid colon
• 9click to revealRectum
• 10click to revealAnal canal

Real tissue — colon mucosa & submucosa

MICROGRAPH — Colon mucosa

Flat luminal surface (no villi), deep straight crypts of Lieberkühn, abundant clear goblet cells lining the crypts.

MICROGRAPH — Colon submucosa

Loose CT layer beneath the muscularis mucosae — note the vessels and scattered lymphocytes. NO submucosal glands here (those are exclusive to esophagus and duodenum).

Quick self-check

The four accessory glands at a glance

Four organs empty into the digestive tract but are not part of the tube itself: the salivary glands (into the mouth) and the pancreas, liver, and gallbladder (all into the duodenum). The pancreas and gallbladder ducts often join to form the hepatopancreatic ampulla just before they empty.

Salivary glands — mixed acinitwo acinus colors in one field

Look for a mix of DARK round serous acini and PALE tubular mucous acini in the same low-power field. Parotid is almost all serous; sublingual is almost all mucous; submandibular is mixed. Saliva contains amylase (starch), lingual lipase (fat), lysozyme + IgA (antibacterial), and mucus.

Salivary gland — note the two acinus colors in the same field.

Pancreas — acini + ISLETSthe only organ that's both endocrine and exocrine

Looks like salivary at first — dark acini everywhere. The deal-breaker: a single PALE round Islet of Langerhans. Islets are endocrine (insulin from β cells, glucagon from α cells); acini are exocrine (digestive enzymes into ducts → duodenum). If you see one islet, you know it's pancreas.

Pancreas — find the pale round islet in the sea of dark acini.

Liver — hexagonal lobulescentral vein in middle, portal triad at corners

The liver is built from hexagonal LOBULES, each ~1 mm across. At the center: ONE thin-walled central vein. At each of the six corners: a portal triad — three vessels (bile duct, branch of portal vein, branch of hepatic artery). Hepatocytes radiate outward in plates with sinusoids between them. Blood travels INWARD from triad to central vein; bile travels OUTWARD through bile canaliculi to the bile duct in the triad.

Liver lobule — central vein in the middle.

Liver — hepatocyte plates and portal triad at a corner.

Quick self-check

Why the gut is the immune system's biggest neighborhood

By surface area, the digestive tract is the body's largest interface with the outside world — bigger even than the skin. Every meal carries food antigens AND a population of swallowed microbes. To handle that without constantly being inflamed, the gut wall has lymphoid tissue at every level. Together this is called GALT (gut-associated lymphoid tissue), part of the larger MALT (mucosa-associated lymphoid tissue) network. GALT contains roughly 70% of all the lymphocytes in your body.

The named GALT/MALT structures

Diffuse MALT in the lamina propriascattered everywhere along the tract

Throughout the entire gut, the lamina propria is studded with single lymphocytes and small lymphoid nodules. They are not visible as discrete labeled structures, but they are functionally what makes the gut wall bristle with immune cells. Every section of mucosa you've labeled contains MALT.

Peyer's patches — the ileum's specialtythe largest organized GALT

In the ILEUM, lymphoid follicles cluster into large, organized aggregates spanning the lamina propria AND the submucosa. The overlying epithelium has flat-topped M cells (instead of villi+microvilli) — they "sample" antigens from the lumen and hand them to dendritic cells inside the patch. Activated B cells leave the patch, mature into plasma cells, and secrete IgA back into the gut lumen. This is the body's main way of policing intestinal microbes without full inflammation.

Note: the muscularis mucosae is INTERRUPTED beneath each patch — necessary so cells can move between mucosal and submucosal halves of the follicle.

Clinical aside: patients with selective IgA deficiency get more frequent gut and respiratory infections. Patients on long-term steroids have shrunken Peyer's patches and similar problems. Nurses see this every day on transplant and rheumatology services.

Click to reveal — Peyer's patch structures

Quick self-check