A significant consequence of atrophic gastritis is hypochlorhydria and achlorhyria, which in turn may have the following effects on physiology (Howden & Hunt, 1987; Modlin et al., 1994):
1) Increased microbial enteric infections and small intestinal bacterial overgrowth.
2) Increase in intestinal permeability resulting from malabsorption and/or bacterial overgrowth or alteration of gastric mucosa architecture as a result of low acidity levels.
3) Nutrient malabsorption.
from, http://www.procto-med.com/achlorhydria-and-atrophic-gastritis/
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Yes, Achlorhydria would have an effect on the digestive process. The decreased acid level itself can cause symptoms similar to acid reflux, and impairs protein digestion by inhibiting the activation of the enzyme pepsin, whose activation is dependent upon a low gastric pH. Low acid levels in the stomach can cause bacterial overgrowth (as the stomach does not kill microbes normally present in food), which can manifest as diarrhea or decreased absorption of nutrients or vitamins. Risk of particular infections is increased. Even without bacterial overgrowth, low stomach acid can lead to nutritional deficiencies through mal-absorption of basic electrolytes. A person with achlorhydria can suffer from stomach pains caused by the digestion of food that is not properly broken down by gastric acid.