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Bacterial Stool Culture Interpretation

Gastrointestinal problems, including bacterial flora changes, may underlie numerous health conditions. Common clinical examples include irritable bowel syndrome, inflammatory bowel disease, diabetes, insulin resistance, obesity, autoimmune conditions, and allergies.

While the stool is predominantly composed of anaerobes, most of the accepted bacterial stool pathogens and opportunists grow on aerobic culture plates. Therefore, using aerobic stool cultures is a way to identify bacteria that may be contributing to symptoms in the gastrointestinal tract.

Culture Identification

At DiagnosTechs, we first isolate bacterial colonies on aerobic culture plates. We then use matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry (MALDI-TOF) for precise identification of bacterial species.

In general, bacteria are identified by genus, species and, if known, the strain. Currently, we identify bacteria only to the species level, with the notable exception of E. coli O157. However, as bacterial identification libraries improve, we hope to identify more specific strains of toxigenic E. coli, as well as other bacterial strains.

About 40 percent of the dry matter in stool is composed of bacteria, many of which are still alive. As such, we expect to see moderate to heavy growth of both Gram negative and Gram positive bacteria in a healthy, normal specimen.

Expected Findings

In stool culture, commonly-isolated Gram negative and Gram positive organisms include:

  • Gram negative: E. coli, Citrobacter, Klebsiella, Pseudomonas, Proteus, Enterobacter, and others
  • Gram positive: Enterococcus, Streptococcus, Bacillus, Lactococcus, and others

No growth, scant, or light growth of the total Gram negative bacteria or total Gram positive bacteria could result from a number of causes:

  • Recent antimicrobial use, including herbal antimicrobials
  • Loose watery stools that dilute the specimen
  • Dysbiosis, where the normal flora have been displaced
  • Very low fiber or other extreme diets

Mixed Flora Results

The bacteria listed under “Mixed Flora” are the bacteria growing on the culture plates in moderate to heavy amounts. These bacteria may be commensal and/or mutualistic, opportunistic, or pathogenic. It is important to note that these three categories of organisms are not distinct and may overlap.

Commensal and/or Mutualistic Bacteria

These include nontoxigenic E. coli, certain species of Enterococcus and Streptococcus, and others such as Bacillus, Lactobacillus, and Lactococcus.

  • The majority of E. coli strains are commensal and may provide benefits by preventing more harmful bacteria from overgrowing.
  • Some strains of Enterococcus faecium, E. faecalis, and E. coli have been used as probiotics.
Opportunistic Bacteria

These include Citrobacter, Enterobacter, Klebsiella, Proteus, Pseudomonas, certain species of Streptococcus and Enterococcus, certain strains of E. coli, and others.

Bacterial Pathogens

These include enterohemorrhagic E. coli (e.g., E. coli O157), Salmonella, Shigella, Yersinia, Aeromonas, Vibrio, and others (see previous issue of ChronoBiology for more information on these pathogens).

There is a common misconception that any bacteria present and reported upon testing must be eliminated. This is not correct. A healthy stool sample will contain living bacteria, and we need a healthy microbial balance present throughout the intestinal tract.

Clinical Relevance

For each organism present under Mixed Flora:

  • Consider current understanding of potential pathogenicity; a PubMed search can be very useful
  • Take in context with symptoms
  • Evaluate a patient’s risks and medical history to decide on an appropriate course of action


  • Stool culture results do not reflect the balance of flora that may be present in the small intestine.
  • Stool culture does not identify all bacterial species present, only those that grow robustly on aerobic culture plates; for example Lactobacillus does not grow well from stool on standard culture plates.
  • Stool culture cannot be used for monitoring the complete elimination of a bacterial species from the gastrointestinal tract, although in some cases there may be indications of a reduction in levels.
  • Interpretation of stool culture requires a careful evaluation of the patient’s symptoms and clinical history and a review of the research on any bacterial species identified to decide on an appropriate clinical course of action.