TABLE 2.

Diagnostic tests for small intestinal bacterial overgrowth (SIBO) and small intestinal dysbiosis.

	Test	Advantages	Disadvantages
1	Traditional breath tests.	Non-invasive. Low costs (minimal costs for consumables). Suitable as an office-based test.	Low sensitivity and specificity. Diagnostic thresholds remain controversial, relevance of high baseline for hydrogen and/methane remains uncertain. Optimal substrate (glucose vs. lactulose).
2	Culture based techniques.	Allows quantitation of colony forming units (CFUs). Considered the gold standard for the diagnosis of SIBO.	Invasive. Most appropriate location for aspirate (distal duodenum reachable with a gastroscope vs. jejunum reachable with radiologically place aspiration catheter) undetermined. Small bowel often does not contain fluid that can be readily aspirated. Only small proportion of microbiota can be cultured, using the traditional culture methods. Lack of consensus of diagnostic thresholds in different segments of the small intestine.
3	Culture bases techniques in combination with molecular characterization of the microbes lining the mucosa associated microbiome.	Allows better characterization of microbial communities. Potentially can tailor future treatments based upon the results of the molecular characterization (e.g., use of specific diets, probiotics, or specific antibiotics).	Additional cost. So far, this technique has not been validated but field is rapidly progressing with the development of molecular techniques. Requires specific equipment to avoid cross contamination of mucosal biopsy samples with oro-pharyngeal secretions and luminal contents. Only currently used by small number of centers with good access to microbial research facilities. Thus far widely unknown how analysis and interpretation can account for PPI use, diets and nicotine use.
4	Assessment of bacterial load, calculated utilizing qPCR measurements of the bacterial 16S rRNA gene, normalized to human beta-actin expression.	Simple and well-established technique (qPCR), but limited data in relation to SIBO diagnosis. Can be routinely done during an elective endoscopy.	Limited clinical experience and thus far no formal validation in the relation to the clinical utility.
5	Gas sensing capsules with wireless transmission of data.	Non-invasive. Gases such as hydrogen, carbon dioxide, and oxygen are measured in the lumen of the small intestine with most likely very good signal to noise ratios, compared with breath traditional breath test. Suitable as an office-based test.	If capsule is swallowed the delivery of capsule and substrate (glucose) may not occur at the same time and may require endoscopic delivery of capsule and substrate. Limited clinical experience and thus far no formal validation in the relation to the clinical utility.
6	Mucosal biopsies.	Can be incorporated into routine endoscopy. Especially useful when fluid is not readily available for aspiration from the proximal small intestine. Good concordance between results (total bacterial counts and the type of organisms) obtained using small bowel aspirate and small bowel biopsy. Targets the microbes colonizing the mucosa associated microbiome. Allows culture work to be done (aerobic and anaerobic bacteria), rapid molecular techniques as well metagenomics, metatranscriptomics, metaproteomics, metabonomics and metabolomics.	Specific biopsy technique/device required to avoid cross contamination.