6.3 Interpret Results

When reviewing microbiome or abundance-table outputs, assess at least the following:

• Whether the sample size is sufficient for group comparison.
• Whether group labels are clear and reliable.
• Whether the unclassified proportion is unexpectedly high.
• Whether the observed number of taxa and diversity range are plausible.
• Whether the community composition is consistent with the sample source, such as an oral or intestinal microbiome.

Example interpretations include:

• In an oral-microbiome example, Prevotella, Veillonella, Neisseria, and Streptococcus may be dominant.
• An unclassified proportion of approximately 45% is not necessarily abnormal in a complex community.
• Alpha diversity may show no significant group difference.
• Beta diversity may show no significant separation.
• Differential taxa may lose significance after FDR correction, especially with simulated metadata or inadequate sample size; this can be a reasonable result rather than an analytical failure.