Host stool samples are an excellent source of gut microbial metabolites ( Jacobs et al., 2008 Lamichhane et al., 2015) and can be obtained without any invasive procedures thus, stool represents the most commonly used biospecimen type for the study of the gut microbiota (particularly in health). The net metabolic output of the gut microbiota is reflected in the stool and encompasses both microbe-microbe interactions and potential interactions between the gut microbiota and its host ( Yen et al., 2015). As a result, efforts are being made to further understand the functional output of the ecosystem to provide greater depth of knowledge than can be gained from determining taxonomic composition alone.
This complex ecosystem is known to be metabolically active and is widely associated with many aspects of mammalian health and disease ( Weir et al., 2013).
The gut microbiota is the ecosystem of microorganisms-bacteria, fungi, archaea, protists, and viruses-residing along the gastrointestinal tract ( Kho & Lal, 2018).
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