The gut microbiome consists of a complex amalgamation of diverse bacterial species in the human gastrointestinal (GI) tract. Proliferation and normobiosis of bacteria are dependent on the nutrient intake supplied by the host, intra-and-inter metabolite signaling crosstalk between neighboring species and environmental signals and cues based on the geographical location along the GI tract. With the recent explosion of gut microbiome research, several research groups have identified and elucidated the critical role gut-metabolites play in modulating an individual’s normal physiology and/or contribute to several diseased states, including neuropsychiatric disorders such as Major Depressive Disorder (MDD), and Generalized Anxiety Disorder (GAD) and neurodegenerative disease such as Parkinson’s Disease (PD) and Alzheimer’s Disease. The purpose of this review is to systematically identify recent advancements of major bacteria phyla such as Baceteroidetes and Firmicutes and its relevant genus and species in health and disease, and how some of the specific metabolites produced by the respective genus and species may mediate neuropsychiatric disorder. Further exploration of such metabolites and its dominant bacterial species may provide innovative areas for research and potential novel targets for therapeutics.