Table 1.
Microorganisms found in different parts of the body and their possible effect on human health. Genera tending to fall towards pathogenic and beneficial are indicated by bold and italic, respectively. The * sign next to the genera names indicates that these beneficial microbes are also reported to cause infection; genera that are neither bold, italic, nor have * symbol are unclassified (The list regarding beneficial and pathogenic effects is not exhaustive).
| Body Sites | Common Phyla | Common Genera | Positive Effects of Beneficial Genera |
|---|---|---|---|
| Gut [39] | Actinobacteria | Corynebacterium * | |
| Bifidobacterium | Stimulates immune system, Gut homeostasis, Protection against gastrointestinal infection [40,41,42,43,44], Protective role in TNF-α induced inflammatory response [45]. | ||
| Atopobium | |||
| Firmicutes | Faecalibacterium | Prevention of Inflammatory bowel disease and colorectal cancer, Protection of colon, control of metabolism [46], Immune response/balancing immunity in intestine [46,47]. |
|
| Clostridium * | |||
| Roseburia | Immunity maintenance, Anti-inflammatory response [48,49,50]. | ||
| Ruminococcus | |||
| Dialister | |||
| Lactobacillus | Anti-microbial activity [51,52], Cholesterol metabolism, immunomodulation, anti-allergic effects, anti-diabetic effects [51]. | ||
| Enterococcus * | |||
| Staphylococcus | |||
| Bacteroidetes | Sphingobacterium | ||
| Bacteroides * | |||
| Tannerella | |||
| Parabacteroides | |||
| Alistipes | |||
| Prevotella | |||
| Proteobacteria | Escherichia | ||
| Shigella | |||
| Desulfovibrio | |||
| Bilophila | |||
| Helicobacter | |||
| Fusobacteria | Fusobacterium | ||
| Verrucomicrobia | Akkermansia * | ||
| Oral cavity [53] | Actinobacteria | Actinomyces | |
| Atopobium | |||
| Corynebacterium * | |||
| Rothia | |||
| Proteobacteria | Campylobacter | ||
| Haemophilus | |||
| Neisseria | |||
| Bacteroidetes | Bergeyella | ||
| Capnocytophaga | |||
| Prevotella | |||
| Firmicutes | Granulicatella | ||
| Streptococcus | |||
| Veillonella | Lactate metabolism, NO2 production, Maintain oral health and general health [54] | ||
| Saccharibacteria | |||
| Fusobacteria | Fusobacterium | ||
| Respiratory tract [25,33] | Actinobacteria | Corynebacterium * | |
| Cutibacterium | |||
| Bifidobacterium | Reduction in respiratory tract infections [55,56,57] Reduces the colonization of pathogenic bacteria [55] | ||
| Rothia | |||
| Firmicutes | Dolosigranulum | ||
| Staphylococcus | |||
| Veillonella * | |||
| Lachnospiraceae | |||
| Streptococcus | |||
| Bacteriodetes | Prevotella | ||
| Fusobacteria | |||
| Proteobacteria | |||
| Vagina [58] | Actinobacteria | Gardnerella | |
| Atopobium | |||
| Eggerthella | |||
| Firmicutes | Alloiococcus | ||
| Papillibacter | |||
| Megasphaera | |||
| Aerococcus | |||
| Lactobacillus | Immunomodulation and restoration of healthy microflora in the vagina, The first line of defense against vaginal pathogens [59,60]. | ||
| Streptococcus | |||
| Bacteroidetes | Prevotella | ||
| Fusobacteria | |||
| Skin [61] | Actinobacteria | Propionibacterium | |
| Corynebacterium | |||
| Micrococcus | |||
| Mycobacterium | |||
| Kocuria | |||
| Rothia | |||
| Firmicutes | Staphylococcus | ||
| Streptococcus | |||
| Lactobacillus | Improves skin moisture, color, texture, pores, wrinkles, UV spots, and brown spots [62] Antipathogenic function [63] | ||
| Finegoldia | |||
| Aerococcus | |||
| Anaerococcus | |||
| Proteobacteria | Paracoccus | ||
| Haematobcter | |||
| Sphingomonas | |||
| Hemophilus | |||
| Bacteroidetes | Flavobacterium | ||
| Prevotella |