The gut microbiome is a vast and complex community of microorganisms that live in the gastrointestinal tract, mainly in the large intestine. It plays essential roles in digestion, metabolism, immunity, and even brain function.
Bacteria – These are the most abundant and well-studied members, with trillions of bacterial cells representing hundreds to thousands of different species.
Bacteria are the dominant component making up ~95% of the gut microbiome.
Most are commensal or mutualistic—they help the host while benefiting themselves.
Common groups include Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria.
Other microorganisms include: Archaea (methane-producing microbes) Fungi and yeasts Viruses (including bacteriophages that infect bacteria) Protozoa (single-celled parasites)
Phylum Common Genera Key Functions
Firmicutes Lactobacillus, Clostridium, Ruminococcus, Faecalibacterium Ferment fiber to short-chain fatty acids (SCFAs) like butyrate
Bacteroidetes Bacteroides, Prevotella Break down complex carbohydrates and proteins
Actinobacteria Bifidobacterium Ferment oligosaccharides; produce vitamins
Proteobacteria Escherichia, Klebsiella Some are normal residents; others are opportunistic pathogens
Verrucomicrobia Akkermansia muciniphila Degrades mucin; supports gut barrier integrity
Fungi in the mycobiome Represent <1% of the microbiome. Include yeasts and molds that interact with bacteria and the immune system.
Archaea Single-celled microorganisms distinct from bacteria. Help with methane production and hydrogen regulation in the gut.
Viruses Include bacteriophages (viruses that infect bacteria) and eukaryotic viruses. Regulate bacterial populations and gene transfer within the gut ecosystem.
Protozoa Eukaryotic microorganisms, less abundant but can influence bacterial balance. Some are commensal, others are potentially pathogenic
Phages are involved in horizontal gene transfer, influencing bacterial evolution and antibiotic resistance.