Understanding the Gut Microbiome
The gut microbiome refers to the entire ecosystem of microorganisms — including their genes, metabolites, and surrounding environment — that inhabits the human gastrointestinal tract. It is important to distinguish the microbiome (the ecosystem) from the microbiota (the organisms themselves): the gut microbiota are the trillions of bacteria, fungi, archaea, and viruses that physically live in your gut, while the gut microbiome encompasses these organisms plus all of their genetic material and metabolic activity.
This distinction matters because the gut microbiome's influence on health extends far beyond the organisms themselves. The collective genome of the gut microbiota encodes over 3 million genes — roughly 150 times more than the human genome — giving this ecosystem extraordinary metabolic capabilities that affect digestion, immunity, mental health, metabolism, and more.
Browse our database of 100+ microbiota profiles below to explore the bacteria, fungi, archaea, and viruses that make up this complex ecosystem. Each profile includes health impacts, clinical evidence, and the prebiotics and dietary strategies that influence their abundance. You can also explore how these organisms produce key metabolites or read our guide on prebiotics vs probiotics.
Microbiome Database
Explore our comprehensive collection of microbiome components and discover their health impacts
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Acinetobacter baumannii
Anelloviridae
Torque teno viruses (TTV)
Anelloviridae
Anelloviruses
Aspergillus fumigatus
A. fumigatus
Bacteroides thetaiotaomicron
B. thetaiotaomicron
Bifidobacterium animalis subsp. lactis
B. animalis subsp. lactis
Burkholderia cepacia complex
B. cepacia complex (Bcc)
Candidatus Methanomassiliicoccus intestinalis
Ca. M. intestinalis
Corynebacterium diphtheriae
Diphtheria bacillus
Haemophilus influenzae
H. influenzae
Klebsiella pneumoniae
K. pneumoniae
Lactobacillus delbrueckii subsp. bulgaricus
L. bulgaricus
Lactobacillus plantarum
L. plantarum
Mycobacterium leprae
Leprosy bacillus
Mycobacterium tuberculosis
M. tuberculosis
Papillomaviridae
Human papillomaviruses (HPV)
Prevotella melaninogenica
P. melaninogenica
Propionibacterium acnes
P. acnes, Cutibacterium acnes
Pseudomonas aeruginosa
P. aeruginosa
Streptococcus pyogenes
Group A Streptococcus (GAS)
Frequently Asked Questions About the Human Microbiome
What is the human microbiome?
The human microbiome is the collection of trillions of microorganisms — bacteria, fungi, viruses, and archaea — that live in and on the human body. The gut microbiome alone contains over 1,000 species and plays critical roles in digestion, immunity, metabolism, and mental health.
How many bacteria live in the human gut?
The human gut harbors approximately 38 trillion bacteria, roughly matching the number of human cells in the body. These organisms collectively encode over 3 million genes — about 150 times more than the human genome — giving them enormous metabolic capacity.
What is the difference between beneficial and harmful gut bacteria?
Beneficial bacteria (like Lactobacillus and Bifidobacterium) produce vitamins, short-chain fatty acids, and anti-inflammatory compounds. Harmful or pathogenic bacteria (like certain E. coli strains or C. difficile) can produce toxins and trigger inflammation. Many species are context-dependent — beneficial in balance but problematic when overgrown.
How can I improve my gut microbiome diversity?
Eating a diverse range of plant-based foods (aim for 30+ different plants per week), consuming fermented foods, getting regular exercise, managing stress, and avoiding unnecessary antibiotic use all support microbiome diversity. Prebiotic fibers like inulin and resistant starch specifically nourish beneficial bacteria.