Interactive Microbiome Explorer

Visualize the human microbiome through interactive taxonomy maps, condition-microbe networks, and side-by-side organism comparisons. Filter by health condition, effect, or genus across 152 organisms backed by 841+ peer-reviewed studies.

Legend: Beneficial Harmful Mixed Neutral | 5 Studies | Prevalence

Lactobacillus

Lactobacillaceae 9 species

Bifidobacterium

Bifidobacteriaceae 8 species

Streptococcus

Streptococcaceae 7 species

Bacillus

Unknown 4 species

Bacteroides

Bacteroidaceae 4 species

Clostridium

Clostridiaceae 4 species

Neisseria

Unknown 4 species

Candidatus

Unknown 3 species

Corynebacterium

Corynebacteriaceae 3 species

Malassezia

Malasseziaceae 3 species

Prevotella

Prevotellaceae 3 species

Staphylococcus

Staphylococcaceae 3 species

Anelloviridae

Unknown 2 species

Blautia

Lachnospiraceae 2 species

Candida

Saccharomycetaceae 2 species

Cutibacterium

Propionibacteriaceae 2 species

Dorea

Lachnospiraceae 2 species

Enterococcus

Enterococcaceae 2 species

Mycobacterium

Mycobacteriaceae 2 species

Propionibacterium

Propionibacteriaceae 2 species

Ruminococcus

Oscillospiraceae 2 species

Saccharomyces

Saccharomycetaceae 2 species

Treponema

Spirochaetaceae 2 species

Other Bacteria

65 species

Other Fungi

2 species

Other Viruses

5 species

Other Organisms

3 species

How to Use This Explorer

Taxonomy Map

Groups organisms by biological genus (Lactobacillus, Bifidobacterium, etc.). Colored by health effect, sized by prevalence. Lines connect organisms sharing two or more conditions.

Conditions Map

Bipartite network: health conditions on the left, microorganisms on the right. Click a condition to see all linked microbes. Shows disease associations.

Outcomes Map

Positive health goals on the left, beneficial microbes on the right. Explore which organisms support digestive health, immunity, metabolism, and other health outcomes.

Compare

Select up to three organisms for side-by-side comparison. Highlights shared conditions and key differences between organisms.

Key Statistics

152

Organisms Mapped

40%

Beneficial

Unique Genera

418

Health Conditions Tracked

131

Bacteria

Fungi

841+

Research References

Connections Found

About the Data

The organisms and relationships shown in this explorer are sourced from peer-reviewed research and curated by the Biome Guide editorial team. Each organism profile includes references to published studies in journals such as Nature, Cell, Nature Medicine, Gut, and The Lancet.

Health effect classifications (Beneficial, Harmful, Mixed, Neutral) reflect the current scientific consensus based on available human studies. These classifications may evolve as new research emerges. Connections between organisms are derived from shared associations with specific health conditions documented in the literature.

Disclaimer: This visualization is for educational purposes only and is not intended as medical advice. The relationships shown represent research-documented associations, not causation. Always consult a qualified healthcare provider for medical decisions.

Frequently Asked Questions

What is the Microbiome Explorer?

The Microbiome Explorer is an interactive visualization tool that maps the relationships between over 100 microorganisms in the human microbiome. It shows how bacteria, fungi, and viruses connect through shared health conditions, taxonomic classification, and health impacts.

How are organisms grouped in the Taxonomy Map?

Organisms are clustered by their biological genus (e.g., Lactobacillus, Bifidobacterium, Bacteroides). Genera with only one species are grouped into "Other" categories by organism type. Edges connect organisms that share two or more associated health conditions.

What does the Conditions Map show?

The Conditions Map is a bipartite network showing health conditions on the left and microorganisms on the right. Lines connect each microbe to its associated conditions. Click any condition to see which microbes are linked to it, or click a microbe to see all its associated conditions.

What does the Outcomes Map show?

The Outcomes Map shows positive health outcomes and goals on the left (like Digestive Health, Immunity, Metabolism) and beneficial microorganisms on the right. It visualizes which microbes contribute to which health benefits, helping you find organisms that support specific health goals.

What do the colors and sizes mean?

On the Taxonomy Map, node colors represent the overall health effect: green for Beneficial, red for Harmful, amber for Mixed, and gray for Neutral. Node size represents prevalence in the population. On the Conditions Map, condition nodes are colored by category (gut, immune, metabolic, etc.) and sized by the number of linked microbes.

Can I filter organisms by health condition?

Yes. Use the Condition filter dropdown to select a condition like IBS, Obesity, or Eczema. The explorer will highlight only organisms associated with that condition while dimming the rest. You can combine this with Health Effect and Genus filters.

Can I compare different microorganisms?

Yes. Use the Compare tab to search for and select up to three organisms for side-by-side comparison. The comparison view highlights shared associated conditions between selected organisms and shows key attributes like health effect, prevalence, and body location.

What research backs up the organism data?

Each organism profile includes references to peer-reviewed studies. Click on any organism in the explorer to see its evidence panel with study titles, journals, publication years, and DOI links. Study count badges on network nodes indicate evidence depth.

Microbiome Database

The interactive explorer requires JavaScript. Below is a complete listing of all organisms in our database.

Organism	Type	Health Effect	Genus	Prevalence	Studies
Acinetobacter baumannii	Bacterium	Harmful	Acinetobacter	Common	6
Actinomyces israelii	Bacterium	Mixed	Actinomyces	Common	6
Akkermansia muciniphila	Bacterium	Beneficial	Akkermansia	Common	8
Alistipes putredinis	Bacterium	Mixed	Alistipes	Common	7
Anaerobutyricum hallii	Bacterium	Beneficial	Anaerobutyricum	Common	3
Anelloviridae	Virus	Neutral	Anelloviridae	Universal	3
Anelloviridae	Virus	Neutral	Anelloviridae	Universal	3
Aspergillus fumigatus	Fungi	Harmful	Aspergillus	Common	2
Bacillus cereus	Bacterium	Harmful	Bacillus	Common	0
Bacillus clausii	Bacterium	Beneficial	Bacillus	Uncommon	3
Bacillus coagulans	Bacterium	Beneficial	Bacillus	Uncommon	10
Bacillus subtilis	Bacterium	Beneficial	Bacillus	Common	14
Bacteriophages	Virus	Beneficial	Bacteriophages	Universal	3
Bacteroides dorei	Bacterium	Mixed	Bacteroides	Common	4
Bacteroides fragilis	Bacterium	Mixed	Bacteroides	Common	11
Bacteroides thetaiotaomicron	Bacterium	Beneficial	Bacteroides	Common	15
Bacteroides vulgatus	Bacterium	Mixed	Bacteroides	Common	12
Bifidobacterium adolescentis	Bacterium	Beneficial	Bifidobacterium	Common	19
Bifidobacterium animalis subsp. lactis	Bacterium	Beneficial	Bifidobacterium	Common	12
Bifidobacterium animalis subsp. lactis	Bacterium	Beneficial	Bifidobacterium	Common	6
Bifidobacterium bifidum	Bacterium	Beneficial	Bifidobacterium	Common	13
Bifidobacterium breve	Bacterium	Beneficial	Bifidobacterium	Common	3
Bifidobacterium lactis	Bacterium	Beneficial	Bifidobacterium	Common	6
Bifidobacterium longum	Bacterium	Beneficial	Bifidobacterium	Common	12
Bifidobacterium longum subsp. infantis	Bacterium	Beneficial	Bifidobacterium	Uncommon	3
Bilophila wadsworthensis	Bacterium	Harmful	Bilophila	Common	3
Blautia obeum	Bacterium	Beneficial	Blautia	Common	3
Blautia wexlerae	Bacterium	Beneficial	Blautia	Common	3
Bordetella pertussis	Bacterium	Harmful	Bordetella	Common	2
Borrelia burgdorferi	Bacterium	Harmful	Borrelia	Common	2
Burkholderia cepacia complex	Bacterium	Harmful	Burkholderia	Uncommon	3
Campylobacter jejuni	Bacterium	Harmful	Campylobacter	Common	11
Candida albicans	Fungi	Harmful	Candida	Very Common	11
Candida glabrata	Fungi	Harmful	Candida	Common	4
Candidatus Methanomassiliicoccus intestinalis	Other	Beneficial	Candidatus	Uncommon	2
Candidatus Methanomethylophilus alvus	Other	Beneficial	Candidatus	Uncommon	0
Candidatus Saccharibacteria	Bacterium	Mixed	Candidatus	Common	3
Chlamydia trachomatis	Bacterium	Harmful	Chlamydia	Common	2
Christensenella minuta	Bacterium	Beneficial	Christensenella	Uncommon	3
Citrobacter freundii	Bacterium	Harmful	Citrobacter	Common	2
Clostridioides difficile	Bacterium	Harmful	Clostridioides	Uncommon	8
Clostridium botulinum	Bacterium	Harmful	Clostridium	Rare	2
Clostridium butyricum	Bacterium	Beneficial	Clostridium	Common	13
Clostridium perfringens	Bacterium	Harmful	Clostridium	Common	8
Clostridium tetani	Bacterium	Harmful	Clostridium	Common	2
Collinsella aerofaciens	Bacterium	Mixed	Collinsella	Common	4
Coprococcus eutactus	Bacterium	Beneficial	Coprococcus	Common	3
Corynebacterium accolens	Bacterium	Beneficial	Corynebacterium	Common	5
Corynebacterium diphtheriae	Bacterium	Harmful	Corynebacterium	Uncommon	3
Corynebacterium jeikeium	Bacterium	Mixed	Corynebacterium	Common	4
crAssphage	Virus	Beneficial	crAssphage	Very Common	3
Cutibacterium acnes	Bacterium	Mixed	Cutibacterium	Common	10
Cutibacterium avidum	Bacterium	Mixed	Cutibacterium	Common	3
Debaryomyces hansenii	Fungi	Mixed	Debaryomyces	Common	5
Deinococcus radiodurans	Bacterium	Beneficial	Deinococcus	Uncommon	5
Desulfovibrio piger	Bacterium	Mixed	Desulfovibrio	Common	3
Dialister invisus	Bacterium	Mixed	Dialister	Common	3
Dorea formicigenerans	Bacterium	Mixed	Dorea	Common	3
Dorea longicatena	Bacterium	Mixed	Dorea	Common	1
Dysosmobacter welbionis	Bacterium	Beneficial	Dysosmobacter	Common	3
Eggerthella lenta	Bacterium	Mixed	Eggerthella	Common	11
Enterobacter cloacae	Bacterium	Harmful	Enterobacter	Common	2
Enterococcus faecalis	Bacterium	Mixed	Enterococcus	Common	7
Enterococcus faecium	Bacterium	Mixed	Enterococcus	Common	10
Escherichia coli	Bacterium	Mixed	Escherichia	Very Common	10
Eubacterium rectale	Bacterium	Beneficial	Eubacterium	Very Common	3
Faecalibacterium prausnitzii	Bacterium	Beneficial	Faecalibacterium	Very Common	8
Fusobacterium nucleatum	Bacterium	Harmful	Fusobacterium	Common	12
Gardnerella vaginalis	Bacterium	Mixed	Gardnerella	Common	9
Haemophilus influenzae	Bacterium	Harmful	Haemophilus	Common	7
Hafnia alvei	Bacterium	Beneficial	Hafnia	Uncommon	3
Helicobacter pylori	Bacterium	Harmful	Helicobacter	Common	9
Herpesviridae	Virus	Harmful	Herpesviridae	Universal	3
Klebsiella pneumoniae	Bacterium	Harmful	Klebsiella	Common	12
Lacticaseibacillus paracasei	Bacterium	Beneficial	Lacticaseibacillus	Common	3
Lactobacillus acidophilus	Bacterium	Beneficial	Lactobacillus	Common	22
Lactobacillus casei/paracasei	Bacterium	Beneficial	Lactobacillus	Common	15
Lactobacillus delbrueckii subsp. bulgaricus	Bacterium	Beneficial	Lactobacillus	Common	9
Lactobacillus gasseri	Bacterium	Beneficial	Lactobacillus	Common	10
Lactobacillus helveticus	Bacterium	Beneficial	Lactobacillus	Uncommon	3
Lactobacillus plantarum	Bacterium	Beneficial	Lactobacillus	Common	17
Lactobacillus reuteri	Bacterium	Beneficial	Lactobacillus	Common	8
Lactobacillus rhamnosus	Bacterium	Beneficial	Lactobacillus	Common	22
Lactobacillus salivarius	Bacterium	Beneficial	Lactobacillus	Common	9
Lactococcus lactis	Bacterium	Beneficial	Lactococcus	Common	3
Legionella pneumophila	Bacterium	Harmful	Legionella	Common	2
Leuconostoc mesenteroides	Bacterium	Beneficial	Leuconostoc	Uncommon	3
Levilactobacillus brevis	Bacterium	Beneficial	Levilactobacillus	Common	3
Limosilactobacillus fermentum	Bacterium	Beneficial	Limosilactobacillus	Common	3
Listeria monocytogenes	Bacterium	Harmful	Listeria	Uncommon	2
Malassezia globosa	Fungi	Mixed	Malassezia	Universal	10
Malassezia restricta	Fungi	Mixed	Malassezia	Universal	3
Malassezia species	Fungi	Mixed	Malassezia	Common	2
Megasphaera elsdenii	Bacterium	Beneficial	Megasphaera	Uncommon	3
Methanobrevibacter smithii	Other	Mixed	Methanobrevibacter	Universal	10
Methanosphaera stadtmanae	Other	Mixed	Methanosphaera	Uncommon	1
Micrococcus luteus	Bacterium	Beneficial	Micrococcus	Common	5
Moraxella catarrhalis	Bacterium	Harmful	Moraxella	Common	3
Morganella morganii	Bacterium	Harmful	Morganella	Common	2
Mycobacterium leprae	Bacterium	Harmful	Mycobacterium	Common	2
Mycobacterium tuberculosis	Bacterium	Harmful	Mycobacterium	Common	2
Mycoplasma pneumoniae	Bacterium	Harmful	Mycoplasma	Common	2
Neisseria gonorrhoeae	Bacterium	Harmful	Neisseria	Common	2
Neisseria lactamica	Bacterium	Beneficial	Neisseria	Common	11
Neisseria meningitidis	Bacterium	Harmful	Neisseria	Common	2
Neisseria subflava	Bacterium	Mixed	Neisseria	Common	0
Nitrososphaera viennensis	Other	Beneficial	Nitrososphaera	Uncommon	2
Nocardia asteroides	Bacterium	Harmful	Nocardia	Rare	2
Oscillospira	Bacterium	Beneficial	Oscillospira	Very Common	7
Oxalobacter formigenes	Bacterium	Beneficial	Oxalobacter	Common	3
Papillomaviridae	Virus	Harmful	Papillomaviridae	Very Common	3
Parabacteroides distasonis	Bacterium	Beneficial	Parabacteroides	Common	3
Parasutterella excrementihominis	Bacterium	Mixed	Parasutterella	Common	2
Pediococcus acidilactici	Bacterium	Beneficial	Pediococcus	Uncommon	3
Polyomaviridae	Virus	Harmful	Polyomaviridae	Very Common	3
Porphyromonas gingivalis	Bacterium	Harmful	Porphyromonas	Common	1
Prevotella copri	Bacterium	Mixed	Prevotella	Common	9
Prevotella histicola	Bacterium	Mixed	Prevotella	Common	3
Prevotella melaninogenica	Bacterium	Harmful	Prevotella	Common	3
Propionibacterium acnes	Bacterium	Mixed	Propionibacterium	Very Common	2
Propionibacterium freudenreichii	Bacterium	Beneficial	Propionibacterium	Uncommon	3
Proteus mirabilis	Bacterium	Harmful	Proteus	Common	2
Pseudomonas aeruginosa	Bacterium	Harmful	Pseudomonas	Common	8
Rickettsia species	Bacterium	Harmful	Rickettsia	Uncommon	2
Roseburia intestinalis	Bacterium	Beneficial	Roseburia	Uncommon	13
Ruminococcus bromii	Bacterium	Beneficial	Ruminococcus	Common	18
Ruminococcus gnavus	Bacterium	Mixed	Ruminococcus	Very Common	4
Saccharomyces boulardii	Fungi	Beneficial	Saccharomyces	Rare	12
Saccharomyces cerevisiae	Fungi	Beneficial	Saccharomyces	Common	6
Salmonella enterica	Bacterium	Harmful	Salmonella	Common	2
Serratia marcescens	Bacterium	Harmful	Serratia	Uncommon	2
Shigella dysenteriae	Bacterium	Harmful	Shigella	Common	3
Staphylococcus aureus	Bacterium	Harmful	Staphylococcus	Common	8
Staphylococcus epidermidis	Bacterium	Mixed	Staphylococcus	Common	7
Staphylococcus hominis	Bacterium	Beneficial	Staphylococcus	Common	2
Streptococcus mitis	Bacterium	Mixed	Streptococcus	Common	2
Streptococcus mutans	Bacterium	Harmful	Streptococcus	Common	8
Streptococcus oralis	Bacterium	Mixed	Streptococcus	Common	1
Streptococcus pneumoniae	Bacterium	Harmful	Streptococcus	Common	3
Streptococcus pyogenes	Bacterium	Harmful	Streptococcus	Common	0
Streptococcus salivarius	Bacterium	Beneficial	Streptococcus	Common	17
Streptococcus thermophilus	Bacterium	Beneficial	Streptococcus	Common	3
Subdoligranulum variabile	Bacterium	Beneficial	Subdoligranulum	Common	3
Sutterella wadsworthensis	Bacterium	Mixed	Sutterella	Common	2
Synergistetes species	Bacterium	Harmful	Synergistetes	Uncommon	3
Tannerella forsythia	Bacterium	Harmful	Tannerella	Common	7
Treponema denticola	Bacterium	Harmful	Treponema	Common	8
Treponema pallidum	Bacterium	Harmful	Treponema	Common	2
Veillonella parvula	Bacterium	Mixed	Veillonella	Common	8
Vibrio cholerae	Bacterium	Harmful	Vibrio	Common	2
Weissella cibaria	Bacterium	Beneficial	Weissella	Uncommon	3
Yersinia pestis	Bacterium	Harmful	Yersinia	Rare	2