The human body is home to a vast and highly diverse community of microorganisms that interact continuously with the host and with one another. These microorganisms are distributed across distinct ecological niches, including the mouth, stomach, gastrointestinal tract, skin, scalp, respiratory tract, and urogenital system, where they can influence digestion, metabolism, epithelial barrier function, immune regulation, and microbial community stability. Among these organisms, probiotics represent specific live microorganisms that, when administered in adequate amounts and supported by appropriate evidence, may provide health benefits to the host. In addition to established probiotic strains, the human microbiome contains numerous commensal microorganisms and emerging next-generation probiotic (NGP) candidates that are being investigated for their potential roles in metabolic, gastrointestinal, immunological, neurological, oral, dermatological, and urogenital health. The following comprehensive reference list brings together these microorganisms according to their principal anatomical location, while preserving individual strain and formulation names as separate records.
PROBIOTICS AND RELATED MICROORGANISMS IN THE HUMAN BODY
Rule: Different strains, combinations, or specific records of the same species are listed as separate entries . The list below is the combined version of all records added throughout the conversation, placed according to the regions where they are found or applied in the human body.
1. MOUTH, TONGUE, TEETH, THROAT AND UPPER RESPIRATORY TRACT
Microorganism / Strain Note Streptococcus salivarius Oral commensal Streptococcus salivarius K12Oral / throat probiotic Streptococcus salivarius M18Oral / throat probiotic Streptococcus salivarius 24SMBOral probiotic research Streptococcus dentisani Oral probiotic candidate Streptococcus mitis Natural oral commensal Streptococcus oralis Natural oral commensal Streptococcus gordonii Early oral colonizer Streptococcus sanguinis Early oral colonizer Weissella cibaria Oral commensal / probiotic candidate Weissella cibaria CMUOral health Weissella cibaria CMS1Oral health Bifidobacterium dentium Oral microbiota Lactiplantibacillus plantarum Oral probiotic candidate Lactiplantibacillus plantarum HEAL9Oral candidate Limosilactobacillus reuteri Oral / periodontal research Limosilactobacillus reuteri ProdentisDSM 17938 + ATCC PTA 5289; oral combination Lactobacillus gasseri Oral candidate Ligilactobacillus salivarius Oral / upper respiratory tract Ligilactobacillus salivarius UCC118Specific strain Latilactobacillus sakei Oral candidate Rothia mucilaginosa Oral commensal Rothia dentocariosa Oral commensal
2. STOMACH
Microorganism / Strain Note Lactobacillus gasseri Gastric microbiota Lactobacillus gasseri OLL2716Stomach / H. pylori research Lactobacillus gasseri LG21Stomach / H. pylori research Lactobacillus acidophilus Gastric transit Lactobacillus acidophilus NCFMSpecific strain Lactobacillus acidophilus LA-5Specific strain Lactobacillus johnsonii Gastric / GI Lactobacillus johnsonii NCC533 / La1Specific strain Lactobacillus helveticus Gastric / GI Lactobacillus helveticus R0052 / R52Specific strain
3. SMALL AND LARGE INTESTINE
3A. Lactobacillaceae and Related Bacteria
Microorganism / Strain Note Lactobacillus acidophilus GI probiotic Lactobacillus acidophilus NCFMSpecific clinical strain Lactobacillus acidophilus LA-5Specific clinical strain Lactobacillus acidophilus DDS-1Specific clinical strain Lactobacillus acidophilus CL1285Bio-K+; specific clinical strain Lactobacillus delbrueckii subsp. bulgaricus Yogurt culture Lactobacillus gasseri GI Lactobacillus gasseri SBT2055Specific strain Lactobacillus gasseri LG2055Specific strain Lactobacillus gasseri BNR17Specific clinical strain Lactobacillus johnsonii GI Lactobacillus johnsonii NCC533 / La1Specific clinical strain Lactobacillus helveticus GI Lactobacillus helveticus R0052 / R52Specific strain Lactobacillus gallinarum Research strains Lactobacillus amylovorus GI research Lacticaseibacillus rhamnosus GI Lacticaseibacillus rhamnosus GGSpecific clinical strain Lacticaseibacillus rhamnosus HN001Specific clinical strain Lacticaseibacillus rhamnosus R0011Specific strain Lacticaseibacillus rhamnosus GR-1Urogenital / clinical strain Lacticaseibacillus casei GI Lacticaseibacillus casei Shirota / YIT9029Specific clinical strain Lacticaseibacillus casei ZhangSpecific strain Lacticaseibacillus paracasei GI Lacticaseibacillus paracasei CRL431Specific strain Lacticaseibacillus paracasei DGSpecific strain Lactiplantibacillus plantarum GI Lactiplantibacillus plantarum 299VSpecific clinical strain Lactiplantibacillus plantarum L-137Specific strain Lactiplantibacillus plantarum PS128Psychobiotic Lactiplantibacillus pentosus Fermented food / GI Lactiplantibacillus paraplantarum Probiotic candidate Limosilactobacillus reuteri GI Limosilactobacillus reuteri DSM 17938Specific clinical strain Limosilactobacillus reuteri ATCC 55730Specific strain Limosilactobacillus reuteri ATCC PTA 6475Specific L. reuteri strain Limosilactobacillus reuteri NCIMB 30242 (LRC)Specific clinical strain Limosilactobacillus fermentum GI Limosilactobacillus fermentum CECT 5716Human milk-derived clinical strain Limosilactobacillus panis Probiotic candidate Limosilactobacillus pontis Probiotic candidate Limosilactobacillus mucosae Mucosal GI Ligilactobacillus salivarius GI Ligilactobacillus salivarius UCC118Specific strain Levilactobacillus brevis GI Levilactobacillus brevis CD2Specific strain Lentilactobacillus kefiri Kefir / GI Lentilactobacillus kefiri LKF01 / DSM 32079Specific strain Lentilactobacillus parakefiri Kefir Lentilactobacillus hilgardii Fermentation / kefir Lactobacillus kefiranofaciens Important member of the kefir microbiota Latilactobacillus curvatus GI Latilactobacillus curvatus HY7601Specific strain Latilactobacillus sakei GI Latilactobacillus sakei CJLS03Specific clinical strain Latilactobacillus sakei OK67 / DW2010Specific clinical strain Fructilactobacillus sanfranciscensis Fermentation
3B. Bifidobacterium
Microorganism / Strain Note Bifidobacterium longum GI Bifidobacterium longum 35624Specific clinical strain Bifidobacterium longum subsp. longum BB536Specific clinical strain Bifidobacterium longum NCC3001Psychobiotic Bifidobacterium longum Rosell-175Psychobiotic strain Bifidobacterium longum subsp. infantis Infant GI Bifidobacterium longum subsp. infantis EVC001Specific strain Bifidobacterium bifidum GI Bifidobacterium bifidum Bb-02Specific strain Bifidobacterium bifidum MIMBb75Specific clinical strain Bifidobacterium breve GI Bifidobacterium breve BB-03Specific strain Bifidobacterium breve M-16VSpecific strain Bifidobacterium breve B-3Specific strain Bifidobacterium animalis subsp. lactis GI Bifidobacterium animalis subsp. lactis BB-12Specific clinical strain Bifidobacterium animalis subsp. lactis HN019Specific clinical strain Bifidobacterium animalis subsp. lactis DN-173 010Specific strain Bifidobacterium animalis subsp. lactis CECT 8145Specific strain Bifidobacterium animalis subsp. lactis Bi-07Specific strain Bifidobacterium animalis subsp. animalis GI Bifidobacterium adolescentis GI Bifidobacterium catenulatum GI Bifidobacterium pseudocatenulatum GI Bifidobacterium gallicum GI isolate Bifidobacterium angulatum GI isolate Bifidobacterium dentium Oral / GI
3C. OTHER BACTERIA AND SPORE-FORMING ORGANISMS
Microorganism / Strain Note Streptococcus thermophilus Yogurt / milk fermentation / GI Lactococcus lactis Fermented food / GI Pediococcus acidilactici GI Pediococcus pentosaceus GI / LP28 Leuconostoc mesenteroides Fermented food Enterococcus faecium SF68Specific strain Enterococcus faecalis Symbioflor 1 / DSM 16440Specific record Enterococcus durans Probiotic candidate Enterococcus lactis Probiotic research Enterococcus hirae Probiotic research Escherichia coli Nissle 1917Mutaflor Clostridium butyricum MIYAIRI 588Specific strain Clostridium butyricum CBM588Specific strain Propionibacterium freudenreichii subsp. shermanii JSSpecific strain Sporolactobacillus inulinus Probiotic candidate Brevibacillus laterosporus Spore-forming candidate Bacillus clausii O/CSpecific strain Bacillus clausii N/RSpecific strain Bacillus clausii SINSpecific strain Bacillus clausii TSpecific strain Weizmannia coagulans ATCC 7050Specific strain Weizmannia coagulans GBI-30, 6086GanedenBC30 Bacillus subtilis DE111Specific strain Bacillus subtilis HU58Specific strain Bacillus subtilis CU1Specific strain Bacillus licheniformis Spore-forming Bacillus pumilus Spore-forming Bacillus indicus HU36Carotenoid-producing Bacillus megaterium Spore formulations
3D. NEXT-GENERATION PROBIOTICS AND COMMENSAL GUT MICROORGANISMS
Microorganism / Strain Note Faecalibacterium prausnitzii Butyrate / NGP Akkermansia muciniphila NGP Akkermansia muciniphila WB-STR-0001Pasteurized form Roseburia spp.Butyrate Bacteroides uniformis Complex carbohydrate metabolism Bacteroides thetaiotaomicron Complex carbohydrate metabolism Bacteroides fragilis NTBFPSA-producing commensal Prevotella copri Carbohydrate metabolism Blautia spp.Fermentation Blautia wexlerae NGP Ruminococcus spp.Fiber metabolism Anaerobutyricum hallii Butyrate Anaerobutyricum soehngenii L6Metabolic NGP Subdoligranulum variable Butyrate Eubacterium rectale Butyrate Intestinimonas butyriciproducens Butyrate / NGP Holdemanella biformis Metabolic NGP Hafnia alvei HA4597Metabolic / appetite Christensenella minuta NGP Oxalobacter formigenes Oxalate metabolism Dysosmobacter welbionis Glucose / lipid metabolism Parabacteroides distasonis Succinate / bile acid metabolism Collinsella aerofaciens Commensal Veillonella atypica Lactate / propionate Veillonella parvula Lactate / propionate Phascolarctobacterium faecium Succinate → propionate Coprococcus comes Commensal Coprococcus eutactus Commensal Alistipes putredinis Commensal
3E. YEASTS
Microorganism / Strain Note Saccharomyces boulardii GI probiotic Saccharomyces boulardii CNCM I-745Specific clinical strain Saccharomyces cerevisiae Fermented / probiotic Saccharomyces cerevisiae CNCM I-3856IbSium; specific strain Kluyveromyces marxianus K. fragilis ; kefirKluyveromyces lactis Fermented dairy
4. VAGINA AND FEMALE UROGENITAL SYSTEM
Microorganism / Strain Note Lactobacillus crispatus Vaginal microbiota Lactobacillus crispatus CTV-05Specific strain Lactobacillus gasseri Vaginal microbiota Lactobacillus jensenii Vaginal microbiota Lactobacillus iners Vaginal microbiota Lacticaseibacillus rhamnosus GR-1Vaginal probiotic Limosilactobacillus reuteri RC-14Vaginal probiotic Limosilactobacillus mucosae Mucosal / vaginal Limosilactobacillus vaginalis Vaginal microbiota Fannyhessea vaginae Formerly Atopobium vaginae Gardnerella vaginalis Vaginal microbiota Lacticaseibacillus rhamnosus GR-1 + Limosilactobacillus reuteri RC-14Combined vaginal probiotic
5. MALE UROGENITAL SYSTEM
Microorganism Note Lactobacillus spp.Urogenital microbiota Lacticaseibacillus rhamnosus Urogenital research Limosilactobacillus reuteri Urogenital research Lactobacillus gasseri Urogenital microbiota Corynebacterium spp.Commensal Staphylococcus spp.Commensal
6. SKIN
Microorganism Note Roseomonas mucosa Skin research Staphylococcus epidermidis Skin commensal Staphylococcus hominis Skin commensal Staphylococcus lugdunensis Skin commensal Micrococcus luteus Skin commensal Cutibacterium acnes Skin microbiota Corynebacterium spp.Skin microbiota Lactiplantibacillus plantarum Topical probiotic candidate Limosilactobacillus fermentum Topical probiotic candidate
7. SCALP
Microorganism Note Cutibacterium spp.Scalp Staphylococcus spp.Scalp Corynebacterium spp.Scalp Malassezia spp.Scalp Malassezia globosa Scalp Malassezia restricta Scalp
8. NOSE AND NASOPHARYNX
Microorganism Note Corynebacterium spp.Nasal microbiota Staphylococcus spp.Nasal microbiota Dolosigranulum spp.Nasal microbiota Dolosigranulum pigrum Nasopharyngeal commensal Streptococcus spp.Upper respiratory tract Moraxella spp.Upper respiratory tract Streptococcus salivarius K12Oral / nasopharyngeal probiotic
9. EYE AND CONJUNCTIVA
Microorganism Note Staphylococcus spp.Ocular surface Corynebacterium spp.Ocular surface Streptococcus spp.Ocular surface
10. LUNGS AND LOWER RESPIRATORY TRACT
Microorganism Note Streptococcus spp.Respiratory microbiota Veillonella spp.Respiratory microbiota Veillonella atypica Lactate metabolism Veillonella parvula Lactate metabolism Prevotella spp.Respiratory microbiota Neisseria spp.Respiratory tract Oral Lactobacillaceae Probiotic / immunological research
11. AREAS NOT NORMALLY CONSIDERED TO HAVE RESIDENT MICROBIOTA
Area Status Blood Not considered resident normal microbiota in healthy individuals Brain Not considered resident normal microbiota in healthy individuals Deep tissues Not considered resident normal microbiota in healthy individuals Peritoneum / sterile internal compartments Not a normal microbiota site
