Yogurt — Probiotic Strains

Homemade live-culture yogurt in glass jars
Homemade live-culture yogurt in glass jars

Yogurt is defined by its starter cultures — the US FDA standard of identity (21 CFR 131.200) describes yogurt as milk ingredients cultured with a characterizing bacterial culture containing Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. Many yogurts also carry added strains of Lactobacillus and Bifidobacterium intended to provide health benefits (Savaiano 2021). This deep dive sets out what the regulations say, what the two starter cultures do, how the term “probiotic” is defined, what is known about survival through the gut, and what trials of named strains tested and found.


Table of Contents

  1. The FDA Standard of Identity (21 CFR 131.200)
  2. The Two Starter Cultures — Symbiosis and Fermentation Roles
  3. Probiotic Adjunct Strains (L. rhamnosus GG, L. casei Shirota, Bifidobacterium, L. reuteri)
  4. The ISAPP Definition of a Probiotic
  5. Surviving Gastric Transit — What Reaches the Gut
  6. CFU Counts on Labels and Through Shelf Life
  7. Strain-Specific Evidence (LGG, B. animalis DN-173 010, L. casei Shirota, L. reuteri)
  8. Heat-Treated Yogurt and the Live-Culture Question
  9. Doses Used in Trials of Named Strains
  10. Cautions (Bacteremia, Pancreatitis Trial, Short-Bowel Syndrome)
  11. Key Research Papers
  12. Connections
  13. Featured Videos

The FDA Standard of Identity (21 CFR 131.200)

The legal definition of “yogurt” in the United States is the FDA standard of identity at 21 CFR 131.200, in its current form from a 2021 final rule (86 FR 31137, June 11, 2021). It describes yogurt as the food produced by culturing cream, milk, partially skimmed milk or skim milk (alone or in combination) with a characterizing bacterial culture that contains the lactic acid-producing bacteria Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. The dairy ingredients must be pasteurized or ultra-pasteurized before the culture is added, and the finished product must have a pH of 4.6 or lower within 24 hours after filling. Cultures in addition to the characterizing culture are listed as optional ingredients, alongside sweeteners, flavorings, color additives, stabilizers, emulsifiers, preservatives and added vitamins A and D.

The standard sets yogurt at not less than 3.25 percent milkfat and not less than 8.25 percent milk solids not fat. A yogurt with between 2.44 and 3.25 percent milkfat must state its milkfat percentage next to the word “yogurt”; below 2.44 percent milkfat, the product is treated as a modified food under a separate section (21 CFR 130.10).

The standard allows yogurt to be treated after culturing to inactivate viable microorganisms and extend shelf life; such a product must carry the phrase “does not contain live and active cultures”. A yogurt may carry the phrase “contains live and active cultures” if it contains at least 107 colony-forming units per gram (CFU/g) at the time of manufacture, with a reasonable expectation of 106 CFU/g through the manufacturer’s assigned shelf life (21 CFR 131.200).

Internationally, the Codex Alimentarius describes yogurt as made with a combination of S. thermophilus and L. delbrueckii subsp. bulgaricus (Marco 2021), and a review of food fermentations notes that in several countries the name yogurt is allowed only for products made with cultures containing both (Sieuwerts 2008).

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The Two Starter Cultures — Symbiosis and Fermentation Roles

Each of the two starter species can ferment milk on its own, but both grow and produce acid faster in mixed culture than alone — a mutual benefit described as protocooperation or mutualism. A 2008 review of food-fermentation microbiology describes the exchange (Sieuwerts 2008):

Some strains of each species also produce bacteriocins that can inhibit the other (Sieuwerts 2008).

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Probiotic Adjunct Strains (L. rhamnosus GG, L. casei Shirota, Bifidobacterium, L. reuteri)

Many yogurts and yogurt-based drinks contain added probiotic strains, which do not necessarily contribute to the fermentation (Sieuwerts 2008); depending on region, these “probiotic” or “bio” yogurts now account for much of the yogurt market (Savaiano 2021). The added strains on this page are those with trials summarised below:

Probiotic effects are generally treated as strain-specific: a meta-analysis of LGG begins from the premise that “the effects of probiotics are strain specific” and that the clinical effects of each strain need to be evaluated separately (Szajewska 2015, LGG). The ISAPP expert panel also judged that some general benefits can be ascribed to strains of well-studied species as a group (Hill 2014; see the next section).

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The ISAPP Definition of a Probiotic

In 2014 an expert panel convened by the International Scientific Association for Probiotics and Prebiotics (ISAPP) reaffirmed the FAO/WHO definition of a probiotic as relevant and sufficiently accommodating (Hill et al., Nature Reviews Gastroenterology & Hepatology):

“Live microorganisms which when administered in adequate amounts confer a health benefit on the host.”

Points from the consensus statement and its 2021 companion on fermented foods:

  1. Live — “Dead microbes, microbial products, microbial components do not come under the probiotic classification” (Hill 2014).
  2. Evidence of benefit — evidence of a health benefit is required, at either a strain-specific or a group level depending on the nature of the benefit. The panel judged that certain effects can be ascribed to strains of well-studied species delivered at a functional dose, and cited Health Canada’s acceptance of named Bifidobacterium and Lactobacillus species, delivered in food at 1 × 109 CFU per serving, for non-strain-specific claims (Hill 2014).
  3. “Live and active cultures” versus “probiotic” — for foods containing live microbes as a diverse, undefined community, the panel found it was not always possible to separate the contribution of the microbes from that of the food matrix; it judged that such microbes fall short of the criteria for “probiotics” and that these foods are best described as “containing live and active cultures” (Hill 2014). The 2021 ISAPP consensus on fermented foods restated that fermented foods are not equivalent to probiotic foods, and described “foods made by fermentation” as acceptable wording for pasteurized fermented foods without live microbes (Marco 2021).

On the yogurt starter cultures themselves, Hill 2014 records that the 2001 FAO/WHO expert consultation said traditional starters are not to be considered probiotics because they lack the ability to proliferate in the intestine, while the 2002 FAO/WHO guidelines recognised probiotic status for the traditional yogurt cultures because they improve lactose tolerance in people who maldigest lactose — a benefit since endorsed by the European Food Safety Authority (EFSA). A 2005 review reached the same conclusion: human studies show that yogurt containing viable S. thermophilus and L. bulgaricus improves lactose digestion and eliminates symptoms of lactose intolerance, so these cultures fulfil the concept of probiotics (Guarner 2005).

EFSA’s 2010 scientific opinion on live yogurt cultures and improved lactose digestion (EFSA 2010) underlies an approved EU claim for live cultures in yogurt or fermented milk to aid lactose digestion (Savaiano 2021). EFSA accepted characterisation at the species rather than the strain level because the mechanism — microbial production of the enzyme β-galactosidase (lactase) — is understood (Hill 2014; Marco 2021). By contrast, health-claim applications for probiotics evaluated by EFSA had, up to 2013, almost completely yielded negative results, and later applications were also rejected (Dronkers 2018); a 2021 review states that no probiotic claim for foods had been granted by EFSA (Marlicz 2021).

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Surviving Gastric Transit — What Reaches the Gut

Fermented-food lactic acid bacteria can transiently make up between 0.1% and 1% of the bacteria in the large intestine. They are unlikely to maintain long-term residence, though some are metabolically active in the gut; the ISAPP panel noted that such interactions would be augmented by repeated daily consumption (Marco 2021).

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CFU Counts on Labels and Through Shelf Life

Counts of live bacteria are given in colony-forming units (CFU). Figures from the sources on this page:

The doses used in trials of named strains are listed with each trial in the next sections.

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Strain-Specific Evidence (LGG, B. animalis DN-173 010, L. casei Shirota, L. reuteri)

Small intestinal bacterial overgrowth is covered on the SIBO page; the trials above did not report results for people with SIBO.

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Heat-Treated Yogurt and the Live-Culture Question

Under the US standard, yogurt may be treated after culturing to inactivate viable microorganisms and extend its shelf life. The product keeps the name “yogurt”, but the label must then carry the phrase “does not contain live and active cultures” in letters at least half the height of the name (21 CFR 131.200). The ISAPP fermented-foods panel described “foods made by fermentation” as acceptable wording for pasteurized fermented foods without live microbes (Marco 2021).

In a 1984 breath-hydrogen study of nine lactase-deficient people, yogurt enhanced lactose digestion, and pasteurizing the yogurt eliminated that effect: pasteurization reduced the yogurt’s lactase activity 10-fold and its cell counts 100-fold. Even so, all subjects fed pasteurized yogurt were symptom-free, whereas eight of nine had gastrointestinal distress after cultured milk (buttermilk), although the amount of lactose malabsorbed was similar (Savaiano 1984). A 2021 systematic review describes another study in which, among flavored and frozen yogurts, ice cream and ice milks, only fresh yogurt significantly improved lactose digestion (Savaiano 2021).

The same review describes two trials in which both pasteurized and non-pasteurized yogurt, eaten for 12 weeks, lowered total cholesterol (by 5% and 10%, respectively), suggesting that a milk component may have contributed (Savaiano 2021).

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Doses Used in Trials of Named Strains

Each trial tested one preparation at one dose and schedule. As reported in the trial abstracts:

Strained and unstrained yogurt are compared on the Greek vs Regular page.

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Cautions (Bacteremia, Pancreatitis Trial, Short-Bowel Syndrome)

Decisions about probiotic products during serious illness belong with a clinician.

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Key Research Papers

  1. Hill C et al. (2014). Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology — PubMed PMID: 24912386
  2. Gorbach SL (1996). The discovery of Lactobacillus GG. Nutrition Today 31(Suppl 1):5S — doi:10.1097/00017285-199611001-00002
  3. Goldenberg JZ et al. (2017). Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database of Systematic Reviews — PubMed PMID: 29257353 (updated in 2025: see Esmaeilinezhad et al. 2025 below)
  4. Schnadower D et al. (2018). Lactobacillus rhamnosus GG versus placebo for acute gastroenteritis in children. NEJM — PubMed PMID: 30462938
  5. Besselink MGH et al. (2008). Probiotic prophylaxis in predicted severe acute pancreatitis: a randomised, double-blind, placebo-controlled trial (PROPATRIA). The Lancet — PubMed PMID: 18279948 — Expression of concern (Lancet 2010: PubMed PMID: 20226971)
  6. Marteau P et al. (2002). Bifidobacterium animalis strain DN-173 010 shortens the colonic transit time in healthy women. Alimentary Pharmacology & Therapeutics — PubMed PMID: 11876714
  7. EFSA Panel on Dietetic Products, Nutrition and Allergies (2010). Scientific Opinion on the substantiation of health claims related to live yoghurt cultures and improved lactose digestion (ID 1143, 2976) pursuant to Article 13(1) of Regulation (EC) No 1924/2006. EFSA Journal 8(10):1763 — doi:10.2903/j.efsa.2010.1763
  8. Sanders ME et al. (2019). Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nature Reviews Gastroenterology & Hepatology — PubMed PMID: 31296969
  9. Szajewska H, Kolodziej M (2015). Systematic review with meta-analysis: Lactobacillus rhamnosus GG in the prevention of antibiotic-associated diarrhoea in children and adults. Alimentary Pharmacology & Therapeutics — PubMed PMID: 26365389
  10. Mimura T et al. (2004). Once daily high dose probiotic therapy [product name omitted] for maintaining remission in recurrent or refractory pouchitis. Gut — PubMed PMID: 14684584
  11. Sazawal S et al. (2006). Efficacy of probiotics in prevention of acute diarrhoea: a meta-analysis of masked, randomised, placebo-controlled trials. Lancet Infectious Diseases — PubMed PMID: 16728323
  12. Suez J et al. (2018). Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell — PubMed PMID: 30193113
  13. Esmaeilinezhad Z, Ghosh NR, Walsh CM, et al. (2025). Probiotics for the prevention of Clostridioides difficile-associated diarrhea in adults and children. Cochrane Database of Systematic Reviews 9:CD006095 — PubMed PMID: 40931979
  14. Hempel S, Newberry SJ, Maher AR, et al. (2012). Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. JAMA 307(18):1959-69 — PubMed PMID: 22570464
  15. Szajewska H, Kołodziej M (2015). Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Alimentary Pharmacology & Therapeutics 42(7):793-801 — PubMed PMID: 26216624
  16. Marco ML, Sanders ME, Gänzle M, et al. (2021). The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Reviews Gastroenterology & Hepatology 18(3):196-208 — PubMed PMID: 33398112
  17. Guarner F, Perdigon G, Corthier G, Salminen S, Koletzko B, Morelli L (2005). Should yoghurt cultures be considered probiotic? British Journal of Nutrition 93(6):783-6 — PubMed PMID: 16022746
  18. Savaiano DA, Hutkins RW (2021). Yogurt, cultured fermented milk, and health: a systematic review. Nutrition Reviews 79(5):599-614 — PubMed PMID: 32447398
  19. Savaiano DA, AbouElAnouar A, Smith DE, Levitt MD (1984). Lactose malabsorption from yogurt, pasteurized yogurt, sweet acidophilus milk, and cultured milk in lactase-deficient individuals. American Journal of Clinical Nutrition 40(6):1219-23 — PubMed PMID: 6439026
  20. Elli M, Callegari ML, Ferrari S, et al. (2006). Survival of yogurt bacteria in the human gut. Applied and Environmental Microbiology 72(7):5113-7 — PubMed PMID: 16820518
  21. Goldin BR, Gorbach SL, Saxelin M, Barakat S, Gualtieri L, Salminen S (1992). Survival of Lactobacillus species (strain GG) in human gastrointestinal tract. Digestive Diseases and Sciences 37(1):121-8 — PubMed PMID: 1728516
  22. Capurso L (2019). Thirty years of Lactobacillus rhamnosus GG: a review. Journal of Clinical Gastroenterology 53(Suppl 1):S1-S41 — PubMed PMID: 30741841
  23. Sieuwerts S, de Bok FA, Hugenholtz J, van Hylckama Vlieg JE (2008). Unraveling microbial interactions in food fermentations: from classical to genomics approaches. Applied and Environmental Microbiology 74(16):4997-5007 — PubMed PMID: 18567682
  24. Tian H, Yu B, Yu H, Chen C (2020). Evaluation of the synergistic olfactory effects of diacetyl, acetaldehyde, and acetoin in a yogurt matrix using odor threshold, aroma intensity, and electronic nose analyses. Journal of Dairy Science 103(9):7957-7967 — PubMed PMID: 32684481
  25. Shida K, Sato T, Iizuka R, et al. (2017). Daily intake of fermented milk with Lactobacillus casei strain Shirota reduces the incidence and duration of upper respiratory tract infections in healthy middle-aged office workers. European Journal of Nutrition 56(1):45-53 — PubMed PMID: 26419583
  26. Nagata S, Asahara T, Wang C, et al. (2016). The effectiveness of Lactobacillus beverages in controlling infections among the residents of an aged care facility: a randomized placebo-controlled double-blind trial. Annals of Nutrition and Metabolism 68(1):51-9 — PubMed PMID: 26599038
  27. Sung V, D’Amico F, Cabana MD, et al. (2018). Lactobacillus reuteri to treat infant colic: a meta-analysis. Pediatrics 141(1):e20171811 — PubMed PMID: 29279326
  28. Su GL, Ko CW, Bercik P, et al. (2020). AGA clinical practice guidelines on the role of probiotics in the management of gastrointestinal disorders. Gastroenterology 159(2):697-705 — PubMed PMID: 32531291
  29. Marlicz W, Skonieczna-Żydecka K, Krynicka P, Łoniewski I, Rydzewska G (2021). Probiotics in irritable bowel syndrome – is the quest for the right strain over? Rapid review of existing guidelines and recommendations. Przegląd Gastroenterologiczny 16(4):369-382 — PubMed PMID: 34976247
  30. Dronkers TMG, Krist L, Van Overveld FJ, Rijkers GT (2018). The ascent of the blessed: regulatory issues on health effects and health claims for probiotics in Europe and the rest of the world. Beneficial Microbes 9(5):717-723 — PubMed PMID: 29798707
  31. Salminen MK, Rautelin H, Tynkkynen S, et al. (2004). Lactobacillus bacteremia, clinical significance, and patient outcome, with special focus on probiotic L. rhamnosus GG. Clinical Infectious Diseases 38(1):62-9 — PubMed PMID: 14679449
  32. Ioannou P, Ziogou A, Giannakodimos I, et al. (2024). Infective endocarditis by Lactobacillus species – a narrative review. Antibiotics (Basel) 13(1):53 — PubMed PMID: 38247612
  33. Bianchetti DGAM, Amelio GS, Lava SAG, et al. (2018). D-lactic acidosis in humans: systematic literature review. Pediatric Nephrology 33(4):673-681 — PubMed PMID: 29218437
  34. Łukasik J, Salminen S, Szajewska H (2018). Rapid review shows that probiotics and fermented infant formulas do not cause d-lactic acidosis in healthy children. Acta Paediatrica 107(8):1322-1326 — PubMed PMID: 29603358
  35. U.S. Food and Drug Administration. 21 CFR 131.200 — Yogurt (standard of identity; 86 FR 31137, June 11, 2021, as amended) — eCFR: 21 CFR 131.200

PubMed Topic Searches

  1. PubMed: LGG clinical trials
  2. PubMed: B. animalis subsp. lactis trials
  3. PubMed: Strain-specific probiotic effects
  4. PubMed: Gastric survival of yogurt cultures
  5. PubMed: ISAPP probiotic definition

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Connections

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