Experiment with Kefir

A reader asked to look at the data from an experiment she did.

I have provided two biomesight results from biomesight (BS) to microbiome prescription (MP). The sample consuming kefir daily was sent first (both to BS and MP). The second sample was after stopping kefir consumption between the two samples.

This was not the ideal sequence, getting a sample before doing Kefir and one after would be the typical approach. This approach should indicate what is lost by stopping. There was 3 weeks washout time before samples.


The stopped Kefir sample is higher quality, so the expectation would be for the numbers to be higher. This is not the case. Stopping resulted in more extreme ranges for bacteria(1.5x more), less types of bacteria, dramatic drop in the count of bacteria out of range (93% decrease in Outside Lab Range). There was a significant in compounds being produced by the microbiome that were more extreme (8x increase) and enzymes also (3.6x increase).

CriteriaOn KefirStopped Kefir
Lab Read Quality3.95.3
Bacteria Reported By Lab470404
Bacteria Over 99%ile110
Bacteria Over 95%ile305
Bacteria Over 90%ile4319
Bacteria Under 10%ile1074
Bacteria Under 5%ile139
Bacteria Under 1%ile07
Lab: BiomeSight
Rarely Seen 1%22
Rarely Seen 5%1214
Outside Range from JasonH44
Outside Range from Medivere1414
Outside Range from Metagenomics77
Outside Range from MyBioma55
Outside Range from Nirvana/CosmosId1919
Outside Range from XenoGene2121
Outside Lab Range (+/- 1.96SD)181
Outside Box-Plot-Whiskers7329
Outside Kaltoft-Moldrup8174
Condition Est. Over 99%ile00
Condition Est. Over 95%ile00
Condition Est. Over 90%ile11
Enzymes Over 99%ile10
Enzymes Over 95%ile32
Enzymes Over 90%ile2441
Enzymes Under 10%ile79240
Enzymes Under 5%ile26158
Enzymes Under 1%ile147
Compounds Over 99%ile02
Compounds Over 95%ile4113
Compounds Over 90%ile29453
Compounds Under 10%ile44163
Compounds Under 5%ile1861
Compounds Under 1%ile28

As often happens, there is a Yin/Yang with some indicators improving and other worst. My general impression is that this microbiome does better on Kefir.

Bacteria Specifics

I then went to compare specific bacteria shifts that had special interest or large shifts

BacteriaOn Kefir Percentile (Percentage)Stop Kefir Percentile (Percentage)
(genus) Bifidobacterium3572
(genus) Lactobacillusnone43
(genus) Blautia38 (6.5%)46 (7.2%)
(genus) Faecalibacterium34 (8.4%)62 (14.6%)
(genus) Lachnospira21 (0.6%)70 (3.5%)
(genus) Bacteroides66 (29.1%)88 (40.5%)
(genus) Phocaeicola79 (15%)93 (23%)

In terms of the literature, I could only find Bacteroides and Phocaeicola, which are both reported to increase (agrees). Different Kefirs will have different impact because each has different bacteria in it. “The kefir granules are a consortium of bacteria and yeasts embedded in a exopolysaccharide matrix. ” [2022]

See Milk kefir: composition, microbial cultures, biological activities, and related products [2015] for various lists of bacteria in different kefir tested.

List of Possible Bacteria in Kefir

The following list illustrates why I tend not to recommend Kefir — too many possible bacteria, some good and some bad. It’s probiotic roulette! If you buy commercial Kefir, have some fun — email the producer and ask which strains are in it, and the last full shotgun lab report verifying it.

  1. Acetobacter acetic
  2. Acetobacter fabarum
  3. Acetobacter lovaniensis
  4. Acetobacter orientalis
  5. Acetobacter rancens
  6. Acetobacter sp.
  7. Acetobacter syzygii
  8. Acinetobacter sp.
  9. Bacillus sp.
  10. Bacillus subtilis
  11. Bifidobacterium bifidum
  12. Bifidobacterium sp.
  13. Brettanomyces sp.
  14. Candida inconspicua
  15. Candida krusei
  16. Candida lambica
  17. Candida maris
  18. Candida sp.
  19. Cryptococcus sp.
  20. Dekkera anomala
  21. Dysgonomonas sp.
  22. Enterococcus durans
  23. Enterococcus faecalis
  24. Enterococcus sp.
  25. Escherichia coli
  26. Gluconobacter frateurii
  27. Gluconobacter japonicus
  28. Halococcus sp.
  29. Kazachastania khefir
  30. Kazachstania aerobia
  31. Kazachstania exigua
  32. Kazachstania unispora
  33. Kluyveromyces lactis
  34. Kluyveromyces marxianus
  35. Kluyveromyces marxianus var. lactis
  36. Lachancea meyersii
  37. Lactobacillus acidophilus
  38. Lactobacillus amylovorus
  39. Lactobacillus brevis
  40. Lactobacillus buchneri
  41. Lactobacillus casei
  42. Lactobacillus casei ssp. pseudoplantarum
  43. Lactobacillus crispatus
  44. Lactobacillus delbrueckii ssp. bulgaricus
  45. Lactobacillus helveticus
  46. Lactobacillus kefir
  47. Lactobacillus kefiranofaciens
  48. Lactobacillus kefiranofaciens ssp. kefiranofaciens
  49. Lactobacillus kefiranofaciens ssp. kefirgranum
  50. Lactobacillus kefiri
  51. Lactobacillus lactis
  52. Lactobacillus lactis ssp. lactis
  53. Lactobacillus parabuchneri
  54. Lactobacillus paracasei
  55. Lactobacillus parakefir
  56. Lactobacillus parakefiri
  57. Lactobacillus plantarum
  58. Lactobacillus satsumensis
  59. Lactobacillus sp.
  60. Lactobacillus uvarum
  61. Lactococcus cremoris
  62. Lactococcus lactis
  63. Lactococcus lactis ssp. cremoris
  64. Lactococcus lactis ssp. lactis
  65. Lactococcus lactis ssp. lactis biovar diacetylactis
  66. Lactococcus sp.
  67. Leuconostoc lactis
  68. Leuconostoc mesenteroides
  69. Leuconostoc paramesenteroides
  70. Leuconostoc pseudomesenteroides
  71. Leuconostoc sp.
  72. Naumovozyma sp.
  73. Pelomonas sp.
  74. Pichia guilliermondii
  75. Pichia kudriavzevii
  76. Pseudomonas sp.
  77. Saccharomyces cerevisiae
  78. Saccharomyces sp.
  79. Saccharomyces turicensis
  80. Saccharomyces unisporus
  81. Saccharomycodes sp.
  82. Shewanella sp.
  83. Streptococcus durans
  84. Streptococcus sp.
  85. Streptococcus thermophilus
  86. Weissella sp.
  87. Zygosaccharomyces sp.

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