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).
|Criteria||On Kefir||Stopped Kefir|
|Lab Read Quality||3.9||5.3|
|Bacteria Reported By Lab||470||404|
|Bacteria Over 99%ile||11||0|
|Bacteria Over 95%ile||30||5|
|Bacteria Over 90%ile||43||19|
|Bacteria Under 10%ile||10||74|
|Bacteria Under 5%ile||1||39|
|Bacteria Under 1%ile||0||7|
|Rarely Seen 1%||2||2|
|Rarely Seen 5%||12||14|
|Outside Range from JasonH||4||4|
|Outside Range from Medivere||14||14|
|Outside Range from Metagenomics||7||7|
|Outside Range from MyBioma||5||5|
|Outside Range from Nirvana/CosmosId||19||19|
|Outside Range from XenoGene||21||21|
|Outside Lab Range (+/- 1.96SD)||18||1|
|Condition Est. Over 99%ile||0||0|
|Condition Est. Over 95%ile||0||0|
|Condition Est. Over 90%ile||1||1|
|Enzymes Over 99%ile||1||0|
|Enzymes Over 95%ile||3||2|
|Enzymes Over 90%ile||24||41|
|Enzymes Under 10%ile||79||240|
|Enzymes Under 5%ile||26||158|
|Enzymes Under 1%ile||1||47|
|Compounds Over 99%ile||0||2|
|Compounds Over 95%ile||4||113|
|Compounds Over 90%ile||29||453|
|Compounds Under 10%ile||44||163|
|Compounds Under 5%ile||18||61|
|Compounds Under 1%ile||2||8|
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.
I then went to compare specific bacteria shifts that had special interest or large shifts
|Bacteria||On Kefir Percentile (Percentage)||Stop Kefir Percentile (Percentage)|
|(genus) Blautia||38 (6.5%)||46 (7.2%)|
|(genus) Faecalibacterium||34 (8.4%)||62 (14.6%)|
|(genus) Lachnospira||21 (0.6%)||70 (3.5%)|
|(genus) Bacteroides||66 (29.1%)||88 (40.5%)|
|(genus) Phocaeicola –||79 (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. ” 
See Milk kefir: composition, microbial cultures, biological activities, and related products  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.
- Acetobacter acetic
- Acetobacter fabarum
- Acetobacter lovaniensis
- Acetobacter orientalis
- Acetobacter rancens
- Acetobacter sp.
- Acetobacter syzygii
- Acinetobacter sp.
- Bacillus sp.
- Bacillus subtilis
- Bifidobacterium bifidum
- Bifidobacterium sp.
- Brettanomyces sp.
- Candida inconspicua
- Candida krusei
- Candida lambica
- Candida maris
- Candida sp.
- Cryptococcus sp.
- Dekkera anomala
- Dysgonomonas sp.
- Enterococcus durans
- Enterococcus faecalis
- Enterococcus sp.
- Escherichia coli
- Gluconobacter frateurii
- Gluconobacter japonicus
- Halococcus sp.
- Kazachastania khefir
- Kazachstania aerobia
- Kazachstania exigua
- Kazachstania unispora
- Kluyveromyces lactis
- Kluyveromyces marxianus
- Kluyveromyces marxianus var. lactis
- Lachancea meyersii
- Lactobacillus acidophilus
- Lactobacillus amylovorus
- Lactobacillus brevis
- Lactobacillus buchneri
- Lactobacillus casei
- Lactobacillus casei ssp. pseudoplantarum
- Lactobacillus crispatus
- Lactobacillus delbrueckii ssp. bulgaricus
- Lactobacillus helveticus
- Lactobacillus kefir
- Lactobacillus kefiranofaciens
- Lactobacillus kefiranofaciens ssp. kefiranofaciens
- Lactobacillus kefiranofaciens ssp. kefirgranum
- Lactobacillus kefiri
- Lactobacillus lactis
- Lactobacillus lactis ssp. lactis
- Lactobacillus parabuchneri
- Lactobacillus paracasei
- Lactobacillus parakefir
- Lactobacillus parakefiri
- Lactobacillus plantarum
- Lactobacillus satsumensis
- Lactobacillus sp.
- Lactobacillus uvarum
- Lactococcus cremoris
- Lactococcus lactis
- Lactococcus lactis ssp. cremoris
- Lactococcus lactis ssp. lactis
- Lactococcus lactis ssp. lactis biovar diacetylactis
- Lactococcus sp.
- Leuconostoc lactis
- Leuconostoc mesenteroides
- Leuconostoc paramesenteroides
- Leuconostoc pseudomesenteroides
- Leuconostoc sp.
- Naumovozyma sp.
- Pelomonas sp.
- Pichia guilliermondii
- Pichia kudriavzevii
- Pseudomonas sp.
- Saccharomyces cerevisiae
- Saccharomyces sp.
- Saccharomyces turicensis
- Saccharomyces unisporus
- Saccharomycodes sp.
- Shewanella sp.
- Streptococcus durans
- Streptococcus sp.
- Streptococcus thermophilus
- Weissella sp.
- Zygosaccharomyces sp.