We often talk about fixing and restoring the microbiome. What does that actually mean?

I believe the ideal microbiome would be one seen in healthy 20 year olds. There are actually some studies of those (and younger individuals) too. “when an individual’s large intestinal gut microbiota has reached its stable climax community, it appears to be stable for a significant period of time as Faith and colleagues showed (200). This study followed 37 health adults and reported that after 5 years 60% of the original strains were still present.” [2015] In other words, about 8% of the strains disappear each year.

“Furthermore, centenarians had a different and less diverse microbiota than adults and younger elderly people.” [2015] – this suggests that a supplementation of a very diverse collection of probiotic species and families may slow aging. see The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations[2014].

The article Role of the normal gut microbiota[2015] illustrates the multiple regions of the microbiome and how they are different.

The study below is on some healthy individuals in their 20’s.

Bifidobacterium

“B. longum and B. pseudocatenulatum, which are detected at levels of 10(7) CFU/g (wet) in samples and the detection rates are 90.48% [of study individuals] and 85.71% [of study individual] respectively. In addition, B. adolescentis, B. bifidum, B. infantis and B. thermacidophium have also been found.” [2005]

Lactobacillus

“L. mucosae, L. fermentum, L. salivarius, L. ruminis [Catenabacterium catenaforme], L. gasseri and L. plantarum are isolated from the stools. L. mucosae (3.68 log10 CFU/g (wet), detection rate 71.43%) and L. fermentum (3.97 log10 CFU/g (wet), detection rate 52.38%) are two dominant species of Lactobacillus.” [2005]

So, L. Acidophilus is NOT found!!!!!! It is found only in certain cultures/life styles/diets.

Infants Differences

“It has been reported that a ‘geographical gradient’ exists in the European infant microbiota where infants from Northern areas have higher levels of Bifidobacterium spp. and some Clostridium spp. and Atopobium spp., while Southern infants had a higher abundance of Eubacteria, Lactobacillus, and Bacteroides (50). Significant differences between the microbiota of Finnish and German infants (57) or between that of Estonian and Swedish ones (58) have been also reported.” [2015]

“Malawian infants had higher counts of lactobacilli than their Finnish counterparts (7.45 log cells/g vs 6.86 log cells/g, P < 0.001, respectively) and the Lactobacillus community was richer and more diverse in the Malawian infants. Leuconostoc citreum and Weissella confusa were the predominant species in both study groups… Moreover,

• Lactobacillus ruminis(59.1% vs 0.0%, P < 0.001),
• Lactobacillus gasseri (38.6% vs 9.7%, P = 0.004;),
• Lactobacillus acidophilus (29.5% vs 0.0%, P < 0.001;), and
• Lactobacillus mucosae (22.7% vs 3.2%, P = 0.017, ) were detected more often in the Malawian infants .
• Lactobacillus casei group species, however, were only detected in the Finnish infants.” [2015]

So Lactobacillus acidophilus is missing from the western infant gut (0.0%)!! So where do we get a Lactobacillus ruminis probiotic????

“Bifidobacteria were dominant at 6 months of age in all of the infants, although in greater proportions in Malawian (70.8%) than in Finnish infants (46.8%; P<0.001). Additional distinctions in bacterial group composition comprised

• Bacteroides-Prevotella (17.2% vs 4.7%; P<0.001) and
• Clostridium histolyticum (4.4% vs 2.8%; P=0.01), respectively. The species
• Bifidobacterium adolescentis, Clostridium perfringens, and Staphylococcus aureus were absent in Malawian but detected in Finnish infants.” [2012]

Bottom Line

We really do not know what a “restored microbiome” should be.  Diet impacts the microbiome. Environment impacts the microbiome. I suspect it should include significant of:

• B. longum – probiotic exists
• B. pseudocatenulatum – unknown
• L. mucosae, – unknown
• L. fermentum, – unknown
• L. salivarius – in a mixture L.Plantarum/Rhamnosus/Salivari 100c (F) Allergy Research
• L. ruminis – unknown
• L. casei – multiple probiotics for western life style.
• L. acidophilus – most common probiotic
• L. gasseri – multiple probiotics
• L. Reuteri – multiple probiotics
• L. plantarum – multiple probiotis