afh gut microbiome restorative program diversity 62bc49b957f3a

AFH Gut Microbiome Restorative Program: Diversity


Highlights (4 minutes):


Webinar (23 minutes):



AFH Restoring the Gut Microbiome:  Diversity

The human microbiome is composed of all the microorganisms colonizing the body.  The gut microbiome can be considered an organ in its own right. It weighs 1.5 kg, it has high metabolic or processing capability that rivals that of the liver, and is plays a vital role in immune and GI maturation. It also plays a role in normal central nervous system development, allows for a reservoir or backup function of essential microflora in case of infection or damage, regulates the immune system, and influences our metabolic GI function


There are 5 main areas of discussion regarding the microbiome. To help you remember we’ll call them the 5 Ds.







Today, we’ll be discussing the Gut Microbiome in terms of Diversity, and give you a tour of the major beneficial microflora and why you want them in your microbiome.


What constitutes a healthy gut microbiome has not been defined. However,  we know that a healthy gut microbiome consists of a high level of diversity, is stable and resists changed when stressed with infection or antibiotics, and has redundant systems in place to allow for multiple ways to process nutrients. It is dominated by Firmicutes, Bacteroides, and Proteobacteria.


Although we don’t have a specific map for the ideal microbiome that fits everyone, we do know through numerous studies that certain microflora and bacterial species are beneficial and that individuals with high numbers of these species are in good health. There are also species that are harmful and we will have a future discussion on the microbiome and disease.


We have a specific stool test that gives an individual a unique map of their microbiome. Here is an example. Included is a snapshot of the 7 major phyla of bacterial.  Yeast, parasites, and pathogenic bacteria may also be revealed.


There are several species of bacteria that seem to have more importance in determining and maintaining health.  Studies have shown an association between the amount of Bifidobacteria species and overall health. Bifidobacteria are present at their highest in the younger years of our lives and the numbers get lower as we age.


There are 3 main ways to increase the diversity in the microbiome.  Certain foods in the diet can support certain bacterial phyla such as resistant starches. Certain polyphenols and nutrients enable and promote the production of short-chain fatty acids which can promote lactobacillus species. AFH PomBioX is a special blend of Pomegranate and citrus to promote short-chain fatty acids, which in turn promote lactobacillus species (see why they are so highly desired below).  These are considered prebiotics. Direct ingestion of probiotics may also promote diversity. Lastly, a fecal microbial transplant may also increase microbial diversity by restoring missing bacterial phyla.


Let’s now look at the microflora that you want to have in abundance in your microbiome.


Beneficial bacteria can be divided into lactic acid-producing bacteria and non-lactic acid-producing bacteria. 


We’ll discuss three of the most important lactic acid bacteria Lactobacillus, Bifidobacteria, and Streptococcus thermophiles.  We will also discuss the non-lactic acid bacteria Bacillus and the nonpathogenic yeast species saccharomyces boulardii.  For a more in-depth discussion please see the written article on our website AFH Gut Microbiome Restoration: Diversity.


The key benefits of lactobacillus bacteria include aiding the digestion and metabolization of proteins and carbohydrates, making B vitamins and vitamin K, breaking up bile salts, enhancing innate and acquired immunity, decreasing inflammatory signals, and has antimicrobial effects against several pathogenic bacteria including Salmonella, C. difficile, candida, and Helicobacter pylori.


Here are some highlights of four of the most studied bacteria in this group: Lactobacillus acidophilus, lactobacillus rhamnosus, Lactobacillus casei, and Lactobacillus plantarum.


Lactobacillus acidophilus is a transient GI species meaning it doesn’t colonize the GI tract but gets ingested, reproduces to makes its contribution to the GI tract and microbiome, and then is gone unless more is ingested. It breaks down casein and gluten, ferments lactose and other sugars, inhibits a host of other pathogens, and reduces the GI concentrations of carcinogenic enzymes.

Lactobacillus rhamnosus is also a transient species. It has a lot of peptidases which means it can break down proteins. It enhances innate or natural immunity using macrophage white blood cells and acquired immunity with T and B white blood cells, which produce antibodies. It inhibits inflammatory signaling, opposes rotavirus and C. difficile, and suppresses enterohemorrhagic E. Coli (a pathologic E. coli causing bloody diarrhea).


Lactobacillus casei is also a transient GI species that is very closely related to L. rhamnosus. It plays a critical role in dendritic cell (nerve cell) differentiation, increases the number of intestinal immunoglobulin A (IgA) producing cells which are protective antibodies in the mucosal layer. It decreases inflammatory cell signaling, suppresses enterohemorrhagic E. Coli (a pathologic E. coli causing bloody diarrhea) from sticking to intestinal cells and invading.


Lactobacillus plantarum is found in all plants and is also a transient GI species.  It helps regulate a key cytokine (inflammatory cell signal) IL-10. It decreases the production of inflammatory signals, supports intestinal barrier function (helps fix intestinal permeability or leaky gut), help keep other bacteria and microbes “in the gut” and not get into the bloodstream and opposes Clostridium Difficile.


The key characteristics of Bifidobacteria are that they are anaerobic or grow in the absence of oxygen, metabolize lactose, ferment non-digestible oligosaccharides, synthesize B vitamins and vitamin K, enhance innate and acquired immunity (see above) , and decrease inflammatory cell signals.


Here is a look at four of the bacteria in this group: Bifidobacterium longum, Bifidobacterium bifidum, Bifidobacterium infantis, and Bifidobacterium breve.

Bifidobacterium longum if the dominant bifidobacteria. If ferments oligosaccharides (non-digestible carbohydrates), inhibits binding of pathogenic E Coli, (enterotoxigenic E. Coli), inhibits Clostridium growth, increases secretory immunoglobulin function and induction, and modulates inflammatory response to respiratory inflammatory cell signaling.


Bifidobacterium Bifidum is present in large numbers but decreased in infants with allergies. It decreases in numbers as we age. It suppresses total and antigen-specific immunoglobulin E (IgE) production which is associated with the “allergic response.”  It also enhances the other immunoglobulins immunoglobulin M, G, and A which can be modulatory type immunoglobulins (IgM, IgG, and IgA) as well as defensive/protective antibodies.


Bifidobacterium infantis is frequently found in infants, rarely found in adults, and reduces inflammatory cell signaling. It improves inflammatory signaling to regulatory quieting signaling ratios in irritable bowel syndrome (IBS).  Together with L. acidophilus, it reduces the risk of necrotizing enterocolitis in very low birth weight infants, promotes normal microflora in children with diarrhea, and can shorten diarrheal courses by several days.


Bifidobacterium breve reduces harmful bacteriodes species, improves weight gain from low birth weight infants, increases B cell proliferation (white blood cells that make antibodies) in Peyer’s patches or lymph tissue scattered across the GI tract, enhances antibody production, eliminates campylobacter jejuni, and inhibits rotavirus.


Here are some key characteristics of Bacillus bacteria. They are gram-positive spore-based probiotics and many species can be used to inhibit the growth of other bacteria in the small bowel. They can grow without with or without oxygen and are transient and non-colonizing. They help ferment and create breakdown products that include acetate, ethanol, acetone, and 2.3 butandiol.  They enhance innate and acquired immunity and promote colonocyte health. While the vast majority of probiotic research has focused on LactobacilliBifidobacterium, and even the yeast probiotic Saccharomyces boulardii; there has been a growing interest in the use and research of the spore-forming Bacilli species (i.e., B. coagulans, B. clausii, B. subtilis, B. indicus). Bacillus species are ubiquitous in nature (almost all are isolated from the soil, water, dust, and air) and have a wide range of characteristics, secondary metabolites, and enzymatic activities. The AFH product BioSpore features Bacillus coagulans (SNZ1969), Bacillus clausii (B106), and Bacillus subtilis (HS43), along with a Serum-Derived Bovine Immunoglobulin Concentrate (ImmunoLin®) and is part of the treatment protocol for small intestinal bacterial overgrowth (SIBO).


Some of the other diverse species of the microbiome that deserve mention are Streptococcus thermophiles. It is used as a yogurt and cheese starter, highly adaptive to lactose, and is transient GI species (see above).  It inhibits pathogen proliferation, reduces DNA damage and premalignant lesions.  It has been used to help with rotavirus infections and in ulcerative colitis. It protects from pathogenic Streptococcus species.

Saccharomyces boulardii is a transient nonpathogenic yeast.  It increases enzymes along the brush border of the intestines which help protect against pathogens, increases secretions of enzymes that help against developing dietary protein allergies, and increases short-chain fatty acid concentrations in the gut. It increases intestinal secretory immunoglobulin A, a protective immunoglobulin (IgA), secretes enzymes that inhibit Clostridium Difficile toxins, inhibits and opposes candida albicans, entamoeba hystolytica, and giardia.


One of our bestselling All Functional Health brand of probiotics is Probio 30 SB, which contains medical dosage of :

Saccharomyces boulardii

Lactobacillus acidophilus La-14®

Bifidobacterium longum Bl-05TM

Lactobacillus plantarum Lp-115®

HOWARU® Bifido

(Bifidobacterium lactis HN019®)


There are studies that show probiotics can be used in the following settings:

Microbiome diversity and balance is important. Since the ideal balance and diversity have not been defined and may be more complex and vary depending on the individual we strive to have a good number of the beneficial bacteria and microflora outlined above. We can obtain a map of one’s microbiome and see if there are deficiencies of the beneficial microflora or excesses of the harmful microflora.   You can contact us at for more information on this special microbiome study. Here are some AFH probiotics that the high concentrations and pharmacologic potency of this beneficial microflora.


Probio 350 or ProBio Plus have high concentrations of Lactobacillus species. Probio 350  as 350 billions colony-forming units of 18 species of bacteria including:

Lactobacillus acidophilus La-14®

Lactobacillus bulgaricus Lb-87

Lactobacillus plantarum Lp-115®

HOWARU® Rhamnosus (Lactobacillus rhamnosus HN001®)

Lactobacillus rhamnosus Lr-32®

Lactobacillus brevis Lbr-35

Lactobacillus gasseri Lg-36

Lactobacillus casei Lc-11®

Lactobacillus salivarius Ls-33®

Lactococcus lactis Ll-23



AFH Probio 350  has a high concentration and variety of bifidobacter species including:

Bifidobacterium lactis Bl-04®

Bifidobacterium longum subsp. Infantis Bi-26

HOWARU® Bifido (Bifidobacterium lactis HN019®)

Bifidobacterium longum Bl-05

Bifidobacterium bifidum Bb-06

Bifidobacterium breve Bb-03

Bifidobacterium bifidum

Bifidobacterium lactis Bb-02


Probio 350  also contains Streptococcus Themophilus.


ProbioPlus has 225 billion colony forming units of 6 highly concentrated bacteria including these lactobacillus species:

Lactobacillus plantarum (Lp-115) *

Lactobacillus acidophilus (La-14) *

Lactobacillus salivarius (Ls-33) *

Lactobacillus casei (Lc-11)


ProBio Plus  also has these bifidobacter species:

Bifidobacterium lactis (Bl-04) *

Bifidobacterium bifidum (Bb-06)


The AFH product BioSpore features Bacillus coagulans (SNZ1969), Bacillus clausii (B106), and Bacillus subtilis (HS43), along with a Serum-Derived Bovine Immunoglobulin Concentrate (ImmunoLin®) and is part of the treatment protocol for small intestinal bacterial overgrowth (SIBO).

. AFH Probio 30 SB has

Saccharomyces boulardii

Lactobacillus acidophilus La-14®

Bifidobacterium longum Bl-05

Lactobacillus plantarum Lp-115®

HOWARU® Bifido

(Bifidobacterium lactis HN019®)



Pomegranate Fruit Extract (Pomanox®) [Standardized to contain 30% Total Punicalagins (A & B) and Punicalins (A & B)]

Citrus Bioflavonoid Complex (MicrobiomeX®)


To get an evaluation of your microbiome, start the AFH gut microbiome restoration program, or order an online functional medicine assessment with functional test kits.  Please email   with any questions or, or call (925)736-9828 for more information.  

Take Care and Stay Healthy

Jeffrey Mark, M.D.



Our offices are conveniently accessible from San Francisco, Berkeley, Piedmont, Orinda, Lafayette,  Walnut Creek, Alamo, Danville, Pleasanton, Dublin, Livermore, Fremont, Marin County, Napa, Sonoma County, and the Central Coast.  Telemedicine appointments make our services easily accessible to virtually anywhere you have internet or cell phone access to utilized our HIPPA compliant video chat telehealth appointments.

Jeffrey Mark, M.D.

Helping clients with compassionate and comprehensive medical care for over 25 years with 4 board certifications in functional medicine, gastroenterology, internal medicine, and anti-aging/ regenerative medicine . IFMCP, ABIM Gastroenterology, NPAS Internal Medicine, ABAARM.

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