microbiome modification for immunotherapy response improvement

[Olga]

Commentaries:

We wrote this article (below) about 6 month ago but were reluctant to share it with the public, as the level of evidence is low re. doses and types of supplements and no testing/feedback on any of it avail. The patient would need to find out what is his microbiome content currently is, but the testing is unreliable, hard to get and it apparently fluctuates so ideally you would need to test it multiple times. We tested Ivan microbiome, it was hard to arrange, the result was pretty good but not typical for the area we live now and lived before.
In essence - the microbiome you already have might be pretty good and trying to change it drastically by modifying a diet may in fact harm it.
But there is still some info to think about and to review what the current diet might be lacking,
The microbiome is located past the stomach so you need to give that lower part society of helpful microbes enough food that would pass trough the stomach undigested - non-soluble fiber for example, eat less salt and fat as they suppress of the most helpful (Akkermansia). And you have to feed the supportive bacteria in stomach that produces butyrate that is needed for the microbiome growth.
In general, a diet with non-or less refined grains such as brown rice, buckwheat, millet, not bleached nuts and seeds esp. pumpkin seeds due to higher zinc content, berries with seeds and skin, good variety of fruits and veggies would provide enough non-soluble fiber. The good quality supplement with below mentioned strains would support the butyrate producing bacteria. Some of the veggies should be eaten raw as it increases the chance that they will not be completely broken down in the stomach and pass trough.
The main warning - do no jump on the supplements, Ivan tried and some of them are so hard do digest that it caused severe vomiting and nausea so after that he only takes high quality fresh (sold from the freezer at the store) probiotics with the good amount of the Bifidobacterium breve and longum. The rest comes from the food. He always ate tons of berries when in season, fruits and veggies. Now he tries to have a good variety of the raw veggies and fruits every day so these helpful bacteria could find something they like:) Cabbage of all types, chick peas, garlic, onions, tomatoes, cucumbers, green peppers, herbs, avocados are the reg. part of his diet.

I am posting what we wrote, read, ask questions. It is pretty raw text with the used articles posted after the text.

Adjuvant microbiome modification for immunotherapy

Introduction

Two novel human studies of microbiome interaction with PD-1 and PD-L1 blockers demonstrate a need to investigate specific human microbiome modification strategies for optimizing immunotherapy effectiveness.1,2,4 They follow two 2015 animal studies which identified strong interactions between the microbiome and PD-1/CTLA-4 immunotherapy treatments.3,35 In each of the four studies, particular gut bacteria abundances resulted in a better response to immunotherapy. The mechanisms of action discussed suggest that a favorable microbiome benefit immunotherapy in diverse tumor types.

A recently announced clinical trial at MD Anderson will attempt to test the effectiveness of microbiome modification strategy in a homogeneous group of human melanoma patients beginning in the second half of 2018.10 It’s reasonable to study a group of patients receiving immunotherapy with heterogeneous disease to observe microbiome effects in treating other tumor types. If a relationship is found, a microbiome modification strategy can be implemented in the following phase. The magnitude of the treatment response can be tracked and compared between the two groups.

Discussion

Gopalakrishnan et. al (2017) identified Ruminococcaceae and Faecalibacterium among those promoting a response to PD-1 therapy in human melanoma (see Figure 1 below for full breakdown).1,20 The patients with those abundances were said to have “enhanced systemic and anti-tumor immune responses mediated by increased antigen presentation, and improved effector T cell function”.1 A study of a CTLA-4 blocker in melanoma patients also found Faecalibacterium and Firmicutes associated with a better response, as well as higher rates of colitis.31 Therefore, similar microbiome abundances were shown to be strongly associated with immune responses achieved by both PD-1 and CTLA-4 blockers in melanoma. Among other things, this suggests that other ways of potentiating the immune response, such as the abscopal effect from radiotherapy, may be aided by the right microbiome composition, and warrants further investigation.

Routy et. al (2017) identified Akkermansia muciniphila in promoting a response to PD-1 therapy in epithelial tumors.2 These bacteria could be responsible for releasing IL-12 cytokines that are required for the expansion of tumor-reactive CD8+ T-cells.5,6 CD8+ T-cells activated in the presence of IL-12 were shown to provide better tumor control in a mouse study.7 Correspondingly, an increased tumor infiltration by CD8+ T-cells in responders was noted.2 This mechanism could be beneficial in other tumor types, and should be investigated further.

Sivan et. al (2015) identified Bifidobacterium breve and longum in promoting a response to PD-1 inhibition in mouse melanoma.3 Treated mice displayed significantly improved tumor control, accompanied by robust induction of tumor-specific T-cells in the periphery, and an increased tumor infiltration by the CD8+ T-Cells. Bifidobacterium may not have a similar effect in stimulating an immune response in humans due to differences in TLR9 expression.32 However, a 2017 study showed B. longum supplementation increasing the abundance of A. muciniphila, which could be useful.22

Vetizou et. al (2015) identified Bacteroides fragilis and Bacteroides thetaiotaomicron in promoting a response to CTLA-4 inhibition in mouse sarcoma.35 The authors also tested the effect of microbiome depletion via antibiotics on melanoma and colon cancer CTLA-4 treatment in mice. Consistent with other studies, treatment was thwarted by antibiotic use.

Analysis

In all four cases, study designs and findings suggest a causal link between specific bacterial abundances, and the magnitude of the immune response. Two of the studies show that a general lack of microbiome diversity negatively impacts treatment effectiveness in various tumor types. Therefore, strong recommendations can be made to immunotherapy patients:

Avoid antibiotics whenever possible, or attempt to counteract their effects on the microbiome.
Eat a healthy diet that promotes a diverse microbiome.

These two simple recommendations can play a crucial role in treatment decisions. Any surgery is usually accompanied by prophylactic antibiotic use, and could therefore be highly detrimental to immunotherapy. Something as simple as a routine infection treated with antibiotics could lead to devastating tumor progression. A poor diet low in fibre and variety could deplete microbiome diversity, wiping out bacteria crucial to the mounting of an appropriate immune response.

Possible role of short-chain fatty acids

Ruminococcaceae and Faecalibacterium produce butyrate. Bacteroides fragilis and Akkermansia muciniphila produce propionate as a major metabolite. Faecalibacterium likely benefit from Bacteroides thetaiotaomicron metabolite acetate.33 Bacteroides fragilis consume Bifidobacteria metabolite exopolysaccharides.39

Propionate and butyrate are short-chain fatty acids that play a mediating role between the microbiome and the immune system. The precise mechanisms are currently an active and important area of research.37,42 Butyrate was shown to provide an anti-inflammatory effect, while inhibiting IL-12 and up-regulating IL-10.36 Interestingly, IL-10 was recently shown to be an immune-activating agent in patients with advanced solid tumors.38 The authors recommended it as a good combination agent for future immunotherapy trials. It’s plausible that the right microbiome could be providing a natural source of such a combination therapy. However, in a study of murine ovarian cancer treatment with PD-1 therapy, IL-10 up-regulation was shown to be immunosuppressive.40 This could be a potential explanation for why different tumor types require different commensal bacterial abundances for optimal response.

Practically, SCFA’s are well-known to protect from colitis, which is a common and serious side-effect of immunotherapy.41 Minimizing the odds or severity of colitis leading to a discontinuation of immunotherapy is an important treatment consideration. Therefore, commensal bacteria that produce SCFA’s are beneficial for that purpose.

Relevance

The modification strategy outlined here may be tested in conjunction with Keytruda (pembrolizumab), Opdivo (nivolumab), Tecentriq (atezolizumab), Bavencio (avelumab), Imfinzi (durvalumab) or other effective PD-1 and PD-L1 blockers, which may be interchangeable.17 Response to prospective therapies such as knocking out PD-1 from T-Cells with CRISPR and re-infusing them back into the patient could also be enhanced.11,16,18 There is a chance that even without PD-1 therapy, disease progression may be slowed.3 General microbiome studies suggest that the bacteria in question are conducive to overall well-being, so supplementation side effects may be generally positive.13,14,23,25

The interactions between gut bacteria are complex, and poorly understood. Testing the microbiome remains the only sure way of knowing whether desired modifications have been achieved. Therefore, a baseline composition and relative abundance analysis of the microbiome should be undertaken in the beginning. After the supplementing for a sufficient period of time, a subsequent analysis can be performed to evaluate effectiveness of the intervention.19 If certain target bacteria are still underrepresented, or overall microbiome diversity is lacking, additional measures can be attempted. Successful supplementation can continue for the duration of immunotherapy treatment.

Fecal transplantation

The four studies made extensive use of fecal matter transplantation (FMT) which was effective in modifying the microbiome, and affecting treatment responses. FMT and subsequent good nutrition may indeed be fast and effective shortcut to acquiring a favorable microbiome for immunotherapy. This is an emerging area of research.

Antibiotic use

Once again, antibiotics are best avoided. What strategies can we employ if the patient was recently treated with antibiotics, or has to undergo a treatment?

If the patient is responding well to immunotherapy, a fecal matter autotransplant could be performed after antibiotic treatment to help safeguard the diversity.

Diet and supplementation

Ruminococcaceae are promoted by eugenol.8 Faecalibacterium are promoted by inulin, short-chain FOS, and somewhat decreased by Omega-3.21,28 F. prausnitzii may require the presence of metabolically complementary Bacteroides thetaiotaomicron.33 They are promoted by a diet high in Galactooligosaccharides (GOS) which can be found in legumes, asparagus, and broccoli.34 Ruminococcaceae abundances were reduced following antibiotic treatment in an animal model.15

Akkermansia muciniphila is promoted by FOS, inulin, and polyphenols.9,24 Patients with IBS should beware of possible FOS intolerance.12 Mouse and human studies report Omega-3 consumption as beneficial.27,28 An alarming case report noted a significant decrease in A. muciniphila with Omega-3 use exists.26 This reiterates the highly individual nature of promotional strategies, and serves as a reminder that microbiome testing is imperative to verify their effectiveness in the individual. No simple relationship between Omega-3 and gut microbiota exists.28 Additionally, a FODMAP diet was found generally beneficial to A. muciniphila.29

Bifidobacterium breve and longum strains can be increased through direct supplementation. Significantly, B. longum supplementation was shown to lead to an A. muciniphila abundance.22

Dosing

Since many microbiome modification studies are performed on lab animals, human dose conversion is necessary. In mg/kg of substance per body weight, the human dose can be estimated as the mouse dose divided by 12.3.30 Consider a typical lab mouse weighing 0.019 kg that receives 100 mg of substance for a dose of 100 mg / 0.019 kg = 5.26 g/kg. The human equivalent would be 5.26 g/kg / 12.3 = 0.427 g/kg. So, a typical human weighing 62 kg would receive 62 kg * 0.427g/kg = 26.5 g. It is a pretty big dose that may cause an adverse effects, a distress of the digestive system and may be not tolerable or even counter-productive, overloading by the single type at the expense of the overlooked other. So direct extrapolating might not work.

Sample supplementation
There might be numerous heath reason when the supplements or high-dose dietary intake of the high content non-soluble fiber or other are not recommended. For example, my sister has the intestinal diverticulitis so if she eats non-bleached seeds or nuts or other large fraction non solible fiber, these diverticules trap the fractions and inflame severely. So it is hard to say for the particular person if any of the discussed approaches is safe for them? start from gradually increasing the intake.
Please consult a medical professional before starting any supplementation to understand all the risks and minimize chances of adverse drug interactions. Any high quality substitutes to the specific products below are acceptable.

Eugenol
Short chain FOS & inulin & GOS
Polyphenols
Bifidobacterium breve and longum

Conflict of interests

The authors generally despise alternative medicine, and non-evidence-based supplementation. There is no affiliation with any supplement, or pharmaceutical company.

Citations

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients
Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors
Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy
Gut microbes can shape responses to cancer immunotherapy
Gut microbes shape response to cancer immunotherapy
CpG-induced antitumor immunity requires IL-12 in expansion of effector cells and down-regulation of PD-1
IL-12 and Type I IFN differentially program CD8 T cells for PD-1 re-expression levels and tumor control
Phytonutrient diet supplementation promotes beneficial Clostridia species and intestinal mucus secretion resulting in protection against enteric infection
Responses of Gut Microbiota and Glucose and Lipid Metabolism to Prebiotics in Genetic Obese and Diet-Induced Leptin-Resistant Mice
Seres Therapeutics, MD Anderson Cancer Center, and the Parker Institute for Cancer Immunotherapy Announce a Collaboration to Support the Investigation of Microbiome Therapeutics for Immuno-Oncology
CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells
Fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs) and nonallergic food intolerance: FODMAPs or food chemicals?
Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila
Enhancement of natural immune function by dietary consumption of Bifidobacterium lactis (HN019)
Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis
CRISPR-Cas9 mediated efficient PD-1 disruption on human primary T cells from cancer patients
Nivolumab and pembrolizumab: Monoclonal antibodies against programmed cell death-1 (PD-1) that are interchangeable
PD-1 Knockout Engineered T Cells for Advanced Esophageal Cancer
Third party testing is available through American Gut Project and uBiome uBiome currently tests for the required bacteria in their SmartGut test that is only available in the US at the moment. A sample report can be viewed at https://explorer.ubiome.com/ by logging in with email: preview@ubiome.com password: ilovebacteria.
ASCO 2017: Higher Gut Bacteria Diversity Tied to Slower Metastatic Melanoma Progression
Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii
Effect of Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 on the healthy gut microbiota composition at phyla and species level: A preliminary study.
Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology.
Triggering Akkermansia with dietary polyphenols: A new weapon to combat the metabolic syndrome?
A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice
Understanding the Impact of Omega-3 Rich Diet on the Gut Microbiota
Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling
A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota
Intestinal Microbiome, Akkermansia muciniphila, and Medical Nutrition Therapy
A simple practice guide for dose conversion between animals and human
Gut microbiota and melanoma treatment responses
Microbiota: a key orchestrator of cancer therapy
Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent
Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics
Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota
Anti-inflammatory effects of sodium butyrate on human monocytes: potent inhibition of IL-12 and up-regulation of IL-10 production
Regulation of immune cell function by short-chain fatty acids
Interleukin-10: An Immune-Activating Cytokine in Cancer Immunotherapy
Bacteroides fragilis metabolises exopolysaccharides produced by bifidobacteria
IL-10 release upon PD-1 blockade sustains immunosuppression in ovarian cancer.
Short-chain fatty acids in ulcerative colitis.
The role of IL-10 in microbiome-associated immune modulation and disease tolerance

[arojussi]

This is great. As immunotherapy is so new it is really hard to say what is optimal for gut microbiome. However we know that gut microbiome is vital, so people try to optimise it. This is best knowledge that is currently available, so we go with that.

[D.ap]

Olga
Fascinating read .: )

In reading of gut microbrial , from the beginning ( infants)
We are born with a basic flora bacterium Bifidobacterium( genetics ?)

And our future health depends on that very beginning ?
Along with environmental changes ?

The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC137899/

[Olga]

It looks like more than Bifidobacterium:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350424/
The Human Neonatal Gut Microbiome: A Brief Review
The first, and most important, contribution to the genesis of the microbiome is vertical transmission of maternal microbiota. Colonization of mucosa in the digestive, respiratory, urogenital tracts, as well as the skin begins at, or perhaps even before, the time of birth when a newborn is exposed to a mother’s microbiota. It was previously thought that the in utero environment was largely sterile and that a fetus was not colonized with bacteria until the time of birth. Recent studies suggest the presence of a microbiome within the placenta as well as fetal meconium, suggesting that the colonization process begins well before delivery. Aagaard et al. have recently characterized a placental microbiome profile, composed of non-pathogenic commensal microbiota from the Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla which, interestingly, shares some similarities with the human oral microbiome (5). They observed that in the first week of life the full-term neonatal gut microbiome is largely colonized by members of the Actinobacteria, Proteobacteria, Bacteroidetes, and, much less, Firmicutes phyla (Figure ​(Figure1


Some very fascinating read on the subject
The Infant Microbiome: Implications for Infant Health and Neurocognitive Development
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681407/
The gut microbiome influences immunological, endocrine, and neural pathways and plays an important role in infant development. Several factors influence colonization of the infant gut microbiome. Different microbial colonization patterns are associated with vaginal versus surgical birth, exposure to antibiotics, and infant feeding patterns. Because of extensive physiological influence, infant microbial colonization patterns have the potential to impact physical and neurocognitive development and life course disease risk.

The intriguing part is that gut microbiome appears to be a modifiable factor...

[D.ap]

Hi Olga and all
Was reading on gut microbiota( as it is unique to each of us) and found this article on gut to brain thru what’s called the enteric nervous system.

I’m not sure if you want it here Olga .
Let me know

“The microbiome‐gut‐brain axis: from bowel to behavior”
https://onlinelibrary.wiley.com/doi/ful ... 10.01664.x

The above was pulled from this primary article

“Effect of Intestinal Microbial Ecology on the Developing Brain”

https://jamanetwork.com/journals/jamape ... le/1569276

Found it incredibly interesting that over 70% of our immunity is generated by our gut . :)
Under “Immunologic Role” paragraph

[D.ap]

Hello Olga,
I’m reading back thru the discussion and what’s the easiest way to know the gut microbes are imbalanced ?
Should it be determined by a doctor?
And that a patient should look into a fecal transplant ?
Who performs and or does the procedure ?

Thanks in advance .

[Olga]

It is really hard to accurately measure the numbers of the beneficial gut bacteria counts/proportion. The problem is that this is not the common test, not covered by the insurance and hard to find the one with the good quality - some of the best bacteria are anaerobic (can only exist in the absence of free oxygen) so will die in open air. The fecal matter has to be collected and analyzed in some very specific manner. There are labs that do that, and provide the fecal transplant to fix the problems but as far as I know it is limited to some diseases - hard so say, since it is a private clinics performing, they might agree to perform this procedure for the immunotherapy treatment patient based on the recent research. I have seen some clinics in Oregon that perform this treatment and tests. We managed to test Ivan but it was really hard.
Otherwise people can just assume their microbiome is not efficient enough if they recently had the antibiotics treatment especially the broad-spectrum antibiotics - they destroy the microbiome and it takes months to rebuild it, or if they are not responders to ICI - just suspect that one of the reason would be that insufficiency and try to fix it.
there are 2 known deaths on the clinical trial for Fecal microbiota transplantation by oral capsules, they contained E-coli. Perhaps the enema is the more safe way for that.
We now do not recommend taking probiotics as in one clinical trial patients who taken them, had worse results than the ones that had not. Perhaps, the probiotics overwhelm the own patients microbiota.
https://www.sciencemag.org/news/2019/04 ... rapy-drugs