Microbiome Therapies and Inflammation - In Depth Notes

Introduction to Microbiome and Its Importance

• The microbiome consists of a vast number of organisms inhabiting human bodies, primarily in the gut, impacting various physiological functions.

• It has been widely recognized for its crucial role in health and disease management.

Microbiome and Fecal Microbiota Transplantation (FMT)

1. Overview of Microbiome and FMT

   • Definition of Microbiome: The microbiome is characterized as the ecological community of microorganisms in our body, with a significant presence in the gastrointestinal tract.

   • Fecal Microbiota Transplantation (FMT) is the process of transferring fecal bacteria from a healthy donor into the gastrointestinal tract of a patient.

Microbiome Therapies for Clostridioides difficile Infections

2. Clostridioides difficile Infections

   • Symptoms: These infections can lead to severe diarrhea and are often treated by restoring microbial balance through FMT or microbiota therapies.

   • Current Therapies:

     • FMT: Highly effective in restoring gut flora and preventing recurrence of infections.

     • Microbiota therapies like RBX2660 and SER109: These therapies represent advanced treatments currently undergoing clinical trials (Phases 1-3).

Microbiome Therapies for Inflammatory Bowel Disease (IBD)

3. Inflammatory Bowel Disease (IBD)

   • Types include Crohn’s Disease (CD) and Ulcerative Colitis (UC), characterized by chronic inflammation of the digestive tract.

   • Fecal Microbiota Transplantation for IBD: FMT has been investigated for its potential benefits in managing IBD symptoms and restoring microbial diversity.

   • Current trials focus on therapies like SER287 for Crohn’s Disease, which are in Phases 1-2 of development.

Microbiome in Cancer Research

4. The Role of the Microbiome in Cancer

   • There is growing evidence suggesting that the gut microbiome can impact responses to cancer treatments, particularly immunotherapy.

   • Studies are investigating how altering microbiome composition could lead to enhanced cancer treatment responses, potentially recommending FMT as a strategy.

Key Facts About the Human Microbiome

Composition and Impact

• Host Microbial Balance:

  • Approximately 10^14 to 10^15 bacteria exist in the human intestine, far exceeding the number of human cells.

  • This complex community is like an individual fingerprint and plays a role in nutrient absorption and health maintenance.

Distribution of Microbes in the Body

• The largest concentration of microbes is found in the gut, particularly the colon, which is essential for metabolic processes.

• Stool analysis indicates that about 40% of fecal matter consists of bacteria, which facilitates various diagnostic and therapeutic approaches in research.

Functions of the Microbiome

1. Immune Functions

   • Development of the immune system and specific antibody production (e.g., IgA).

2. Metabolic Functions

   • Synthesis of essential vitamins and processing of dietary components.

3. Protective Functions

   • Protects against pathogens through competition and production of antimicrobial substances.

Concept of Dysbiosis

• Dysbiosis refers to the imbalance of microbial communities, often linked to various health conditions such as obesity, diabetes, and IBD.

• Understanding factors that impact microbiome health (genes, environment, diet, antibiotics) is essential for developing therapeutic strategies.

Therapeutic Strategies to Influence the Microbiome

• Approaches to restore microbial balance include dietary changes, use of antibiotics, probiotics, prebiotics, and FMT.

Conclusion

• The microbiome plays a pivotal role in our overall health, and emerging therapeutic strategies utilizing FMT and microbiota-based treatments show promise in managing severe diseases, including C. difficile infections, IBD, and even improving cancer therapies. Understanding the intricate relationships between microbiota and health will pave the way for future research and treatment methodologies in gastroenterology and immunology.

Slide 4: Who are we actually? Some facts regarding the microbiome

Key Points:

• Our body hosts 10× more microbes than human cells — that’s about 10¹⁴ bacteria.

• The total microbiome weight can reach up to 2 kg.

• The microbiome genome is 1,000× larger than the human genome.

• Each person’s microbiome is unique, like a fingerprint.

• Humans act as incubators for these microbes.

• The microbiome functions as a bioreactor, helping to:

  • Digest food

  • Produce energy (contributes up to 10% of our daily energy needs)

Explanation of Visuals:

• A circle chart compares the size of the human genome (20,000 genes) to the human microbiome (3,300,000 genes), illustrating the microbiome’s vast genetic diversity.

Glossary:

• Microbiome: The community of microorganisms (bacteria, fungi, viruses) living in and on the human body.

• Bioreactor: A system (in this case, our body) that supports a biologically active environment, such as microbial metabolism.

Key Takeaway:
The human microbiome is a massive and unique microbial ecosystem that plays a crucial role in our health, metabolism, and individuality.

Slide 5: Where is the human microbiome located?

Key Points:

• Microbiomes are found throughout the body: mouth, skin, airways, urogenital tract, and most importantly, the gut.

• An estimated 95% of all human microbiota reside in the gastrointestinal tract (GIT).

Explanation of Visuals:

• A human body diagram shows different microbiome locations with a red-highlighted gut region and a large red bubble emphasizing that the majority of microbes are in the gut.

Glossary:

• GIT (Gastrointestinal Tract): The digestive tract, including the stomach, intestines, and associated organs.

• Microbiota: The community of microorganisms in a particular environment, such as the gut.

Key Takeaway:
Although microbes live throughout the body, the vast majority are concentrated in the gut, making it the central hub of the human microbiome.

Slide 6: Crowded house... most bacteria reside within the colon

Key Points:

• The colon contains the highest concentration of bacteria.

• Bacterial load increases dramatically along the digestive tract:

  • Stomach: 10¹–10³ CFU/ml

  • Duodenum: 10³–10⁴ CFU/ml

  • Jejunum: 10⁴–10⁷ CFU/ml

  • Ileum: 10⁷–10⁸ CFU/ml

  • Colon: 10⁸–10¹² CFU/ml

Explanation of Visuals:

• An intestinal tract illustration shows increasing bacterial counts from stomach to colon, with a pyramid graphic emphasizing the massive bacterial density in the colon.

Glossary:

• CFU (Colony Forming Units): A measure of viable bacterial or fungal cells.

• Duodenum/Jejunum/Ileum: Sections of the small intestine; the ileum connects to the colon.

Key Takeaway:
Bacterial populations increase throughout the intestines, peaking in the colon, which houses the highest density of microbes in the human body.

Slide 7: The gut is the main interface with the environment

Key Points:

• The gut surface area is about 400 m², making it the largest interface with the outside environment.

• This surface is in constant contact with food, microbes, and antigens.

• The gut is also home to the largest microbial population in the body.

Explanation of Visuals:

• A soccer field comparison illustrates surface areas:

  • Lung: 180 m²

  • Gut: 400 m²

• The large pink rectangle labeled "gut" visually emphasizes its massive size and microbial load.

Glossary:

• Interface: A surface or point of interaction between two systems.

• Antigens: Substances that provoke an immune response, such as parts of microbes or food proteins.

Key Takeaway:
The gut is our body’s largest and most exposed interface with the environment and is densely populated with microbes, highlighting its key role in immune defense and digestion.

Slide 8: The fecal microbiome – A perfect research tool

Key Points:

• Humans excrete ~120 g of stool per day, of which 40% is bacteria.

• Over a lifetime, this adds up to about 42 tons of stool, containing massive amounts of microbial data.

• Feces provide a non-invasive way to study gut microbiota and its changes.

Explanation of Visuals:

• An illustration shows a dump truck metaphorically collecting human feces over a lifetime.

• The message: The large quantity and bacterial content of feces make it a rich source for microbiome research.

Glossary:

• Fecal microbiome: The microbial community present in human stool.

• Non-invasive: Methods or techniques that do not require penetration of the body or removal of tissue.

Key Takeaway:
Stool contains vast amounts of bacteria and serves as an ideal, non-invasive resource for studying the human gut microbiome.

Slide 9: Why is the microbiome important for us?

Key Points:

• The microbiome plays roles in three main functions:

  • Protective Functions:

    • Blocks pathogens from colonizing.

    • Produces antimicrobial factors.

    • Strengthens the intestinal mucosa.

  • Immune Functions:

    • Trains and develops the immune system.

    • Reduces inflammation.

    • Breaks down toxins.

  • Metabolic Functions:

    • Synthesizes vitamins and bile acids.

    • Helps digest complex carbohydrates.

    • Produces short-chain fatty acids (SCFAs).

    • Regulates fat storage and energy production.

Explanation of Visuals:

• Diagram of the intestinal wall shows microbial interaction with:

  • Villi, where absorption and immune signaling occur.

  • Associated functional benefits are grouped around the intestinal tissue illustration.

Glossary:

• Pathogens: Harmful microorganisms that can cause disease.

• Short-chain fatty acids (SCFAs): Metabolic byproducts of gut bacteria that have beneficial effects on health.

• Mucosa: The lining of the gastrointestinal tract that protects underlying tissues.

Key Takeaway:
The gut microbiome supports health through protective, immune-regulating, and metabolic functions, making it essential for homeostasis and disease prevention.

Slide 10: The microbiota is influenced by:

Key Points:

• Many factors shape the composition and function of the gut microbiota, including:

  • Genes

  • Age (→The older you get, the less diverse Microbiome you have)

  • Gender

  • Environment

  • Stress

  • Diet

  • Antibiotics

  • Drugs

  • Immune system

• These factors influence whether the microbiota remains balanced (eubiosis) or becomes imbalanced (dysbiosis).

Explanation of Visuals:

• Icons and arrows illustrate how diverse external/internal factors (e.g., food, medications, infections) interact to impact microbiome health.

• Central diagram suggests the microbiota is dynamic and responsive to lifestyle and biological conditions.

Glossary:

• Eubiosis: A balanced and healthy state of the microbiome.

• Dysbiosis: An imbalanced microbiome that may lead to disease.

• Microbiota: The collection of all microbes in a given environment, like the gut.

Key Takeaway:
The gut microbiota is not fixed — it’s shaped by many factors, and understanding these can help manage or prevent disease.

Slide 11: A healthy microbiome is very diverse, but repetitive damage results in dysbiosis

Key Points:

• A healthy microbiome is characterized by high microbial diversity.

  • it is very diverse (or should be) → diversity is the main measure!

• Occasional disturbances (e.g., antibiotics, infections) can lead to partial recovery.

• Repeated or severe damage may cause permanent dysbiosis, reducing diversity and altering microbial composition.

Explanation of Visuals:

• Colored microbial shapes represent different bacteria.

• Arrows show transition from a healthy state → damage → either recovery or dysbiosis.

• Dysbiosis is depicted as a less diverse and more imbalanced community.

Glossary:

• Microbial diversity: The variety of bacterial species within a microbial community.

• Dysbiosis: A state of microbial imbalance often associated with inflammation, infection, or disease.

• Recovery: The process of returning to a balanced microbial state after disturbance.

Key Takeaway:
Microbial diversity is key to gut health — while occasional damage may be reversible, chronic disruptions can lead to long-term imbalances (dysbiosis).

Slide 12: Dysbiosis favours disease onset

Key Points:

• Dysbiosis (an imbalanced microbiome) is linked to the development of various diseases.

• It contributes to:

  • Heart disease

  • Atherosclerosis

  • Hypertension

  • Obesity

  • Type 2 diabetes

  • Inflammatory bowel disease

• Dysbiosis disrupts the immune system and gut barrier, leading to chronic inflammation.

Explanation of Visuals:

• A central diagram shows how dysbiosis affects multiple organs and conditions, with arrows pointing from the gut to disease outcomes like cardiovascular and metabolic disorders.

Glossary:

• Dysbiosis: Disruption in the balance of microbial communities, often leading to disease.

• Atherosclerosis: Buildup of fats and cholesterol in arteries.

• Chronic inflammation: Long-term immune activation that can damage tissues.

Key Takeaway:
An unhealthy microbiome contributes to the onset of various chronic diseases by disturbing immune regulation and metabolic balance.

Slide 13: The role of the Microbiome in the growing list of diseases

Key Points:

• The microbiome is now linked to an increasing range of diseases, including:

  • Autoimmune diseases (e.g., multiple sclerosis)

  • Nonalcoholic fatty liver disease

  • Atherosclerosis

• Genomic studies have found associations between changes in microbial composition and disease development.

• The oral, gut, and plaque microbiomes interact and may contribute to disease progression.

Explanation of Visuals:

• The slide presents snippets from scientific articles highlighting various microbiome-disease links.

• Key terms like "autoimmune demyelination" and "gut microbiota in patients with atherosclerosis" are highlighted to emphasize disease relevance.

Glossary:

• Autoimmune demyelination: The immune system attacks the protective covering of nerves.

• Nonalcoholic fatty liver disease (NAFLD): Fat accumulation in the liver not due to alcohol use.

• Commensal microbes: Non-harmful microbes that naturally live in the body.

Key Takeaway:
Scientific evidence increasingly supports that microbiome imbalances are involved in the onset and progression of many chronic and autoimmune diseases.

Slide 14: Strategies to influence the intestinal microbiome

Key Points:

• Several interventions can modulate the gut microbiota:

  • Diet (fiber-rich, diverse)

    • Problem your adaption on microbiome is very unspecific

  • Antibiotics (though often damaging to the microbiota)

  • Probiotics (live beneficial microbes)

  • Prebiotics (fiber-like substances that feed beneficial microbes)

  • Fecal microbiota transplantation (FMT)

  • Bacteriophage therapy (targeted bacterial viruses)

  • Enzyme replacement

• Personalized medicine approaches can optimize microbiome modulation.

Explanation of Visuals:

• A diagram in the center shows the gut and microbiota surrounded by influencing strategies like diet, antibiotics, probiotics, and more, with arrows showing bidirectional effects.

Glossary:

• Probiotics: Supplements or foods containing beneficial live bacteria.

• Prebiotics: Non-digestible fibers that help healthy bacteria grow.

• Bacteriophages: Viruses that infect and kill specific bacteria.

• Pathogenesis: Development of a disease

Key Takeaway:
A variety of dietary, medical, and biotherapeutic strategies exist to shape the gut microbiota toward a healthier balance.

Slide 15: Fecal Microbiota Transplantation – FMT

Key Points:

• FMT involves transferring stool from a healthy donor into a patient with dysbiosis.

• It aims to restore microbial diversity and treat conditions like:

  • Clostridium difficile infection (CDI)

  • Other gut-related diseases

• FMT can be administered via:

  • Capsules

  • Colonoscopies

  • Nasogastric tubes

• FMT helps re-establish microbiome balance and resilience.

Explanation of Visuals:

• A step-by-step diagram illustrates the FMT process:

  • Feces from a healthy donor → processing → administration to patient → microbiota restored in the gut.

Glossary:

• FMT (Fecal Microbiota Transplantation): A medical procedure transferring fecal bacteria from a healthy individual to a patient.

• Clostridium difficile (C. difficile): A bacterium causing severe diarrhea and inflammation, often after antibiotic use.

Key Takeaway:
FMT is a powerful clinical tool for treating microbiome-related diseases by reintroducing healthy microbial communities.

Slide 16: Microbiome therapies for Clostridioides difficile (C. diff) infection

Key Points:

• This slide serves as a section header introducing microbiome-based therapies targeting C. difficile, a bacterium responsible for severe intestinal infections.

• The upcoming slides explore clinical significance, FMT (Fecal Microbiota Transplantation) trials, and comparisons with traditional treatments like vancomycin.

Explanation of Visuals:

• No figures shown — this is a title slide setting the stage for the next in-depth discussion on C. difficile and microbiome interventions.

Glossary:

• C. difficile: A pathogenic bacterium causing severe diarrhea, particularly after antibiotic use.

• Microbiome therapy: Medical approaches that aim to restore healthy microbial communities to treat disease.

Key Takeaway:
The focus shifts to microbiome-based interventions—especially FMT—for treating C. difficile infections, a serious healthcare concern.

Slide 17: Clostridioides difficile colitis – clinical significance

Key Points:

• C. difficile is the most common nosocomial diarrhea (hospital-acquired).

• Estimated cost: >$1 billion/year.

• Produces two toxins:

  • Toxin A: Increases permeability and secretion.

  • Toxin B: Destroys cells (cytotoxin).

• Dangerous features include:

• Toxin A:

  • New toxin-variant strains (e.g., BI/NAP1/027).

  • Resistance to quinolones and toxin overproduction.

• Toxin B:

  • Cytotoxin; inflammation

• US mortality (2008): C. difficile caused more deaths than all other gastrointestinal pathogens combined.

Explanation of Visuals:

• This is a text-based slide listing key medical and epidemiological data to highlight the public health burden and severity of C. difficile infections.

Glossary:

• Nosocomial infection: An infection acquired in a hospital.

• Toxin A/B: Toxins produced by C. difficile that damage intestinal cells.

• BI/NAP1/027: A highly virulent strain of C. difficile.

• Quinolones: a broad-spectrum group of synthetic antibiotics used to treat bacterial infections

• Cytotoxin: A cytotoxin is a substance that has a toxic effect on cells

Key Takeaway:
C. difficile is a dangerous, costly, and often deadly hospital-acquired infection, driven by toxin production and drug-resistant strains.

Slide 18: Randomized controlled trial on FMT for recurrent C. diff infection

Key Points:

• A clinical trial compared 3 treatment groups for 43 patients with recurrent C. difficile:

  1. Vancomycin (antibiotic) + bowel lavage (Darmspühlung) + FMT

  2. Vancomycin only

  3. Vancomycin + bowel lavage

• Primary endpoint: Resolution of diarrhea without relapse after 10 weeks.

Explanation of Visuals:

• A trial flowchart shows randomization and outcomes:

  • FMT group had a higher cure rate.

  • Non-FMT groups showed lower effectiveness and higher relapse rates.

Glossary:

• Randomized controlled trial (RCT): A scientific study design used to compare treatment outcomes.

• Bowel lavage: Cleansing the bowel, often using fluid solutions.

Key Takeaway:
FMT, in combination with standard treatment, significantly improves outcomes in patients with recurrent C. difficile compared to vancomycin alone.

Slide 19: FMT for recurrent Clostridioides difficile infection – more efficient than vancomycin

Key Points:

• Cure rates after first FMT:

  • 93.8% (13 of 16 patients) in the FMT group had resolution.

  • Only 31.3% (13 of 41) in vancomycin groups showed improvement.

• Second FMT increased cure rate further in relapsing patients.

• The study was stopped early due to significant differences in outcomes.

Explanation of Visuals:

• A bar graph compares resolution rates between groups.

• Visual emphasis on FMT’s superiority over vancomycin, even with bowel lavage.

Glossary:

• Vancomycin: An antibiotic commonly used to treat C. difficile.

• Resolution of symptoms: The end of diarrhea and return to normal function.

• Clostridium difficile (C. difficile) is a bacterium that can cause serious intestinal infections, particularly diarrhea and colitis → gram-positive

Key Takeaway:
FMT shows dramatically higher success rates than standard antibiotic therapy in treating recurrent C. difficile, offering a powerful alternative.

Slide 20: FMT for recurrent C. diff infection – Analysis of fecal microbiota

Key Points:

• Microbiota in patients with recurrent C. difficile is significantly altered before FMT.

• After FMT:

  • Bacterial diversity increases, becoming more similar to healthy donors.

    • FMT is NOT killing any bacteria! it makes just the microbiome more diverse.

  • There's a rise in Bacteroidetes and Clostridium clusters (IV and XIVa).

  • Proteobacteria levels (often pathogenic) decrease.

Explanation of Visuals:

• A box plot compares fecal microbial diversity:

  • Donors have the highest diversity.

  • Pre-FMT patients show reduced diversity.

  • Post-FMT patients show restored diversity, approaching donor levels.

Glossary:

• Bacterial diversity: A measure of the variety of bacterial species in a sample.

• Proteobacteria: A phylum of bacteria that includes many pathogens.

• Clostridium clusters IV/XIVa: Beneficial gut bacteria involved in short-chain fatty acid production.

Key Takeaway:
FMT restores gut microbial diversity in C. difficile patients, making it more similar to that of healthy individuals.

Slide 21: FMT for recurrent and refractory C. diff infection – Effects of delivery and preparation

Key Points:

• Systematic review and meta-analysis of 37 studies shows:

  • FMT is more effective than vancomycin.

  • Clinical resolution rate averages at 92%.

• Delivery route and stool preparation methods:

  • Lower GI (e.g., colonoscopy) more effective (95%) than upper GI (88%).

  • Frozen stool as effective as fresh (92% vs. 93%).

• Multiple FMTs further improve treatment outcomes.

• Serious adverse events (SAEs) were rare.

Conclusion:

• FMT is a safe and effective therapy for both recurrent and refractory C. difficile infections.

• Effectiveness is independent of delivery method and stool form.

Explanation of Visuals:

• Text-based slide summarizing key findings from large-scale evidence.

Glossary:

• Refractory infection: Infection not responding to standard treatment.

• Meta-analysis: A statistical method combining data from multiple studies.

• Lower/upper GI delivery: Colonoscopy vs. nasogastric tube administration.

Key Takeaway:
FMT is a consistently effective treatment for C. difficile, regardless of how it's delivered or whether fresh or frozen stool is used.

Slide 22: FMT OR Fidaxomicin OR Vancomycin for C. diff infection

Key Points:

• Randomized trial compared:

  • FMT (n = 24)

  • Fidaxomicin (n = 24)

  • Vancomycin (n = 16)

• Week 8 resolution rates:

  • FMT: 91.7%

  • Fidaxomicin: 70.8%

  • Vancomycin: 50%

• Clinical effect and negative toxin test were both highest in the FMT group.

Explanation of Visuals:

• Bar chart shows clear differences in treatment efficacy.

• FMT consistently outperforms both antibiotic treatments.

Glossary:

• Fidaxomicin: A narrow-spectrum antibiotic targeting C. difficile.

• Resolution rate: Percentage of patients who fully recover within the study period.

• Negative toxin test: Lab confirmation that C. difficile toxins are no longer present.

Key Takeaway:
FMT is superior to both fidaxomicin and vancomycin for treating C. difficile infection, with the highest cure and clearance rates.

Slide 23: Conclusion on FMT and C. diff. colitis

Key Points:

• FMT prevents recurrence of C. difficile infection in about 90% of cases.

• It is more effective than standard antibiotics (vancomycin, fidaxomicin).

• Caution is advised:

  • There's a risk of transmitting multidrug-resistant organisms (MDROs).

• Rigorous donor screening is crucial to minimize risks.

Explanation of Visuals:

• Plain text-based conclusion slide summarizing major clinical and safety implications of FMT.

Glossary:

• Colitis: Inflammation of the colon, often seen in C. difficile infections.

• Multidrug-resistant organisms (MDROs): Bacteria resistant to multiple antibiotics, posing safety concerns in transplants.

Key Takeaway:
FMT is a highly effective treatment for C. difficile colitis, but must be applied with strict safety protocols due to potential risks.

✅ Why FMT helps so well against recurrent C. difficile:

1. It restores colonization resistance

• A healthy microbiota prevents C. difficile from regrowing by:

  • Competing for nutrients and space.

  • Producing bacteriocins (natural antibiotics from good bacteria).

  • Maintaining gut pH and bile acid balance, which inhibits C. difficile spore germination.

2. Antibiotics disrupt this balance

• Antibiotics like vancomycin kill C. difficile, but also destroy good gut bacteria.

• This leaves an empty ecological niche that C. difficile can easily re-invade — which is why recurrence rates can be so high (up to ~25–30%).

3. FMT fills the microbiome gap

• FMT introduces a full, diverse microbial community from a healthy donor.

• This re-establishes the natural defenses of the gut, making it much harder for C. difficile to come back.

• It's like replanting a healthy forest that can outcompete the invasive weed (C. difficile).

Slide 24: Story of the first FDA-approved microbiota therapy – REBYOTA®

Key Points:

• RBX2660 (Rebyota®) is the first FDA-approved microbiota-based therapy.

• Phase 2 study: 78.9% success after 8 weeks; 91% in responders maintained results at 6 months.

• Phase 3 trial: Success rate of 70.6% for RBX2660 vs. 57.5% for placebo.

• Rebyota is:

  • Approved by the FDA.

  • A single-dose rectal enema.

  • Used to prevent recurrence of C. difficile.

• It consists of donor stool samples screened thoroughly for safety.

Explanation of Visuals:

• A bullet list summarizing clinical trial milestones and approval details.

• Emphasizes trial phases and regulatory outcome.

Glossary:

• FDA (Food and Drug Administration): U.S. agency that approves medical treatments.

• Rectal enema: A treatment delivered through the rectum.

• RBX2660: The product name before branding as Rebyota.

Key Takeaway:
Rebyota® became the first FDA-approved microbiota-based therapy, showing strong clinical efficacy in preventing recurrent C. difficile infections.

Slide 25: First FDA-approved microbiota therapy – REBYOTA®

Key Points:

• Rebyota® is indicated for:

  • Prevention of C. difficile recurrence in adults aged ≥18.

  • Following antibiotic treatment for C. difficile.

• It is not indicated for initial treatment of active infection.

• Contains live microbes (from donor stool), administered rectally.

Explanation of Visuals:

• Product image and clinical use description.

• Regulatory label specifies use limitations and indications.

Glossary:

• Indication: The officially approved use of a drug.

• Limitation of Use: Specifies where the drug should not be used.

Key Takeaway:
Rebyota® is used to prevent, not treat, C. difficile infections and is administered rectally as a single-dose therapy following antibiotics.

Slide 26: Further microbiome therapies for C. diff. infection – SER-109 Phase 3

Key Points:

• A Phase 3 clinical trial (randomized, placebo-controlled) tested SER-109.

• Participants: Adults with ≥3 C. difficile infections.

• Intervention:

  • SER-109 or placebo, post-standard antibiotic treatment.

  • Monitored for 8 weeks.

• Goals:

  • Measure recurrence rates.

  • Analyze safety, microbiome shifts, and bile acid metabolism.

Explanation of Visuals:

• Trial design diagram shows patient enrollment, randomization, and outcome assessments.

• Structure similar to drug development trial phases.

Glossary:

• SER-109: Oral microbiome therapy using bacterial spores.

• Placebo-controlled: A group receives no active drug to compare effectiveness.

Key Takeaway:
SER-109 is being tested in advanced clinical trials as another microbiome therapy to reduce C. difficile recurrence post-antibiotic treatment.

Slide 27: Further microbiome therapies for C. diff. infection – SER-109 Phase 3 (Results)

Key Points:

• Recurrence rates after 8 weeks:

  • 12% in SER-109 group vs. 40% in placebo.

• SER-109 reduced recurrence risk significantly.

• Bacterial spore engraftment observed only in SER-109 group.

• Safety and side effect profile similar to placebo.

Conclusion:

• SER-109 is effective and safe for preventing recurrent C. difficile.

• Spore-based microbiome restoration appears promising.

Explanation of Visuals:

• Bar chart compares recurrence rates between placebo and SER-109 groups.

• Lower recurrence clearly evident in the treatment group.

Glossary:

• Spore-forming bacteria: Hardy microbes capable of surviving harsh conditions.

• Engraftment: Establishment of introduced microbes in the recipient's gut.

Key Takeaway:
SER-109 shows strong potential as an oral, spore-based microbiome therapy to prevent C. difficile recurrence with minimal side effects.

Slide 28: Latest treatment guidelines for C. difficile infections (2021 update)

Key Points:

• Guidelines by ESCMID (2021) summarize treatment based on infection severity:

  • Non-severe 1st episode: Fidaxomicin preferred; vancomycin as alternative.

  • Severe 1st episode: Same as above, but hospitalization may be required.

  • Fulminant disease: Requires high-dose oral vancomycin + IV metronidazole.

  • 1st recurrence: Fidaxomicin or vancomycin with extended tapering.

  • 2nd recurrence or later: Consider FMT (Fecal Microbiota Transplantation).

• Fidaxomicin is prioritized over vancomycin due to better recurrence outcomes.

Explanation of Visuals:

• A table outlines treatment recommendations per disease stage and recurrence status.

• Color-coded rows distinguish between treatment levels.

Glossary:

• Fulminant disease: Sudden, severe illness with high risk of complications.

• Tapering: Gradual reduction in medication dosage.

• ESCMID: European Society of Clinical Microbiology and Infectious Diseases.

Key Takeaway:
Modern guidelines emphasize fidaxomicin and FMT in managing recurrent or severe C. difficile, replacing older metronidazole-based approaches.

Slide 29: Microbiome therapies for Inflammatory Bowel Disease (IBD)

Key Points:

• This is a section header slide introducing microbiome-based therapies for IBD.

• Focus shifts from C. difficile to chronic intestinal inflammatory diseases: Crohn’s disease (CD) and ulcerative colitis (UC).

• Microbiome modulation is a potential tool for managing inflammation and symptoms.

Explanation of Visuals:

• Title slide only; no figures presented — sets up the following slides on IBD.

Glossary:

• IBD (Inflammatory Bowel Disease): Chronic inflammation of the gastrointestinal tract, primarily CD and UC.

Key Takeaway:
New section begins focusing on the role of microbiome therapies in treating IBD, including Crohn’s disease and ulcerative colitis.

Slide 30: Inflammatory bowel disease (IBD)

Key Points:

• Includes Crohn’s disease (CD) and ulcerative colitis (UC).

• Approx. 15,000 patients affected in Switzerland.

• Characterized by chronic, relapsing intestinal inflammation.

• Key distinctions:

  • CD: Segmental and transmural inflammation affecting any GI tract part.

  • UC: Continuous inflammation starting in rectum, confined to colon lining.

• Can also cause extraintestinal symptoms (e.g., eyes, joints, skin, liver).

Explanation of Visuals:

• Three images compare a healthy colon, a Crohn’s-affected colon, and extraintestinal symptoms (e.g., inflamed joints).

Glossary:

• Transmural: Extending through the entire bowel wall.

• Extraintestinal: Symptoms outside the gut (e.g., eyes, joints).

• Segmental: Involving only certain parts, not continuous.

Key Takeaway:
IBD includes CD and UC, which differ in inflammation patterns but share chronicity and systemic involvement.

Slide 31: Symptoms of IBD

Key Points:

• Symptom prevalence in Swiss patients with CD (n = 279) vs. UC (n = 113):

  • Diarrhea: CD (89.5%), UC (96.4%)

  • Bloody stools: CD (27.3%), UC (89.3%)

  • Pain: CD (86.9%), UC (81.3%)

  • Fatigue: CD (81.7%), UC (40.2%)

  • Weight loss: CD (59.6%), UC (38.4%)

  • Arthralgia/arthritis: CD (29.2%), UC (27.7%)

  • Fever: CD (24.7%), UC (20.5%)

  • Skin issues: CD (14.2%), UC (15.2%)

Explanation of Visuals:

• A two-column table lists IBD symptoms with percentages per disease type.

• Highlights differences, especially more bloody stools in UC and more fatigue in CD.

Glossary:

• Fatigue: Persistent tiredness, common in chronic inflammatory diseases.

• Arthralgia: Joint pain.

• Bloody stools: A common symptom of mucosal damage in UC.

Key Takeaway:
Symptoms of IBD vary between CD and UC, with UC more often showing bloody stools, while CD more commonly presents with pain, fatigue, and weight loss.

Slide 32: Incidence of IBD is still increasing

Key Points:

• The number of IBD cases is rising steadily, especially in Western countries.

• Countries like Switzerland, Canada, and Norway show some of the highest incidences.

• The increase is notable across both Crohn’s disease (CD) and ulcerative colitis (UC).

• This trend mirrors that of other immune-related diseases (e.g., multiple sclerosis, type 1 diabetes).

Explanation of Visuals:

• A line graph compares IBD incidence over time among various countries.

• Swiss IBD registry (SWISS IBD) data is included to highlight local trends.

Glossary:

• Incidence: Number of new cases in a population over a specific time.

• IBD: Includes both Crohn’s disease and ulcerative colitis.

Key Takeaway:
IBD is becoming increasingly common, particularly in industrialized countries, reflecting possible links to environmental and lifestyle changes.

Slide 33: Genetic risk factors for IBD: > 200 identified since 2001

Key Points:

• Over 200 genetic risk loci for IBD have been identified, making IBD a model for studying polygenic diseases.

• Some genetic variants are shared between CD and UC, while others are distinct.

• Key genes include:

  • NOD2, ATG16L1 (CD-specific)

  • IL23R, HLA regions (shared or UC-specific)

Explanation of Visuals:

• A Venn diagram displays genetic loci:

  • Left circle: CD-associated genes.

  • Right circle: UC-associated genes.

  • Overlap: Shared risk loci between both conditions.

Glossary:

• Polygenic disease: A condition influenced by many genes.

• Locus/loci: Specific position(s) on a gene or chromosome.

• NOD2: A gene involved in immune recognition of bacteria.

Key Takeaway:
While many genetic risk factors for IBD have been identified, their presence alone doesn't explain the rising incidence, suggesting other contributors.

Slide 34: Environmental factors lead to disease onset (with genetic predisposition)

Key Points:

• Genetics alone (30%) do not explain the increase in IBD cases.

• Environmental factors (70%), especially those associated with the “Westernized lifestyle,” are major contributors.

• This includes:

  • Diet

  • Hygiene

  • Pollution

  • Antibiotic use

Explanation of Visuals:

• A pie chart divides disease risk:

  • 70% environmental factors

  • 30% genetic susceptibility

• Arrows connect both, illustrating interaction between genes and environment.

Glossary:

• Genetic predisposition: Increased likelihood of developing a disease based on genetics.

• Westernized lifestyle: Includes high-fat diets, low fiber, and sedentary behaviors.

Key Takeaway:
Environmental triggers, more than genetics, drive the global rise in IBD cases—especially in regions undergoing lifestyle westernization.

Slide 35: IBD Pathogenesis

Key Points:

• Pathogenesis (disease development) of IBD involves:

  1. Environmental factors: Diet, antibiotics, oxygen levels, pH.

  2. Microbiome changes: Altered gut microbes and their metabolites.

  3. Genetic predisposition: Variants affecting immune function and barrier integrity.

  4. Epigenetic changes: Gene regulation without DNA sequence change.

• These contribute to:

  • Immune system dysregulation

  • Chronic intestinal inflammation

Explanation of Visuals:

• A flow diagram shows how external and internal factors converge to trigger immune dysfunction and IBD symptoms.

Glossary:

• Epigenetics: Modifications that regulate gene expression without altering the DNA sequence.

• Immune dysregulation: Malfunction of immune response, often leading to inflammation.

Key Takeaway:
IBD results from complex interactions among environmental triggers, microbiome disturbances, genetic risk, and immune imbalance.

Slide 36: “Dysbiosis” in IBD: reduced “diversity”

Key Points:

• IBD is associated with reduced microbial diversity, a hallmark of dysbiosis.

• Specific changes in bacterial composition include:

  • Decrease in Firmicutes and Bacteroidetes.

  • Increase in Proteobacteria, including potential pathogens.

• These imbalances impair gut health and contribute to inflammation.

Explanation of Visuals:

• A bar chart compares bacterial diversity in healthy individuals vs. IBD patients.

• Different bacterial phyla and families are shown, highlighting the shift in community structure in IBD.

Glossary:

• Dysbiosis: An imbalanced microbial community that contributes to disease.

• Microbial diversity: The variety of different bacterial species in the gut.

Key Takeaway:
IBD is marked by a less diverse gut microbiome with an increase in harmful bacteria and a loss of beneficial ones—contributing to disease pathology.

Slide 37: Genetic, environmental, and immune-mediated microbiome interactions in the pathogenesis of IBD

Key Points:

• IBD pathogenesis arises from a complex interaction between:

  • Genetic factors (e.g., NOD2, ATG16L1)

  • Environmental influences (e.g., diet, antibiotics)

  • Microbiome imbalance

  • Immune dysregulation

• These factors contribute to:

  • Barrier dysfunction

  • Persistent inflammation

  • Defective microbial tolerance

Explanation of Visuals:

• A detailed diagram integrates multiple components:

  • Top: Environmental and genetic influences.

  • Middle: Intestinal barrier and microbiota interactions.

  • Bottom: Downstream effects on immune activation and inflammation.

Glossary:

• NOD2 / ATG16L1: Genes involved in microbial sensing and immune regulation.

• Barrier dysfunction: Loss of gut lining integrity, allowing bacteria to cross and trigger inflammation.

Key Takeaway:
IBD results from the convergence of genetic predisposition, environmental triggers, microbiome imbalance, and immune malfunction.

Slide 38: Microbiota and FMT for Colitis ulcerosa

Key Points:

• Clinical studies explore FMT for ulcerative colitis (UC) treatment.

• Findings:

  • IBD is not necessarily caused by a single pathogen, but by a microbiota imbalance.

  • Success of FMT in UC depends on:

    • Donor microbiota composition.

    • Recipient response.

• Clinical remission was more likely with microbiota-rich stool donors.

Explanation of Visuals:

• A highlighted excerpt from a clinical trial publication in The Lancet discusses how donor factors influence remission rates in UC following FMT.

Glossary:

• Colitis ulcerosa (UC): Chronic inflammation of the colon lining.

• Clinical remission: Absence or significant reduction of disease symptoms.

Key Takeaway:
FMT can support remission in UC, but its success heavily depends on donor microbiota composition and matching with the patient.

Slide 39: FMT for the treatment of Colitis ulcerosa

Key Points:

• A randomized controlled trial (RCT) showed:

  • FMT induced remission in 24% of UC patients (9 out of 38).

  • In the placebo group: remission in 5% (2 out of 37).

• Indicates statistically significant benefit of FMT for UC patients.

• Both donor stool composition and UC subtype influence outcomes.

Explanation of Visuals:

• Title and abstract of a landmark paper in Gastroenterology highlight FMT’s effects on UC remission.

Glossary:

• Randomized Controlled Trial (RCT): Gold-standard clinical study design comparing treatments with a control group.

• Ulcerative colitis (UC) is a chronic inflammatory disease that affects the large intestine (colon), specifically the inner lining of the colon and rectum.

  It is one of the two main types of Inflammatory Bowel Disease (IBD) — the other being Crohn’s disease.

• Remission: A period during which symptoms of a disease are reduced or disappear.

Key Takeaway:
FMT can induce remission in ulcerative colitis in a subset of patients, but its effectiveness varies depending on both donor and disease factors.

Slide 40: FMT for the treatment of Colitis ulcerosa

Key Points:

• A randomized, double-blind, placebo-controlled, proof-of-concept trial tested FMT in ulcerative colitis (UC).

• Patients received FMT from a single healthy donor via enema.

• Results:

  • No statistically significant difference in clinical remission or endoscopic improvement.

• Suggests that FMT in UC is not "one size fits all".

• Showed you can not use the Stool from 1 Healthy Donor, but there is a personal component that fits for a person.

Explanation of Visuals:

• Abstract from Gastroenterology (2015) outlines study design and main result: lack of consistent benefit from a single donor FMT approach.

Glossary:

• Proof-of-concept trial: A preliminary study to assess feasibility and potential effects.

• Endoscopic improvement: Visible healing of intestinal lining during colonoscopy.

Key Takeaway:
A single-donor FMT may not be sufficient to induce consistent remission in UC—highlighting the need for individualized or optimized approaches.

Slide 41: Multidonor FMT for the treatment of Colitis ulcerosa

Key Points:

• Multicenter, double-blind, placebo-controlled trial across 3 hospitals.

• FMT via rectal enema 5×/week for 8 weeks.

• Multidonor FMT led to:

  • Clinical remission

  • Endoscopic healing

  • Symptom improvement

• The use of multiple donors increased microbiome diversity and treatment success.

Explanation of Visuals:

• Summary of trial design and findings from Paramsothy et al., 2017 in Lancet.

• Bullet points highlight improved outcomes with a more diverse donor pool.

Glossary:

• Multidonor FMT: FMT material sourced from multiple healthy individuals to maximize microbial diversity.

• Rectal enema: Delivery of treatment through the rectum.

Key Takeaway:
Multidonor FMT is more effective than single-donor FMT in inducing remission and mucosal healing in UC.

Slide 42: LOTUS Study – Lyophilised oral faecal microbiota transplantation for ulcerative colitis (UC)

Key Points:

• LOTUS trial tested oral, lyophilized (freeze-dried) FMT capsules vs placebo.

• Design: Randomized, double-blind, placebo-controlled.

• Results:

  • Clinical remission: 15% (FMT) vs 5% (placebo)

  • Clinical response and endoscopic remission also favored FMT.

  • Statistical significance reached for some endpoints (p < 0.05).

Explanation of Visuals:

• Flowchart shows trial design.

• Bar graphs present primary and secondary outcome rates, showing better results with FMT capsules.

Glossary:

• Lyophilized: Freeze-dried to preserve microbes for oral capsule use.

• Clinical response: Improvement in symptoms short of full remission.

Key Takeaway:
Oral FMT capsules are a promising, non-invasive therapy for UC, offering modest but statistically significant clinical benefits.

Slide 43: FMT & AID for the treatment of Colitis ulcerosa

Key Points:

• This study combined:

  • FMT

  • AID (Anti-Inflammatory Diet)

• Design: Open-label randomized controlled trial.

• FMT administered via colonoscopy, followed by enema and dietary intervention.

• Combination therapy aims to:

  • Improve remission rates.

  • Modify gut environment via microbiota and diet synergy.

Explanation of Visuals:

• Diagram shows study arms and timeline for interventions:

  • One group receives FMT + diet.

  • One group receives standard of care.

Glossary:

• AID (Anti-Inflammatory Diet): Nutritional approach aiming to reduce gut inflammation.

• Open-label: Participants and researchers know which treatment is administered.

Key Takeaway:
Combining FMT with a targeted diet may offer enhanced treatment outcomes for UC by addressing both microbial and dietary factors.

Slide 44: FMT & AID for the treatment of Colitis ulcerosa

Key Points:

• Combining FMT with Anti-Inflammatory Diet (AID) shows superior results compared to standard medical therapy.

• Results after 8 weeks:

  • Higher clinical response and endoscopic remission in FMT + AID group.

• AID was continued for 40 weeks, supporting long-term benefits.

Explanation of Visuals:

• Two bar charts compare:

  • Clinical response

  • Endoscopic remission between FMT+AID vs. standard care

• Red arrows highlight statistically significant improvements.

Glossary:

• AID (Anti-Inflammatory Diet): Dietary approach aiming to reduce inflammation.

• Endoscopic remission: Healing of intestinal tissue as seen during colonoscopy.

Key Takeaway:
FMT combined with a targeted diet is more effective than optimized medical therapy alone for UC, supporting an integrated treatment strategy.

Slide 45: Repetitive FMT in Colitis ulcerosa – Systematic Meta-Analysis

Key Points:

• This meta-analysis compared single vs. repeated FMT:

  • Single FMT: 11 studies; remission rate = 19%

  • Repeated FMT: 13 studies; remission rate = 33.8%

    • Or when you pool the stool from multiple donors, higher remission rate.

• Repeated administration clearly increases treatment efficacy.

Explanation of Visuals:

• Two forest plots display remission outcomes:

  • Left: Single FMT

  • Right: Repeated FMT

• Confidence intervals and pooled estimates are shown, with repeated FMT marked superior.

Glossary:

• Forest plot: A graphical summary of results from multiple studies.

• Meta-analysis: A statistical method combining data across studies to identify overall trends.

Key Takeaway:
Repeated FMT treatments yield significantly better outcomes in UC compared to a single treatment session.

Slide 46: Efficacy & safety of FMT in treatment of UC – Systematic Meta-Analysis

Key Points:

• A table summarizes multiple studies assessing:

  • Clinical remission

  • Endoscopic remission

  • Adverse events

• Consistent outcomes across studies demonstrate:

  • FMT is both effective and safe for UC treatment.

Explanation of Visuals:

• Table lists various clinical trials, their design, remission outcomes, and safety data.

• Concludes FMT has reproducible benefit with acceptable safety.

Glossary:

• Adverse events: Unwanted side effects or complications during treatment.

Key Takeaway:
FMT shows consistent efficacy and a good safety profile in treating UC, with strong evidence from multiple clinical trials.

Slide 47: Can we possibly identify the “Super-Donors”?

Key Points:

• A study tested standardized FMT with microbiome-guided donor selection.

• Goal: Identify whether certain “super-donors” consistently produce better outcomes.

• Findings:

  • No significant difference in remission rates across donors.

  • Clinical and microbiota diversity outcomes were similar between donor groups.

• Suggests no clear “super-donor” profile has been identified yet.

Explanation of Visuals:

• Left: Workflow showing donor selection and microbiome profiling.

• Right: Table with remission rates by donor group shows no standout performer.

Glossary:

• Super-donor: Hypothetical donor whose microbiota leads to significantly higher success rates in FMT. → were identified as “not present” in Uni Leuven Trial, the clinical trial had to be stopped since rates where so bad with the chosen super-donors.

• Microbiome-guided selection: Choosing donors based on the composition and diversity of their gut microbes.

Key Takeaway:
Despite efforts to find high-performing “super-donors,” no consistent superiority has been observed—suggesting outcomes depend on multiple factors beyond donor alone.

Slide 48: Improved microbiome therapies for UC – SER-287 Phase 1

Key Points:

• SER-287 is a spore-based microbiome therapeutic tested in mild to moderate UC.

• Phase 1b study evaluated:

  • Safety and tolerability of daily oral SER-287.

  • Efficacy when preceded by vancomycin (to deplete native microbiota).

• Results suggested:

  • SER-287 was well tolerated.

  • Potential for inflammation reduction and remission support.

  • Vancomycin pre-treatment may improve microbial engraftment.

Explanation of Visuals:

• Diagram summarizes trial design: vancomycin → SER-287 → gut microbiome modulation.

• Illustrates mode of action involving immune modulation and barrier support.

Glossary:

• Spore-based therapy: Uses bacterial spores to restore gut microbiota.

• Engraftment: Successful colonization of donor microbes in the recipient gut.

Key Takeaway:
SER-287 showed promise as a safe oral microbiome therapy for UC, particularly when combined with antibiotic pretreatment.

Slide 49: SER-287 failed to improve outcomes in a Phase 2 trial in UC

Key Points:

• Despite early promise, Phase 2 results were disappointing.

• Clinical remission rates were:

  • 10–11% with SER-287.

  • 11% in placebo group.

• No significant improvement compared to control → raises concerns over efficacy.

• Highlights difficulty in translating microbiome-based therapies into consistent clinical outcomes.

Explanation of Visuals:

• A text-based summary from a publication outlines trial failure and implications for future microbiome drug development.

Glossary:

• Placebo: Inactive treatment used to compare effects in clinical trials.

• Phase 2 trial: Mid-stage clinical study to evaluate treatment efficacy.

• SER 287 is an orally administered, donor-derived non-immunosuppressive therapeutic

Key Takeaway:
SER-287 did not outperform placebo in larger trials, highlighting the complexity of applying microbiome interventions in UC.

Slide 50: Summary of FMT studies for UC

Key Points:

• Overview of 20 cohort studies and 6 RCTs in UC:

  • Clinical remission in 39/140 FMT patients vs. 13/137 on placebo (risk ratio: 2.62).

• Key observations:

  • Pre-treatment with antibiotics and repeated FMT improve success.

  • Single donor FMT shows inconsistent results.

  • Some evidence supports oral capsule delivery.

• Research is still heterogeneous:

  • Studies vary in design, donor types, and endpoints.

• FMT remains experimental and should be used within clinical trials only.

• There are still "super donors" (even when pooling multiple donors), but these cannot

  yet be selected or identified.

Explanation of Visuals:

• Bullet point summary emphasizes trends, limitations, and future directions of current FMT research in UC.

Glossary:

• RCT (Randomized Controlled Trial): Study comparing interventions using random assignment.

• Meta-analysis: Combines data from multiple studies for statistical insight.

Key Takeaway:
FMT shows potential for UC but remains a research-based therapy due to inconsistent methodologies and outcomes across studies.

Slide 51: Microbiome in Cancer

Key Points:

• This is a transition slide, introducing a new section focused on the microbiome’s role in cancer.

• Suggests a shift from inflammatory bowel diseases to exploring how microbes influence tumor development, therapy response, or immune modulation.

Explanation of Visuals:

• No figures or data presented — this is a thematic slide divider to start the next topic.

Glossary:

• (None needed on this slide.)

Key Takeaway:
The presentation now shifts focus from IBD to examining how the microbiome intersects with cancer biology and treatment.

Slide 52: Bacteria as cancer therapy

Key Points:

• Investigating whether intestinal microbiota can be used to improve cancer immunotherapy outcomes.

• Specific microbes may:

  • Enhance the immune response.

  • Increase tumor recognition by the immune system.

  • Act as natural adjuvants to cancer treatments.

Explanation of Visuals:

• The left image shows intestinal microbiota as a therapeutic tool.

• The right image shows cancer tissue, indicating the target where immune response might be enhanced.

Glossary:

• Immunotherapy: Cancer treatment that activates the patient’s immune system.

• Adjuvant: A substance that enhances the body’s immune response to an antigen.

Key Takeaway:
Gut bacteria are being explored as supportive agents in cancer immunotherapy, aiming to boost patient response to treatment.

Slide 53: Microbiome impacts on carcinogenesis

Key Points:

• The microbiome influences cancer development in various organs, including:

  • Gut, skin, lung, oral cavity, and genitourinary tract.

• Microbial effects can be:

  • Pro-tumorigenic: Promoting inflammation, DNA damage, or immune suppression.

  • Anti-tumorigenic: Enhancing immune surveillance and barrier function.

• Effects are mediated via immune, metabolic, and inflammatory pathways.

• Micriobiota in the Tumor Microenvironment can have an influence on the polarization of Macrophages, to have an impact from M2 macrophages (pro-tumorgenic) to M2 macrophages (anti-tumorgenic).

• Checkpoint inhibitors work quite wll in Melanoma-patiens but not in Colorectal Cancer patients.

Explanation of Visuals:

• Left: A clock diagram illustrates microbial influence across body sites.

• Right: A circular gut-tumor interaction diagram shows pathways by which microbes can promote or inhibit cancer.

Glossary:

• Carcinogenesis: The process by which normal cells transform into cancer cells.

• Immune surveillance: The immune system’s ability to detect and destroy abnormal cells.

Key Takeaway:
Microbes can both promote and suppress cancer development through complex interactions with host immunity and metabolism.

Slide 54: Direct and indirect interaction between Microbiome and cancer cells

Key Points:

• Microbes influence cancer via:

  • Direct interactions: Bacteria invade or bind to tumor cells.

  • Indirect interactions: Bacteria activate immune responses or affect systemic inflammation via the metabolites in the blood

• The gut–tumor axis allows communication between distant microbiota and tumor sites (e.g., colon, liver, lung).

Explanation of Visuals:

• Anatomical diagram shows local and systemic effects:

  • Gut bacteria influence tumors in the gut and other organs via immune signaling and microbial metabolites.

Glossary:

• Gut–tumor axis: Concept that gut microbes affect distant tumors via systemic mechanisms.

• Systemic inflammation: Widespread immune activation that can support or inhibit tumor growth.

Key Takeaway:
The microbiome can affect cancer locally or from a distance, influencing tumor growth through immune and metabolic pathways.

Slide 55: Bacteria are located in cancer and immune cells within the cancer tissue

Key Points:

• Studies show bacteria present inside tumor tissues, including:

  • Tumor cells

  • Macrophages

  • Other immune cells

• These intratumoral bacteria:

  • May interact with the immune system.

  • Can influence treatment response.

  • Are identified via LPS (Marker of persistence of Bacteria → in the tumor visible), LTA, and FISH staining.

Explanation of Visuals:

• Microscopy images show:

  • LPS and LTA staining indicating bacterial components.

  • FISH (fluorescence in situ hybridization) to visualize bacteria.

  • Bacteria observed inside immune cells and tumor cells.

Additional Slide shown (not in this desk):

• Showing that not only in the Primary Tumor the LPS marker is visible in the staining picture but also in some metastasis of the same patient.

• Indicating that the bacteria has traveled also somehow through the system.→ question is this, how are they traveling? by the tumor cells? by the immune cells?

• In some patients also shown that you have a quite similar microbiome setting in the Primary Tumor tissue and the Metastatic Tumor tissue.

Glossary:

• LPS (Lipopolysaccharide): A bacterial cell wall component found in Gram-negative bacteria.

• LTA (Lipoteichoic acid): A Gram-positive bacterial cell wall marker.

• FISH (Fluorescence in situ hybridization): A technique to detect specific DNA/RNA sequences.

Key Takeaway:
Bacteria are found not only in the gut but also within tumors and immune cells, suggesting a direct microbial presence in the tumor microenvironment.

Slide 56: The location of bacteria within cancer tissue is organized

Key Points:

• Bacteria within tumors are not randomly distributed.

• They reside in organized micro-niches—specific regions within tumor tissue.

• These regions have:

  • Unique protein expression profiles.

  • Bacteria-positive vs. bacteria-negative zones (AOIs = Areas of Interest).

• Different microenvironments within a tumor may host different bacterial profiles.

Explanation of Visuals:

• Left: Microscopic images of colorectal cancer tissue show bacteria localized to defined areas.

• Right: Protein expression data highlight differences between bacteria-rich and bacteria-free tumor regions.

Glossary:

• AOI (Area of Interest): Specific tissue zone selected for molecular analysis.

• Micro-niches: Small, spatially distinct environments with unique biological properties.

Key Takeaway:
Intratumoral bacteria inhabit specific, structured microenvironments, possibly influencing local immune activity or treatment response.

Slide 57: Differential microbiome composition in tumor patients responding or not responding to checkpoint-inhibitor therapy

Key Points:

• Microbiome composition differs between:

  • Responders to checkpoint inhibitors (e.g., anti-PD-1 therapy).

  • Non-responders.

• Certain bacterial species are enriched in each group:

  • Responders show higher levels of Ruminococcaceae, Bifidobacterium.

  • Non-responders have more Bacteroides species.

• Gut microbes may influence immune activation and therapeutic efficacy.

Explanation of Visuals:

• Left: Bar chart shows key microbial taxa distinguishing responders vs. non-responders.

• Right: PCoA plot separates patient groups based on microbiota profiles.

Glossary:

• Checkpoint inhibitors: Drugs that help immune cells recognize and attack cancer.

• PCoA (Principal Coordinates Analysis): Visualizes differences in complex microbial datasets.

Key Takeaway:
The gut microbiome can influence cancer treatment outcomes, with distinct microbial signatures linked to therapy success or failure.

Slide 58: Bacteria as cancer therapy in humans?

Key Points:

• Fecal Microbiota Transplantation (FMT) may improve cancer immunotherapy.

• Clinical trials in melanoma patients show:

  • FMT induces immune reactivation in patients previously resistant to anti-PD-1 therapy.

  • Increased CD8+ T cell infiltration in tumors after FMT.

• Suggests therapeutic potential of microbiome modulation in oncology.

• Studies were done in rather small populations (10-15 patients)

Explanation of Visuals:

• Two study excerpts:

  • Left: FMT overcomes therapy resistance.

  • Right: FMT promotes immune responses and partial remission.

Glossary:

• Anti-PD-1 therapy: A form of immunotherapy targeting PD-1 to boost T cell activity.

• CD8+ T cells: Cytotoxic immune cells that kill cancer cells.

Key Takeaway:
FMT may enhance cancer immunotherapy by altering the gut microbiome to support anti-tumor immunity.

Slide 59: FMT-induced therapy response in initially therapy-resistant patients

Key Points:

• FMT leads to clinical response in some patients previously resistant to immunotherapy.

• Study example:

  • Patients receiving FMT show reduction in tumor burden.

  • PET scans reveal therapy responders post-FMT.

• Suggests the microbiome can shift immune dynamics even in advanced cancer stages.

Explanation of Visuals:

• Left: Line plots show tumor size changes in FMT-treated patients (responders vs. non-responders).

• Right: PET scans from one patient before and after treatment show reduction in tumor activity.

Glossary:

• PET scan (Positron Emission Tomography): Imaging to visualize metabolic activity in tissues.

• Therapy-resistant: Patients who do not initially respond to conventional treatment.

Key Takeaway:
FMT has shown the ability to induce therapeutic responses in otherwise immunotherapy-resistant cancer patients, underscoring its potential in precision oncology.

Slide 60: FMT alters the microbiome composition and induces CD8⁺ cytotoxic T-cells in the tumor tissue

Key Points:

• Fecal Microbiota Transplantation (FMT) leads to:

  • Changes in gut microbiome composition

  • Increased infiltration of CD8⁺ cytotoxic T cells into melanoma tumor tissues

• These effects were observed in patients who previously did not respond to immunotherapy.

  • So patients who had a good response where acting as donors to patients with no response so far acting as recipients.

Explanation of Visuals:

• Upper panels show microbiome shifts between responders and non-responders post-FMT.

• Lower panels present tissue staining, highlighting increased CD8⁺ T cells in tumors after FMT.

Glossary:

• CD8⁺ T cells: Immune cells that kill tumor cells.

• Melanoma: A type of skin cancer that can respond to immune-based treatments.

Key Takeaway:
FMT can enhance anti-tumor immunity by both reprogramming the gut microbiome and promoting immune cell infiltration into tumors.

Slide 61: Bacteria promote the efficacy of cancer immunotherapy

Key Points:

• The Comprehensive Cancer Center Zurich Lighthouse Project integrates FMT with cancer immunotherapy.

• Approach includes:

  • Patient stratification via microbiome biomarkers

  • Use of mechanistic analysis to predict therapy response

  • A precision FMT trial aiming to match patients with “super donors”

• Goal: Enhance overall response rate (ORR) to immunotherapy through targeted microbial modulation.

Clinical Study in USZ:

• Donors were defined as patients who had a response to the cancer treatment and had a perfect microbiomal profile acting as donor for recipients

• Multiple cancer patient types were used, besides also Melanoma and HCC (liver) patients

• It has shown in the clinical trial of USZ that the patients who had the best response to the donor FMT where the ones in which their microbiome profile was “the furthest” apart, when on a PCA the profile was similar to the donor, the recipient did not respond well

• Diversity of microbiome has again shown to be an important feature, the higher the diversity the better the response was.

Explanation of Visuals:

• Flowchart outlines the clinical pipeline:

  • Patients → biomarker-based screening → matched FMT donor → immunotherapy

• Emphasis on combining systems biology and machine learning with clinical intervention.

Glossary:

• Precision FMT: Tailoring donor selection to patient-specific microbiome profiles.

• ORR (Overall Response Rate): Proportion of patients who experience tumor reduction.

Key Takeaway:
FMT can be systematically integrated into cancer treatment pipelines to enhance immunotherapy efficacy using personalized, biomarker-guided approaches.

Slide 62: Cancer immunotherapies have limited efficacy in colorectal carcinoma

Key Points:

• Immunotherapy (e.g., checkpoint inhibitors) has limited success in colorectal cancer (CRC), especially in most microsatellite-stable tumors.

• This leads to the question:

  • Could bacteria alone (via FMT or other delivery) serve as a standalone therapy?

• The slide sets the stage for exploring microbiome-based monotherapy in CRC.

Explanation of Visuals:

• Left: Illustration of colon anatomy and CRC location.

• Right: Image of a CRC lesion during colonoscopy.

Glossary:

• CRC (Colorectal Carcinoma): Cancer of the colon or rectum.

• Monotherapy: Treatment using a single therapeutic agent.

Key Takeaway:
Since immunotherapy alone is often ineffective in CRC, microbiome-based therapies could offer a new therapeutic avenue—possibly even as monotherapy.

Slide 63: Clostridiales bacteria are underrepresented in the colon of CRC patients

Key Points:

• CRC patients show significantly lower levels of Clostridiales, a beneficial bacterial group.

• Clostridiales play roles in:

  • Immune regulation

  • Butyrate production (an anti-inflammatory metabolite)

• Loss of these bacteria may contribute to:

  • Tumor-promoting inflammation

  • Weakened gut barrier integrity

Explanation of Visuals:

• Left: Volcano plot showing microbial abundance differences between CRC patients and healthy controls.

• Right: Box plots confirm underrepresentation of Clostridiales in CRC across multiple datasets.

Glossary:

• Butyrate: A short-chain fatty acid with anti-inflammatory effects, produced by gut bacteria.

• Volcano plot: Graph showing statistical significance vs. fold change in data.

Key Takeaway:
A lack of Clostridiales in CRC patients suggests these microbes may protect against colorectal cancer, highlighting their therapeutic potential.

Slide 64: 4 Clostridiales bacteria mix (CC4) acts as a systemic immunotherapy in vivo

Key Points:

• A mixture of 4 Clostridiales strains (CC4) significantly reduces tumor volume in mouse models (MC-38 tumors).

• CC4 treatment:

  • Increased infiltration of CD8⁺ T cells in tumors.

  • Elevated immune checkpoint marker expression (e.g., CTLA4, PD1), suggesting immune activation.

• Indicates systemic immunomodulation from gut bacteria.

Explanation of Visuals:

• Top: Tumor volume images from mice; bar plot shows tumor size reduction.

• Middle: CD8⁺ T cell staining shows increased immune cell presence.

• Bottom: Immune gene expression profiles reveal elevated T cell activation markers in treated mice.

Glossary:

• MC-38: A murine colon cancer cell line.

• CTLA4 / PD1: Immune checkpoint proteins involved in T cell regulation.

Key Takeaway:
A defined Clostridiales mix (CC4) can serve as a potent systemic immunotherapy by stimulating CD8⁺ T cell–driven tumor control.

Slide 65: Single bacterial strains are more efficient than CC4 mix

Key Points:

• Testing individual strains from the CC4 mix revealed that some single strains:

  • Achieve stronger tumor reduction than the full mix.

• Suggests that specific strains drive the therapeutic effect more efficiently.

• Supports the idea of developing strain-specific therapies rather than general mixes.

Explanation of Visuals:

• Tumor images from mice injected with MC-38 cells and treated with different bacteria.

• Bar chart quantifies tumor volume, highlighting top-performing strains.

Glossary:

• Subcutaneous injection: Injection under the skin, common in tumor mouse models.

Key Takeaway:
Individual Clostridiales strains may outperform bacterial mixes in reducing tumors, paving the way for precise microbiome-based cancer therapies.

Slide 66: Serum transfer from CC4 mix–treated mice is efficient to induce therapeutic tumor shrinkage

Key Points:

• Transferring serum (blood fraction) from CC4-treated mice to untreated mice:

  • Led to reduced tumor growth.

• Implies that soluble factors (not the bacteria themselves) mediate immune effects.

• Observed increases in CD8⁺ T cells and granzyme B expression.

Explanation of Visuals:

• Diagram of serum transfer experiment.

• Tumor growth curves show slower progression in serum-recipient mice.

• Bar plots show immune marker increases.

Glossary:

• Serum: Fluid portion of blood containing proteins, antibodies, and signaling molecules.

• Granzyme B: A protein released by cytotoxic T cells to kill tumor cells.

Key Takeaway:
Therapeutic effects of Clostridiales may be mediated by serum-borne immune modulators, not just direct bacterial presence.

Slide 67: Specific bacteria as a novel cancer immunotherapy approach

Key Points:

• Conceptual summary of microbiome-based cancer treatment:

  • Identify beneficial bacterial strains (e.g., Clostridiales).

  • Use them to boost CD8⁺ T cell activity.

  • Result: Tumor cell reduction and enhanced therapy outcomes.

• Personalized microbiome therapy can be:

  • Delivered to the gut or systemically.

  • Tailored to individual patients (precision medicine).

• Project supported by Wyss Zurich and ReCOLONY initiative.

Explanation of Visuals:

• Left: Tumor and microbiome interaction in the gut.

• Right: Future application using capsules or personalized bacteria cocktails.

Glossary:

• Precision medicine: Tailored treatment based on individual characteristics, including microbiome.

• ReCOLONY: Initiative to develop microbial-based cancer therapeutics.

Key Takeaway:
Specific gut bacteria hold promise as next-generation immunotherapies, potentially revolutionizing cancer treatment by activating the patient’s immune system.