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Dr. Shustina is an incredibly knowledgeable doctor who truly takes time to find root cause.
RG
Rochel Gordon
Condition · Gastrointestinal
Gut Microbiome & Dysbiosis
Persistent digestive issues, unexplained fatigue, and mysterious food sensitivities aren't just random health problems—they're often signs of dysbiosis, an imbalance in your gut microbiome affecting the trillions of microorganisms that play crucial roles in digestion, immunity, mood, and overall health. Research shows that a balanced gut microbiome is connected to almost every aspect of wellness, with studies revealing that microbial diversity and balance directly influence everything from metabolic health and immune function to brain health and disease prevention. Our comprehensive approach focuses on restoring optimal microbiome diversity and function through personalized protocols that address the root causes of microbial imbalance.
What Exactly Is the Gut Microbiome?
The gut microbiome is a complex ecosystem of approximately 100 trillion microorganisms—including bacteria, fungi, viruses, and other microbes—that inhabit your gastrointestinal tract and work symbiotically with your body to maintain health. This microbial community functions almost like an additional organ, performing essential functions including breaking down indigestible fibers, producing vital nutrients like short-chain fatty acids and vitamins, regulating immune function, and communicating with your brain through the gut-brain axis. A healthy microbiome is characterized by high diversity, balanced populations of beneficial bacteria, and resilience to environmental stressors. When this delicate ecosystem becomes imbalanced—a condition called dysbiosis—it can lead to widespread health issues affecting digestion, immunity, mood, metabolism, and numerous other body systems.
Types of Dysbiosis and Their Characteristics
Dysbiosis can manifest in several distinct patterns, each requiring specific assessment and targeted restoration strategies for optimal microbiome recovery.
| Type | Primary Characteristics | Common Manifestations | Considerations |
|---|---|---|---|
| Beneficial Bacteria Depletion | Loss of key beneficial species (Bifidobacterium, Lactobacillus, Faecalibacterium) | Poor digestion, compromised immunity, increased infections | Often responds well to targeted probiotic restoration |
| Pathogenic Bacterial Overgrowth | Proliferation of harmful bacteria (Clostridium difficile, pathogenic E. coli, Proteus) | Chronic inflammation, digestive upset, systemic symptoms | Requires antimicrobial treatment followed by beneficial bacteria restoration |
| Loss of Overall Diversity | Reduction in total microbial species and genetic diversity | Multiple food sensitivities, poor stress resilience, accelerated aging | Needs comprehensive diversity restoration through varied fiber sources |
| Small Intestinal Bacterial Overgrowth (SIBO) | Beneficial colon bacteria migrating to small intestine | Bloating, malabsorption, nutrient deficiencies, food intolerances | Requires specialized treatment and motility restoration |
Why Gut Microbiome Health Impacts More Than Digestion
The gut microbiome influences virtually every aspect of health through complex interactions with multiple body systems, earning recognition as a "hidden organ" essential for optimal wellness. Beyond digestion, your microbiome produces neurotransmitters that affect mood and cognitive function, trains and regulates your immune system (which is 70% located in the gut), influences hormone production and metabolism, and communicates directly with your brain through the vagus nerve and microbial metabolites. Beneficial bacteria produce short-chain fatty acids that fuel your intestinal cells, reduce inflammation, and support cardiovascular health, while also synthesizing essential vitamins like B12, K2, and folate. When dysbiosis occurs, these vital functions become compromised, leading to systemic inflammation, compromised immunity, mood disorders, metabolic dysfunction, and increased susceptibility to chronic diseases.
Common Signs of Gut Microbiome Dysbiosis Include
Digestive and Gastrointestinal Symptoms:
- Chronic bloating, gas, and abdominal discomfort
- Irregular bowel movements (diarrhea, constipation, or alternating patterns)
- Food intolerances and sensitivities that seem to multiply over time
- Acid reflux, heartburn, and digestive discomfort after meals
- Abdominal pain and cramping
Immune and Inflammatory Symptoms:
- Frequent infections (colds, flu, UTIs, yeast infections)
- Skin issues including eczema, acne, rashes, and poor wound healing
- Seasonal allergies and environmental sensitivities
- Autoimmune conditions or chronic inflammatory symptoms
- Slow recovery from illness or injury
Neurological and Cognitive Symptoms:
- Brain fog, difficulty concentrating, and memory issues
- Mood swings, anxiety, depression, and irritability
- Chronic fatigue and low energy levels
- Sleep disturbances and poor sleep quality
- Headaches and migraines
Metabolic and Systemic Symptoms:
- Unexplained weight gain or difficulty losing weight
- Sugar and carbohydrate cravings
- Blood sugar imbalances and energy crashes
- Nutrient deficiencies despite adequate dietary intake
- Hormonal imbalances affecting various body systems
Diagnostic Options at Whole Gut Health
Comprehensive microbiome assessment goes beyond basic stool testing to evaluate the complex ecosystem of your gut and identify specific imbalances affecting your health. At Whole Gut Health, we use advanced diagnostics to map your unique microbiome and develop personalized restoration protocols.
Testing options may include:
Comprehensive Gut Microbiome Analysis using advanced DNA sequencing to assess bacterial diversity, beneficial vs. pathogenic ratios, and functional capacity of your microbial community.
SIBO Breath Testing to identify bacterial overgrowth in the small intestine and determine specific gas patterns (hydrogen, methane, hydrogen sulfide).
Comprehensive Stool Analysis evaluating digestive function, inflammation markers, beneficial bacteria levels, and potential pathogenic organisms.
Applied Kinesiology or Muscle Testing to identify dietary or other triggers that may be contributing to microbiome imbalance and chronic inflammation. This is also used to help refine and personalize treatment.
Nutritional Assessment including vitamins, minerals, and metabolites produced by gut bacteria to assess functional status.
Inflammatory and Immune Markers to evaluate the systemic impact of microbiome imbalance on overall health.
Metabolomic Analysis when indicated to assess microbial metabolite production and functional pathways.
We customize testing protocols based on your symptoms, health history, and suspected dysbiosis patterns to ensure comprehensive evaluation and optimal restoration planning.
Our approach
Why Whole Gut Health is different.
At Whole Gut Health, we go beyond conventional symptom management and traditional functional medicine protocols. We trust your body's innate ability to heal itself when given the right support.
In Dr. Shustina's many years of practice, she has seen that many digestive diseases have their root cause in emotional traumas and unhealed wounds. When these underlying causes are healed, the body can heal from the inside out in a lasting way.
We focus on the mind-gut connection, incorporating energy healing techniques, personalized nutrition that evolves as you heal, and integrative approaches addressing mind, body, and spirit. If this resonates with you, contact our office to schedule your consultation and take the first step on your healing journey.
Our Gut Microbiome Restoration Approach
Our Three-Phase Microbiome Optimization Protocol Includes:
Phase 1 — Assessment and Dysbiosis Pattern Identification
- Comprehensive evaluation of microbiome composition, diversity, and functional capacity
- Detailed analysis of dietary, lifestyle, and environmental factors affecting microbial health
- Antibiotic and medication history affecting microbial populations
- Dietary patterns promoting beneficial vs. harmful bacteria
- Stress and sleep factors influencing microbiome resilience
- Environmental toxins and chemicals disrupting microbial balance
- Infections and pathogens requiring targeted treatment
- Environmental Optimization: Assessment and reduction of microbiome-disrupting chemicals, toxins, and lifestyle factors
Phase 2 — Targeted Microbiome Restoration
- Digestive dysfunction affecting microbial ecosystem health
- Pathogen Elimination: When indicated, targeted antimicrobial protocols to address harmful bacterial, fungal, or parasitic overgrowth while preserving beneficial species
- Beneficial Bacteria Restoration: Strategic probiotic protocols using specific strains to restore depleted beneficial populations and improve microbial diversity
- Prebiotic Optimization: Personalized fiber and prebiotic protocols to feed beneficial bacteria and promote healthy microbial metabolite production
- Dietary Microbiome Support: Anti-inflammatory nutrition plans emphasizing diverse plant foods to maximize microbial diversity and function
Phase 3 — Long-Term Microbiome Maintenance and Resilience
- Treatment of stress induced microbiome changes with energy medicine, and other mindful practice strategies.
- Sustained Diversity Protocols: Long-term strategies for maintaining optimal microbial diversity through varied nutrition and lifestyle practices
- Microbiome Resilience Building: Comprehensive approaches to enhance your microbiome's ability to recover from stressors and maintain stability
- Ongoing Monitoring: Regular assessment of microbiome health and function to prevent dysbiosis recurrence
- Lifestyle Integration: Sustainable practices for supporting lifelong microbiome health through diet, stress management, and environmental awareness
- Personalized Maintenance: Individualized protocols for maintaining your unique optimal microbiome composition
Expert-Led, Personalized Care
Dr. Alexandra Shustina is a board-certified gastroenterologist and internist specializing in complex digestive disorders, gut health, and the gut–brain connection. Drawing from both conventional gastroenterology and integrative medicine, she takes a comprehensive approach to uncovering the underlying factors contributing to illness and guides patients toward lasting wellness.
At Whole Gut Health, every patient receives highly personalized care rooted in a deep understanding of digestive health, nutrition, the gut microbiome, and the interconnected systems that influence overall well-being. By combining evidence-based medicine with a thoughtful, individualized approach, we help patients move beyond symptom management and create a clear path toward long-term healing and vitality.
Frequently Asked Questions
Common questions, answered.
What is the gut microbiome?
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The gut microbiome is a complex ecosystem of approximately 100 trillion microorganisms that inhabit your gastrointestinal tract and work symbiotically with your body. This includes bacteria, fungi, viruses, and other microbes that perform essential functions including digestion, immune regulation, neurotransmitter production, and communication with your brain through the gut-brain axis.
What are the different types of dysbiosis?
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Beneficial Bacteria Depletion
- Primary characteristics: Loss of key beneficial species
- Common manifestations: Poor digestion, compromised immunity, increased infections
- Often responds well to targeted probiotic restoration
Pathogenic Bacterial Overgrowth
- Primary characteristics: Proliferation of harmful bacteria
- Common manifestations: Chronic inflammation, digestive upset, systemic symptoms
- Requires antimicrobial treatment followed by beneficial bacteria restoration
Loss of Overall Diversity
- Primary characteristics: Reduction in total microbial species and genetic diversity
- Common manifestations: Multiple food sensitivities, poor stress resilience
- Needs comprehensive diversity restoration through varied fiber sources
Small Intestinal Bacterial Overgrowth (SIBO)
- Primary characteristics: Beneficial colon bacteria migrating to small intestine
- Common manifestations: Bloating, malabsorption, nutrient deficiencies
- Requires specialized treatment and motility restoration
What are the common signs of gut microbiome dysbiosis?
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- Digestive: Chronic bloating, irregular bowel movements, food intolerances, acid reflux, abdominal pain
- Immune/Inflammatory: Frequent infections, skin issues, allergies, autoimmune conditions, slow recovery
- Neurological: Brain fog, mood swings, chronic fatigue, sleep disturbances, headaches
Metabolic: Weight gain, sugar cravings, blood sugar imbalances, nutrient deficiencies, hormonal imbalances
How is gut microbiome health assessed?
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Comprehensive microbiome assessment includes multiple evaluation approaches:
- Comprehensive Gut Microbiome Analysis: Advanced DNA sequencing to assess bacterial diversity and function; beneficial vs. pathogenic bacteria ratios
- SIBO Breath Testing: Identifies bacterial overgrowth in small intestine
- Comprehensive Stool Analysis: Evaluates digestive function and inflammation markers
- Applied Kinesiology or Muscle Testing: Identifies dietary or triggers contributing to microbiome imbalance and helps refine treatment.
- Nutritional Assessment: Evaluates vitamins, minerals, and bacterial metabolites
- Inflammatory Markers: Assesses systemic impact of microbiome imbalance
Testing protocols are customized based on symptoms and suspected dysbiosis patterns.
What does gut microbiome restoration involve?
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Our comprehensive three-phase microbiome optimization protocol includes:
Phase 1: Assessment and Dysbiosis Pattern Identification
- Comprehensive evaluation of microbiome composition, diversity, and functional capacity
- Detailed analysis of dietary, lifestyle, and environmental factors affecting microbial health
- Identification of dysbiosis drivers including medication history, dietary patterns, stress factors, and environmental toxins
Phase 2: Targeted Microbiome Restoration
- Pathogen elimination with targeted antimicrobial protocols when indicated
- Treatment of stress induced microbiome changes with energy medicine, and other mindful practice strategies.
- Beneficial bacteria restoration using strategic probiotic protocols
- Prebiotic optimization with personalized fiber protocols
- Dietary microbiome support emphasizing diverse plant foods
- Environmental optimization to reduce microbiome-disrupting factors
Phase 3: Long-Term Microbiome Maintenance and Resilience
- Sustained diversity protocols for maintaining optimal microbial diversity
- Microbiome resilience building to enhance recovery from stressors
- Ongoing monitoring and lifestyle integration for lifelong microbiome health
Why is microbiome diversity so important?
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Microbiome diversity is connected to virtually every aspect of health. Higher diversity is associated with better immune function, improved mood, enhanced metabolism, better stress resilience, and reduced risk of chronic diseases. Diverse microbiomes are more stable and resilient to disruption, while low diversity is linked to increased inflammation, compromised immunity, and higher disease risk.
Can gut microbiome imbalances be effectively restored?
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Yes, with comprehensive functional medicine approaches addressing root causes. The microbiome is remarkably adaptable and can be restored through targeted interventions including pathogen elimination, beneficial bacteria restoration, prebiotic support, optimization of the nervous system, anti-inflammatory nutrition, and lifestyle optimization. The key is identifying specific dysbiosis patterns and implementing personalized restoration protocols.
What makes your approach to microbiome restoration different?
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At Whole Gut Health, we take a comprehensive, personalized, and proven approach to microbiome health:
- Advanced microbiome analysis using cutting-edge testing technologies
- Personalized restoration protocols based on individual dysbiosis patterns
- Integration of conventional gastroenterology with functional medicine approaches
- Focus on building long-term microbiome resilience rather than temporary fixes
- Comprehensive lifestyle and environmental optimization for sustained microbial health
Who provides gut microbiome care at your practice?
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Dr. Alexandra Shustina is a board-certified gastroenterologist and internist who serves as NYC's and Miami's premier gut health specialist. She has training in both conventional gastroenterology and functional gut health, with expertise in the gut microbiome and its role in health and wellness.
How do I get started with gut microbiome assessment and restoration?
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The first step is scheduling a comprehensive consultation where we'll:
- Review your symptoms, health history, and current microbiome-affecting factors in detail
- Determine the most appropriate microbiome testing strategy for your case
- Develop a personalized microbiome restoration plan based on your specific dysbiosis patterns and health goals
Contact our office to schedule your initial consultation and begin your journey toward optimal gut microbiome health and the comprehensive wellness benefits it provides.
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Dr. Shustina is a great doctor and healer! She is an expert and has great results. She has helped me and my family and I highly recommend her.
I know doctor Alexandra Shustina very well. She is a great physician. High integrity and good a good diagnostic.
Dr. Shustina is an incredible professional. She goes to the root level of the issue, not only superficial, so in reality there’s healing. And she is holistic meaning that her approach is from a whole, complete point of view and she provides it through her education, knowledge, wisdom and experience. Dr. Shustina was so patient with me, asking me question and guiding me how I could take charge of my health. Thank you Dr. Shustina
Dr. Shustina is truly exceptional! I met her at a health and wellness event and I was so blown away by her perspective on health. Dr. Shustina combines expertise in gastrointestinal health with a holistic approach, considering not just the physical symptoms but the whole person. Since meeting her I have invited her to talk at an event that I put together and I have also had my daughter be seen by her. She is now my go to person for everything Holistic and Gut related. Thank you Dr Shustina for everything!
Dr. Shustina is an incredibly knowledgeable doctor who truly takes the time to find the root cause of every patient’s illness. I am constantly awed by her excellent diagnostic ability and her efforts on behalf of her patients. She really goes above and beyond to treat and cure.
Dr Shustina is an outstanding and brilliant holistic physician with a wonderful understanding of the whole body. I highly recommend her!!
Dr. Shustina has helped me and my family improve our health. She is very knowledgeable in medical and in holistic and natural treatments and was able to find the source of the problem whc=ic created lasting results
Dr shustina is a wise and helpful doctor. She talks to you and consults with you about everything and spends a generous amount time asking questions about your health, grasping a full understanding of how your symptoms are making you feel, and what lifestyle you have. Our first appointment we spoke for a complete hour. I had struggled on and off with sibo for about 3 years before seeing her. I was extremely tired and had lots of symptoms of digestive issues. I saw 2 gastroenterologist before me they didn’t help much and they definitely did not consult with me for as thoroughly as she did. But upon seeing dr Shustina she was able to diagnosis me immediately and start a treatment plan that helped and got to the root cause of the issue. She has given me health and my life back and I can’t be grateful enough. Dr Shustina is the last gastroenterologist I need to see because I’m healthy and if problems happen in the future I trust her.
Dr. Shustina is the best doctor I have ever been to. She really takes the time and makes the effort to assess the root of the problem. She went above and beyond to help me a number of times with a variety of tools. She has the medical training and specialty along with a broad range of tools and experience to help patients in a natural and holistic way.
Dr. Shustina is very kind and very patient and has helped me change my lifestyle in a way that I thought I could not. By changing some things, she was able to help me heal my gut which was an area that I thought could not be healed. I highly recommend her!!
Doctor Shustina is the absolute best! It is hard to put into words how significant of an impact she has had on my well-being. She has helped me resolve numerous issues - from physical to mental- that other doctors dismissed, and she has spent countless hours answering my questions and teaching me lifestyle changes that have enabled me to thrive. She takes a whole person approach, focusing on root causes and not simply symptoms. She is not only a doctor but a friend, and she cares deeply about her patients. It gives me a lot of comfort knowing that whatever the issue is, I can come to Doctor Shustina for guidance and support. I could not recommend her enough! Thank you Dr. Shustina!
I recently had the privilege of consulting with Dr. Shustina. She is an outstanding doctor who truly understands the body's ability to heal itself and focuses on holistic remedies. I highly recommend Dr. Shustina for anyone seeking natural solutions and long-lasting relief. She patiently listened to me and answered all my questions. She provided me with holistic supplements and remedies that not only improved my symptoms but also enhanced my overall well-being. If you're looking for a knowledgeable and caring gastroenterologist who prioritizes natural remedies, Dr. Shustina is undoubtedly the ideal choice.
I have been under Dr. Shustina's care for the past 5 months which have been excellent. In these months, my digestive system has improved considerably. In my experience she is the first doctor which listens to her patients and works in treating the conditions and not only the symptoms. She is willing to explore alternative ways to achieve a better health. I highly enjoy the doctor-patient relation. I do highly recommend her.
Dr. Shustina is a fantastic doctor who truly cares for the patient. Her holistic approach attacks the root cause, leading to healing that lasts. Her expertise in gut health is evident, and the results reflect her vast knowledge and dedication towards each patient.
“I found Dr. Shustina after many months of searching for a board certified doctor who was able to incorporate holistic healing and nutrition into a treatment plan rather than simply diagnosing my symptoms and prescribing medication. Dr. Shustina has a wealth of knowledge and is helping me a heal years of gastrointestinal issues. p.s Her podcast, available on her site, is a GOLD MINE.”
Reviews
The body remembers when it's finally heard.
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Dr. Shustina goes to the root level of the issue, not only superficial, so there's healing.
LG
Leah Glickman
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She has significantly improved my health. I was suffering from Ulcerative Colitis and now live normally.
ML
Monica LaBadia
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Dr. Shustina has helped me change my lifestyle and heal my gut in a way I thought impossible.
DL
Dalit Lonstein
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She listens to patients and treats conditions, not symptoms.
GS
Gabriela Salazar
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Dr. Shustina is the best doctor I have ever been to. She assesses the root of the problem.
MS
M. S.
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She is an outstanding doctor who understands the body's ability to heal itself and holistic remedies.
SS
Sibel Sebi Sharabi
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Dr. Shustina has a wealth of knowledge and is helping me heal years of gastrointestinal issues.
DC
Daniela Chaparro
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Dr. Shustina is an amazing doctor. She diagnosed my cancer early and saved my life.
MW
Mordechai Weinstein
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After one session with Dr. Shustina, my digestive pain went away.
TP
Taryn Parascand
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Doctor Shustina is the absolute best. She has helped me resolve numerous issues other doctors dismissed.
RS
Rachel S.
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Dr. Shustina is a fantastic doctor who truly cares. Her holistic approach attacks the root cause.
CS
Clay Simonsen
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