Gut health and the microbiome: a foundational guide

A Foundational Guide for Gut Health, Digestion, Hormones and Immunity

Quick summary

Gut health plays a foundational role in digestion, immune function, hormone balance and overall health and wellbeing. This guide explains:

• What are the gut and the microbiome: functions and key factors influencing them
• How the gut microbiome influences whole-body health
• Why digestive issues often emerge or worsen after 40
• How to support gut health using evidence-informed natural approaches

What Is the Gut? (Simple Digestive Map)

The journey of food through your body

Mouth → Stomach → Small Intestine → Large Intestine

• Mouth: starts digestion
• Stomach: breaks food down
• Small intestine: absorbs nutrients
• Large intestine: processes fibre and hosts gut microbes

The large intestine is where your microbiome mainly lives.

Definition: Gut Microbiome

The gut microbiome refers to the trillions of microorganisms including bacteria, fungi and protozoa, that live primarily in the large intestine and play a critical role in human health.

The Gut as a Living Garden (Microbiome Explained)

Your gut is like a living garden ecosystem.

• Beneficial bacteria = healthy plants
• Fibre = fertiliser for microbes
• Plant diversity = garden diversity
• Processed food/stress = disruption to balance

A healthy gut is a balanced, diverse ecosystem.

What the Gut Actually Does (Beyond Digestion)

1. Immune system support

Most immune activity is linked to gut function.

2. Hormone regulation

Gut microbes help process and regulate hormones.

3. Gut–brain communication

The gut communicates constantly with the brain via nerves and chemical signals.

Why Gut Health Underpins Whole-Body Health

The gastrointestinal tract is more than a digestive system. It’s a complex, intelligent network that influences:

• Nutrient absorption
• Immune regulation
• Hormone metabolism
• Nervous system signalling
• Inflammation control

An imbalanced gut can contribute to symptoms far beyond digestion, including fatigue, mood changes, skin issues, hormone disruption and immune dysfunction.

What Disrupts Gut Health?

Common disruptors include:

• Low fibre diets
• High processed food intake
• Pesticides residues in non-organic foods
• Chronic stress
• Poor sleep
• Inactivity
• Disrupted circadian rhythms
• Certain medications

Medications That Affect the Gut Microbiome

Antibiotics

Reduce both harmful and beneficial bacteria.

NSAIDs (e.g. ibuprofen)

Can irritate gut lining and affect gut microbial balance.

PPIs (acid reflux medications)

Reduce stomach acid, changing microbial environment further down the digestive tract.

Metformin (diabetes medication)

Alters gut bacteria composition.

Environmental Factors and Gut Health

Glyphosate (Roundup)

Glyphosate-based herbicides are the most heavily applied herbicide in the world and usage continues to rise. Glyphosate is frequently found in the food chain because it is directly sprayed on edible crops.

Studies suggest glyphosate can:

• Negatively influence microbial balance
• Reduce beneficial bacteria and promote harmful bacteria impacting overall health
• Alter gut ecosystem diversity

Research is ongoing and effects depend on exposure levels.

Study examples

1. Low-dose glyphosate exposure alters gut microbiota composition and modulates gut homeostasis (PMID: 37196884) ^[1]
2. Glyphosate may affect human gut microbiota, Science Daily, 2020 ^[2]
3. Impact of glyphosate (Roundup^TM) on the composition and functionality of the gut microbiome, 2023 (PMID: 38099711) ^[3]
4. Research presentation: Mesnage, Robin, “Effects of dietary exposures to pesticide residues on the gut microbiome,” 2019 ^[4]

What Gut Microbes Eat

The microbiome bacteria thrive on:

• Fibre (including soluble, insoluble, resistant starch)
• Polyphenols present in brightly coloured fruit and vegetables
• Plant diversity in the diet

More plant variety = more microbial diversity = healthier microbiome.

Find out more about what types of fibre the microbiome likes to eat preferably in my post: Dietary fibre: the ultimate guide to eating more fibre everyday. ^[5]

Microbiome Balance vs Dysbiosis

A healthy gut microbiome is diverse, resilient and balanced. Dysbiosis (gut bugs imbalance) occurs when: ^[6]

• Beneficial bacteria are reduced
• Opportunistic organisms overgrow
• Microbial diversity declines

Common contributors include:

• Chronic stress
• Poor diet quality
• Antibiotics or medications
• Infections or travel
• Hormonal changes
• Pesticides and environmental disruptors

Symptoms may include bloating, irregular bowel habits, reflux, food sensitivities, fatigue and brain fog.

One of the simplest ways to improve gut diversity is increasing plant variety by eating 30 plant foods for gut health each week. Learn how to do it simple and effectively and understand why plant diversity matters for your gut in my article: How to improve gut health naturally: why 30 plant foods per week changes everything ^[7].

For clients with significant dysbiosis, I employ the GAPS diet which significantly restricts fibre (food for microbiome bacteria) to starve the unfriendly bacteria – this also starves the beneficial bacteria, and then rebuild the microbiome diversity and leaky gut through specific nutritional protocol. Find out more about this approach in my post: GAPS diet: what is it and how and when to apply it. ^[8]

Parasites, Bacteria and Opportunistic Organisms

Modern stool testing has increased detection of organisms such as:

• Blastocystis hominis
• Dientamoeba fragilis
• Opportunistic bacteria or yeasts such as Candida

Importantly, presence does not always equal disease. Some organisms may be harmless in certain contexts and problematic in others. Parasites and microbes must be interpreted clinically. Effective care depends on:

• Symptoms
• Immune resilience
• Overall gut environment
• Individual health history

Learn more about gut parasites and testing for their presence in my blog: Parasite treatment considerations: Blastocystis hominid and Dientamoeba fragilis ^[9].

The Gut–Brain–Hormone Connection

The gut communicates continuously with the brain and endocrine system via:

• The vagus nerve
• Neurotransmitter production (e.g. serotonin)
• Immune signalling molecules
• Hormone metabolism and recycling

Disruptions in gut health can influence:

• Stress resilience
• Mood and anxiety
• Sleep quality
• Estrogen balance

Circadian rhythm is e key influencer of hormones, gut function, immunity, sleep and metabolism. Find out how and why in my article: Melatonin, sunlight and circadian rhythm: a complete guide for hormones, sleep and midlife health ^[10]

Read more about gut parasites and testing in my blog: Parasite treatment considerations: Blastocystis hominid and Dientamoeba fragilis ^[9].

Gut Inflammation and Immune Activation

Approximately 70% of the immune system resides in the gut, mostly around small intestine (GALT = Gut-associated lymphoid tissue) ^[11]. Chronic gut inflammation can:

• Increase intestinal permeability (leaky gut) ^[12]
• Activate immune responses
• Drive systemic inflammation
• Affect hormone signalling

Triggers may include:

• Food intolerances ^[13]
• Chronic infections
• Stress
• Dysbiosis

Supporting gut integrity is therefore central to immune balance. ^[14] Learn about home methods of supporting gut wall repair and integrity in this post: Healing bone broth recipes. ^[15]

Gut Health After 40

Hormonal shifts during perimenopause and menopause can affect:

• Gut motility
• Microbiome composition
• Inflammatory responses
• Metabolic balance
• Nervous system function

At the same time, digestive symptoms may worsen due to:

• Slower metabolism
• Reduced digestive secretions
• Cumulative stress load
• Cumulative toxic load

Addressing gut health at this life stage can significantly improve energy, sleep, hormone balance (including decrease in menopause symptoms) and overall quality of life.

Read more about hormones and menopause HERE. ^[16]

Foundational Gut Support (Evidence-Informed)

Rather than aggressive interventions, gut health is best supported through foundations first approach:

Core Principles:

• Regular, balanced meals (not overeating)
• Wholefood nutrition, preferably organic produce
• Avoiding processed foods and additives/ preservatives/ pesticides residue in foods
• Gentle digestive support where needed
• Adequate hydration
• Stress and nervous system regulation
• Sleep improvement
• Circadian rhythms regulation – download my Circadian Health Guide for explanation and practical steps ^[17]

Targeted treatment protocols should always be individualised and based on clinical context supported by gut and microbiome testing, where appropriate.

5 Simple Ways to Support Gut Health Naturally

1. Eat a wide variety of plants (aim for 30 plants food per week)- feeds beneficial gut bacteria
2. Include fermented foods – supports microbial diversity
3. Move your body regularly – helps gut motility and digestion
4. Spend time outdoors – supports circadian rhythm and microbial diversity
5. Prioritise sleep – gut microbes follow daily biological rhythms

Bringing It All Together

Your gut is a living ecosystem that affects your entire body. When supported well, it can improve:

• Digestion
• Immune function
• Energy stability
• Mental clarity

Small daily habits matter more than perfection.

Key Takeaways

• Gut health is central to whole-body health
• The microbiome acts like a living garden
• Dysbiosis can affect whole-body health
• Diversity of plants consumed is critical
• Lifestyle strongly influences gut health and the microbiome
• Gut health influences digestion, immunity, hormones, weight and mood
• Gut health becomes increasingly important after 40
• Foundational support is essential before targeted treatment

FAQs

Next steps

If you’d like help with improving your gut health and re-balancing your microbiome, book an online naturopathic consultation ^[22]with me to discuss your circumstances and how I could help. Please note that at present I’m able to consult with Australia-based clients only.

To book an online or phone consultation, click the button below. I also offer a free 20-minute initial discussion to talk about your circumstances and how I could assist you.

I look forward to connecting with you and supporting you on your health journey.

Best of Health

Joanna Sochan
Wholistic Health and Lifestyle Therapist
Natural and Lifestyle Solutions for Abundant Health and Wellbeing

Related posts

• Gut health and hormones: how microbiome regulates estrogen levels ^[23]
• Rebuilding your natural melatonin cycle: practical strategies for hormonal harmony ^[24]
• Digestive first aid for bloating, indigestion, reflux, constipation and diarrhoea ^[25]
• Parasite treatment considerations ^[9]

Disclaimer: The above material is for informational and/or educational purposes only. It should not be used to self-diagnose and it is not a substitute for a medical advice, diagnosis, treatment, prescription or recommendation. All viewers of this content, especially those taking prescription or over-the-counter medications, should not make any changes in their health regimen or diet before first consulting a doctor or other qualified health provider with any questions they may have regarding a medical condition or their particular circumstances.

Joanna Sochan is a Wholistic Natural Therapist and founder of Naturimedica Wholistic Health & Wellcare. She has a passion for helping her clients transform their lives by becoming healthy and well naturally. Joanna has 15+ years experience in clinical practice and has special interest in solving complex cases, gut health, food sensitivities, hormone imbalances, detox and weight loss. She helps clients individually (mostly online) Australia-wide and also offers online therapeutic programs, eCourses and self-help books. View full bio ^[26].