Understand the gut microbiome for improved health outcomes

Microbiome management is for people who:

• need more energy
• suffer chronic pain conditions
• have disturbed sleep
• experience low immune responses
• experience digestive discomfort
• suffer autoimmune disorders
• are stressed or overwhelmed
• have mood disturbance
• practice restrictive diets or fasting

Explain the microbe world residing in the human gut, and how it effects nutrition, immunity, mental health, mood, and behaviour.

This is an experiential learning-based course. Throughout your studies you will have the opportunity to network with and learn from a variety of industry professionals. Establishing real-world relationships and confidence is key to career success. 

Lesson Structure

There are 8 lessons in this course:

1. Scope and Nature of the Human Gut Microbiome
   • Introduction - What is the microbiome?
   • The Gastrointestinal Tract
   • Stomach, Small Intestine, Large Intestine
   • How the Gut Microbiome is Established (Birth and Breastfeeding)
   • Maintaining the Gut Microbiome as Adults
   • Diet and Nutrition
   • Lifestyle and Other Factors
   • The Gut Microbiome Effect
   • Contribution to Metabolic Function
   • Protect Against Pathogens
   • Educating the Immune System
   • Gut Microbe Disruption and Dysbiosis
   • Dysbiosis
2. Genetics, Metagenomics and Metabolomics
   • Bioinformatics
   • Microbiome Heritability
   • Health Hereditary
   • Metabolomics
   • Technologies
   • Bacteria Metabolism
   • Short-Chain Fatty Acids
   • Organic Acids
   • Vitamins
   • DNA Sequencing Technologies
   • Next Generation Sequencing
   • Applications of PCR and DNA Sequencing
   • Metagenomics
   • Samples and Sampling Techniques and Considerations
   • The Human Microbiome Project
   • Bacterial Genomic Contribution to Human Survival
3. Diversity and Characteristics of Biota
   • Introduction
   • A fine balance - beneficial and detrimental biota
   • Prebiotics
   • Probiotics
   • Natural Probiotics
   • Probiotic Supplements
   • Symbiotics
   • Understanding Microbe Classification
   • Types of Bacteria
   • Major Bacterial Phylum Present in the Gut
   • Actinobacteria
   • Bacteroidetes
   • Firmicutes
   • Proteobacteria
   • Bad Biota
   • Nurturing a Healthy Gut
   • Diet and Antibiotics Typical Reponses
4. Maintaining the Gut Environment
   • Introduction
   • Anatomy Overview
   • Stomach
   • Small Intestine Environment
   • Large Intestine Environment
   • Managing the Large Intestine
   • Diarrhoea
   • Digestion
   • Microbiome & Hormones
   • Microbiome and Allergies
   • Microbe Imbalance
   • Gut Dysbiosis
   • Inflammation - Function and Process
   • Biosensors
   • Gut Health Treatment
   • Probiotics and Other Supplements
   • Nutrition-based Interventions
   • Lifestyle Practices including Stress
   • Faecal Microbiota Transplant
5. Diseases and Immunity
   • Introduction
   • Immunity
   • Types of Resistance
   • Phagocytes
   • Natural Killer Cells
   • The Inflammatory Response
   • Nausea and Vomiting
   • Digestive Disorders
   • Irritable Bowel Syndrome (IBS)
   • Crohn's Disease and Ulcerative Colitis
   • Diverticulitis
   • Polyps
   • Future Research
   • Fungi and Bacteriophages - Treatment in Disease
   • Beyond Traditional Probiotics
6. Managing Diet and Nutrition
   • Homeostasis and Microbiota
   • How Nutrition affects Homeostasis
   • Function Foods and Gut Health
   • Fermented Foods
   • Prebiotic Foods
   • Probiotics
   • Plant Foods
   • Polyphenols
   • Fibre
   • Dairy Produce
   • The Importance of Water
   • Water Absorption
   • Practical Ways to Improve the Gut
   • Supplements
   • Gut Transit Time
   • Coeliac Disease
   • Intermittent Fasting & Microbial Activity
7. The Gut-Brain-Axis
   • What Are Psychobiotics?
   • Probiotics
   • The Interaction Between the Mind and Body
   • The Gut-Brain Axis
   • Animal Research on Psychobiotics
   • Neurotransmitters
   • Tryptophan and Serotonin
   • GABA
   • Stress Hormones
   • Human Research on Psychobiotics
   • Findings on Depression and Anxiety
   • Psychobiotics and Other Mental Health Conditions
   • Issues with Psychobiotic Research
   • The Future of Psychobiotics
8. Applications of Gut Microbiome Management
   • Cultivate and Grow the Gut Microbiome
   • Pre-Schoolers and Young Children
   • Behaviour and Temperament
   • Sleep Disturbance
   • Cognition and Learning
   • Teenagers and Young Adults
   • Endocrine system support supporting hormonal changes
   • Immunity
   • Adults
   • Autoimmune (conditions)
   • Stress
   • Arthritis & Pain Management
   • Grief and Emotional Disturbances
   • Eating to Improve Microbiota
   • Other Strategies to Enhance Microbiota

Each lesson culminates in an assignment which is submitted to the school, marked by the school's tutors and returned to you with any relevant suggestions, comments, and if necessary, extra reading.

Aims

• Describe the nature of the human gut microbiome and its overall effect on the body.
• Describe how genetics influence the gut microbiome and how the use of metagenomics and metabolomics has enhanced our understanding of its functioning.
• Distinguish influencing factors on microbial colonies, which produce good or bad outcomes on human health.
• Explain how the gut can be managed to achieve good health, thus avoiding dysbiosis.
• Distinguish common diseases of the GI tract, the role of immunity in fighting gastrointestinal disease and advances in microbiome treatments of disease.
• Explain the effect diet and nutrition has on the gut microbiome.
• Explain the gut-brain axis and how it affects our mood, behaviour, and mental health.
• Analyse and combine theory with functional strategies to enhance microbiome diversity and abundance.

What You Will Do

• Investigate how gut microbes are established at the beginning of life.
• Produce a glossary of key terms to support foundational information.
• Research companies online that conduct metagenomics for consumers in your country.
• Go to a health food store, pharmacy, chemist, or other retailer selling biota as dietary supplements. Review the range of products on the shelves.
• Research tests which can be conducted to check for dysbiosis.
• Consider an immune centric or inflammatory diet. Draw up an appropriate diet plan.
• Create an educational resource resembling an information leaflet found in a healthcare setting.
• Connect with organisations that support sufferers of the nutrition disease/disorder – subscribe to newsletters, follow blogs and social media pages, sign up for quality resources such as Ebooks.
• Talk with people who have experienced any of the conditions outlined in the lesson and who have used probiotic supplements to ‘treat’ the condition or support their health.
• Design a specific set of guidelines for microbiome management for a specified scenario.
• Watch 2-3 videos on one of the following topics: dysregulation of intestinal mucosal immunity or regulation of behaviour through microbiome management.
• Write a lunch or dinner recipe for someone who has been purging the upper GI tract for 3 weeks and has returned to taking high potency multi-species probiotics but wants to add a selection of prebiotics.

Take hold of your microbiome health!

This course is:

• rooted in cutting-edge nutritional science
  
• for those who want to understand "why"
• an opportunity to delve into microbiology  
  
• written by experts in microbial science, nutrition and psychology 
  
• tutor-supported for help and guidance if needed 
  
• designed with tasks which encourage authentic learning 
  
• suited for a learner with no prior knowledge of the subject 
  
• a complementary subject to therapeutic nutrition, health food production, microbiology and mental health courses 

HOW THE GUT MICROBIOME IS ESTABLISHED

Under normal conditions, the formation of the adult microbiome occurs over the first three years of life. This is affected by life events such as birth method, weaning, starting solid food, and primarily cessation of breastfeeding. At birth, the most common bacteria are aerobic bacteria such as Enterococcus and Staphylococcus. Later in adulthood, anaerobes prevail, with a prevalence of Firmicutes and Bacteroidetes species the most common types.

Birthing

The gut microbiome begins developing in the womb, however much of the gut microbiome is environmentally acquired from birth. It is majorly affected by the type of birth delivery (vaginal or caesarean) and early feeding (breast or bottle). 

The vaginally delivered baby is initially colonised with the vaginal and distal gut bacteria of the mother, while babies delivered by Caesarean section (C-section) are colonised predominantly with the skin bacteria from the mother. Difference in the gut microbiome composition based on delivery type can be seen for several years. Caesarean delivery has been shown to influence the microbiota composition, and this change is associated with medical complications, such as coeliac disease, asthma, autism, and obesity.

The vaginal microbiome undergoes a dramatic shift in bacterial species in preparation for birth, principally characterised by a decrease in species diversity. Diversity is a measure of the richness and evenness characteristics of a community, often calculated as a specific "diversity index".  The dominance of Lactobacilli species has been observed throughout pregnancy (and up to 6 weeks post birth for some women). These species are protective. It is understood that lactic acid produced by Lactobacilli, increase the pH of the vagina and prevent pathogens colonising the environment. The microbiome of the vagina following birth experiences another shift, and in most cases the return to species richness. That is linked to lowering oestrogen levels after the delivery or removal of the placenta. 

Lactobacilli are important – these normally are the first to colonise in the infant’s guts as he/she passes through the birth canal. The passage through the birth canal gives the baby its first dose of microbes. A newborn is a sponge as it populates its own microbiome after leaving the sterile womb. The infant gut microbiome continues to develop until 2-3 years, after which it remains relatively stable throughout adulthood.

Breastfeeding

The initial microbial exchanges between mother and infant at birth and shortly thereafter by early feeding, are fundamental to a newborn’s microbiota, as these early colonisers play a very important role in the development of the newborn’s immune system and long term in the activity and function of the microbiome, particularly in the gut. The feeding method (breastfeeding vs. formula) along with weaning (timing of the introduction of solid foods) are important contributors in the development of an individual’s gut microbiome. 

MAINTAINING THE MICROBIOME AS ADULTS 

Is the gut microbiome unique to each person?

Everyone has a unique gut microbiome. But herein lies the problem. It’s difficult for scientists to determine a “normal” or “healthy” pattern of microbes because every body’s microbiome is different – even in identical twins! This makes working out what a healthy microbiome looks like challenging.

Diet and Nutrition for Improving the Microbiome

Feeding the gut microbiome is essential for its longevity. The types of food consumed has a significant impact on the population that survives. The typical Western diet is high in fat and low in fibre and has been linked to a decrease in overall bacteria and of the beneficial species. High fibre diets are more beneficial as this will provide good nutrients to the gut microbiome, increase the bacterial richness (the number of distinct species in the community) and boost production of short-chain fatty acids.  

People can eat their way to good gut health. To do that, people must expand their food horizon.

For adults, diet is the most powerful influence on the microbiome. By regulating the food items consumed and in what quantities, it is possible to manipulate the population densities of the different microflora. The consumption of fibres (or prebiotics) can proportionately increase the diversity of these probiotic bacterial species in the gut. Bacteria metabolise these fibres, and the fermentation results in the production of short chain fatty acids, which nourish the gut barrier, enhance immunity, and reduce inflammation. Vegetables, herbal tea, fruits, red wine, and dark chocolate can come in handy in regaining the lost bacterial diversity. The essential components in these food items are the polyphenols—which have unique properties—the most important being their antioxidant characteristic.

The Gut Project is a citizen science project based in the UK. The project is an open-source crowd funded project that relies on volunteers sending their faecal samples in the post for analysis. The key finding in the project is that microbial diversity is key. A diet rich in prebiotics seems essential.

Eating a wide-range of plant-based foods such as seeds, herbs, spices, nuts, legumes, fruits, and vegetables – all provide fuel for microbes. Conversely, sugar, antibiotics and processed foods decrease the number and diversity of human microbiota.

Lifestyle and Other Factors

There are a variety of other factors that can influence the gut microbiome including:

• Exposure to pathogens – colonisation by pathogenic bacteria can induce inflammation in the GI tract which can destabilise the gut microbiome or outcompete the commensal bacteria causing further illness. 
• Age – as people get older, their microbial diversity decreases and this reduction in diversity is correlated with nutritional status, increased inflammation, and frailty. Research now shows that long-living people (including those that live to 100 years) exhibit increased gut microbial diversity. If people want to live long lives, then it is critical to nourish gut microbes.
• Stress and Anxiety – stress and anxiety can affect gut motility, visceral perception, GI secretion and intestinal permeability. These can in turn negatively alter the composition of the gut microbiome.
• Medication – medications such as antibiotics and proton pump inhibitors (typically prescribed for acid reflux), can disrupt or diminish taxonomic diversity which can persist over time.

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