FREE Discovery Call
FREE Burnout Test

What Happens In The Gut, Does Not Stay In The Gut

Sep 26, 2022

“It turns out that we are only 10% human: for every human cell that is intrinsic in our body, there are 10 resident microbes” ~ Michael Pollen.

Ummm, how mind blowing is that?!?! We are more microbe than human!

When you consider this, it makes complete sense that the health of your microbiome (the bugs inside and on you) are crucial to the function of your body. In my blog post today, I’m going into the nitty-gritty of different types of bugs in your gut, and health benefits and issues they have been linked to. 

(Warning: this is a very research-based article. If you love the facts: great! You’ll love this article. But if you don’t, you might not want to read, and just trust me that the bugs in your gut are dictating SO MUCH about your health!!!).


So What is The Microbiome?

The microbiome is the centre of it all. The empire of your health. In recent times, there has been a plethora of research linking good health - and not so good health - to the state of your microbiome.

The microbiome compromises trillions of microbes - bacterial, fungal, viral and protozoa. If your microbiome is healthy, you will have a good amount of beneficial bacteria, like bifidobacterium species, lactobacillus species, akkermansia muciniphila and faecalibacterium prausnitzii (try to say those ten times!). These lovely lads help you to break down food to a useable form, support the gut lining and regular bowel movements, produce anti-inflammatory metabolic by-products, and make up a large chunk of your immune system.

When the microbiome - your good bugs - are depleted, it can lead to poor nutrient absorption, leaky gut, immune system issues, alternating bowel movements, and pathogen overgrowth. A depleted microbiome has even been linked to metabolic diseases like diabetes, cardiovascular disease, and autoimmunity.

The microbiota can decrease in diversity due to lack of plant-foods, Western diet, restrictive high- fibre diets (Keto, Paleo, Low FODMAP, etc.), antibiotics, C-section, bottle-fed, NSAID use, PPI use, urban upbringing, alcohol binge-drinking, Chemotherapy, Crohn’s disease & Coeliac disease.
Researchers are still discovering new strains of bacteria in the microbiome. There’s so much we don’t know. But there are some specific microbes that we do know a lot about, and today I want to do a spotlight on these and the health issues/benefits associated with these microbes we can discover in functional lab testing (FYI, medical doctors are not routinely looking at ANY of these microbes, which is crazy once you see all the diseases they are linked with). Much of this research comes from PhD scholar, Dr Jason Hawrelak. 


The Bad Bugs

Proteobacteria & Bacteroidetes
Proteobacteria & Bacteroidetes are gram-negative bacteria that produce lipopolysaccharide (LPS), aka endotoxins (Cani et al, 2008). In healthy adults with good intestinal integrity, a balanced GIT ecosystem and consuming fibre-rich diets, only minuscule amounts of LPS can be found in blood plasma.

Western-style diets low in fibre, prebiotic-rich foods, and resistant starches; whilst being rich in fats significantly increase LPS absorption (Laugerette et al., 2011) (Ghanim et al., 2009) (Pendyala, Walker, & Holt, 2012) (Caniand Delzenne 2009) (Cani et al., 2007)(Hildebrandt et al., 2009) (Martinez- Medina et al., 2013).

LPS release a number of pro-inflammatory cytokines, leading to low-grade systemic inflammation, and conditions such as:

  • Depression & Mood disorders (causes inflammation of the brain)
  • Alcoholic liver disease (Malaguarnera, Giordano, Nunnari, Bertino, & Malaguarnera, 2014)
  • Alzheimer’s disease (Lukiw, 2016)
  • Atherosclerosis (Wang et al., 2012) - LPS enhances arterial lipid deposition
  • Congestive cardiac failure (Charalambous, Stephens, Feavers, & Montgomery, 2007)
  • Chronic Fatigue Syndrome (Giloteaux et al., 2016)
  • Metabolic syndrome (Jialal & Rajamani, 2014)
  • Non-Alcoholic Fatty Liver Disease (Alisi, Ceccarelli, Panera, & Nobili, 2012)
  • Obesity (Cani et al., 2007)
  • Type 2 Diabetes (Pussinen, Havulinna
  • Lehto, Sundvall, & Salomaa, 2011)
  • Systemic inflammation

Escherichia coli
Member of the Proteobacteria phylum (LPS/endotoxin). Pathobiont potentially related to:

  • Colorectal cancer (Prorok-Hamon et al., 2014)
  • Crohn’s disease (Barnich, Denizot, & Darfeuille-Michaud, 2013)
  • NAFLD (Zhu et al., 2013)
  • Excessive weight gain during pregnancy (Santacruz et al., 2010)
  • Recurrent UTIs (Russo, Stapleton, Wenderoth, Hooton, & Stamm, 1995)
  • Small Intestinal Bacterial Overgrowth (SIBO) (Bouhnik et al., 1999)
  • PPI-induced Dysbiosis in Stomach and Small Intestine (Del Piano et al, 2012)
  • Alcoholic liver disease via LPS production (Malaguarnera, Giordano, Nunnari, Bertino, & Malaguarnera, 2014)
  • NSAID- and aspirin-induced intestinal damage via endotoxin production and beta-glucuronidase activity (Syer et al., 2015)
  • Metabolic syndrome via LPS production (Jialal & Rajamani, 2014) 
  • Type 2 diabetes via LPS production (Pussinen, Havulinna, Lehto, Sundvall, & Salomaa, 2011) 
  • Obesity via LPS production (Cani et al., 2007)

Bacteroides spp.
Member of the Bacteroidetes phylum (LPS/endotoxin). Dominant microbe in those consuming a high-fat, high-protein, low-fibre diet. Pathobiont potentially related to (Wexler, 2007):

  • Most commonly isolated anaerobic pathogen in human infections - bacteraemia; osteomyelitis; appendicitis
  • Can cause abscess formation
  • Highest antibiotic resistance rates of all anaerobic pathogens
  • High Bacteroides counts associated with: (Le Chatelier et al., 2013) 
    • Reduced microbiota diversity (low gene counts) 
    • Adiposity
    • Insulin resistance

    • An inflammatory phenotype
  • Protein putrefier (Vince & Burridge, 1980)(Macfarlane & Macfarlane, 1995) - contributes to production of amines, indoles, & ammonia
  • One of the main producers of β-glucuronidase (Skar, Skar, & Stromme, 1988)
  • Produces secondary bile acids (Fukiya et al., 2009)
  • Increased risk of colon cancer
  • May play a role in Alzheimer's (Lukiw, 2016) 

Desulfovibrio spp. & Bilophyla spp.
Hydrogen Sulphide (H2S) gas producers from the proteobacteria phylum. Pathobiant related to:

  • H2S may be toxic to colonocytes via inhibition of butyrate oxidation.


  • H2S production linked to increased risk of IBD, colorectal cancer, increased colon visceral hypersensitivity & increased intestinal permeability.
  • Common symptoms: swelling, weight gain, inflammation, gas, bloating, constipation, headaches, eye inflammation, skin issues, feeling toxic & exhausted, sometimes an ammonia like smell.

Methanobrevibacter spp.
These bugs produce methane in the gut which decreases gas “bulkiness”, leading to decreased intestinal gas-related symptoms. HOWEVER, too much methane can result in slowing of GIT transit, leading to constipation. High counts are often seen in some constipated patients and some IBS constipated patients (Kim et al., 2012) (Attaluri, Jackson, Valestin, & Rao, 2010).

The Good Bugs
Bifidobacterium spp.
Health benefits include (Romond, Haddou, Mielcareck, & Romond, 1997)(Ballongue, 1998)(Hsieh et al., 2015)(Marin, Miguelez, Villar, & Lombo, 2015):

  • Colonisation resistance
  • pH balance
  • Important role in polyphenol transformation
  • Protects against GIT damage
  • Promotes healing of the GIT
  • Immune stimulation/modulation
  • Vitamin production - B1, B2, B3, B6, folate, B12, biotin
  • Negatively correlated with insulin resistance
  • Some strains can produce GABA
  • Patients with major depression found to have significantly lower bifidobacteria counts compared to healthy controls

Lactobacillus spp.
Health benefits include:

  • Colonisation resistance (Reid, Bruce, McGroarty, Cheng, & Costerton, 1990)
  • Short chain fatty acids (SCFA’s) & lactate production (van Limpt, Crienen, Vriesema, & Knol, 2004)
  • Pathogen growth-inhibition
  • Some strains produce GABA (Cryan & Dinan, 2012)
  • Polyphenol transformations (Marin, Miguelez, Villar, & Lombo, 2015)
  • Important for activity of many medicinal herbs and absorption of dietary polyphenols

Akkermansia spp.
Health benefits include:

  • Associated with a healthier metabolic status and better outcomes from weight loss dietary interventions (Dao et al., 2015)(Miura & Ohnishi, 2014)
  • Akkermansia abundance inversely associated with body fat mass, waist-to-hip ratio, glucose intolerance
  • Akkermansia associated with a more diverse and healthy GIT microbiota
  • Low levels associated with increased gut permeability 


Faecalibacterium prausnitzii & other Butyrate Producers

Health benefits include (Canani et al., 2011)(Zhou et al., 2017)(Canani et al., 2011)(Vinolo, Rodrigues, Nachbar, & Curi, 2011)(Bourassa, Alim, Bultman, & Ratan, 2016)(Berni Canani, Di Costanzo, & Leone, 2012):

  • Maintains and promotes intestinal barrier integrity in the colon and small intestine
  • Decreases endotoxin absorption
  • Decreases abdominal pain and sensation of faecal urgency in patients with visceral hypersensitivity
  • Enhances colonic motility 

  • Enhances insulin sensitivity & reduces obesity & diabetes
  • Protects against neural cell death
  • Upregulates mitochondrial function
  • Attenuates endotoxin-induced neural inflammation
  • Upregulation of brain-derived neurotrophic factor (BDNF) & improves mood
  • Decreases systemic inflammation via suppression of the release of pro- inflammatory mediators in the liver, adipose tissue, and WBCs

Pretty amazing bugs we have living inside our system, hey?! Not only do they affect the state of our gut, but also our whole biology! Put another way: Your gut is not Las Vegas. What happens in the gut does not stay in the gut ;)

If you want to learn more about the microbiome and how we test and recorrect the gut in our functional medicine practice, sign up to (free) 10-Part Gut & Hormonal Mini-Course. 


Filipa Bellette is Co-Founder of Chris & Filly Functional Medicine. She is an accredited Clinical Nutritionist & Functional Medicine Practitioner. She is also a Ph.D. thought-leader, award-winning writer, and regularly published as a guest blogger & in the media. Together with her husband Chris Bellette, Filipa has worked with over 2,000+ busy, burnout clients in the last 10+ years, and specialises in producing healthy, balanced, and happy Mums & Dads...or as she calls it, a Power Parent! Filipa’s own passion for producing high-performance Power Parents came from her own personal experience of Mummy Burnout, after having babies and juggling the demands of business, family, and her failing health.

Stay connected with news and updates!

Join our mailing list to receive the latest news and updates from our team.
Don't worry, your information will not be shared.

We hate SPAM. We will never sell your information, for any reason.