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  • Writer's pictureJoan Rothchild Hardin

Good vs Bad Bacteria in the Gut

Source: Aspen Clinic

Our gut microbiomes are home to several pounds of minuscule microorganisms whose jobs include helping digest our food, producing certain vitamins, regulating our immune system, and keeping us healthy by protecting us against disease-causing bacteria. A ‘microbiome’ is defined as the collection of microbes or microorganisms inhabiting an environment, creating a mini-ecosystem. (Baylor College of Medicine, 2017)

These tiny residents in our gut microbiomes include numerous colonies of bacteria, fungi, viruses, and  other microbes. Of the bacterial colonies living in our guts, some are probiotic (beneficial – good for us) and some are pathogenic (disease causing – bad for us). If your gut microbiome contains too few good bacteria and too many bad ones, you’re either already sick or on your way there.


In case you find the idea of pounds of gut-dwelling microbes disgusting, you should know that they (along with the microbes in the other microbiomes in and on our bodies) far outnumber our human cells.

“From the Human Genome Project we learned that the human genome has about 20,000 protein-coding genes—no more than a mouse has, and fewer than some common laboratory plants! How could such intelligent, exquisite, complicated beings as ourselves get by with so few genes? It turns out that we humans are not simply just humans. Each one of us is an ecosystem with an estimated one trillion other microscopic organisms living in and on us at any given time. And these organisms, collectively known as our microbiome, contain about 300 times the number of genes than our own genomes express.” (Perkins, 2017)

Those other nonhuman cells reside in the colonies of bacteria and other microorganisms living in and on us – representing about 10,000 different species.  Contrary to what we see in the mirror and how we understand our physical SELF, it turns out each of us is actually a complex ecosystem made up of some human and many many more non-human cells. An estimated 30 trillion cells in your body—less than a third—are human. The other 70-90% are bacterial and fungal.

Source: Gaby D’Allesandro/ American Museum of Natural History

“‘The human we see in the mirror is made up of more microbes than human,’ said Lita Proctor of the National Institutes of Health, who’s leading the Human Microbiome Project.

“The definition of a human microbiome is all the microbial microbes that live in and on our bodies but also all the genes — all the metabolic capabilities they bring to supporting human health,’ she said.

“These microbes aren’t just along for the ride. They’re there for a reason. We have a symbiotic relationship with them — we give them a place to live, and they help keep us alive.

“‘They belong in and on our bodies; they help support our health; they help digest our food and provide many kinds of protective mechanisms for human health,’ Protor said.” (Stein, 2012) 99% of the unique genes in your body are bacterial. Only about 1% is human.

Source: Gaby D’Allesandro / American Museum of Natural History

This human-microbial ecosystem arrangement works quite well unless the balance of good to bad microbes becomes chronically disturbed – especially in the gut microbiome, which bears the largest responsible for keeping us healthy.

Gut dysbacteriosis (also called gut dysbiosis) is an imbalance in the gut flora caused by too few beneficial (probiotic) bacteria and an overgrowth of bad (pathogenic) bacteria, yeast, and/or parasites.

SIBO (Small Intestinal Bacterial Overgrowth) refers to a condition is which a mixture of gut flora and partially digested food from the colon has worked its way back through the ileocecal valve into the small intestine and taken up residence there.

Source: Alternavita

The ileocecal valve is a sphincter muscle situated at the junction of the ileum (the final portion of the small intestine) and the colon (the first portion of the large intestine).

The small intestine is where 90% of digestion takes place. It’s main job is to absorb the nutrients and minerals from your food.

The function of the ileocecal valve is to allow the partially digested food materials to pass in only one direction: from the small intestine into the large intestine. When this valve is working poorly, it can allow some of that partially digested food, mixed with gut flora and toxins that belong only in the large intestine, to ‘back flow’ into the small intestine.

Source: Triad of Health

Unfortunately, the symptoms of gut dysbiosis and SIBO can be vague and often go unnoticed, undiagnosed, and dismissed by  conventional health care clinicians.

Source: The Eco Well


“Generally speaking, if you have frequent digestive symptoms and/or discomfort, you likely have an issue with the balance of good and bad bacteria in the gut.

“What is often overlooked, however, is that many other ongoing health problems can be related to unhealthy digestive microflora as well. Sometimes the issues are due to an overgrowth of pathogenic bacteria like candida, but they also may result from weaknesses in the gut membrane. Healthy gut bacteria produce byproducts that help keep the intestinal lining strong, and without enough good bacteria to manufacture these substances, the intestinal tract becomes highly susceptible to damage. Inflammation then leads to ulceration, which destroys areas of the mucosal lining of the intestinal wall. These “breaks” allow disease-causing bacteria, toxins, and undigested food particles to pass directly into the bloodstream, where they disrupt the the body’s normal function in many ways.”  (Williams, 2017)


Dr Williams lists these digestive symptoms as evidence of too much bad bacteria in the gut microbiome:

  • Constipation

  • Excess intestinal gas

  • Too little or no intestinal gas

  • Chronic diarrhea

  • Chronic bad breath

He lists these symptoms elsewhere in the body as evidence of a gut flora imbalance:

  • Hormonal problems

  • PMS

  • Menstrual complaints

  • Prostate trouble

  • Breast enlargement in men

  • Need for sexual hormone medication

  • Candida infection (candidiasis)

  • Chronic anemia

  • Chronic respiratory problems

  • Dairy product allergies and intolerances

  • Vitamin B deficiencies

  • High cholesterol levels

  • Neurological problems

  • Severe bruising problems

  • Chronic vaginal infections

  • Chronic bladder infections

  • Osteoporosis

  • Sarcopenia

– (Williams, 2017)

There are actually many other physical warning symptoms of gut microbe imbalance stemming from a chronic overrun of bad bacteria in the gut microbiome. Here’s another list from Functional Medicine doc Sara Gottfried MD:

  • Frequent gas or bloating on most days of the week

  • Cramping, urgency, and/or mucus in your poop once per week

  • Brain fog, anxiety, or depression

  • Food sensitivities

  • Missing micronutrients

  • Chronic bad breath

  • Loose stool, diarrhea, constipation, or a combination

  • Diagnosis of Irritable Bowel Syndrome (IBS)

  • History of “stomach bugs,” gastroenteritis, and/or food poisoning

  • History of prolonged antibiotics such as for acne or sinusitis

  • Carbohydrate intolerance, particularly after eating fiber and/or beans

  • Fatigue or low energy

  • Use of anti-acids for heartburn, reflux, or hiatal hernia

  • Autoimmunity, or an autoimmune condition such as Hashimoto’s thyroiditis, psoriasis, or multiple sclerosis *

  • Sinus congestion

Dysbiosis in the gut microbiome sets up a sequence of events leading to chronic inflammation in the body, followed by a multitude of vague symptoms … and ultimately to problems such as:

  • Suppression of the control system for making hormones, called the Hypothalamic-Pituitary-Adrenal-Thyroid-Gonadal Axis

  • Breast cancer

  • Colorectal cancer

  • Irritable bowel syndrome

  • Inflammatory bowel disease

  • Autoimmunity *

  • Metabolic diseases such as obesity, diabetes, and gestational diabetes

  • Autism

  • Other neurological conditions such as Parkinson’s disease

  • How effectively you detoxify endocrine disruptors or xenobiotics

  • Plus many other conditions and diseases with linkage still emerging, such as chronic venous insufficiency

 – (Gottfried, 2017)  * See AUTOIMMUNE DISORDERS for a  more complete list of autoimmune diseases and conditions.

Source: Huffington Post


4 Steps to Heal Leaky Gut and Autoimmune Disease by Dr Josh Axe gives information on how to improve a dysbiotic, leaky gut and  heal autoimmune disorders.

To read more about what’s already known about some of the other microbiomes that make up the body’s ecosystem – the mouth, lungs, genitals, womb, and skin microbiomes, see THE BODY’S ECOSYSTEM: Research on the human microbiome is booming, and scientists have moved from simply taking stock of gut flora to understanding the influence of microbes throughout the body.

See MALFUNCTIONING PYLORIC & ILEOCECAL VALVES – AND HOW TO FIX THEM for information on how to improve the functioning of your ileocecal valve.

INCREASED GUT PERMEABILITY – CAUSES & CONSEQUENCES explains how the mucosal lining of the gut can become damaged and lead to chronic inflammation in the body, in turn creating chronic autoimmune conditions and diseases.

To read more about autoimmune diseases, their symptoms, and causes, see AUTOIMMUNE DISEASE SYMPTOMS YOU NEED TO KNOW ABOUT by Dr Josh Axe.

Source: Healing From Scratch

“Humanity is just a speck in the massively bacterial world. We need to get used to that idea.”

“Given that fact, it shouldn’t surprise us that microbes occupy most of us as well. Seventy to ninety percent of all cells in the human body are bacterial, representing perhaps 10,000 different species. Genetically we get even less real estate: 99 percent of the unique genes in our bodies are bacterial. This population of over 100 trillion microorganisms makes up our microbiome: a collection of microbial communities that has evolved along with homo sapiens to help orchestrate basic life processes, beginning the moment we’re born.”

DR. MARTIN BLASER Author of Missing Microbes Professor of Translational Medicine, Director of the New York University Human Microbiome Program, former Chair of the Department of Medicine, and Professor of Microbiology at NYU School of Medicine. His work focuses on the human microbiome.


Axe, J. (2017). Autoimmune Disease Symptoms You Need to Know About.See:

Axe, J. (2017). 4 Steps to Heal a Leaky gut and Autoimmune Disease. See

Baylor College of Medicine. (2017). The Human Microbiome Project. See:

Gottlfried, S. (2017). Dysbiosis Decoded: Symptoms, Why You Get It, and Link to Autoimmunity, Breast Cancer, Irritable Bowel Syndrome, Plus Other Common Conditions. See:



Perkins, S. (2017). Meet Your Microbiome. American Museum of Natural History. See:

Stein, R. (2012).  THE HUMAN MICROBIOME: GUTS AND GLORY – Finally, A Map Of All The Microbes On Your Body. NPR. All things Considered. See: The Scientist Staff. (2014). The Body’s Ecosystem: Research on the human microbiome is booming, and scientists have moved from simply taking stock of gut flora to understanding the influence of microbes throughout the body. See:

Williams, D. (2017). Signs You Have too Much Bad Bacteria in Your Gut. See:

© Copyright 2017. Joan Rothchild Hardin. All Rights Reserved.

DISCLAIMER:  Nothing on this site or blog is intended to provide medical advice, diagnosis or treatment.


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