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Bad times for good bacteria: how modern life has damaged our internal ecosystems

Bad times for good bacteria: how modern life has damaged our internal ecosystems

"Every adult is made up of 100 million, million human cells (that’s a one followed by 14 zeroes). But the human body is also home to ten times this number of bacterial cells, which, collectively, are called the microbiota.


Exactly the same processes we see in external ecosystems – loss of diversity, extinction, and introduction of invasive species – are happening to our own microbiota. And damaged ecosystems don’t function as well as they should.



Modern medicine has been very successful at controlling bacterial diseases with antibiotics. Unfortunately, antibiotics cause considerable collateral damage to innocent and beneficial bacteria. After antibiotic therapy, the microbiota may never return to their original abundance, and genetic diversity is reduced in those bacteria that remain.

Collectively, these changes mean that our microbial ecosystems have become degraded, much like natural ecosystems globally. The microbiota are less functional and resilient than they should be. And it turns out they have essential roles in developing our immune systems, and in regulating metabolism. So it shouldn’t be surprising that altered microbiota are now being associated with many diseases of the modern world.

These diseases include obesity, allergic reactions, chronic inflammatory conditions and autoimmune disorders. More recently, it’s also been suggested that psychological conditions, such as depression and anxiety, are linked to the bacteria that live inside us."

Chris/Cllcanada, will be pleased to know the article continues on to discuss how a “poo transplant”) can help restore a healthy ecosystem after Clostridium difficile (C diff) infection :) .

Complete article by Michael Gillings, Professor of Molecular Evolution, Macquarie University, Australia:

So why is this relevant to us? With our compromised immune systems, we are much more likely to need antibiotics to help us fight off bacterial infections and these infections are likely to last longer than is the case in otherwise healthy people - even with antibiotic assistance. So we are therefore more at risk of health challenges caused by having a damaged internal ecosystem. Also, because we have compromised immune systems, probiotics may not be appropriate for us. Here are some previous community discussions on probiotics:


Photo: Mosses don't flower, they produce spores:

5 Replies

Great post :) was just talking about that with my gf and my need to buld up good bacteria

What i recomend she was not inpressed :o

But for years they have removed apendix and its been descoverd that is bad idea as that is where reserve of good bacteria is kept just in case of what as been talked about in this post

Great post always intresting



The other big player is h.pylori... it has links to ITP in CLL.. get it checked... also

involved in MALT...bad gut troubles...



I've been following the biome research at a distance for almost 5 years now. I participated in the American Gut Project:

Some of you can participate in the British Gut Project if you are so inclined:

From what I've read, there are a few critiques of current, seemingly enlightened advice to try to increase diversity of our gut biomes by ingesting a variety of alternative foods.

The are so many species of bacteria, fungi, and archaea that inhabit out gut, it is still impossible to catalog them. Scientists sample the RNA16S, often from fecal swabs, with hopes of extrapolating the bacteria elsewhere in the digestive system. This provides the families of microbes, but not usually the species. A few have sampled the whole path, and found widely varying families from mouth on down, but most of the bulky data is from the far end. So it's not quite representative. The family level studies are all they can do, hence the concentration on diversity more than on actual species.

The modern hunter gatherers suffer from short lives due to disease and accidents. Their digestive diseases are a particular problem, especially in childhood. Of course, they have a diverse biome. But the evidence that that is better is scant. Despite our lack of diversity, we do live a long time.

Experiments on changing the biome permanently by ingesting various probiotics have not been very successful. When subjects revert to the previous diet, the biome reverts. You are what you eat. In addition, no magic bullet has been found. A few careful studies of 1 or 2 species have shown promise for IBS, IBD, and Crohn's disease in a percentage. It's nowhere near as dramatic as a fecal transplant, which can indeed interrupt a seriously disturbed biome.

The biome also has far more viruses than bacteria, and these are key to the balance between bacteria, fungi, etc. To my knowldge, there's no attempt to massive catalog them. It's even more difficult, because they are so small, and there are micro environments - cracks and crevices - that hold biofilms - a matrix of various bacteria, viruses, and segments of DNA and remains of dead cells in the mucous membranes.

All that said, I do eat yogurt daily. I have IBS-C. I've had a 2 bouts with diverticulitis and gastritis. I have a gene that makes me a little more susceptible to noro virus (the cruise ship virus). I've had disturbed digestion since childhood - long before I received antibiotics. But I've also had antibiotics and antivirals.

So I think the picture of how our inner jungle works is far from complete, and it's too soon to make drastic changes. I recommend making small changes, and observing carefully via a detailed food diary. Also, what you find in the store is not at all representative of the research - it's representative of what can be manufactured and marketed easily.


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One of the leaders in fecal research and fecal banking is the nonprofit OpenBiome, located in Boston...


"Bad Times For Good Bacteria" by Australian professor Michael Gillings is a fascinating expose on microbiota and modern day molecular evolution. A really good read. If you thought about the impact of triclosan on your immune system or a "poo transplant" or even the impact of cooking our food you should read this. Thanks Neil



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