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Lactobacillus: Colonist, Probiotic, or Both?

A misunderstood microbe.

by Malay Nanavaty

Setting the Scene for the Lactobacillus Conversation

Lactobacillus is an oxygen-tolerant genera within the phylum of Firmicutes. To most people, the word Lactobacillus is synonymous with a few others (probiotics, yogurt, and gut health come to mind). With all of the hype around this particular class of bacteria, you may be wondering where in the microbiome they reside. In this post, I will do my best to answer this question...but the answer may surprise you.

Microbiome Basics

Lets go over the basics of the microbiome before getting into the details. In humans, the microbiome is concentrated in the distal gut (the end of the large intestine). This is mostly because the pH of the small intestine is too low for most bacteria to thrive in. Additionally, the flow of food through the small intestines is very fast, making colonization difficult. As a result, the primary energy sources used by the microbiome are:
- Undigested foods/fibers that make it into the distal gut
- Mucus secretions and dead cells from the intestinal epithelium

Most of the microbes that live inside your gut rely on these core energy sources. Over time, a community of different bacteria developed. Some bacteria convert the raw ingredients in your gut into energy and generate waste. Other bacteria use these waste products as sources for energy themselves. In this way, microbes adapted to each other’s presence, developing niches in the gut community to occupy. This explains why it is so hard to drastically change the composition of an adult’s microbiome. Trying to colonize your gut with new bacteria is like dropping a grizzly bear in the savannah and expecting it to outcompete the lion; the new colonists lack the ability to thrive in the new niche. Enter Lactobacillus:

Permanent Resident or Just Passing Through?

There is a fundamental issue in using fecal samples as the source for all of your microbiome knowledge. The issue is that of bacterial origin. Where in the gut does the bacteria you detect live? Is it a rare colonist of the small intestine? Maybe it lives in the mouth? Or, maybe, it doesn’t even live inside you! The food you eat has plenty of bacteria growing all over it. Perhaps what you detect in your fecal sample is just a bacterial species present on your food that got flushed through your system. In fact, this may be exactly what is happening with Lactobacillus.

History of Lactobacillus Research

At this point, a lot of you may be doubtful of the claim that Lactobacillus is not a part of the microbiome. To understand why we place so much value on this particular group of bacteria, we need to look into the past.

In the early 1900s, the scientist Elie Metchnikoff noted that fermented foods do not spoil as quickly as their nonfermented counterparts. He reasonably concluded that the same principle must apply to the human gut. He thought that bacteria that produce lactic acid must be warding off more harmful bacteria in the body. Thus, he expected that fecal sample cultures would reveal a large number of Lactobacillus growth. He did the experiment and found exactly what he expected. This experiment set the foundation that Lactobacillus is an important member of the microbiome.

Analysis of Elie’s Work

While Elie did all of his experimentation properly, the limitations of the technology available to him was a major source of error. When this experiment was performed, there was little to know understanding of anaerobic bacteria. As a result, when Elie grew fecal sample cultures, he grew them in the high oxygen atmosphere of the outside world. In this environment, it was impossible for the commonplace gut bacteria to survive (remember, most Bacteroidetes and Firmicutes strains depend on other phyla to reduce oxygen levels in the early stages of gut colonization). As a result, Elie only saw bacteria that could tolerate oxygen on his culture plates.

Modern Analyses of Lactobacillus Abundance

Modern technology paints a very different picture of the abundance of Lactobacillus in the human gut. When accounting for anaerobic bacteria in the gut, it is revealed that Lactobacilli make up only 0.01% of the total bacterial count in the gut. And there's more. As we mentioned earlier in this post, established microbiome populations are extremely stable over time due to the checks and balances different strains place on each other. We do not see this for the Lactobacilli populations. Within one person, the levels of Lactobacillus swing wildly across time. This suggests that these bacteria do not have an established spot in our microbiomes.

This data points towards the fact that oral consumption is the major source of lactobacilli in our guts. In fact, the only place in our bodies where Lactobacillus is seen in large numbers is in our oral cavity. Thus, it is possible that any small amount of Lactobacillus population seen in fecal samples may be originating from swallowed saliva.

Lactobacillus in Other Mammal Guts

Unlike humans, there is substantial evidence that Lactobacillus colonizes the guts of mice, pigs, and rats. How is this possible? The answer is quite simple; while human guts are entirely lined with mucus secreting glands, the guts of these other mammals have patches of intestine that are free of mucus. It is at these locations that Lactobacillus grows and forms biofilms to anchor itself. Without these patches, these bacteria can easily get washed out of the gut by mucus. In fact, this membrane anchoring is exactly how Lactobacilli survive in our oral cavities. Common bacteria like Bacteroidetes and Actinobacteria survive in the mucus by reproducing faster than the mucus pushes them out. Lactobacilli have not evolved to survive in such an environment.

Role of Lactobacillus as a Probiotic

While the case against Lactobacillus residence is strong, their role as a probiotic is still undisputed. Since these bacteria are mostly foreign to the microbiome, their ingestion stimulates the activity of the gut immune system, which may be useful when trying to recover from a gut disease (or just for general health). In the case of IBS and IBD, the problem is often an overstimulated gut immune system. In that instance, it may be useful to seek probiotics with bacteria that have co-evolved with humans. That way, their presence in the gut will not trigger a hyper-immune response.


The story of Lactobacillus is quite an interesting one. It is a class of bacteria that has been the attention of many people. This attention is not misplaced; these bacteria impart objective benefits to people who consume them. However, it is important to remember that their origins are not as straightforward as most other bacteria in your gut. Detection of Lactobacilli in your microbiome samples means that you either harbor a very rare strain of this bacteria, or those bacteria have made a very long journey to end up on your report.

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