Microbiome: Bolster Your Bifidos

Microbiome: Bolster Your Bifidos


Last week I talked about the ability of microbes to produce B vitamins. Bifidobacteria are the star of that show (among many others). So I wanted to write a post about ways we can help our own bifidos along.

[There many other microbes that we know affect our health, and probably a lot that are still ?undiscovered?. I?d like to address these other microbes as well, but will do so in a future post. Of note, there are entire populations of people that don?t have bifidobacteria as part of their microbiomes. So these particular microbes are clearly not mandatory for health and wellness. We do know, however, that Bifidobacteria have numerous beneficial health effects and are ubiquitous throughout the world, so it is certainly worth looking at ways to help them out.]


Prebiotics are carbohydrates that feed our beneficial gut bacteria. We can?t digest prebiotics on our own, so they make it all the way down to our colon, where our gut bacteria digest them and create compounds that are beneficial to our health. They preferentially increase populations of ?good?* bacteria, including lactobacillus and bifidobacteria. This means that they don?t feed pathogenic bacteria and therefore help keep a healthy microbe balance in our guts. Without them, our beneficial gut bacteria may not get enough food and can reduce in numbers.

honeyIsomalto-oligosaccharides are a type of prebiotic that appear to be very effective for biotin production by B. bifidum. They are found naturally in honey, starches such as tapioca and potatoes, and in several fermented foods such as miso and kimchi. Evidence suggests that eating these types of foods can promote growth of beneficial Bifidobacterium sp. and potentially improve overall gut health.

B. infantis subspecies is one of the first species to colonize the guts of infants. As discussed last week, it also appears to be one of the better producers of B-vitamins. Galacto-oligosaccharides (GOS) are a type of prebiotic present in human milk and are reported to stimulate growth of many different bifidobacteria, particularly B. infantis, and result in an improved intestinal environment. This is another reason for the importance of breast-feeding babies as a way to bolster the gut microbiome from the very beginning. Due to the beneficial effects of GOS on infant gut health, the prebiotic is now often added to infant formula.

artichokeFructo-oligosaccharides (FOS) have also been shown to increase Bifidobacteria concentration in the gut. These compounds occur naturally in many plants. Onions and garlic may be the most well-known sources, but FOS can also be found in asparagus, chicory, artichoke, banana, and many other plants. It is well-established that consuming FOS-rich foods helps to increase populations of Bifidobacteria. Add this to your list of reasons to eat your alliums.

A couple of weeks ago, I wrote a post about the potential beneficial impacts of of polyphenol-rich foods on the gut microbiome. There is evidence that consumption of foods that are high in polyphenols can increase concentrations of Bifidobacteria, including those I mentioned last week as being good B-vitamin producers. For individuals who can?t tolerate oligosaccharides, consuming high polyphenol foods might be a good option.

Antibiotics – Steer Clear When Possible

I don?t think that antibiotics are evil. They have saved many lives and will continue to do so. However, they are sorely overused, and one of the repercussions of this overuse is major disruption of our gut flora. The change in gut flora following short-term antibiotic treatment is long term and may sometimes be permanent. This means that our microbiome may never return to the level and type of diversity it had before antibiotic treatment.

So whenever possible, avoid antibiotics. In part, this means doing everything possible to stay healthy in the first place. Following a nutrient-dense, low-inflammation diet is critical here. It also means making sure that, if you do get sick, you don?t take antibiotics unless the infection is bacterial. Too often, antibiotics are prescribed for viral infections, for which antibiotics are not at all effective. Even most ear infections, often thought to be bacterial, are in fact viral. Antibiotics were long thought to be completely harmless, but we now know that isn?t the case. On top of gut disruption, antibiotic use can increase the recurrence of ear and other infections. This is probably because antibiotics disrupt the immune system through effects on the microbiome.

Bifidobacteria in particular are highly susceptible to most antibiotics, which may be part of the reason some people get sick following a course of antibiotic treatment. It?s valuable not only to take probiotics following a course of antibiotics, but also to eat prebiotics, minimize consumption of processed and inflammatory foods, and keep stress down.

Stress Management

There?s a lot to talk about here, but I?ll keep it brief for now. High levels of stress lead to decreased populations of yogaBifidobacteria in the gut, which can then contribute to a variety of other health issues. Both psychological and physical stress
can have an effect. It is therefore important the work on stress management through activities such as yoga, meditation, walking, or whatever helps you to destress. Sleep is also extremely valuable.

In addition, it is important to keep physical stress in check. This means avoiding foods that stress your body and promote inflammation. Ancestral diets are an excellent start (starting to see a trend?). Exercise is very beneficial, as long as it is done in moderation. Over-exercising can be a major stressor and can ultimately have detrimental health effects.


It may be the case that we can also supplement with Bifidobacteria-rich foods and supplements. Bifidobacteria don?t do well in oxygen-rich environments, so they are found in only a limited number of fermented foods (usually only when they are specifically added). Some suggest taking a high-quality probiotic supplement, though the research isn?t very clear here. There are so many bacteria in our guts, that the relatively small amount in a probiotic supplement may not do much to increase populations of certain strains.

There is evidence, however, that supplementation with Lactobacillus helveticus and Bifidobacterium longum has beneficial psychological and physiological effects, indicating that probiotic supplements do impact the gut microbiome. At the very least, it might be a good safety net. In combination with the prebiotics mentioned above, this could be a good way to help your improve your microbiome.


Eat your fruits and veggies, avoid processed and inflammatory foods, minimize stress, and avoid antibiotics when possible. I would also strongly recommend a paleo-type ancestral diet to anyone. We don?t know exactly what?s going on in our guts. But there?s still a lot that we know we can do to help our microbes along and consequently improve our own health.

*When I say ?good? bacteria, I?m talking about those bacteria that appear to be beneficial based on existing research. There?s a lot more to a healthy microbiome than knowing which bacteria are ?good? and ?bad?. It may be more of an issue of ratios, or interactions with other bacteria, or how the environment outside our bodies interacts with certain microbes. Our gut microbiome is a bit of a moving target, but we?re not completely in the dark. There is a great deal of research-based evidence we can use, and I think it?s important to focus on what we do know and how we can use that evidence to optimize our health and wellness.



Bailey et al. (2004). Prenatal stress alters bacterial colonization of the gut in infant monkeys. Journal of Pediatric Gastroenterology & Nutrition, 38(4), 414-421.

Bouhnik et al. (2006). The capacity of short-chain fructo-oligosaccharides to stimulate faecal bifidobacteria: A dose-response relationship study in healthy humans. Nutrition Journal, 5(8), 1-6.

Jakobsson et al. (2010). Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLOS One, 5(3), 1-12.

Ketabi (2011). Isomalto-oligosaccharides as prebiotics: In vitro metabolism by lactobacilli and bifidobacteria and in vivo effects in rodent models. Lambert Academic Publishing.

Messaoudi et al. (2011). Beneficial psychological effects of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in healthy human volunteers. Gut Microbes, 2(4).

Sebater-Molina et al. (2009). Dietary fructooligosaccharides and potential benefits on health. Journal of Physiology and Biochemistry, 65(3), 315-328.

Whisner et al. (2013). Galacto-oligosaccharides increase calcium absorption and gut bifidobacteria in young girls: A double-blind cross-over trial. British Journal of Nutrition, 110(7), 12929-12303.


Yen et al. (2011). Beneficial effects of fructo-oligosaccharides supplementation on fecal bifidobacteria and index of peroxidation status in constipated nursing-home residents – A placebo-controlled, diet-controlled trial. Nutrition, 27(3), 323-328.

3 thoughts on “Microbiome: Bolster Your Bifidos”

  • Hi Ellen! Just found you today thru Ms. Google. I developed a candida overgrowth after a series if utis + strep inections for which I stupidly took antibiotics each time. 🙁 Excellent information here. Thank so much for your research and writings. Much appreciated. I see now that I probably knocked out the Bifido bacteria and lactobacillus. Oddly enough, I twice ate active yogurt (first time also with probiotics) and had severe die off with very high fevers in the evenings (102), severe might sweats, complete exhaustion and zero appetite. Have u ever heard of this type of reaction? Now I’m scared to eat yogurt! I think I will start again at maybe a tablespoon a day and see what happens. Oh, also, i developed white tongue (thrush? Some people differentiate between them… I don’t know why) after my last go around with antibiotics, which is how I knew I had candida… only minor symptoms otherwise, like dandruff, a small bit of eczema. Thx for any info re if u have heard of severe die off after yogurt/probiotics.

    • Hi! I can’t say I know too much about die off in response to yogurt, but I have heard from some people that they have strong responses to taking probiotics. If you can find a functional medicine practitioner near you, it might be worth asking them if you continue to have severe negative responses to foods like yogurt. They also might be able to help you pinpoint any candida or potential SIBO issues.

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