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Bifidobacteria and Lactobacilli: deficiency and what kind of food contains them

Bifidobacteria and Lactobacilli

In this article, we discuss two kinds of bacteria that constitute a major part of our intestinal microbiota: Bifidobacteria and Lactobacilli. The two are important as they determine the health of our immune system and gut.

What is the human microbiota

These days, the concept of microbiota is becoming increasingly popular. More and more people are getting interested in learning how to look after their inner world of microbes.

The somewhat outdated assumption that the human body is no longer a mystery, which was largely inspired by the advancements in our understanding of the human genome, has given way to the world of the unknown which is the human microbiome. Indeed, we live in symbiosis with a huge microbial community inside of our bodies.

But this fact was completely overlooked until 2012 when the results of the Human Microbiome Project shed some light on the mysteries of the microbiome. This ground-breaking study revealed that the human body is inhabited by over 10,000 different species of microorganisms.

What is the human microbiota

Since then, studies into the human microbiome have distinguished several classes of microorganisms: helminths, fungi, protozoa, bacteria, and viruses. These microorganisms colonize different organs in our bodies. For example, we have the skin microbiota; the vaginal microbiota; the urinary system microbiota; the respiratory microbiota; the ear, nose, and throat (ENT) microbiota; and the most numerous gut microbiota, also known as the intestinal microbiota.

The composition of the microorganisms differs depending on their location. By far the largest microbial community in the body is found in the microbiota of the gastrointestinal tract. It consists of over 100 trillion microbial cells – the number which is 5-10 times greater than the number of cells anywhere else in the body.

Research: Guinane CM, Cotter PD. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therap Adv Gastroenterol. 2013 Jul;6(4):295-308. doi: 10.1177/1756283X13482996. PMID: 23814609; PMCID: PMC3667473

The gut microbiota i) receives resources from our food (in particular, from dietary fiber) which are used in the metabolic processes, and ii) is directly involved in the process of food digestion (in fermentation, nutrient absorption, vitamin synthesis, etc.). As such, the gut microbiota is extremely important for the normal functioning of the intestinal immune system.

One of the fascinating facts about the human microbiota relates to its development. In the past, it was believed that a womb is a sterile place and a baby’s microbiota starts to form at the time of birth, and more precisely when the baby passes through the birth canal where it gets exposed to microorganisms. But now there is evidence to suggest that the colonization of the human intestines by microorganisms starts during fetal development.

Research: Nyangahu DD, Jaspan HB. Influence of maternal microbiota during pregnancy on infant immunity. Clin Exp Immunol. 2019 Oct;198(1):47-56. doi: 10.1111/cei.13331. Epub 2019 Jun 21. PMID: 31121057; PMCID: PMC6718277

Microorganisms are transmitted from the mother to the fetus during gestation in addition to the transmission that occurs during the labor itself. Because of the gestational transmission, it is very important that during pregnancy expectant mothers maintain healthy diets with plenty of nutrient-dense foods.

There are two types of microbiota: the parietal and the luminal. The parietal microbiota is inherited and cannot be influenced in any way. By contrast, the composition of the luminal microbiota can be altered.

Nata Gonchar

Holistic Nutritionist, founder
of the project WOW Bali

TOP-10 ingredients
for your health and
balanced meal plan
Nata Gonchar

Holistic Nutritionist, founder
of the project WOW Bali

As Hippocrates said, you are what you eat. The meaning of this phrase concerns every person, who takes care of his health. The food we eat has a big impact on our vital activity, state of health and quality of life.

Nowadays healthy diet is very popular and everyone knows that he should give up junk food. But not everyone knows what he must eat except for grain, vegetables and protein food.

It's essential to diversify your diet. Every bite of food should provide you with vitamins, minerals and phytonutrients that are necessary for good health.

So how can we have a proper nutrition plan?

We prepared a PDF-file to help you. It contains TOP-10 ingredients, which should be added to everyone's diet.

Luminal microbes are located in the opening of the gastrointestinal tract, known as the intestinal lumen. They feed on insoluble dietary fiber, by connecting to it, digesting it, and then delivering the micro- and macronutrients to the parietal microbiota. The parietal microbiota lives in the parietal mucus of the gastrointestinal tract and feeds on the soluble dietary fiber.

The role of Lactobacilli and Bifidobacteria in human health

Bifidobacteria are gram-positive anaerobic bacteria that do not require oxygen to survive. One of the main functions of this bacteria is to maintain parietal digestion, which is the digestion responsible for the absorption of minerals.

In addition, Bifidobacteria create a natural barrier that prevents the penetration of pathogens and toxins. Bifidobacteria live in symbiosis with their human hosts: they receive nutrients from us and i) produce the amino acids, proteins, and B vitamins that are necessary for our health and ii) promote the normal absorption of proteins, fats, vitamin D, calcium, and iron.

Lactobacilli can exist both in the presence of oxygen and in its absence. One of the main functions of Lactobacilli is the production of the enzyme lactase, which breaks down sugars in milk (lactose). Lactobacilli form a natural immune defense, accelerate the process of outer skin layer regeneration, and play an active role in phagocytosis – a process that destroys foreign particles or pathogens such as inflected cells or bacteria.

Bifidobacteria and Lactobacilli both have health benefits, but there are also differences between the two. These differences include:

  • Abundance. Under normal circumstances – when the intestinal microbiota is in balance – Bifidobacterium is the major bacterial form in the intestines. Lactobacillus constitutes only about 1% of the gastrointestinal microbiota.
  • Location. Bifidobacteria live mainly in the lumen of the large intestine, while Lactobacilli are a part of the digestive, urinary, genital, and oral systems.
  • Shape and motility. Lactobacilli do not move (are non-motile) and are rod-shaped, while Bifidobacteria can occur either in single or branched rods, or clubs and are motile.

Research: Vlasova, Anastasia N et al. “Comparison of probiotic lactobacilli and bifidobacteria effects, immune responses and rotavirus vaccines and infection in different host species.” Veterinary immunology and immunopathology vol. 172 (2016): 72-84

Both varieties of microorganisms are beneficial to humans, so it is very important to maintain a perfect balance of Bifidobacteria and Lactobacilli in our bodies.

Intestinal dysbiosis and Bifidobacteria and Lactobacilli deficiency: causes, signs, and treatment

A number of different external and internal factors can disturb the balance between the beneficial and the pathogenic intestinal microbiota. The main factors that can lead to changes in the composition of the microbiota are:

  • long-term use of medications
  • surgical interventions
  • poor nutrition
  • chronic stress
  • intestinal infections
  • various diseases of the digestive system (for example, gastritis, hepatitis, etc.)
  • metabolic diseases
  • untreated thyroid problems

Intestinal dysbiosis and Bifidobacteria and Lactobacilli deficiency

The imbalance in the gut microbiota can result in the development of a condition called dysbiosis. This condition is associated with a number of unpleasant symptoms and can negatively affect digestion. The main symptoms of intestinal dysbiosis include:

  • Excessive flatulence
  • Alternating constipation and diarrhea
  • Abdominal pain
  • Nausea
  • Irritability, sleep disturbances, apathy

In addition to intestinal dysbiosis, the bacterial imbalance in the microbiota can lead to deficiencies of vitamins and minerals. Also, when the normal balance in the gut is disturbed and there are less of beneficial bacteria than normal, other inhabitants of the intestine such as fungi, pathogenic bacteria, and parasitic worms, are allowed to overgrow.

Nutrition significantly affects the composition of bacteria. For example, excessive consumption of simple carbohydrates, fatty and fried food, and lack of dietary fiber causes a significant reduction in the beneficial microbiota.

In addition, certain health conditions are associated with low numbers of Bifidobacteria and Lactobacilli in the intestines. Among these are diabetes, obesity, asthma, coeliac disease, dermatitis, psoriasis, and irritable bowel syndrome (IBS).

Research: Collado MC, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y. Imbalances in faecal and duodenal Bifidobacterium species composition in active and non-active coeliac disease. BMC Microbiol. 2008 Dec 22;8:232. doi: 10.1186/1471-2180-8-232. PMID: 19102766; PMCID: PMC2635381
Gao X, Jia R, Xie L, Kuang L, Feng L, Wan C. Obesity in school-aged children and its correlation with gut E.coli and Bifidobacteria: a case-control study. BMC Pediatr. 2015 May 30;15:64. doi: 10.1186/s12887-015-0384-x. PMID: 26024884; PMCID: PMC4448301.
Akay HK, Bahar Tokman H, Hatipoglu N, Hatipoglu H, Siraneci R, Demirci M, Borsa BA, Yuksel P, Karakullukcu A, Kangaba AA, Sirekbasan S, Aka S, Mamal Torun M, Kocazeybek BS. The relationship between bifidobacteria and allergic asthma and/or allergic dermatitis: a prospective study of 0-3 years-old children in Turkey. Anaerobe. 2014 Aug;28:98-103

Studies have also found a link between low levels of beneficial bacteria and depression, ulcerative colitis, chronic fatigue syndrome, and neurodegenerative disorders.

Research: Groeger D, O’Mahony L, Murphy EF, Bourke JF, Dinan TG, Kiely B, Shanahan F, Quigley EM. Bifidobacterium infantis 35624 modulates host inflammatory processes beyond the gut. Gut Microbes. 2013 Jul-Aug;4(4):325-39. doi: 10.4161/gmic.25487. Epub 2013 Jun 21. PMID: 23842110; PMCID: PMC3744517
O’Mahony L, McCarthy J, Kelly P, Hurley G, Luo F, Chen K, O’Sullivan GC, Kiely B, Collins JK, Shanahan F, Quigley EM. Lactobacillus and bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology. 2005 Mar;128(3):541-51. doi: 10.1053/j.gastro.2004.11.050. PMID: 15765388

The principles of fighting intestinal dysbiosis are i) elimination of its causes, ii) restoration of normal intestinal microbiota, and iii) effective treatment of the disease itself.

With respect to i), it is necessary to first remove excess pathogenic microbes from the intestines, the biliary tract, and other organs. Concerning ii), it is important to eliminate the inflammation in the intestines, normalize the activity of the small intestine, restore the normal pH balance, and stimulate the growth of the beneficial microbiota whilst suppressing the growth of the opportunistic and pathogenic microbes.

As with any treatment, it is always important to pay attention to our general and local immune responses and work in parallel on strengthening the immune system.

Reversing the Bifidobacteria and Lactobacilli deficiencies has been shown to lead to stress reduction and improvements in the psychological well-being in patients with depression. Other benefits of replenishing the levels of the Bifidobacteria and Lactobacilli are as follows: lower cholesterol levelsand reduced symptoms associated with irritable bowel syndrome, such as pain, bloating, cramps, constipation, and diarrhea.

Research: Whorwell PJ, Altringer L, Morel J, Bond Y, Charbonneau D, O’Mahony L, Kiely B, Shanahan F, Quigley EM. Efficacy of an encapsulated probiotic Bifidobacterium infantis 35624 in women with irritable bowel syndrome. Am J Gastroenterol. 2006 Jul;101(7):1581-90. doi: 10.1111/j.1572-0241.2006.00734.x. PMID: 16863564
Messaoudi M, Lalonde R, Violle N, Javelot H, Desor D, Nejdi A, Bisson JF, Rougeot C, Pichelin M, Cazaubiel M, Cazaubiel JM. Assessment of psychotropic-like properties of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects. Br J Nutr. 2011 Mar;105(5):755-64. doi: 10.1017/S0007114510004319. Epub 2010 Oct 26. PMID: 20974015
Pinto-Sanchez MI, Hall GB, Ghajar K, Nardelli A, Bolino C, Lau JT, Martin FP, Cominetti O, Welsh C, Rieder A, Traynor J, Gregory C, De Palma G, Pigrau M, Ford AC, Macri J, Berger B, Bergonzelli G, Surette MG, Collins SM, Moayyedi P, Bercik P. Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: A Pilot Study in Patients With Irritable Bowel Syndrome. Gastroenterology. 2017 Aug;153(2):448-459.e8. doi: 10.1053/j.gastro.2017.05.003. Epub 2017 May 5. PMID: 28483500
Ejtahed HS, Mohtadi-Nia J, Homayouni-Rad A, Niafar M, Asghari-Jafarabadi M, Mofid V, Akbarian-Moghari A. Effect of probiotic yogurt containing Lactobacillus acidophilus and Bifidobacterium lactis on lipid profile in individuals with type 2 diabetes mellitus. J Dairy Sci. 2011 Jul;94(7):3288-94. doi: 10.3168/jds.2010-4128. PMID: 21700013

There are several ways of replenishing Bifidobacteria and Lactobacilli. One of them is by taking probiotic supplements and adding more probiotic-rich foods to the diet. Another is by adding more prebiotics. We will examine each in turn.

Probiotics and prebiotics


Probiotics are live bacteria and yeasts that help your body maintain a healthy community of microorganisms in the intestinal microbiota. As such, probiotics are very beneficial to us. Probiotics are widely used as dietary supplements and can also be found in yogurts and other dairy products.

The effectiveness of probiotics depends on many factors, such as their composition, the way they were produced, the condition of the human intestinal microbiota, our lifestyle, and much more.


Prebiotics are defined as non-digestible food that promotes the growth of beneficial microorganisms in our gut. For food to be classified as a prebiotic, it must not be processed by digestive enzymes in the upper digestive tract. They go to our lower digestive tract where they act as food for healthy bacteria instead. In addition to probiotics, prebiotics is used to normalize the intestinal microbiota.


Dietary fiber, oligosaccharides, fructo-oligosaccharides, galacto-oligosaccharides, inulin, and raffinose (found in beans) all have the properties of prebiotics. For example, fructo-oligosaccharides – found in artichokes, onions, chicory, garlic, corn flakes, oatmeal, rye, and beer – are carbohydrates consisting of monosaccharide molecules. Fructo-oligosaccharides tend to significantly increase the levels of Bifidobacteria and Lactobacilli and at the same time decrease the number of harmful bacteria.

An increase in the Bifidobacteria and Lactobacilli suppresses the growth and reproduction of such pathogens as salmonella, listeria, campylobacter, shigella, and vibrio. Small amounts of oligosaccharides are found in the milk of mammals. Human breast milk contains about 130 different oligosaccharides, which act as a kind of soluble dietary fiber. The oligosaccharides in breast milk increase the abundance of Bifidobacteria and regulate the pH balance of the colon in babies.

Research: Underwood M.A., Gaerlan S., De Leoz M.L., Dimapasoc L., Kalanetra K.M., Lemay D.G., German J.B., Mills D.A., Lebrilla C.B. Human milk oligosaccharides in premature infants: Absorption, excretion, and influence on the intestinal microbiota. Pediatr. Res. 2015;78:670–677. doi: 10.1038/pr.2015.162


A combination of probiotics and prebiotics, known as synbiotics, can be used in supplementation. The benefits of synbiotics are that it improves the survival and colonization potential of probiotics in the intestines, and selectively stimulate the growth and metabolism of Lactobacteria and Bifidobacteria.

The supplements usually come in the form of a powder containing Bifidobacteria, Lactobacilli, and their combinations.

What to look for in probiotic and prebiotic supplements:

  • they should not cause side effects even when used long-term
  • they must have a colonization potential: this means that they can stay in the digestive tract until a positive effect is achieved
  • they should have a stable clinical efficacy and their production technology must not be overly complex

For most of us, probiotic and prebiotic supplements are considered safe. However, is important to remember that not all supplements are the same and different strains and doses can have different health effects and benefits. Certain strains of Lactobacillus and Bifidobacterium, for example, have clinically proven efficacy so it’s better to choose products with formulas created according to scientific evidence.

It is important to know that probiotic supplementation is prohibited in conjunction with certain health conditions including acute pancreatitis, oncology, and ulcers. Some probiotic strains should not be used if suffering from irritable bowel syndrome (IBS), bacterial overgrowth syndrome (SIBO), and fungal overgrowth syndrome (SIFO).

Bifidobacterium and Lactobacillus supplementation is also contradictory during immunosuppressive treatments. Due to a lack of clinical evidence on their impact on immunocompromised patients, probiotic supplementation is generally not recommended.

Research: S. P. Borriello, W. P Hammes, W. Holzapfel, P. Marteau, J. Schrezenmeir, M. Vaara, V. Valtonen, Safety of Probiotics That Contain Lactobacilli or Bifidobacteria, Clinical Infectious Diseases, Volume 36, Issue 6, 15 March 2003, Pages 775–780

Always consult your healthcare provider or nutritionist who will advise you on the best probiotic strain for your supplementation.

Top foods high in probiotics

Here we present the top 11 foods high in Lactobacilli and Bifidobacteria.


Yogurt is one of the best sources of probiotics. Natural yogurt is made of milk that has been fermented by bacteria, mainly lactic acid bacteria and Bifidobacteria. Yogurt is very beneficial to human health, especially as far as the health of the musculoskeletal system (bones) is concerned. Yogurt is also beneficial to those with a tendency for high blood pressure.

In children, yogurt can help to relieve diarrhea caused by antibiotics. In adults, yogurt can help to relieve symptoms of irritable bowel syndrome. In addition, yogurt may be suitable for people with lactose intolerance, as the bacteria used in the production of yogurt convert some of the lactose into lactic acid thereby significantly reducing the lactose content in the final product. By the way, it is the lactic acid that makes yogurts taste sour.

However, it should be noted that not all yogurts contain live probiotics. In some cases, all live bacteria are killed during the heat treatment used in the production of yogurt. This is why it is important to choose yogurt where active or live cultures of bacteria are listed on the label. Yogurt that does not contain added sugar is also a better option.


Whilst yogurt is probably the best-known probiotic food; kefir is much more beneficial. It is a fermented probiotic drink made from either cow’s or goat’s milk by adding kefir grains. These grains contain colonies of around 20 types of microorganisms including lactic acid bacteria, yeasts, and acetic acid bacteria. The word “kefir” supposedly comes from the Turkish word keyif which means “good feeling”, arguably because that is how one feels after drinking kefir.

Kefir is incredibly beneficial for the whole body including the skeletal system and the gastrointestinal tract. In addition, kefir is also highly regarded for its protective properties against viral infections. In addition to the probiotic bacteria, kefir also contains several major strains of yeast, which makes it also a powerful prebiotic. Just like yogurt, kefir is generally well tolerated by people with lactose intolerance.

Research: Safety of Probiotics That Contain Lactobacilli or Bifidobacteria


Sauerkraut is a finely chopped cabbage mixed with salt and allowed to ferment in its juices containing lactic acid. In addition to its probiotic properties, sauerkraut is rich in fiber and vitamins C, B, and K. It also contains sodium, iron, and manganese. When buying sauerkraut, make sure to choose the unpasteurized type because pasteurization kills live and active bacteria.


Tempeh is a fermented soy product that originates in Indonesia. These days tempeh is well-known around the world as a high-protein meat substitute.

Research: Andreas Romulo, Reggie Surya, Tempe: A traditional fermented food of Indonesia and its health benefits, International Journal of Gastronomy and Food Science, Volume 26

Tempeh is made from whole soybeans. The soybeans are softened, dehulled, boiled in water, and then fermented with the help of an acidifier (usually in vinegar) and a starter containing the fungal culture of Rhizopus oligosporus.

Fermentation actually has an amazing effect on the nutritional profile of soybeans which ordinary are high in phytic acid – a plant compound that interferes with the absorption of minerals like iron and zinc. During fermentation, however, the amount of phytic acid in the soybeans is reduced, which means more minerals can be absorbed from tempeh than from unfermented soybeans.

In addition, vitamin B12 is synthesized during the fermentation of tempeh. Overall, tempeh is an excellent choice for both vegetarians and those looking to add some probiotic foods to their diet.


Kimchi is a Korean dish containing spicy fermented vegetables, primarily Chinese cabbage. Kimchi is seasoned with a mixture of salt, herbs like green onion, and spices like chili pepper, garlic, and ginger. Kimchi contains the lactic acid bacteria Companiactobacillus kimchi, as well as other lactic acid bacteria. The presence of these bacteria in kimchi helps to support gut health and aid digestion. The main ingredient of Kinchi – the Chinese cabbage – is rich in vitamins and minerals, including vitamin K, riboflavin (vitamin B2), and iron.



Miso is a traditional Japanese paste, produced by fermenting soybeans, rice, wheat, or their mixture with salt and Koji mold (Aspergillus oryzae) – a fungus widely used in fermentation in East Asia. This paste is used in miso soup which is served with most meals in Japan. Miso is a good source of protein and fiber.

It is also rich in vitamins, minerals, and plant compounds, including vitamin K, manganese, and copper. It has been shown that adding miso soup on the regular basis to the diet may reduce the risk of breast cancer in women over 40.

Research: Yamamoto S, Sobue T, Kobayashi M, Sasaki S, Tsugane S; Japan Public Health Center-Based Prospective Study on Cancer Cardiovascular Diseases Group. Soy, isoflavones, and breast cancer risk in Japan. J Natl Cancer Inst. 2003 Jun 18;95(12):906-13

Another study has reported an association with a reduction of stroke risk in women who consumed miso regularly.

Research: Ito, K. Review of the health benefits of habitual consumption of miso soup: focus on the effects on sympathetic nerve activity, blood pressure, and heart rate. Environ Health Prev Med 25, 45 (2020)


Kombucha is a fermented drink made with black or green tea, sugar, and SCOBY – a symbiotic colony of bacteria and yeast. Kombucha is popular in many parts of the world. These days the internet is full of claims about the benefits of kombucha to human health, however, these claims are yet to be verified by quality scientific research since only animal and in vitro studies are available to date. However, since kombucha is a fermented product, it does contain probiotics beneficial to our health.

Fermented pickles

Pickled cucumbers are popular around the world. There is a number of ways to make them, but here we will only discuss salt fermentation since this is the only type of pickles that is beneficial to our gut. With the addition of salt, cucumbers release lactic acid bacteria, and this allows them to ferment. Pickled cucumbers are a great source of probiotic bacteria that aid digestion.

They are low in calories and are an excellent source of vitamin K. However, pickles should not be consumed in large quantities as they are also high in sodium. It is also important to note that pickles made with vinegar do not contain live probiotics.


The term buttermilk refers to a range of fermented milk drinks. There are two main types of buttermilk: traditional and cultivated. Traditional buttermilk is the liquid left in the process of butter-making. This type of buttermilk is of interest here as it contains probiotic strains. The cultivated buttermilk, by contrast, does not have these beneficial properties. Traditional buttermilk also contains important vitamins and minerals such as vitamin B12, riboflavin, calcium, and phosphorus; and is low in fat and calories.


Natto is another traditional Japanese product made from fermented soybeans. It contains the bacterial strain of Bacillus subtilis. Natto is one of the staples of Japanese cuisine. It has a characteristic odor and a slimy texture. Natto is usually mixed with rice and served for breakfast. In addition to digestive benefits, it is rich in protein and vitamin K2 which is important for bones and cardiovascular health. As such, Natto is highly recommended for adults over 40.

Certain types of cheese

Although most types of cheese are fermented, this does not mean that all of them contain probiotics. When buying cheese, it is important to look for live active cultures on food labels. Beneficial bacteria can survive during the aging process in some cheeses, including gouda, mozzarella, and cheddar.


Cheese is an excellent source of protein and is also rich in important vitamins and minerals, including calcium, vitamin B12, phosphorus, and selenium. Moderate consumption of dairy products, such as cheese, may help reduce the risk of heart disease and osteoporosis.

The material is based on research: