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BRMI Article Archive - Probiotics and the Microbiome

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The human gastrointestinal system is a huge, complex ecosystem where microbiota, nutrients, and host cells interact extensively in a process crucial for body homeostasis and regeneration. The various bacterial communities that make up the gastrointestinal microbiota have many functions including metabolic and trophic functions.


The gastrointestinal tract functions as a barrier against antigens from microorganisms and undigested food. Dysbiosis or microbe-imbalance can have negative consequences in terms of health and many diseases have been associated with impairment of the gastro-intestinal microbiota.


These close relationships between gastro-intestinal microbiota, health, and disease have led to great interest in using probiotics (i.e. live micro-organisms), or prebiotics (i.e. non-digestible substrates) to positively modulate the intestinal microbiota to prevent or treat diseases. Research shows that probiotics can be used as innovative tools to alleviate intestinal inflammation, normalize gastrointestinal mucosal dysfunction, and down-regulate hypersensitivity reactions.  


Basically, probiotics are microbial cell preparations or components of microbial cells that have a beneficial effect on the health and well-being of the host. Probiotics were first described by a few visionary scientists like Metchnikoff, Nissle, and Shirota about a century ago. This concept of “useful microbes” as written by Metchnikoff in his publication On the prolongation of life, in 1907, has led many years later to the use of “probiotic” strains to deliberately manipulate the microbiota. This concept was largely forgotten during the expansion of the era of antibiotics and vaccines. Research on the roles of the commensal microbiota, however, brought a renewed interest in these beneficial microorganisms. Probiotic formulations are now intensively being developed and standardized for both human and animal consumption. 


A prebiotic is a non-digestible food ingredient that confers benefits on the host by selectively stimulating the growth and/or activity of one bacterium or a group of bacteria in the colon, thereby improving the health of the host. Prebiotics are dietary carbohydrates that escape digestion in the upper gastrointestinal tract, altering the bacterial composition of the gut by changing the type of the substrate provided to the existing microbial population in the gastrointestinal tract e.g. fructooligosaccharides, glucooligosaccharides and inulin. Together probiotics and prebiotics have a greater effect - symbiotics that improve the survival of the bacteria in the gastrointestinal tract.


Probiotics may contain a variety of microorganisms. The most common are bacteria that belong to groups called Lactobacillus and Bifidobacterium. Other bacteria may also be used as probiotics, including many yeasts such as Saccharomyces boulardii. Different types of probiotics may have different effects. For example, if a specific kind of Lactobacillus helps prevent an illness, that doesn’t necessarily mean that another kind of Lactobacillus or any of the Bifidobacterium probiotics would do the same thing. 

Lactobacillus and Bifidobacterium species have been shown to enhance the innate immune system and to enhance macrophage phagocytosis. Scientific results also provide evidence of the advantages of the utilization of certain Bacillus strains as probiotics. These bacteria can produce a very stable duration form called the endospore. Compared to the widely used lactic acid bacteria, bacterial spores offer the advantage of a higher survival rate during the acidic stomach passage and better stability during the processing and storage of food products.


The articles on this page describe the functions of probiotics and specific bacteria. 

Abhari, K., Shekarforoush, S. S., Hosseinzadeh, S., Nazifi, S., Sajedianfard, J., and Eskandari, M. H. (2016). The effects of orally administered Bacillus coagulans and inulin on prevention and progression of rheumatoid arthritis in rats. Food Nutr. Res. 60:30876. doi: 10.3402/fnr.v60.30876.


AlFaleh, Khalid, and Jasim Anabrees. Probiotics for prevention of necrotizing enterocolitis in preterm infants. Evidence‐Based Child Health: A Cochrane Review Journal 9, no. 3 (2014): 584-671.


Aponte, Guillermo Bernaola, Carlos Alfonso Bada Mancilla, Nilton Yhuri Carreazo, and Raúl Alberto Rojas Galarza. Probiotics for treating persistent diarrhoea in children. Cochrane Database of Systematic Reviews 8 (2013).


Bäckhed, Fredrik, Claire M. Fraser, Yehuda Ringel, Mary Ellen Sanders, R. Balfour Sartor, Philip M. Sherman, James Versalovic, Vincent Young, and B. Brett Finlay. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell host & microbe 12, no. 5 (2012): 611-622.


Baker, Hannah Claire, Dang Ngoc Tran, and Linda Valerie Thomas. Health benefits of probiotics for the elderly: a review. Journal of Foodservice 20, no. 5 (2009): 250-262.


Berthold-Pluta, A., Pluta, A., and Garbowska, M. (2015). The effect of selected factors on the survival of Bacillus cereus in the human gastrointestinal tract. Microb. Pathog.82, 7–14. doi: 10.1016/j.micpath.2015.03.015.


Butel, M. J. (2014). Probiotics, gut microbiota and health. Med. Mal. Infect. 44, 1–8. doi: 10.1016/j.medmal.2013.10.002.


Casula, G., and Cutting, S. M. (2002). Bacillus probiotics: spore germination in the gastrointestinal tract. Appl. Environ. Microbiol. 68, 2344–2352. doi: 10.1128/AEM.68.5.2344-2352.2002.


Ciorba, Matthew A. A gastroenterologist's guide to probiotics. Clinical gastroenterology and hepatology 10, no. 9 (2012): 960-968.


Doron, S., and Snydman, D. R. (2015). Risk and safety of probiotics. Clin. Infect. Dis. 60, S129–S134. doi: 10.1093/cid/civ085.


Duc, L. H., Hong, H. A., Barbosa, T. M., Henriques, A. O., and Cutting, S. M. (2004). Characterization of Bacillus probiotics available for human use. Appl. Environ. Microbiol. 70, 2161–2171. doi: 10.1128/AEM.70.4.2161-2171.2004.


Farnworth, Edward R. The evidence to support health claims for probiotics. The Journal of Nutrition 138, no. 6 (2008): 1250S-1254S.


Figueroa-González, I., A. Cruz-Guerrero, and G. Quijano. The benefits of probiotics on human health. J Microbial Biochem Technol S 1 (2011): 1948-5948.


Floch, Martin H., W. Allan Walker, Mary Ellen Sanders, Max Nieuwdorp, Adam S. Kim, David A. Brenner, Amir A. Qamar et al. Recommendations for probiotic use — 2015 update: proceedings and consensus opinion. Journal of clinical gastroenterology 49 (2015): S69-S73.


Fuller, Roy. Probiotics in human medicine. Gut 32, no. 4 (1991): 439-442.


Ghoneim, M. A. M., Hassan, A. I., Mahmoud, M. G., and Asker, M. S. (2016). Effect of polysaccharide from Bacillus subtilis sp. on cardiovascular diseases and atherogenic indices in diabetic rats. BMC Complement. Altern. Med. 16:112. doi: 10.1186/s12906-016-1093-1.


Gill, H., & Prasad, J. (2008). Probiotics, immunomodulation, and health benefits. In Bioactive components of milk (pp. 423-454). Springer, New York, NY.


Goldenberg JZ, Ma SS, Saxton JD, Martzen MR, Vandvik PO, Thorlund K, et al. Probiotics for the prevention of Clostridium difficile–associated diarrhea in adults and children. Cochrane Database Syst Rev 2013;CD006095. doi: 10.1002/14651858.CD006095.pub3. PubMed PMID: 23728658.


Goldin, Barry R. Health benefits of probiotics. British Journal of Nutrition 80, no. S2 (1998): S203-S207.


Gomes, Ana MP, and F. Xavier Malcata. Bifidobacterium spp. and Lactobacillus acidophilus: biological, biochemical, technological and therapeutical properties relevant for use as probiotics. Trends in Food Science & Technology 10, no. 4-5 (1999): 139-157.

Green, D. H., Wakeley, P. R., Page, A., Barnes, A., Baccigalupi, L., Ricca, E., et al. (1999). Characterization of two bacillus probiotics. Appl. Environ. Microbiol. 65, 4288–4291.


Guo, Z., Liu, X. M., Zhang, Q. X., Shen, Z., Tian, F. W., Zhang, H., et al. (2013). Influence of consumption of probiotics on the plasma lipid profile: a meta-analysis of randomized controlled trials. Nutr. Metab. Cardiovasc. Dis. 21, 844–850. doi: 10.1016/j.numecd.2011.04.008.


Hill, Colin, Francisco Guarner, Gregor Reid, Glenn R. Gibson, Daniel J. Merenstein, Bruno Pot, Lorenzo Morelli et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11, no. 8 (2014): 506-514.


Hong, H. A., Huang, J. M., Khaneja, R., Hiep, L. V., Urdaci, M. C., and Cutting, S. M. (2008). The safety of Bacillus subtilis and Bacillus indicus as food probiotics. J. Appl. Microbiol. 105, 510–520. doi: 10.1111/j.1365-2672.2008.03773.x.


Horosheva, T. V., Vodyanoy, V., and Sorokulova, I. (2014). Efficacy of Bacillus probiotics in prevention of antibiotic-associated diarrhoea: a randomized, double-blind, placebo-controlled clinical trial. JMM Case Rep. 1, 1–6. doi: 10.1099/jmmcr.0.004036.


Hungin, A. P. S., C. Mulligan, B. Pot, P. Whorwell, L. Agréus, P. Fracasso, C. Lionis et al. Systematic review: probiotics in the management of lower gastrointestinal symptoms in clinical practice–an evidence‐based international guide. Alimentary pharmacology & therapeutics 38, no. 8 (2013): 864-886.


Kalliomäki, M., Salminen, S., Arvilommi, H., Kero, P., Koskinen, P., and Isolauri, E. (2001). Probiotics in primary prevention of atopic disease: a randomised placebo-controlled trial. Lancet 357, 1076–1079. doi: 10.1016/S0140-6736(00)04259-8.


Khochamit, N., Siripornadulsil, S., Sukon, P., and Siripornadulsil, W. (2015). Antibacterial activity and genotypic–phenotypic characteristics of bacteriocin-producing Bacillus subtilis KKU213: potential as a probiotic strain. Microbiol. Res. 170, 36–50. doi: 10.1016/j.micres.2014.09.004.


Khodadad, A., Farahmand, F., Najafi, M., and Shoaran, M. (2013). Probiotics for the treatment of pediatric Helicobacter pylori infection: a randomized double blind clinical trial. Iran J. Pediatr. 23, 79–84.


Kim, Ji Yeun, Jung Hyun Kwon, So Hyun Ahn, Sang Il Lee, Young Shin Han, Young Ok Choi, Soo Young Lee, Kang Mo Ahn, and Geun Eog Ji. Effect of probiotic mix (Bifidobacterium bifidum, Bifidobacterium lactis, Lactobacillus acidophilus) in the primary prevention of eczema: a double‐blind, randomized, placebo‐controlled trial. Pediatric Allergy and Immunology 21, no. 2p2 (2010): e386-e393.


Kimura, Katsunori. Health benefits of probiotics: probiotics for Helicobacter pylori infection. Food science and technology research 10, no. 1 (2004): 1-5.


Kolsto, A. B., Tourasse, N. J., and Okstad, O. A. (2009). What sets Bacillus anthracis apart from other Bacillus species. Annu. Rev. Microbiol. 63, 451–476. doi: 10.1146/annurev.micro.091208.073255.


Kosak, T., Maeda, T., Nakada, Y., Yukawa, M., and Tanaka, S. (1998). Effect of Bacillus subtilis spore administration on activation of macrophages and natural killer cells in mice. Vet. Microbiol. 60, 215–225. doi: 10.1016/S0378-1135(97)00102-8.


Lee, Y., Yoshitsugu, R., Kikuchi, K., Joe, G. H., Tsuji, M., Nose, T., et al. (2016). Combination of soya pulp and Bacillus coagulans lilac-01 improves intestinal bile acid metabolism without impairing the effects of prebiotics in rats fed a cholic acid-supplemented diet. Br. J. Nutr. 116, 603–610. doi: 10.1017/S0007114516002270.


Lefevre, M., Racedo, S. M., Ripert, G., Housez, B., Cazaubiel, M., Maudet, C. P., et al. (2015). Probiotic strain Bacillus subtilis CU1 stimulates immune system of elderly during common infectious disease period: a randomized, double-blind placebo-controlled study. Immun. Ageing 12, 24. doi: 10.1186/s12979-015-0051-y.


London, L. E., Kumar, A. H., Wall, R., Casey, P. G., O’Sullivan, O., Shanahan, F., et al. (2014). Exopolysaccharide-producing probiotic Lactobacilli reduce serum cholesterol and modify enteric microbiota in ApoE-deficient mice. J. Nutr. 144, 1956–1962. doi: 10.3945/jn.114.191627.


Mallappa, R. H., Rokana, N., Duary, R. K., Panwar, H., Batish, V. K., and Grover, S. (2012). Management of metabolic syndrome through probiotic and prebiotic interventions. Indian J. Endocrinol. Metab. 16, 20–27. doi: 10.4103/2230-8210.91178.


Maneerat, S., Lehtinen, M. J., Childs, C. E., Forssten, S. D., Alhoniemi, E., Tiphaine, M., et al. (2014). Consumption of Bifidobacterium lactis Bi-07 by healthy elderly adults enhances phagocytic activity of monocytes and granulocytes. J. Nutr. Sci. 44, 1–10. doi: 10.1017/jns.2013.31


McFarland, Lynne V. Systematic review and meta-analysis of Saccharomyces boulardii in adult patients. World journal of gastroenterology: WJG 16, no. 18 (2010): 2202.


Messaoudi, Michaël, Nicolas Violle, Jean-François Bisson, Didier Desor, Hervé Javelot, and Catherine Rougeot. Beneficial psychological effects of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in healthy human volunteers. Gut microbes 2, no. 4 (2011): 256-261.


Nichols, Andrew W. Probiotics and athletic performance: a systematic review. Current sports medicine reports 6, no. 4 (2007): 269-273.


Ozawa, Kyosuke, Kanji YABU-UCHI, Kumiko Yamanaka, Yutaka Yamashita, Keizo Ueba, and Toshio Miwatani. Antagonistic effects of Bacillus natto and Streptococcus faecalis on growth of Candida albicans. Microbiology and immunology 23, no. 12 (1979): 1147-1156.


Picard, C., J. Fioramonti, A. Francois, T. Robinson, F. Neant, and C. Matuchansky. Review article: bifidobacteria as probiotic agents–physiological effects and clinical benefits. Alimentary pharmacology & therapeutics 22, no. 6 (2005): 495-512.


Ranji, P., Akbarzadeh, A., and Rahmati-Yamchi, M. (2015). Associations of probiotics with vitamin D and leptin receptors and their effects on colon cancer. Asian Pac. J. Cancer Prev. 16, 3621–3627. doi: 10.7314/APJCP.2015.


Salminen, Seppo, Sonja Nybom, Jussi Meriluoto, Maria Carmen Collado, Satu Vesterlund, and Hani El-Nezami. Interaction of probiotics and pathogens — benefits to human health? Current opinion in biotechnology 21, no. 2 (2010): 157-167.


Sanders, Mary Ellen. Probiotics: definition, sources, selection, and uses. Clinical Infectious Diseases 46, no. Supplement_2 (2008): S58-S61.


Scott, K. P., Antoine, J. M., Midtvedt, T., and van Hemert, S. (2015). Manipulating the gut microbiota to maintain health and treat disease. Microb. Ecol. Health Dis. 26, 25877. doi: 10.3402/mehd.v26.25877.


Shida, K., and Nomoto, K. (2013). Probiotics as efficient immuno potentiators: translational role in cancer prevention. Indian J. Med. Res. 138, 808–814.


Shimizu, K., Ogura, H., Asahara, T., Nomoto, K., Morotomi, M., Tasaki, O., et al. (2013). Probiotic/synbiotic therapy for treating critically ill patients from a gut microbiota perspective. Dig. Dis. Sci. 58, 23–32. doi: 10.1007/s10620-012-2334-x.


Stamatova, Iva, and Jukka H. Meurman. Probiotics: health benefits in the mouth. American Journal of Dentistry 22, no. 6 (2009): 329.


Suvarna, V. C., and V. U. Boby. Probiotics in human health: A current assessment. Current science 88, no. 11 (2005): 1744-1748.


Vandenplas, Yvan, Geert Huys, and Georges Daube. Probiotics: an update. Jornal de Pediatria (Versão em Português) 91, no. 1 (2015): 6-21.


Weichselbaum, Elisabeth. Potential benefits of probiotics – main findings of an in-depth review. British journal of community nursing 15, no. 3 (2010): 110-11.

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