The Modern Era of Microbiome Science
Jun 29 2021
| Our Blog
| Jacqueline Rizo
The human microbiome refers to the organisms (bacteria, fungi, and viruses) that reside in and on our body. When using microbiome in this article, it is being limited to the bacteria that make their home in and on the human body.
The Human Genome Project, which cost an estimated $3 billion, was a 13-year (1990-2003) project that resulted in the first successful sequencing of the human genome. Scientists had hoped that sequencing the human genome would lead to cures for many of today’s chronic degenerative diseases. That goal failed, and as we know, sequencing the human genome never led to successful treatments for any diseases.
However, one great benefit that emerged from the Human Genome Project was the development of incredible technology, which allows scientists to sequence genomes at a fast, affordable pace. For example, in January 2017, Illumina, which is the world’s leading producer of next-generation sequencing technology, announced that their new NovaSeq™ could sequence a genome in one day for only $100. (1)
The incredible power and speed of the new gene sequencing technology were partly responsible for the government’s funding of the Human Microbiome Project (2007-2012). (2) Subsequently, the Human Microbiome Project resulted in the publication of over 350 studies, which are viewed as the “birth” of the modern era of microbiome science.
Nena Dockery, Scientific and Regulatory Manager at Stratum Nutrition, explains, “There was a tremendous amount of knowledge gained from the Microbiome Project and subsequent research on the human microbiome. Families of microbes (mostly bacteria) were identified and their relative numbers began to be associated with various health benefits and disease susceptibility. Some of the bacterial species that were shown to be particularly beneficial were isolated from human or food sources and commercially grown as a supplemental source of these beneficial species – and the probiotics industry took off. Along the way, it was discovered how important specific strains of bacteria were, which narrowed commercialization down to bacterial strains that could be patented for their benefits.
Prebiotics then began to become recognized as food sources both for the supplemented probiotics and to encourage growth of the body’s own beneficial species. If combined in a product with specific bacteria shown to thrive with certain prebiotics, the term “synbiotic” was used.”
Dockery continues, “And that is where the research began to get very interesting. As part of the research on the body’s native bacteria, it was found that certain bacteria produce byproducts of their metabolism that have substantial benefits to their human host. For example, some produce digestive enzymes, like lactase. Lactase breaks down milk sugar (lactose) and its absence in the body leads to lactose intolerance. Other bacteria, especially those in the colon produce short-chain fatty acids, such as butyrate, that are very protective against the development of colon cancer. Of course, this type of research was a big Ah Ha moment for scientists because the microbes (again mostly bacteria) could produce these byproducts in the broth used to ferment them for commercial production into probiotics; and that resulted in a further study that led to the introduction of postbiotics.”
Most probiotics currently on the market are designed to work in the gut. The intestinal tract, particularly the lower intestine, is the home to trillions of microorganisms that provide a variety of benefits, mostly related to digestion and immune functioning. However, medications, especially antibiotics, along with certain disease conditions, diet, genetics and lifestyle choices all play a role in the composition of an individual’s microbiome. Probiotics are designed to support healthy functioning of our body’s own microbiome and fill in the gaps where deficiencies have developed.
It is now known that the immune benefits of the body’s protective microbiome don’t begin in the gut, but in the oral cavity, where pathogenic microbes most often enter the body. The oral cavity is home to as many different species of bacteria as the gut; and these bacteria can form an extremely strong barrier against invaders, influencing the health, not only of the teeth and gums, but extending into the throat and ear canals, and indirectly, throughout the entire body. (3)
Dockery continues, “To a certain extent, these good bacteria function through competitive inhibition, but more importantly, some strains of bacteria like the beneficial oral cavity species, Streptococcus salivarius, can produce compounds called Bacteriocin-Like-Inhibitory-Substances (BLIS). These compounds are highly inhibitory to specific pathogenic bacteria. Probiotics derived from indigenous strains of these beneficial bacteria may help provide a front-line protection against unfavorable strains entering the body through the mouth and nose. Some of these strains, such as S. salivarius K12 have been extensively researched for safety and their ability to colonize in the human oral cavity. (4-10)
Another indigenous strain of S. salivarius is M18. This strain has several unique characteristics that make it a beneficial component of the oral microbiome. S. salivarius M18 produces BLIS compounds that inhibit several species of common bacterial species that contribute to tooth decay and gingivitis. It also secretes two enzymes that make the oral cavity less favorable to deleterious species. Urease is an enzyme produced by M18 that helps raise the pH of the oral cavity environment, making it less conducive to acidogenic bacterial strains that weaken tooth enamel. M18 also produces a dextranase that helps break down dextran, a carbohydrate that is an integral component of dental plaque. BLIS M18 is a probiotic sourced from S. salivarius M18 that has been shown in several studies to help promote healthy teeth and gums. (11-14)
Prebiotics are a type of fiber that the human body cannot digest. They are present in fiber-rich foods, such as fruits, vegetables, and whole grains. According to Dockery, “the benefits of dietary fiber are well-known, impacting such diverse areas as cardiovascular health, digestive health and weight. Most dietary fiber sources are complex polysaccharides. However, this has expanded to include oligosaccharides, which are composed of fewer monosaccharides (simple sugars). Oligosaccharides now make up most commercially marketed prebiotic fiber. (15)
Prebiotics persist intact through the digestive tract to the colon where they are fermented by bacteria and other microorganisms. Consumption of prebiotic foods or supplements can help ensure an optimal food source for colonic bacteria and production of the beneficial compounds (such as the short chain fatty acids) resulting from the fermentation process.
Though prebiotics can fairly easily be obtained through the ingestion of certain foods (such as oats that contain beta glucan, and apples, which contain pectin), many of the best sources for prebiotic fiber are foods such as Konjac root and seaweed, that are not regular parts of the western diet. Therefore, prebiotics are available in supplemental form. Some prebiotics are also antioxidants and can provide additional benefits to the human host.”
“Currently, there is no consistency in what is sold as a postbiotic,” said Dockery. “Some companies market products identified as postbiotics that are a blend of the beneficial by-products of microbial metabolism found in the supernatant or even single by-products such as butyrate. However, the International Scientific Association of Probiotics and Prebiotics (ISAPP) has recently set the definition as 'A preparation of inanimate microorganisms and/or their components that confers a health benefit on the host'. This definition includes the presence of killed microbial cells and cell fragments (usually from heat treatment) but notably omits the requirement of the supernatant, though it could be included in a postbiotic product.
Postbiotics appear to be the latest trend in the Biotics industry and do have some distinct manufacturing and marketing advantages over probiotics. Since they are not live microbes, shelf stability and survival through the gut can be much more predictable.”
Alexis Collins, Product Manager at Stratum Nutrition, said, “It is a relief to have an esteemed scientific body such as ISAPP provide us with a comprehensive definition of postbiotics. This will not only provide much-needed clarity for our customers but will also be the kick-off for postbiotic education for the end consumer. Stratum is proud to be the distributor of LBiome™, which fits the ISAPP postbiotic definition.
LBiome™ is a human strain-derived, heat-treated postbiotic (Lactobacillus LB) that has been used as a digestive aid for over a century. Researched in postbiotic form for over 100 years, LBiome™ is the “Pioneer in Postbiotics”, with 12 published clinical studies showing digestive health support for both adult and pediatric populations. (16-23) LBiome™ provides the digestive benefits of a probiotic and the formulation flexibility of a spore, with none of the stability or manufacturing concerns.
LBiome™ cells adhere to the gut lining, forming an enhanced environment for the gut microbiome, all while simultaneously strengthening the gut lining by supporting a healthy brush border and tight junctions. In addition, recent published research has shown LBiome™ to be bifidogenic, increasing populations of several species of beneficial Bifidobacterium in both an in vitro cell culture and in an ex vivo human fecal fermentation system. (24) These mechanisms of action produce fast results for calming lower GI upset, as seen in the many published LBiome™ clinical studies.
Growth of the Biotic Industry
According to the market research report "Human Microbiome Market by Product (Prebiotics, Probiotics, Food, Diagnostic Tests, Drugs), Application (Therapeutic, Diagnostic), Disease (Infectious, Metabolic/Endocrine), Research Technology (Genomics, Proteomics, Metabolomics) - Global Forecast to 2028", published by MarketsandMarkets™, the global Human Microbiome Market is projected to reach USD 1,598 million by 2028 from USD 894 million in 2025, at a CAGR of 21.3% from 2025 to 2028.
Dockery concludes, “Few other segments within the dietary supplement and functional foods industries have expanded and diversified to the extent that the “-biotics” segment has. This has presented tremendous opportunities for continued growth, and at the same time has resulted in the expected challenges such as where and when NDI notifications might be required, to the splitting of the Lactobacillus genus. At the same time, this expansion provides exciting opportunities for the introduction of new ingredients that will safely and effectively provide tremendous benefits that can potentially be customized to meet specific needs in the end-consumer.”
The research on prebiotics, probiotics, and postbiotics continues to expand as more and more information is uncovered about the positive functions that the human microbiome provides in supporting and maintaining human health.
For more information on formulating your next product with LBiome or one of our BLIS ingredients, BLIS K12 & BLIS M18, contact us here.
Illumnia Press Release: https://www.illumina.com/company/news-center/press-releases/press-release-details.html?newsid=2236383.
The NIH Human Microbiome Project. https://www.genome.gov/pages/about/nachgr/february2018agendadocuments/hmp_talk_feb_council_final_0206.
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