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The study of the gut microbiome has evolved over centuries, with innovative discoveries paving the way for disease treatment today. Extensive research has opened avenues of different areas of gut microbiology; from identifying common gut commensals to establishing new treatments such as faecal microbiota transplantation (FMT), scientists have expanded knowledge on the gut microbiome, beyond the imagination of the dedicated scientists who began this research centuries ago.
Advancements in technology have had a colossal impact on our understanding of gut microbiology. We now understand that all human faecal samples will yield numerous anaerobic bacteria when cultured appropriately. Indeed, 87% of the human intestinal microbiota can now be cultured using optimal conditions [1]. Since most of the gut microbiome comprises anaerobes, high quality anaerobic incubation conditions are essential. Anaerobiosis has been pivotal in the clinical setting, for example, with blood cultures previously yielding minimal anaerobic growth, but stricter anaerobic conditions have allowed more fastidious obligate anaerobes to thrive and grow. This has aided patient diagnosis and treatment, which is often a matter of life or death for blood infections.
From the 4th century to today, there have been countless developments in the world of gut microbiology. Probiotics and prebiotics have become popular worldwide, with supplementation being marketed in different forms, from yogurt drinks to capsules. On the other hand, treatments such as FMT have become established in the world of Clostridioides difficile infections (CDI), which if left untreated can be fatal.
Year |
Details |
|
4th century |
The first records of FMT note how Chinese physicians treated patients with human faecal slurry, termed as "yellow soup". This was used to treat severe diarrhoea and food poisoning - there was reported success. [2] |
|
1900 |
Bifidobacterium is found to be less abundant in formula-fed babies compared to breastfed babies, and this is subsequently associated with diarrhoea and gut disorders. H. Tissier proposes the idea of supplementing with Bifidobacterium, forming the foundation for prebiotics and probiotics. [3] |
|
1905 |
Pharmacies begin to sell lactic acid bacteria tablets, establishing the beginning of commercial probiotics and gut microbiome interventions. [3] |
|
1916 |
The first anaerobic jar is invented by McIntosh and Fildes. This is imperative for successfully growing anaerobes that colonise the gut. |
|
1919 |
Inspired by the work of Elie Metchnikoff, Issac Carasso begins producing and marketing yogurts containing strains collected from the Pasteur Institute. [3] |
|
1935 |
Minoru Shirota identifies a strain of L. casei isolated from the human gut microbiota that can tolerate the harsh conditions of the digestive tract. This strain was used by Shirota in Yakulk, a milk probiotic drink, that is still consumed today. [3] |
|
1958 |
Faecal enemas were used to treat 4 patients with pseudomembranous colitis. It is likely this was caused by a CDI, though FMT was not successfully used for CDI until the 1980s. [4] |
|
1971 |
Moringaga, a Japanese company, produces dairy products containing Bifidobacterium longum BB536 isolated from infant faeces. This leads to the launch of bifidobacteria-containing yogurts in France during the 1980s. [3] |
|
1980 |
Don Whitley Scientific launch the Whitley MK1 Anaerobic Workstation. A cabinet designed to incubate larger volumes of anaerobic samples but also provide space for anaerobic working conditions. |
|
1983 |
Lactobacillus rhamnosus GG is isolated and becomes one of the most studied probiotic strains. [3] |
|
2001 |
The first human genome is sequenced, marking a monumental step towards understanding the role of genetics, not just of humans but of our microbiomes, in chronic disease development. [3] |
|
2006 |
A model study shows obesity can be transferred by gut microbiota, establishing a link between metabolic diseases and the gut microbiota. This is pivotal for future research into metabolic disease treatment. [3] |
|
Late 2000s |
METAgenomics of the Human Intestinal Tract (MetaHIT) and International Human Microbiome Standards lay the groundwork for bioinformatics needed to analyse the gut microbiota. [3] |
|
2019 |
Akkermansia muciniphila improves metabolic parameters in humans in a clinical trial. This lays groundwork for the use of next-generation probiotics as postbiotics in nutrition. [3] |
|
2020 |
Don Whitley Scientific launches the GMP Isolator Range. These cabinets are designed for clinical and biopharmaceutical facilities, including those working in FMT. They combine strict anaerobic conditions with Grade A ISO3 laminar airflow meeting FDA, EU and PIC/S latest standards. |
|
2022 |
FDA approves the use of RBX2660 (Rebyota) for prevention of recurrent CDI in adults. [2] |
|
2022 |
Don Whitley Scientific launches the Whitley Incubation Box. A rectangular, transparent and stackable anaerobic box, designed to incubate small volumes of anaerobic work but stackable to save bench or incubator space. |
|
2025 |
Gut microbiology continues to be linked to diseases in other human organs. In addition to the link to metabolic diseases, dysbiosis of the gut microbiome is associated with liver disease. [5] |
|
2026 |
Don Whitley Scientific continue to work on product development and prepare to launch the new generation workstations. |
Gut microbiology is destined to evolve, and genetic technology advancements will likely be at the forefront of its future success. The use of multi-omics approaches as well as conducting larger-scale studies will provide novel results and help advance precision medicine. Next-generation microbiome studies are set to delve deeper into the gut microbial communities of the public and how they interact with the host. Along with larger cohort studies, this will provide a wider representation of gut microbial communities and understanding of how they can cause disease. Gut microbiology will continue to be a frontier in human medicine, and it is hoped that successful advancements will aid disease treatments and therapies.
Written by DWS Microbiologist Kirsty McTear
References
- Rosenberg E. Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts. npj Biofilms and Microbiomes [Internet]. 2024 Nov 23;10(1). Available from: https://www.nature.com/articles/s41522-024-00580-y
- Barron M. Fecal Microbiota Transplants (FMT): Past, Present and Future [Internet]. ASM.org. 2024. Available from: https://asm.org/Articles/2024/February/Fecal-Microbiota-Transplants-Past-Present-Future
- Hiol A, Veiga P. From the Laboratory to the Plate: How Gut Microbiome Science Is Reshaping Our Diet. The Journal of Nutrition. 2025 Sep. Available from: From the Laboratory to the Plate: How Gut Microbiome Science Is Reshaping Our Diet - ScienceDirect
- EISEMAN B, SILEN W, BASCOM GS, KAUVAR AJ. Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis. Surgery. 1958 Nov;44(5):854-9. PMID: 13592638.
- Yasmina Tashkent, Choo JM, Richard A, Wang Z, Calzadilla‐Bertot L, Vasil E, et al. Steatotic Liver Disease in Younger Adults is Associated With Altered Gut Microbiology. Liver International. 2025 Feb 25;45(3).
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