It is well known that a fibre-rich diet has beneficial effects on human health. What is less well known is that these effects are co-mediated by the gut microbiota, which converts dietary fibre into metabolites with unique physiological functions. And very few know how exactly gut microorganisms can utilize these complex carbohydrates. The molecular underpinnings of this process take us back to the beginnings of microbiome research and the laboratory of avant-garde researcher Abigail Salyers in Urbana, Illinois, United States in the late 1980s.
At that time, microbiology was dominated by the simplistic notion that a few model bacteria could help us understand the entire bacterial diversity. Abigail Salyers and her laboratory, instead, focused on anaerobic bacteria of the genus Bacteroides from the human colon. Her laboratory was particularly interested in how Bacteroides thetaiotaomicron degrades starch and other complex polysaccharides, a highly unusual research topic in those days. Using biochemical assays, they had already convincingly demonstrated that starch-degrading enzymes are associated with cells rather than being extracellularly secreted. In addition, they had shown that starch utilization included a binding step to a protein at the cell surface. They assumed that polysaccharides are subsequently transported across the outer membrane into the periplasmic space, where they are then degraded. Such an import process would ensure that only bacteria catabolizing starch profit from the degradation products, thus avoiding cross-feeding of other bacterial species of the microbiota and providing starch-utilizing bacteria with the ability to occupy a unique metabolic niche in the human gut. However, evidence for binding of starch to a cell surface site does not prove that such a binding is necessary for starch utilization. For the ultimate proof, it was important to show in intact cells that starch can only be used after binding. To address this, the genetic tools for Bacteroides, in particular transposon mutagenesis with Tn4351, which the laboratory had developed in previous years, proved to be groundbreaking. By characterizing a set of B. thetaiotaomicron transposon mutants, which could not grow on starch, Salyers and her team were finally able to elegantly show that binding of starch to the cell surface is required for starch utilization, and that the genes encoding binding site components are under the same regulatory control as the degradative enzymes. Although they were unable to grow on starch, the receptor mutants were still able to grow on shorter-chain oligosaccharides. This was to be expected, as the biochemical analyses had already revealed that the receptor prefers longer-chain polysaccharides.
In subsequent years, this early work served as the basis for the discovery of countless polysaccharide utilization loci in Bacteroides. Each locus is specialized in the degradation of specific plant or host glycans, and is crucial for the establishment of a niche in the host. Its genetic tractability turned B. thetaiotaomicron into one of the most-studied and thus best-understood gut microorganisms. Abigail Salyers herself became a strong advocate of the importance of microbial genetics in exploring the functions of gut microorganisms in their environment. Knowing full well that setting up a new genetic system is a tricky task and that overcoming the genetic intractability barrier is a mentally challenging and “lonely struggle”, she dreamed of a team effort, and a “well-funded army of scientists dedicated to constructing a genetic system for most of the organisms for which such systems are needed”.
Today, some three decades later, there are still no genetic tools for most of the species found in the human gut. Our poor understanding of something relatively ‘simple’ such as the transformation of gut microbiota species with DNA remains a major obstacle to broad-scale engineering of the gut microbiome. Although there have been notable advancements, such as the development of high-throughput genetic tools for key microbiota members and the ability to manipulate certain species in situ within communities, a significant breakthrough is still needed to increase the number of genetically tractable species. This breakthrough is essential for unlocking the functions of the millions of enigmatic genes in the human gut microbiome, which could prove to be important contributors to human health. Salyers’ pioneering efforts to go beyond traditional model organisms, her tireless promotion of genetic tools and her foresight that microbiome research could become a pre-eminent discipline in the coming decades seem more timely and more visionary than ever.
Anderson, K. L. & Salyers, A. A. Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron. J. Bacteriol. 171, 3199–3204 (1989)
Salyers, A. A., Bonheyo, G. & Shoemaker, N. B. Starting a new genetic system: lessons from Bacteroides. Methods 20, 35–46 (2000)
The author declares no competing interests.
About this article
Cite this article
Maier, L. Pioneering microbiome engineering. Nat Rev Microbiol 21, 630 (2023). https://doi.org/10.1038/s41579-023-00949-4