The most significant achievements in gut microbiome science in 2018

In 2018, the Gut Microbiota for Health (GMFH) digital community has reached an audience that includes scientists, healthcare professionals, and the general public, with 60,000 visits every month from all over the world.

These changes reflect an increased awareness of how the gut microbiome influences health. Meanwhile, the number of publications focusing on the gut microbiota in 2018 has hit 4,900, which represents the highest number of published scientific papers on the topic over the past two decades.

Here are some of the areas that have shown the most significant progress this year in gut microbiome science:

Early life gut microbiome

Three longitudinal studies with large cohorts have shown the potential role of the early-life gut microbiome as a biomarker for identifying children at risk of developing obesity and type 1 diabetes (T1D) later in childhood. These findings reinforce the fact that genes related to important functions—including fermentation and the biosynthesis of short-chain fatty acids—are more relevant than particular taxa in predicting the subsequent development of metabolic and autoimmune diseases in childhood.

Particular attention has also been paid to the role of early-life mycobiome establishment in infant health.

Nutrition and the gut microbiome

Environmental factors related to diet and drugs are the largest determinants of gut microbiota composition. In fact, the World Gastroenterology Organization has launched new guidelines to provide physicians with science-based recommendations to improve patients’ gut health through diet.

Instead of studying the impact of isolated nutrients on the gut microbiome, scientists have started elucidating how macronutrients (e.g. omega-3 polyunsaturated fatty acids), micronutrients and food additives affect the gut microbiota in the context of broader dietary patterns. The metabolic outputs of those processes may have significant impacts on human physiology, as in the colonization resistance effects mediated by propionate.

Regarding the effects of specific food groups and nutrients, new observational data has found that fermented dairy products are associated with a healthier lifestyle and greater adherence to the Mediterranean Diet in people with high cardiovascular risk. On the other hand, a review reveals that the benefits of fiber for the gut microbiota in healthy adults rely on the type of fiber being ingested, as the key element is the degree of fermentability rather than fiber solubility.

Non-antibiotic drugs and the gut microbiome

In vitro research has found that many non-antibiotic human-targeted drugs—including proton-pump inhibitors, antipsychotics, and metformin—may have a direct effect on the gut microbiome that potentially contributes to their gastrointestinal side effects, therapeutic actions, and even antibiotic resistance.


A new review updates evidence-based probiotic interventions considers fermented foods in relation to probiotics and addresses some regulatory challenges in the probiotic field. The new scientific evidence that supports probiotic use in healthy adults is also worth mentioning, including the role of probiotics in changing brain activation patterns.

When it comes to commercialized probiotics, changes are coming in the nomenclature of the genus Lactobacillus. Many probiotic lactobacilli will likely be renamed and no longer be part of the Lactobacillus genus, which will have scientific, commercial, regulatory and intellectual property implications. In addition, specific probiotic health benefits are beginning to be associated with higher taxonomic groups rather than strain.

Gut barrier

The protective effects of the gut microbiota on intestinal homeostasis and beyond the gastrointestinal tract are determined by a functional intestinal barrier. New research in mice has provided relevant mechanistic insights into how gut microbes are critical for the maturation of the intestinal barrier’s structure and functionality.

When restoring high fat diet-induced intestinal barrier dysfunction, the probiotic strain Lactobacillus rhamnosus CNCM I-3690 has been shown to have beneficial effects in mice.

Antibiotic resistance

We are currently facing a disproportionate antibiotic resistance epidemic, led by both an increase in outpatient antibiotic use and the high amounts of antibiotic-resistance genes in gut commensals. It has been found that the mother’s gut and breast milk microbiota constitutes a significant source of antibiotic resistance genes in the infant gut.

Scientists have also developed a new method that provides a mechanistic understanding of the genes that confer resistance to antibiotics in the gut microbiota. Although the human intestinal microbiome is considered a major reservoir for antibiotic resistance genes (over 6,000 genes), fortunately, most of them are associated with intrinsic commensal microbiota and are rarely shared with bacterial pathogens.

The gut-brain axis

The past decade has seen a paradigm shift in our understanding of the microbiota-gut-brain axis. With the discovery of “neuropod cells”, scientists have found new evidence detailing how nutrients in the gut lumen communicate rapidly with the brain. The researchers conclude that these new mechanisms may be the first to sense nutrients that immediately reach the gut after a meal, even before the gut hormones involved in satiety are released.

Gut microbiota resilience

Although we still lack a definition of a healthy gut microbiome due to its complexity and intra- and inter-subject variability, gut microbiota resilience is emerging as a potential biomarker of health. Indeed, the resilience of the gut microbiota in response to different perturbations may be considered a healthy feature. After receiving doses of 3 powerful antibiotics, the gut microbiota in healthy people made a nearly full recovery after 1.5 months with no intervention (only 9 species were missing after 6 months).

In 2019, GMFH will continue to cover the important progress made in our knowledge of the gut microbiota’s impact on wellbeing and disease. We will also bring you more information on the 8th edition of the GMFH World Summit, to be held in Miami on March 23-24, 2019.

We wish you a very happy 2019. Don’t forget to stay tuned over the coming year!