The human microbiome has not only captured the attention of scientists, but also healthcare practitioners and the lay press. While initial studies focused on characterizing the gut microbiome in the context of both health and disease and the influence of environmental factors, there has been a shift in the field towards mechanistic research focusing on microbiome influence on host phenotype, with lots of unknowns, thus emphasizing the need for further advances.

Such increased interest in information related to the microbiome is reflected in the way the Gut Microbiota for Health (GMFH) digital community has reached more than 80,000 members from all over the world in 2019, including scientists, healthcare professionals and the general public.

Here are some of the breakthroughs in the field in 2019:


Host-microbe symbiosis in early life and its impact on maternal and neonatal health

Although current ongoing debate among scientists asks whether gut colonization starts during pregnancy or at birth, it is widely accepted that birth is the major microbial encounter for newborns.

A wide range of factors can affect microbial compositions in both the gut and human milk. After controlling for maternal antibiotics during labor, researchers showed that Caesarean sections may predispose newborns to respiratory infections in the first year of life, with Enterococcus, Bifidobacterium and Klebsiella driving the prediction.

The human milk microbiota is also a hot topic in early life research. Scientists have found that breast milk is an important source of fungi for the growing infant. Human milk oligosaccharides are also present in serum and may be predictors of gestational diabetes mellitus development in pregnancy.


Members of the gut microbiome beyond bacteria also matter

The contribution of non-bacterial microbial communities to shaping the gut ecosystem’s stability and affecting health outcomes remains poorly understood. Scientists from University College Cork have revealed that the viral component of the gut microbiome is highly individual and stable in healthy individuals, and correlates with predominant gut bacterial taxa.

Likewise, the fungal microbiota has been overlooked in digestive diseases. Although the gut mycobiota represents a tiny part of gut microorganisms, scientists’ main interest lies in understanding the influence bacteria and fungi can have on each other in the macro-environment.


Time to focus on the small intestinal microbiome for functional gastrointestinal symptom prediction

The majority of studies into irritable bowel syndrome (IBS) have focused mainly on the fecal or colonic microbiome. Saffouri and colleagues found that a different duodenum microbiome composition assessed using 16S ribosomal ribonucleic acid gene sequencing is a good predictor of functional gastrointestinal symptoms. In contrast, neither the appearance or resolution of small intestinal bacterial overgrowth (SIBO)—a classic reported cause of common functional gastrointestinal symptoms diagnosed by using quantitative cultures of jejunal aspirates or hydrogen breath tests—correlated with symptoms.


Beyond dietary fiber: sun exposure and cooking may also explain interindividual variability in gut microbiome

Diet and lifestyle may outweigh genetics in shaping gut microbiome. As nutrients are rarely consumed in isolation, scientists are exploring how dietary patterns affect the gut microbiota (e.g. in the context of inflammatory bowel diseases and non-Westernized populations).

Also interesting is the fact that mechanistic evidence has shown that the gut microbiota could mitigate the potentially detrimental effects of certain food groups such as red meat and may contribute to increasing the amount of blood available for transfusions.

Beyond microbiota accessible carbohydrates as a major fuel for gut microbes, scientists have recently turned to other nutrients to explain interindividual gut microbiome variability. A small new intervention study in healthy females is the first to report changes in the gut microbiota in response to ultraviolet light. And the effect was more vigorous in the subjects with vitamin D deficiency. Additionally, in both mice and humans, cooking can affect the gut microbiome and should therefore be considered a new covariable in microbiome studies.


Microbiota-gut-brain communication

Most of what we know about the relationship between gut microbes and mental health has been explored in animal studies. In 2019, Valles-Colomer and colleagues strengthened the link between changes in gut microbiota composition and depression and quality of life scores in two large population cohorts. The researchers also curated from literature 56 compounds that play an important role in proper nervous system function, which gut microbes either synthesize or metabolize, which represents a leap forward in mental health research.

However, scientists still struggle to elucidate the mechanistic underpinnings of gut-brain communication. Writing in Nature, Chu and colleagues have unraveled, in unprecedented detail, mechanisms by which the gut microbiota affects mice fear conditioning.


The human gut microbiome as a potential source of novel therapeutics and precision diagnostics

Non-invasive gut microbiome data is starting to be used as a means of developing tailored diagnoses and monitoring gut-related conditions. In 2019, Versalovic and colleagues developed a disease classifier based on microbial features and biochemical and molecular characteristics that enabled pediatric cases of IBS to be distinguished with an accuracy rate of around 80%.

Metagenomic analyses have allowed for a better understanding of gut microbes’ contribution to predicting clinical response to dietary interventions and exercise and to disease phenotypes.

The second phase of the 10-year NIH-funded Human Microbiome Project has provided one of the most comprehensive multi-omic datasets to date of host-microbiome dynamics in inflammatory bowel disease and prediabetes.

Finally, moving to a smaller scale, scientists have discovered 4,539 previously undescribed polypeptides with fewer than 50 amino acids produced by the commensal gut microbiome. Altogether, these data underscore the importance of moving from a one-size-fits-all to precision approaches for diagnosing and treating disease.


Probiotics and prebiotics

Research on the gut microbiome has also been accompanied by increased interest in probiotics and prebiotics as modulators of intestinal physiology. Moreover, rational selection of beneficial bacteria is being applied to the discovery of novel probiotics for controlling metabolic syndrome—as in the case of Akkermansia muciniphila—and stress relief—with Bifidobacterium longum 1714 presenting as a good candidate within probiotics, with its antidepressant and anxiolytic potential.

Although the effects of probiotics have been extensively evaluated under disease states, their role in healthy situations remains to be seen. A double-blind, placebo-controlled trial has found that the probiotic Bifidobacterium breve Bif195, taken for 8 weeks, is effective in alleviating Aspirin-induced ulcers in healthy adults. Additionally, prebiotics and probiotics could be used to improve the immune response of healthy volunteers receiving the influenza vaccination.

GMFH will continue to cover the important progress made in 2020 in understanding how our gut microbiota affects wellbeing and disease. We will also bring you more information on the 9th edition of the GMFH World Summit, to be held in Madrid (Spain) on March 7 and 8, 2020.


We wish you a very happy 2020. Don’t forget to stay tuned over the coming year!