Over the last few years, scientists have found that the microbes hosted in the digestive tract (the gut microbiota or gut flora) perform key functions for health. Digestion, immunity and even mental health are extremely dependent on tasks carried out by the gut bacteria.
Now, two studies have found that the human gut hosts five hundred species of microbes – and seven million microbial genes – that were unknown until now. The proportion of the gut flora that had been hidden until now may hold essential information on the origin of a range of diseases (IBD and metabolic syndrome, among others), as well as the clues on how to cure them.
The two studies were published in Nature Biotechnology in July, and come from the efforts of the MetaHIT (METAgenomics of the Human Intestinal Tract) project, a European consortium working to explore the composition of human gut microbiota.
The first of the two studies focuses on expanding the catalogue of genes that belong to microbes of the gut flora. Previously, scientists had sequenced the genes in the intestine of 124 individuals, obtaining a list of 3.3 million genes belonging to microbes that live there. The current number of samples has increased to 1000, coming from patients from three continents (America, Europe and Asia). As a result, the catalogue has increased to 10 million genes. The next step for the scientists is to find what these genes do, in order to have a better understanding of the functions performed by the microbiota.
The second of the two studies pursues an even more ambitious goal: identifying new organisms in the microbiota, rather than identifying new genes. The expanded catalogue obtained in the first study is a list of genes; genes, however, don’t exist on their own: they are part of the genomes of organisms. It is not easy to identify to which microbe each gene of the catalogue belongs to, so to do this, researchers developed a new bioinformatics method that allows scientists to group genes in the catalogue to guarantee that each group makes up the genome of a specific microbe. By applying this method, the authors have found 500 species whose existence in the microbiota was previously unknown.
The basic idea behind the method is to find genes that always occur in similar abundance in different individuals. The group of genes that are in the same number in many people are likely “packed” together within the genome of the same microbe; this probably means that the genes are present in all those subjects. Using a computer method based on this idea, scientists have found many genomes of microbes. Surprisingly, not all of them were known to be present in the microbiota: rather, 500 organisms were new species.
“[In this work] you have a novel approach that is telling you that, still, today, most of the microorganisms inside the human gut have not been characterized, are not known. This is, to me, the lesson in this study”, said Professor Francisco Guarner, head of the Experimental Laboratory at the University Hospital Vall d’Hebron (Barcelona), and co-author of both studies.
Interestingly, some of the subjects analysed in the study had very few of these new species. By checking who these individuals were, the authors found that they all had Crohn’s disease, ulcerative colitis, or metabolic syndrome with an inflammatory component. These findings suggest that there is a correlation between suffering from these diseases and having less diversity in these unknown species. “These species, unknown until now, will possibly make the difference between healthy and unhealthy people”, said Guarner.
This information may open the door to new strategies aimed at recovering the presence of these species through nutritional intervention. In particular, providing patients with probiotics or prebiotics, that may help to balance their microbiota.
Giovana Martucelli is a nutritionist with a specialization in Clinical and Hospital Nutrition and practical training in Nutritional Therapy. She is currently a Master’s student in Gastroenterology at the Faculty of Medicine of the University of São Paulo (FMUSP), where she works as a researcher at the Laboratory of Nutrition and Metabolic Surgery of the Digestive System (METANUTRI/LIM-35).
With over seven years of research experience, she has built a strong background in the field of gut microbiota, with a particular focus on precision medicine. She is the author of several works presented at national and international conferences and has received awards such as the Best of ASPEN – GI Topics (2025) and the Research Travel Award (ESPEN, 2024).
Mónica Quinzo is a biomedical researcher working on her PhD about gut parasitic nematodes and vaccine research at the National Center of Microbiology in Madrid. She holds a bachelor’s in Biochemistry and a master’s in Immunology. She is passionate about the role of the gut microbiome in the modulation of host immunity in health and disease. She is really concerned about the importance of empowering people through scientific communication to enable conscious and healthier decisions. Follow Mónica on twitter: 
Konstantina Zafeiropoulou is a dietitian with strong scientific interest in the diet-microbiota interactions and their role in human health and disease. She holds a Master of Science in Human Nutrition from the University of Glasgow, during which she explored the involvement of gut microbiota in the etiopathogenesis of Celiac Disease and evaluated the gluten free diet-microbiota interactions. She is currently a PhD candidate at Amsterdam UMC unraveling the role of gut microbiota and long-term dietary patterns in the development of postoperative colorectal anastomotic leakage. Follow Konstantina on Twitter 