Coloured scanning electron micrograph of bacteria on the surface of a human tongue. The study reconstructed with unprecedented detail how the oral and gut microbiome are transmitted from person to person. Credit: Steve Gschmeissner/Spl/Getty.
The microbiome, the ensemble of microorganisms that live in the gut, mouth, and skin, influences general health, and is linked to diabetes, cardiovascular diseases, and cancer. The microbiome mainly reflects our mother’s, and then its composition evolves through adulthood, partly through social interactions.
Until now there was limited knowledge about how microbiome is transmitted, but a new extensive study1 shows that people in close social contact share a significant percentage of the bacterial strains in their gut and mouth. The study, coordinated by Nicola Segata from the University of Trento, shows that cohabitation influences transmission more than kinship. For example, in twins the rate of shared bacterial strains decreases as they grow older living apart. These results are consistent across populations in different areas with very distinct lifestyles and diets.
The researchers used data from nearly 7,000 stool and saliva samples used in previous studies and added nearly 3,000 newly-sequenced samples, obtaining thousands of metagenomes, each made of combined genetic data from all the microorganisms from a single individual.
“We included individuals from communities less often considered in microbiome studies, working with centres in Africa and South America to diversify our dataset”, says Mireia Valles-Colomer, post-doctoral researcher in the Segata Lab, and first author of the study.
The scientists estimated that on average mothers and their children share 34% of the bacterial strains in the gut , whereas members of the same household have 12% of the strains in common, and those who live in the same village share only 8%. On average, people living in different villages do not share any bacterial strains. As for the oral microbiome, people living together share on average 32% of strains regardless of kinship.
The researchers developed new computational strategies for the study. First, they needed to identify the bacterial strains in each metagenome. This is challenging since “each metagenome contains tens of millions of fragments made by around 100 nucleotides and each bacterial genome has around one million nucleotides”, explains Segata. “Understanding to which genome each fragment belongs is like facing the pieces of several puzzles all mixed up, and having to figure out to which puzzle each piece belongs”.
In 2019 Segata’s lab devised a method that allowed them to analyse fragments in the metagenome and compile a catalogue of nearly 150,000 bacterial genomes grouped in species2. “In the new work, we expanded it up to one million genomes”, Segata says.
The second step was to establish when two people really share the same strain. Since bacteria accumulate mutations, two samples taken from the same individual at different times do not have exactly the same genomes. The researchers built phylogenetic trees of each bacterial species, and found that the genetic distance between a pair of samples, taken from the same person, fewer than six months apart, is smaller than the distance between two samples from unrelated individuals. This allowed to find a threshold distance below which the two genomes could be associated to the same strain.
Scientists compared results in westernized (Europe, the US and Shanghai) and non-westernized populations (Argentina, a rural community in China, Colombia, Ghana, Guinea-Bissau, Tanzania), finding no significant differences. “Even if the microbiome of non-westernized populations is genetically richer, the transmission pattern is similar”, says Valles-Colomer.
“This is a comprehensive study that confirms some hypotheses on gut microbiome transmission and adds new knowledge on the oral microbiome”, says Maria Rescigno, who leads the Mucosal Immunology and Microbiota Lab at Humanitas Research Hospital in Milan. “Many of the highly transmissible species were unknown before this study, and this could inform research on the microbiome’s impact on non-communicable diseases.”
