UPFRONT | News and events NUTRITION Persistence pays off in the human gut microbiome The human gut microbiome How is the human gut micro-biome sustained? Researchers in the UK and Germany, alongside other international collaborators, have investigated the evolu-tion of bacteria in the human gut microbiome --asking how these microbes persist throughout their lifetimes --taking into account internal and external influencing factors. The results of the study will help inform tailored probiotics, live bacteria found in particular foods or supplements, as well as die-tary or medical interventions, to treat gut disease and main-tain a healthy gut microbi-ome. Lead author and Group Leader Dr Falk Hildebrand from the Quadram Institute and Earlham Institute, ex-plains: “We know that certain microbes colonize us at birth, and some can live with us for decades. Yet, although stud-ies have looked at individual microbe species, the mecha-nisms and scale of persis-tence in the microbiome as a whole haven’t been ex-plored.” Scientists at the Earlham Institute and Quadram Insti-tute on the Norwich Re-search Park, along with the European Molecular Biology Laboratory (EMBL) in Ger-many, used metagenomics to analyse the evolutionary strategies and persistence of different bacteria in the hu-man gut microbiome. Metagenomics is the study of all of the genes from many different organisms in a pop-ulation. This process not only provides detailed informa-tion about the bacteria strains present but also indicates the enhancing ca-pabilities of those different strains, based on their genet-ics, to keep the gut in good working order. From analysing stool sam-ples, the team re-examined metagenomes from over 2,000 adult and infant sam-ples, including several from the same families and found three major dispersal strate-gies underlying human gut bacterial persistence. The data came from previously published studies looking at microbiome changes over time, with each individual providing on average 2-3 samples several months apart. The data was built into a diverse dataset of 5,278 metagenomes, which were probed to analyse patterns of persistence in the different types of bacteria and how these were influenced by the common factors: age, family members, geographic region, and antibiotic usage. “Some microbe species did show consistent differ-ences being either highly persistent taxonomic groups, or being low-persistent, rely-ing more on exchanges be-tween family members. In babies, however, the average persistence of bacterial strains dropped to 80%. This isn’t unexpected; we know that especially in newborn babies there is an ongoing exchange of gut microbes,” said Dr Hildebrand. “Antibiotics had different effects of different types of bacteria, with the overall ef-fect depending on how resil-ient different bacteria are, their intrinsic persistence, and to what extent they were replaceable within the micro-biome.” To delve deeper into what drives persistence, the re-searchers compared microbi-ome communities beyond an individual level, but also across families, countries and regions. This allowed them to group bacteria based on their persistence characteristics and, through genomic analy-sis, look for clues to the evo-lution of these groups’ strat-egies in dispersing among new human hosts. The first group, termed ‘tenacious’ bacteria, were the most persistent and well adapted for survival in the human gut. For example, these bacteria were able to survive by switching to differ-ent nutrition sources as the host moved through infancy and into adulthood. Tenacious bacteria, how-ever, are the ones most likely to be lost from the microbi-ome following antibiotic use. If we have been carrying these bacteria in us since childhood, their loss may be permanent. This is a particu-lar concern in relation to over-and misuse of antibiot-ics. Another group was termed the ‘heredipersistent’ bacte-ria, which are strains that are ‘inherited’ and cluster within families. These have a lower persistence in childhood and a higher turnover rate, sug-gesting cycles of reinfection is key to their persistence in an individual. Genomic analysis showed that these bacteria tend to have genes allowing them to spread by spores, which would help transmission from, say, a parent to child, but also across a family unit. A third group, named ‘spa-tiopersistent,’ appear to cluster to their own geo-graphic areas, but not associ-ated with families. With much current inter-est in maintaining or manip-ulating the microbiome for health, the research team hopes their holistic explora-tion of the evolution of differ-ent persistence in gut mi-crobes will lead to better, more well-informed clinical strategies. “Our study gave us a much better idea of which gut bac-teria are closely associated with their host, and which are more prone to switch be-tween hosts. This is impor-tant information to inform pro-prebiotics and most medical applications,” added Dr Hildebrand. — Earlham Institute. www.Cndoctor.ca 6 Chiropractic and Naturopathic Doctor July/August 2021 Photo: ovocheva / Adobe Stock
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