Ultra-deep sequencing of the gut microbiomes of 167 Hadza people revealed an average of 730 species, compared to just 277 for an average Californian, while farmers in Nepal had an average of 436 microbe species.
The study, led by Justin Sonnenburg at Stanford University in California, also found the Hadza have diversities of not just bacteria, but also bacteriophages and archaea.
“We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing,” wrote the researchers in Cell.
“Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes.
“This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.”
Increased industrialization after the Second World War has been accompanied by dramatic increases in metabolic disease, cognitive diseases, and immune diseases, and there is a school of thought that the common underlying factor in all of this is a shift in our gut microbiota, or to put it another way, a loss of diversity. This was perhaps most famously summarized by Prof Martin Blaser in his book, Missing Microbes.
Prof Blaser (Rutgers) is one of the leaders of the Microbiota Vault, along with Maria Gloria Dominguez-Bello (Rutgers) and Professors Rob Knight and Jack Gilbert at the University of California at San Diego.
Outlining their proposal for the Vault in 2018 in the journal Science, the four researchers wrote: “A global repository of human-associated microbes should back up existing research collections, similar in principle to the inspiring example of the Seed Vault established in the permafrost of Svalbard Island in Norway to preserve the natural biodiversity of plants. We owe future generations the microbes that colonized our ancestors for at least 200,000 years of human evolution. We must begin before it is too late.”
There is also the suggestion that these vanishing microbes could be cultured and open up opportunities in the future for novel probiotics to support health.
One of the key groups in studies of disappearing gut bacteria are the Hadza people in East Africa. Previous studies have described that their gut microbiota is much more diverse and resilient to challenges like antibiotics than the gut microbiota of people in the Western world.
Sonnenburg and his team applied ultra-deep metagenomic sequencing to 351 fecal samples from the Hadza and comparative populations in California and Nepal. This led to sequencing of over 90,000 genomes from gut microbes, including bacteria, bacteriophages, archaea, and eukaryotes.
The data revealed that 44% of these were previously unrecorded in existing datasets such as the Unified Human Gastrointestinal Genome database and the Metagenomic Gut Virus (MGV) catalog.
Digging into the microbiomes further, the researchers identified a species of bacteria called Treponema succinifaciens that was completely absent from the Californian samples. Data from the Nepali microbiomes showed only partial presence for this microbe, a result that suggested this bacterium is vanishing as societies industrialize.
“The data generated in this study represents a one-of-a-kind collection of the human gut microbiome data from one of the last remaining hunter-gatherer populations,” they wrote.
“The Hadza are a modern people facing challenges related to land dispossession, hunger, and lack of access to education, healthcare, and political decision-making, although technologies, food, and medicines from urban centers are becoming increasingly available. The data generated from Hadza fecal samples in this study (collected in 2013–2014) may thus represent a critical permanent reference point for microbiome scientists to understand the impacts of industrialization on the gut microbiome.”
Published online ahead of print, doi: 10.1016/j.cell.2023.05.046
“Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes”
Authors: M.M. Carter, et al.