What our stomach microbes reveal about ancient human diets

Human diets have long served as a window into the past, offering insights into the habits and lifestyles of our ancestors.

These dietary patterns not only shaped early human survival but also influenced the evolution of our digestive systems.

Now, researchers have taken this concept further by examining the bacteria in our stomachs to uncover what our earliest human ancestors consumed.

The bacterial clue: A tale of Helicobacter

Helicobacter pylori, discovered in 1983, is a bacterium notorious for causing significant gastric diseases, including around a million cases of stomach cancer annually.

Its long association with humans – dating back to more than 100,000 years – suggests its likely role in many prehistoric stomach aches.

The study was conducted by Professor Daniel Falush of the Shanghai Institute of Immunity and Infection (SIII) of the Chinese Academy of Sciences, Professor Yoshio Yamaoka of Oita University, and Professor Kaisa Thorell of Gothenberg University.

Specialized strain of bacteria

The researchers analyzed nearly 7,000 Helicobacter genomes from around the world. Among their key findings was a highly distinct variant of Helicobacter, termed the Hardy ecospecies.

This variant emerged hundreds of thousands of years ago and spread around the world alongside humanity. It’s a specialized strain, designed to live in the stomachs of people with a principally carnivorous diet – those who consumed a lot of meat or fish.

This discovery suggests that our stomach bacteria today can inform us about the diet of our ancestors.

“We have made a substantial effort to collect bacteria from around the world, involving clinicians and researchers from more than 20 countries. This unprecedented collection of genomes will allow us to develop interventions and treatments suitable for every context,” said Professor Yamaoka.

Insights into early human diets

These bacteria were already silent passengers in our stomachs, adapting and evolving as our species stepped out of Africa more than 50,000 years ago.

The new ecospecies of Helicobacter identified in the study, known as Hardy, is significantly different from the more common type (Ubiquitous) by over 100 genes.

This discovery offers great insight into what these bacteria need to survive in our stomach and how diversity is maintained within bacterial species.

Exploring the diet of ancestral humans, it appears that in some parts of the world people relied heavily on fish or meat for sustenance due to the seasonal unavailability of plant material. These locations include Indigenous regions of Siberia and Northern Canada.

Intriguingly, the Hardy ecospecies has key genetic differences that could adapt it to the conditions found in a carnivore’s stomach, hinting at the dietary habits of early humans.

Bacteria surviving in acidic stomachs

One critical genetic difference between the Hardy and Ubiquitous strains lies in genes called ureases.

Ubiquitous Helicobacter pylori makes a urease protein that incorporates nickel atoms while most Hardy Helicobacter includes iron atoms instead of nickel.

This alternative urease helps Helicobacter survive in carnivores’ more acidic stomachs, which also tend to have higher iron availability and lower nickel.

Helicobacter’s battle with the immune system

“Helicobacter pylori can live in our stomachs for decades, in a constant running battle with the human immune system, which can result in gastric disease,” said Professor Thorel.

“The Hardy ecospecies differs from the normal Ubiquitous Helicobacter in many genes it uses to interact with stomach cells and immune system cells, implying a completely different strategy.”

“Understanding this strategy can provide new insights into the development of gastric diseases, including the often deadly gastric cancer.”

Ancestral tale of gastric bacteria

The analysis of nearly 7,000 Helicobacter pylori genomes from around the world concluded that the first modern humans were infected by two distinct types of this bacterium – the Hardy and Ubiquitous.

Both ecospecies spread out of Africa during the early human migrations; however, the Hardy ecospecies appears to have gone extinct in many locations.

Understanding why these ecospecies coexist in some populations but not others promises to shed new light on our prehistory and the ongoing burden of gastric disease that we continue to grapple with today.

The study is published in the journal Nature.

—–

Like what you read? Subscribe to our newsletter for engaging articles, exclusive content, and the latest updates. 

Check us out on EarthSnap, a free app brought to you by Eric Ralls and Earth.com.

—–