Lost Species and Vanishing Microbes
The impact of industrialisation on our gut microbiome
The story of human evolution is intertwined with a vast and complex microbial world. For millennia, our ancestors coexisted with a diverse array of microbes that played vital roles in digestion, immunity, and even mood regulation. However, with the dawn of industrialisation, this ancient partnership has been dramatically altered. Modern lifestyles — characterised by processed diets, reduced exposure to natural environments, widespread antibiotic use, and urbanisation — have triggered a profound shift in our gut microbiota.
Emerging research reveals that industrialisation has not only reshaped our microbial communities but has also led to the alarming loss of microbial species critical to our health. These changes have profound implications, many of which are only beginning to be understood.
The decline of fiber-degrading bacteria
One of the most significant casualties of the modern lifestyle is the population of fiber-degrading bacteria in our gut. In industrialised societies, there is a marked reduction in bacterial groups such as Ruminococcus, which specialize in breaking down complex plant fibers. This decline is largely driven by low-fiber diets, dominated by processed and refined foods, that fail to nourish these beneficial microbes. As a result, the gut ecosystem becomes less diverse and less resilient, weakening its ability to support overall health.
Increased horizontal gene transfer and emerging risks
Compounding the problem, gut bacteria in industrialised populations exhibit elevated rates of horizontal gene transfer — the exchange of genetic material between bacterial species. While this can sometimes lead to beneficial adaptations, it also facilitates the spread of harmful traits, such as antibiotic resistance. This hidden consequence of modern life threatens not only our gut microbiome but also broader public health.
Irreversible microbial loss across generations
Research suggests that the effects of industrialisation are not confined to one generation. Studies involving animal models show that a sustained low-fiber diet can lead to the extinction of specific microbial species. Once lost, these microbes may not be recoverable even if fiber intake is restored in subsequent generations. This irreversible depletion highlights the urgent need for preventive measures to protect microbial diversity before it is too late.
Environmental exposure and the microbial connection
In addition to dietary changes, reduced exposure to biodiverse natural environments plays a critical role in gut microbiome decline. Traditional societies, with their close interactions with soil, animals, and plants, harbor a far richer and more diverse gut microbiota. In contrast, urban dwellers living in sanitized, concrete environments miss out on this essential microbial enrichment. Reconnecting with nature — through gardening, outdoor activities, and less sterile living — may offer a pathway to restoring some lost microbial allies.
Health implications of a disturbed microbiome
The consequences of a disrupted gut microbiome are far-reaching. Decreases in beneficial bacteria that produce key metabolites, such as short-chain fatty acids, have been linked to a rise in inflammatory bowel diseases, obesity, diabetes, cardiovascular conditions, and even mental health disorders. What was once a harmonious partnership between humans and their gut flora is increasingly becoming a battlefield, with serious implications for modern health.
Conclusion: Charting a new path forward
Industrialisation has undoubtedly brought remarkable advances to human society, but it has also exacted a hidden toll on the invisible world within us. By understanding the depth of our connection to our gut microbes — and the factors threatening their survival — we can begin to make informed choices. Prioritising high-fiber, plant-rich diets, minimizing unnecessary antibiotic use, and fostering regular interaction with natural environments are vital steps toward rebuilding the rich, diverse microbiota that once thrived alongside us.
Our health, and the health of future generations, may well depend on it.
Additional Reading
Carter MM et al. 2023. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell https://doi.org/10.1016/j.cell.2023.05.046
Gopalan S et al. 2022. Hunter-gatherer genomes reveal diverse demographic trajectories during the rise of farming in Eastern Africa. Current Biology 32: 1852-1860. https://doi.org/10.1016/j.cub.2022.02.050
Guglielmi G. 2024. Industrial societies may be losing gut microbes that help digest plants. Microbiome Post
Tomofuji Y. et al. 2022. Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases. Cell Genomics 2, 100219. https://doi.org/10.1016/j.xgen.2022.100219
Willis K. 2024. To improve your gut microbiome, spend more time in nature. Wired https://www.wired.com/story/to-improve-your-gut-microbiome-spend-more-time-in-nature-kathy-willis/?utm_source=chatgpt.com
Very informative article