The Human Intestinal Microbiome—Its Development and Evolution

Klaus Mager

The article elaborates on the relationship between soil microbiomes and human gut microbiomes, emphasizing the interconnectedness and the impact of modern lifestyle changes on both. Here are the key points:

Abstract

Soil and the human gut contain approximately the same number of active microorganisms, while human gut microbiome diversity is only 10% that of soil biodiversity and has decreased dramatically with the modern lifestyle. We tracked relationships between the soil microbiome and the human intestinal microbiome. We propose a novel environmental microbiome hypothesis, which implies that a close linkage between the soil microbiome and the human intestinal microbiome has evolved during evolution and is still developing.

From hunter-gatherers to an urbanized society, the human gut has lost alpha diversity. Interestingly, beta diversity has increased, meaning that people in urban areas have more differentiated individual microbiomes. On top of little contact with soil and feces, hygienic measures, antibiotics and a low fiber diet of processed food have led to a loss of beneficial microbes.

At the same time, loss of soil biodiversity is observed in many rural areas. The increasing use of agrochemicals, low plant biodiversity and rigorous soil management practices have a negative effect on the biodiversity of crop epiphytes and endophytes. These developments concur with an increase in lifestyle diseases related to the human intestinal microbiome.

We point out the interference with the microbial cycle of urban human environments versus pre-industrial rural environments. In order to correct these interferences, it may be useful to adopt a different perspective and to consider the human intestinal microbiome as well as the soil/root microbiome as ‘superorganisms’ which, by close contact, replenish each other with inoculants, genes and growth-sustaining molecules.

Keywords:?soil biodiversity, human health, land use, lifestyle, gut microbiota, soil microbiology, global change, nutrition, organic-agriculture, urbanization

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In view of the functional similarities between the intestinal microbial community and the soil microbial ecosystem, a relationship between both appears possible. Looking at the entire ecological system, the human body and its microbes can be regarded as an extended genome [8].

In this context, we discuss the soil microbiome and its potential link to the (human) intestinal microbiome and assess the possible interrelation of the human intestinal microbiome and the soil microbiome.

The main factors that presumably determine the human intestinal microbiome are (i) host genetics and metabolism (heritage), (ii) lifestyle (environment) in particular, and (iii) diet and nutritional habits.

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The Human Intestinal Microbiome—Its Development and Evolution

The microbial diversity in the human gut is a coevolution between microbial communities and their hosts. “Ancient” microbes evolved symbiotically or communally with humans and are most likely beneficial rather than pathogenic.

Nutrition/diet was of paramount importance for the clustering pattern in primates. The microbial population of the human gut derived from the ancestors, individually from the mother through vertical transmission during gestation, during birth, and after birth through contact with maternal body sites, with the greatest contribution of the maternal gut. Within the first three years of life, the gut bacterial phylogenetic composition evolves to an adult-like community independent of the geographic area. Mothers are the source for the transmission of microbes and gut colonization during and after birth.

It is suggested that over time dietary intake has a stronger influence on gut microbial composition than host genetics. The GI microbiota can even influence host genes, thereby regulating energy expenditure and storage. Thus, gut community composition must be predominantly shaped by non-genetic factors related to the environment, including lifestyle and diet.

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The close link between reduced soil biodiversity (due to alkaline soil conditions) and gut microbial richness in baboons is an aspect that deserves particularly critical scrutiny in view of the global megatrend of biodiversity loss, especially for sustaining human health. Rural environments that are rich in microbiota, such as traditional farms, have been shown to have health benefits in humans. In pre-industrial times, small structured farms dominated and a large part of the population was working in the agricultural sector, pastoralists or hunter gatherers, and so their lifestyle was in close direct contact with nature (i.e., soil, plants,?Figure 1).

Our ancestors lived in close contact with the environment (a, a cycle for pre-industrial microbiota). In contrast, human activities such as urbanization, industrialization of agriculture, and the modern lifestyle, including the use of pesticides and antibiotics as well as hormones (medication), together the loss of direct contact with soil and feces has depleted the richness of and overlapping with microbiota (b, a cycle for industrial microbiota). This depletion of microbial richness in all compartments can substantially affect human health.

Therefore, we assume that the modern human lifestyle and the loss of direct contact with soil cause interruptions in the microbiological cycle in urban environments in contrast to pre-industrial rural environments. Soil is therefore a key primary source of a healthy intestinal microbiome of humans. However, the exact way how soil and the environment shape the human gut microbiome and how lifestyle changes affect the gut microbiome needs to be further elucidated. It is a dynamic research topic with relevance for preventive medicine.

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As these microbes disappear, the soil and its plants suffer; and so does our health, as we take in significantly fewer, and fewer types, of tiny organisms into our gut microbiomes; some of these microbes may actually be in danger of extinction, with the effects on human health not fully understood. Additionally, our diets have become reliant on monocultures of processed and fatty foods that do not properly “feed” our tenant microbes and keep them in balance, leaving us susceptible to diseases such as obesity, diabetes, and colon cancer.

In the same way that microbial diversity in?soil?is decreased by agricultural chemicals, our microbial gut diversity is reduced by antibiotics. Both antibiotics and synthetic pesticides have been critically important societal interventions, but the collateral damage to human and soil microbiomes has been “tremendous.” Figuring out how to restore and protect microbiomes —?in soil, in people, in oceans, and air — will be the work of researchers for many years to come, and essential to supporting all life on our planet. “Nurture your ecosystem,” says Mayer, “and it will take care of everything else.”

As quickly as we’re learning about the essentialness of these systems, though, we’re also actively destroying them with a variety of unsustainable practices. These have grave implications for climate change and the ways it affects disease, ecosystem function and food security.

Sources:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6780873/

https://foodprint.org/blog/soil-microbiomes/

https://www.nature.com/articles/s41579-022-00779-w

https://www.mdpi.com/2076-2607/7/9/287

Summary generated by ChatGPT 4.o?

The provided documents elaborate on the relationship between soil microbiomes and human gut microbiomes, emphasizing the interconnectedness and the impact of modern lifestyle changes on both. Here are the key points:

Abstract

• Microbiome Diversity: Soil and the human gut have similar numbers of active microorganisms, but the human gut microbiome diversity is only 10% of that found in soil. This diversity has decreased significantly due to modern lifestyles.
• Environmental Microbiome Hypothesis: There is a proposed close linkage between soil and human intestinal microbiomes that evolved over time. Urbanization and modern practices have led to a loss of beneficial microbes in the human gut due to reduced contact with soil, increased hygiene measures, use of antibiotics, and low fiber diets.
• Soil Biodiversity Decline: Agricultural practices, such as the use of agrochemicals, low plant biodiversity, and rigorous soil management, negatively impact soil microbiome diversity, which mirrors the decline in human gut microbiome diversity.
• Health Implications: These changes correlate with increased lifestyle diseases related to the human intestinal microbiome.

Introduction

• Soil Microbial Ecology: The diverse microbiota in soil are crucial for its primary productivity and nutrient cycling. Soil is a part of the human habitat, impacting health through direct contact and the ingestion of plants grown in it.
• Human Microbiome Research: The human microbiome, particularly the intestinal microbial community, plays a major role in health and disease. The microbiome is influenced by genetic, dietary, environmental factors, and microbial agents from soil.

Relationship Between Soil and Gut Microbiomes

• Microbial Ecosystem: Both the soil and human gut microbiomes are dynamic ecosystems that interact closely. The human body and its microbes can be seen as an extended genome, impacted by environmental microbial exposure.
• Microbial Diversity: Soil harbors more diverse microbial species than the human gut. The microbial composition of the human gut has evolved through close contact with soil over time.

Human Intestinal Microbiome Development

• Coevolution: Human gut microbiomes coevolved with their hosts. "Ancient" microbes that evolved with humans are typically beneficial.
• Environmental Impact: The human intestinal microbiome is shaped more by environmental factors than by host genetics. Urbanization and reduced contact with natural environments lead to lower microbial diversity in urban populations compared to rural ones.

Human Intestinal Microbiome and Lifestyle

• Impact of Urbanization: Urban lifestyles show lower exposure to beneficial environmental microbes, impacting the gut microbiome negatively. Early exposure to diverse environments can protect against autoimmune diseases.
• Hygiene Hypothesis: Less hygienic environments with rich microbial diversity can protect against allergies and autoimmune disorders.

Diet and Nutrition

• Dietary Influence: Modern diets high in processed foods and low in fibers reduce gut microbiome diversity. Traditional diets rich in plant-derived carbohydrates and fibers support a more diverse gut microbiome.
• Agricultural Practices: Conventional farming practices reduce soil biodiversity, whereas organic farming enhances it. The intake of diverse, unprocessed foods from biodiverse soils positively influences the gut microbiome.

Summary and Conclusion

• Interconnectedness: The soil microbiome is a crucial contributor to the human gut microbiome. Both systems are interlinked, and modern practices disrupting soil biodiversity also affect human health.
• Future Research: Further research is needed to explore the geographical and functional relationships between soil and human gut microbiomes to develop practices that support both human health and environmental sustainability.

For more detailed insights, the document suggests investigating the soil and root microbiota in greater detail, adopting sustainable agricultural practices, and considering traditional dietary habits to improve human health and maintain ecological balance