From the Gut Up: The Latest Breakthroughs in Microbiome Research

Gut health is one of the hottest trends of the last few years, yet many people are confused about what it actually means and how it impacts our daily lives. While the idea of having a healthy gut may seem like just another fad, the science behind it is rooted in decades of research and studies. In this series of articles, we aim to delve into the mechanisms and science behind gut health, including its composition, functions, and how to maintain a healthy gut with longevity in mind. Whether you’re already a health enthusiast or just looking to improve your overall well-being, this series is for you.

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This article is part one of a four-part series on the microbiome and longevity.

1. From the Gut Up: The Latest Breakthroughs in Microbiome Research
2. Gut Feelings: The Surprising Links Between Gut and Your Body’s Vital Organs
3. The Clockwork of Microbiome-Based Aging: Tracing the Lifelong Impact of the Gut Microbiome
4. Bacterial Botox: Microbiome-Based Interventions for Timeless Health

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A First Look at your Microscopic Allies

Getting punished for not washing your hands before eating might feel familiar, and that’s because of the importance of keeping our hands clean to avoid the spread of harmful microbes. We grew up thinking that microorganisms such as bacteria, viruses, or fungi are bad, and they must be annihilated to preserve our health and well-being. On top of that, COVID has taken this conception to the extreme, pushing us to isolate ourselves from one another, sanitise our hands hourly, and wipe up any surface. 

Surely, this is justified by the multitude of debilitating diseases that are caused by germs. They span from pneumonia (Streptococcus pneumoniae) to meningitis (Haemophilus influenzae), food poisoning (Escherichia coli and Salmonella), and more (Chess & Talaro, 2021). However, not all microorganisms are harmful. There are 10 to 100 trillion microorganisms (Sender et al., 2016) that are essential for the human body to survive and thrive. 

The Essential Role of Microorganisms in Human Health

Scientists have long believed that there must be a purpose behind our preservation of microbes, as humans have never existed without a microbiome. Years of research led to the discovery that microbes play a crucial role in a variety of human physiological processes, including digestion, immunity, and mental health (Gilbert et al., 2018). As a result, experts have reached a consensus to proclaim the microbiome – a new and vital organ of the human body (The Human Microbiome Project Consortium, 2012). 

Microbes are found all over our body: on our skin, in the cavities of the ear, nose, and throat, in the lungs, intestine, reproductive organs, and urinary tract (Gilbert et al., 2018). We are basically home to several microorganism ecosystems, and despite this universal presence, as humans, we share 99.9% of our genome, but 80-90% of a person’s microbiome profile is unique (Lloyd-Price et al., 2016).

The Human Microbiome and its Various Components

The largest reservoir of microbes and bacteria is the intestine, and the study of the gut microbiome refers to the vast research around the bacterial composition (bacteriome) of the intestinal environment (The Human Microbiome Project Consortium, 2012). However, there is a rapidly expanding field of research that is focused on exploring the remaining components of this wide ecosystem, including viruses (virome), fungi (mycobiome), archaea (archaeome), and helminths (macrobiome) (Vemuri et al., 2020) which exert significant influence in preserving the delicate balance within the gut. 

In addition to the term “microbiome,” there are several other keywords to become familiar with to have a comprehensive understanding of this field. For example, while people have used them interchangeably, “microbiome” and “microbiota” have a distinct difference. 

“Microbiota” refers to the actual microorganisms found in each environment, while “microbiome” encompasses both the microorganisms and their genetic information (Lloyd-Price et al., 2016). Additionally, “metagenome” refers only to the genes of microorganisms in that specific environment (Handelsman, 2004). 

Regarding general health and self-care, the two important concepts are “dysbiosis,” which stands for an imbalance in the types of microorganisms present in a person’s gut associated with many health problems (Petersen & Round, 2014); and “gut health” which is achieved when there is a lack of gastrointestinal issues and diseases, as well as of other unfavourable local conditions (Staudacher & Loughman, 2021).

Understanding Key Terms and Concepts in Microbiome Research

An illuminating analogy exists to facilitate visualisation of the gut microbiome. Imagine it as a thriving rainforest, where diverse organisms and species coexist in a harmonious balance within your intestine. A greater variety of species makes the ecosystem more productive and resilient to disturbances or change; as a result diversity is a hallmark of a healthy microbiome (Lozupone et al., 2012). 

Like in ecology, the diversity of the human gut microbiome is critical and can be described through the concepts of species evenness, which refers to the distribution of various species within the community, and species richness, which refers to the number of unique species present (Costello et al., 2012). 

Each species (e.g., Acidophilus) is assigned to a genus, resulting in a two-part scientific name (e.g., Lactobacillus Acidophilus). This naming system is based on a hierarchy of ranks that groups species based on common traits (Fig 1).

The breakthroughs in the realm of gut microbiome and the identification of numerous microorganisms have been achieved through the advent of the Next Generation Sequencing (NGS) technologies in the 21^st century (Wensel et al., 2022). Some of the most used methods, also utilized by gut microbiome sequencing companies worldwide, include:

• 16S ribosomal RNA (rRNA): it is based on the sequencing of the 16S rRNA gene, which is present in all bacteria and is highly conserved among different species.
• Whole genome shotgun (WGS): involves sequencing of the entire DNA content of a microbial sample.
• Metagenomics: encompasses all methods of analysing the genetic material of complex microbial communities. It can be performed using any of the above methods, or a combination of them.
• Metatranscriptomics: focuses on analysing the transcripts, or RNA, of a microbiome. This approach provides insight into the functional potential of a microbiome, as transcripts reflect the genes that are actively being expressed and translated into proteins.

The Gut Microbiome Beyond Digestion

Despite their tiny size, the human gut microbiome is an organ of substantial weight, averaging at an impressive three pounds. This is even heavier than the human brain. The sheer number of microorganisms in the microbiome is staggering, equating to the number of cells in an average human body (Sender et al., 2016; The Human Microbiome Project Consortium, 2012). Thus, it is correct saying that we are 50% human and 50% bacteria (Sender et al., 2016).

Yet, the true marvel of the gut microbiome lies in its gene expression, which outpaces that of human cells by a factor of 100. This capability gives rise to functions beyond the potential of the human body, rendering it a critical and integral component of human physiology (Gilbert et al., 2018).

The Multifaceted Functions of the Gut Microbiome

Given its location, it must not be surprising that bacteria in the gut play a crucial role in aiding the digestive process (Oliphant & Allen-Vercoe, 2019). Normally, the human digestive system undergoes a process of breaking down food into smaller components, which are then made accessible for assimilation. This involves mainly the reduction of carbohydrates, proteins, and fats. However, the large intestine (also known as colon) receives, in addition, undigestible carbohydrates from our diet that would otherwise be eliminated through the stool. But thanks to the activity of some of the bacteria in the gut, these undigested substances are transformed into useful compounds that support our health (Oliphant & Allen-Vercoe, 2019). 

Studies conducted among malnourished children found that a group of 14 gut bacteria was associated with the severity of stunning. To investigate the causal relationship, the authors transplanted these 14 strains into germ-free mice (raised under sterile conditions with no microbiomes). The mice that received the gut microbes from the malnourished children developed the characteristic inflammatory changes and disruption of the small intestine lining seen in environmental enteric dysfunction (Chen et al., 2020), supporting the evidence that the gut microbiome plays a critical role in nutrient absorption. 

Among the microbiome products, the short-chain fatty acids (SCFAs): butyrate, propionate, and acetate are the most studied. SCFAs can act as signalling molecules, able to reprogram gene expression in humans. They stimulate G protein-coupled receptors (GPCRs), the largest group of membrane receptors, and suppress histone deacetylases (HDACs), a well-studied anti-cancer function (Koh et al., 2016). 

• Butyrate serves as a crucial source of energy for the cells that compose the inner lining of the human colon (colonocytes). It also induces apoptosis (self-destruction) in colon cancer cells and activates intestinal gluconeogenesis (production of glucose in the body), which is significant for energy balance and diabetes management (De Vadder et al., 2014). 

• Propionate regulates gluconeogenesis in the liver and plays a role in regulating feelings of satiety (Canfora et al., 2015). 

• Acetate has a notable impact on the regulation of metabolism in tissues outside of the intestine, including cholesterol metabolism and lipogenesis (creation of fats) (Perry et al., 2016). 

Nutrient Absorption and Vitamin Synthesis by the Gut Microbiome

The gut microbiome also plays a crucial role as a provider of essential vitamins. While vitamins can be found in many different types of food, vitamin deficiencies are still a common issue, largely due to poor nutrition resulting from inadequate food intake and unhealthy eating habits. Studies have shown that some members of the gut microbiota (Lactic acid bacteria, Bifidobacteria, Pseudomonas, Klebsiella sp.) can synthesize vitamin K and most of the water-soluble B vitamins, such as biotin, cobalamin, folates, nicotinic acid, pantothenic acid, pyridoxine, riboflavin, and thiamine (LeBlanc et al., 2013). 

Unlike dietary vitamins, which are absorbed in the upper part of the small intestine, the majority of the vitamins produced by gut bacteria are taken up in the colon and assimilated into host tissues. This suggests that microbiome-produced vitamins have higher bioavailability than the common multivitamin pill (Albert et al., 1980; LeBlanc et al., 2013).

Pathogen Defense and Immune System Development

Another crucial function of the gut microbiome is to keep pathogens at bay by occupying all the available niche in the human gut and thus outcompeting them for the liveable space (Kamada et al., 2013). Commensal bacteria produce bacteriocins, which are protein toxins that specifically target members of the same or similar bacterial species. Additionally, they help to prevent pathogen infection by altering the host environment in a way that makes it inhospitable to pathogens. 

For example, bacteriocins consume unused oxygen, compete for nutrients, and change the pH levels to make it unfavourable for pathogen colonisation. 

Going back to the rainforest analogy, the bacterial species in our gut live a delicate balance competing for survival (Kamada et al., 2013). In an elegant mouse study, the authors found that the disruption of the gut microbiome via antibiotics increases susceptibility to Clostridium difficile infection (Theriot et al., 2014), supporting the idea that a strong gut microbiome is needed to fight pathogens and infections.

Moreover, the gut microbiome indirectly safeguards the host by participating in the development of the immune system. The intestine, being abundant in immune cells, allows for active interactions between these cells and microorganisms, fostering immune tolerance. It is estimated that 70-80% of the body’s immune cells are in the gut forming what is known as the Gut Associated Lymphoid Tissue (GALT) (Mörbe et al., 2021; Wiertsema et al., 2021). Small immune cells within the GALT use their dendrites to probe the gut barrier and assess the antigens present in the lumen. Based on this evaluation, trained by the individual’s own microbiome, they can either initiate an inflammatory response by activating T-helper cells or an anti-inflammatory response by activating T-regulatory cells (Mörbe et al., 2021). 

In another brilliant animal study, inflammation of the lungs and allergic airway was observed after inducing alteration of the gut-microbiome using antibiotics (Cavalcante et al., 2022).

Impacts on Human Health and Disease

The training of the GALT begins immediately upon the rupture of the amniotic sac when the newborn gets exposed to millions of bacteria from the external environment. Following the baptism with outside bacteria, it takes approximately three years for the gut microbiome to build up, diversify, and stabilise through a variety of factors such as the consumption of breast milk, exposure to pets, interaction with siblings, and more (Romano-Keeler & Sun, 2022; Ronan et al., 2021). 

It has been demonstrated through research that the reduced diversity and imbalanced microbiome development, typically occurring within the first 1000 days of life, may result in an increased susceptibility to allergies and autoimmune diseases in the long term (Hu et al., 2021). Birth via caesarean section, for instance, has been shown to result in a substantially different microbial composition compared to those delivered through the vaginal canal, and is also associated with heightened occurrences of asthma and allergies (Stokholm et al., 2020).

With the aim to illustrate the up-to-date crucial role of the gut microbiome in immunity, a group of scientists investigated the microbiome diversity of 106 individuals who had varying levels of COVID-19, in comparison to a control group of 68 individuals who were COVID-free. Long-COVID, which is marked by persistent symptoms that can last for weeks or months after infection, is characterised by widespread symptoms such as fatigue, weakness, and insomnia. The results showed that patients who experienced long-covid had a microbiome that was less diverse and abundant, whereas those who did not experience long-covid had a gut microbiome that was similar to those who had never had COVID-19. Further analysis of the microbiome of those with long-covid revealed that it was deficient in bacteria known for boosting immunity (Liu et al., 2022).

Beyond the above mentioned essential functions, the gut microbiome has a significant impact on human health. It has been shown to have a direct connection with a variety of diseases, including mental health disorders, cancers, autoimmune and inflammatory conditions, metabolic disorders, and others. The relationship between the gut microbiome and sickness has been widely documented, leading to the consensus that as much as 90% of all diseases can be traced back to the health of the gut microbiome (Ahlawat et al., 2021). The interconnection between the gut and other vital organs results in the formation of “gut-organ axis” which refers to the wide-reaching effects of the gut microbiome, which we will be covering in the next article of this series. 

The Dynamics of the Gut Microbiome 

As previously mentioned, the microbial makeup of an individual changes throughout their lifespan and is most consistent during adulthood, with species belonging to Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria dominating the gut (Rinninella et al., 2019). However, after the age of 60, the gut microbiome undergoes a final rearrangement, losing diversity due to a weakened immune system, increased medication use, and residing in care homes. 

Unique Composition and Healthy Aging

Besides the diversity, recent research featuring 9,000 individuals across three different cohorts suggests that an increasingly unique composition of the gut microbiome is a crucial component of healthy aging (Wilmanski et al., 2021). In mid-to-late adulthood, microbiomes become more personalized, and those with a more individualized microbiome tend to have better clinical laboratory results, physical health, mobility, and require fewer medications (Wilmanski et al., 2021). 

Gut Microbiome in Centenarians

Recent studies on centenarians from various countries, including Italy, Russia, China, and India, found that their microbiomes are characterized by lower levels of symbionts associated with younger age groups and higher levels of alternative health-associated taxa, such as Akkermansia spp., and disease-associated bacteria (pathobionts) (Kashtanova et al., 2020; Tuikhar et al., 2019; Wang et al., 2019; Wu et al., 2019). 

Another study conducted on 160 centenarians with an average age of 107, found that they had higher levels of bacterial species producing secondary bile acids (isoalloLCA) which act as a natural antibiotic in the gut, pacifying pathogenic species and maintaining immune homeostasis (Sato et al., 2021). 

Enterotypes and Diet Influence

Although it’s difficult to distinguish between cause and effect in the relationship between microbiome and aging, there are certain functions that could contribute to a negative cycle of health decline. For example, some of the pathobionts that increase with age, release lipopolysaccharides (LPS) and DNA-damaging toxins that contribute to inflammation, oxidative stress, and cancer (Ghosh et al., 2022). 

Although there is still some disagreement on what constitutes a healthy gut microbiome (Rinninella et al., 2019), studies on large groups of humans have uncovered some consistent characteristics of the intestinal microbiota that are associated with health or, more accurately, with the absence of disease. In the effort to group people based on their gut microbiome, the term “enterotype” was introduced in the scientific community in 2011 to describe clusters of bacterial communities in the gut that are linked to specific long-term dietary habits (MetaHIT Consortium (additional members) et al., 2011):

• Enterotype 1: Bacteroides-dominant, which is found in individuals who consume high levels of animal protein and fats, as well as refined sugars.
• Enterotype 2: Prevotella-dominant, which is found in individuals who consume high-fiber, whole-food diets that include grains, legumes, vegetables, and fruits, as well as refined carbohydrates like sweets and pastries. 
• Enterotype 3: Ruminococcus-dominant, which is found in individuals who consume a diet that is rich in dietary fiber and resistant starches but has limited variety. This enterotype reflects the dietary choices and stability found in rural, farming communities. 

It should be noted that the concept of enterotypes is still contentious due to the difficulty of developing rules and identifying systems to organize such a dynamic ecosystem as the human gut microbiome. Nonetheless, there is currently enough theory and evidence to suggest that enterotypes represent a promising direction for microbiome research.

Among other factors such as medication, exercise, stress levels, social life, and chronic diseases, diet is the most extensively studied that affects the gut microbiome composition. A 2013 pilot study found that microbial communities could respond to dietary changes within just three days (David et al., 2014), but such changes are usually temporary and do not affect the core taxa, which remain stable (Leeming et al., 2019). 

Shaping Your Inner Ecosystem

Long-term dietary changes are required to make lasting alterations to the gut microbiota. Recently, a randomized clinical trial from Stanford University showed that a 17-week fermented foods diet is an effective approach for improving decreased microbiome diversity and increased inflammation that are prevalent in industrialized society (Wastyk et al., 2021).

What small, evidence-based, long-term changes can you introduce to improve your gut health? 

High-fiber diet: this is not another blog telling you that the only way to increase fiber and optimal gut health is via consumption of a variety of fruit and vegetables. Surely, veggies and fruit are great sources of undigestible fibers that benefit the good bacteria in your gut and health, as we described above. A high fiber diet was proven to lead to changes in microbiome function and personalized immune responses (Wastyk et al., 2021). However, there are other more creative ways to consume a high-fiber diet such as including seeds, nuts, and legumes to your meals, as we recommend in the NOVOS Longevity Diet. Seeds (e.g., chia, sunflower, flax, pumpkin, sesame seeds) are great toppings for your smoothies, yogurt, salad, bread, granola, and more. Similarly, nuts (e.g., almonds, Brazilian nuts, cashew, hazelnuts) can be added to many foods, or consumed as separate snacks. Legumes are a perfect substitute for refined carbohydrates, like rice or pasta. Due to the presence of raffinose, a complex carbohydrate, legumes might cause a little extra gas at first. However, studies have shown that the gas levels will return to normal once you are eating legumes regularly (Winham & Hutchins, 2011).

Fermented food: this is ideal to introduce new bacteria into your gut ecosystem and increase microbiome diversity (Wastyk et al., 2021). However, not all fermented products are created equal, and it is important to be wary of false advertising. Many brands market their products as containing living cultures and probiotics when they do not. Additionally, some fermented products may contain high amounts of sugar (>10g per 100ml), which negates the potential health benefits of the probiotics. Therefore, it is best to opt for sugar-free options like kombucha, yogurt, kefir, buttermilk, kimchi, sauerkraut, nato, fermented vegetables, and vegetable brine drinks.

Drink coffee: an investigation into the microbiome uncovered a robust correlation between the ingestion of coffee and the structure of the gut microbiome. The research demonstrated that individuals who consumed coffee had a propensity towards greater microbiome diversity, in a dose-dependent manner. More precisely, those who consumed up to four cups of coffee daily exhibited a gut microbiome of increased diversity, in contrast to those who consumed less coffee (Asnicar et al., 2021). We explore further the topic of coffee and its impact on longevity in this article.

Engage in social interactions: a recent study published in Science Advances suggests that social interaction may be linked to a healthier, richer, and more diverse microbiota in chimpanzees, which could lead to a longer and healthier life. After an eight-year research project in Gombe National Park in Tanzania, scientists discovered that chimpanzee social interactions spread gut microbiome diversity within and between host generations. More frequent social interaction increases microbial species diversity within individual microbiomes and promotes similarity in the gut microbial community across different chimpanzees (Moeller et al., 2016). Supporting this idea, unlike industrialized populations where the microbiome diversity tends to decrease with age, the microbiome of the Hadza, a group of indigenous people from Tanzania, increases in diversity over time. The reason for this is believed to be that older Hadza members continue to interact and live with younger members of the tribe in closely-knit communities, which contrasts with older people in our society who are often left in care homes (Schnorr et al., 2014). Read more about positive relationships and the role they play in longevity here.

The Path Ahead: Exploring The Gut Microbiome’s Crucial Role in Human Health

In conclusion, the gut microbiome is an incredibly complex and dynamic ecosystem that plays a vital role in human health. From its involvement in digestion and metabolism to its influence on immunity, the gut microbiome is a fascinating area of research with immense potential for improving human health. We have only just scratched the surface of our understanding of this fascinating microbial world within us. As we continue to uncover the mysteries of this intricate microbial community, it is clear that there is much more to learn about its functions and how we can manipulate it for the benefit of human health. We are beginning to see the immense potential for personalized medicine, disease prevention, and even mental health interventions. 

In the next articles of this series, we will delve further into the gut-microbiome axes and explore how they affect everything from mental health to hypertension, diabetes, cancer, and much more. We will also look at how the gut microbiome changes as we grow up and what that means for how we age. Finally, we will examine the latest microbiome-based therapies and how they are revolutionizing the field of medicine. Join us as we continue to explore the exciting world of the microbiome. 

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