Keeping up with gut microbiome

About author: Dr. Tarini Shankar Ghosh is a Research Support Officer, currently working in the Alimentary Pharmabiotic Centre (APC) Microbiome Ireland, University College Cork, with Prof. Paul W O’ Toole and group. He did his M.Tech from BSBE, IIT Kanpur in 2007, under the supervision of Prof. R. Sankararamakrishnan. He is a computational biologist investigating gut microbiomes. His main research theme is to identify the generic microbial markers of health, their variation across various population-strata, their alterations in different disease conditions and finally the formulation of personalized diet/symbiotic-based microbiome restoration strategies for improving human health. In the current narrative, he would be discussing some of his recent studies that have provided crucial insights into the above aspects.

How would you explain your paper’s key results to the non-scientific community?

Our body is a complex ecosystem made up of both our own cells and microbes. The gut harbours one of the largest microbial communities found in human body. This community of microbes along with their encoded functions (estimated to be more than 150 times the coding capacity of our own) are collectively referred to as the gut microbiome. The gut microbiome plays a crucial role in modulating almost all aspects of our physiology, including nutrient harvest from our food, modulating our immune system, and even affecting our mood. Changes in lifestyle, medication intake (including antibiotics), age as well as diet affect the make-up of the gut microbiome, which may further increase the risk of non-infectious diseases and metabolic disorders. However, unlike our own genome, the gut microbiome is amenable to changes that can be exploited therapeutically. Thus, it is important to identify the hallmarks of a healthy gut microbiome.

Simplistically, the gut microbial community can be broadly divided into two major constituents, namely the putatively beneficial symbionts and the pathobionts, depending on their functional effects on the host (Figure 1A). Beneficial symbionts are symbiotic species that are normal residents of the gut, while pathobionts are those that under certain conditions produce metabolites/gene-products that detrimentally affect the host. Thus, increasing the representation of the ‘good’ symbionts and depleting the ‘bad’ pathobionts is the objective of microbiome-targeted therapeutic interventions. The exact nature of the intervention, however, would depend on the directionalities of the microbiome changes associated with a given disease. While diseases characterized by gain of pathobionts can be addressed by pathobiont-targeted antimicrobial therapies, those characterized by loss of beneficial species require microbiome restoration strategies aimed at enriching these microbes, like probiotics or prebiotics. Thus, identifying the nature of the microbiome changes associated with various diseases is important.

The challenge is, even among apparently healthy individuals, the composition of the gut microbiome is variable and dependent on several host-associated factors. It is important to explore how the microbiome changes with host-associated factors like social strata and age and how these changes influence the disease-associated microbiome alterations (specifically the generic markers of health). One of these factors is Age. Aging is associated with multiple changes in our body, including a gradual deterioration of physiological function, chronic low-grade inflammation (‘inflamm-aging’) and onset of chronic diseases. These in turn lead to changes in lifestyle including reduced quality of diet and physical activity and intake of medications, all of which have a profound effect on the composition of the gut microbiome (Figure 1B). These changes in the “baseline” gut microbiome are also expected to influence the alterations associated with different diseases. Thus, it is imperative to investigate these variations across the human age landscape.

To probe this aspect, in the first study under this narrative, I profiled the gut microbiome changes in five major diseases (type II diabetes, inflammatory bowel disease, colorectal cancer, cirrhosis and polyps) in a multi-cohort dataset constituting more than 2500 individuals from 20 to 89 years old [1]. We observed that disease-associated changes in the gut microbiome follow specific age-centric trends. While in younger individuals, majority of the five investigated diseases were characterized by a gain of disease-associated pathobionts, then same diseases in elderly were observed to linked to a loss of beneficial taxa usually found in a healthy gut (Figure 1C).

Investigating the overlaps of these microbiome alterations across diseases, we identified a core group of pathobionts that were observed to be enriched across multiple diseases. Notably, this group of species was also observed to be enriched in a completely distinct data set containing gut microbiomes of frail elderly individuals (sequenced as part of the ELDERMET project in Ireland). These species are known to produce cytotoxic compounds like p-Cresol, acetone, ammonia (that are associated with multiple disorders), trimethylamine (that has been associated with atherosclerosis), hydrophobic secondary bile acids (linked to cancer and diabetes) and ethanol (Figure 2A). We also identified 24 taxa that were observed to be depleted across multiple diseases, as well as the frail elderly individuals of the ELDERMET cohort.

Figure 1. A. The two major components of gut microbiota, the pathbionts and beneficial symbionts, and their variable alteration patterns in disease. B. Age-associated changes in physiology and life-style and the associated changes in the gut microbiome. C. Age-specific variations in disease-microbiome alterations and the suggested microbiome-targeted therapeutic strategies.

What are the possible consequences of these findings for your research area?
The findings of this study indicated that, even for the same disease, the approach of microbiome-based therapeutic strategies could vary depending upon the age-group of the target population. Specifically, it showed that microbiome-restoration approaches could be more helpful for addressing disease in the elderly as compared to medication or antimicrobial strategies (Figure 1C). The 24 health-associated taxa identified in this study is a short list of these generic microbial markers of health.

Figure 2. A. Metabolite produced by the generic pathobionts that drive the host to a state of further physiological decline. B. Properties of the health-associated keystone species that facilitate faster gut microbial community growth rate and resilience of the microbiome.

The question that follows is why are these taxa important? Many of them are known to produce short chain fatty acids (SCFAs), like acetate, propionate and butyrate that have a multitude of beneficial functions for the host (Figure 2B). Some of them, like Bifidobacterium, are well known probiotics and neuro-transmitter producers. Another crucial role of these taxa was evident in another study (published in Nature Ecology and Evolution) where we investigated the changes in the gut microbiome post antibiotic treatment [2]. Antibiotics disrupt the gut microbiome and facilitate the entry of antibiotic resistance pathogens. Recovery of the gut microbiome post-antibiotic treatment thus is essential but can be slow and variable across individuals. In this study, while investigating the effects of antibiotic treatment on the gut microbiome of 117 individuals from four geographically distinct cohorts, we identified 21 bacterial species that were associated with faster recovery of the gut microbiome post-antibiotic treatment across multiple cohorts. This encompassed eight of the 24 health-associated markers. These species were observed to have specific carbohydrate degrading capabilities, enabling them to use diet/host-derived energy sources to only for their own growth but also to “feed” other resident microbial community members, thus ensuring a significantly higher community growth rate and finally faster recovery post-treatment. These species could thus be referred to as the ‘key-stone’ members that promote microbiome homeostasis by making the gut microbial community more resistant to external changes. Thus, besides benefiting the host, a subset of these species is also essential for the resilience of the gut microbiome.

What was the exciting moment (eureka moment) during your research?

How you externally restore or enrich these species in individuals? Given their anaerobic nature and complex growth requirements, formulation and production of microbial consortia containing pure cultures of one or more of these species is a costly venture. Here comes the exciting part of this story, the third study, published in the journal Gut [3].

In this study, we were investigating the effect of adopting a Mediterranean Diet (MedDiet) on the gut microbiome of 612 elderly individuals spread across five European nationalities [3]. A MedDiet regime is characterized by increased intake of vegetables, legumes, fruits, nuts, olive oil and fish and a reduction in red meat, dairy product and saturated fat consumption. Previously, the MedDiet has been associated with multiple benefits including reduced mortality as well as incidence of multiple diseases especially in the elderly. However, the exact mechanistic basis of these aspects was never been explored. During this study, we observed that adherence to the diet led to specific changes in the gut microbiome of the individuals. It was these alterations that were then associated with significant improvements in several aspects of host health, like inflammation, cognitive function and frailty.

The eureka moment came upon investigating the exact nature of these changes (findings summarized in Figure 3). Species enriched due to the diet were known as SCFA producers (a hallmark of the generic markers of health, as observed in [1]). Further, using co-occurrence network analysis, we were able to show that these species occupied central nodes in the gut microbiome, indicative of the key-stone nature of these species, that is the presence of these species was important for other members of the microbiome to exist (as observed in [2]). Notably, the species observed to be depleted with increased adherence to the diet were those known to produce hydrophobic secondary bile acids, the cytotoxic p-Cresol, ethanol (pathobiont associated properties observed in [1]).

Figure 3. Microbiome-mediated beneficial effects of the Mediterranean Diet in elderly (as observed in [3]).

Thus, something as simple as adherence to a healthy dietary pattern was observed to enrich the hallmarks of a healthy and resilient gut microbiome (Figure 3), associated with specific phenotypes of healthy aging. What was more important was the observation that the microbiome could act as the key transducer of the signals of a beneficial diet. The food that we eat also feeds our microbiome. This study showed that diet-based therapeutic modulation of the microbiome could therefore act as a relatively inexpensive population level strategy for retention of a beneficial gut microbiome and improving human health.

What do you hope to do next?

Although the findings of the above MedDiet intervention study were remarkable, we also observed a high degree of variability in the individual-specific responses to the MedDiet. In other words, the responses to the intervention were highly personalized. What factors determine these personalized responses? One of these factors is the baseline gut microbiome of an individual. Besides disease and medications, several host-associated factors like the ethnicity, diet, demographics as well as life-style influence the gut microbiome composition even among healthy individuals (Figure 4A). We have recently shown that while the gut microbial community can still be broadly divided into pathobionts and beneficial symbionts (and the keystones) [4], the exact list of members from these two broad groups vary across different populations. The most-stark observations were made between the individuals from westernized/industrialized societies and those from non-industrialized societies. Can we come up with the predictive algorithms that can help to design personalized dietary interventions or combinatorial therapy of diet and probiotic administration, given the profile of an individual (in terms of ethnicity, age, social status, disease, medication, etc)? These are some of the questions that I intend to investigate next.

Figure 4. A. Effect of host-associated factors on the baseline gut mcrobiome. B. Principal coordinate analysis (PCoA) of ~ 7000 gut microbiomes obtained from Westernized populations (EU, North America, Japan and China), non-western industrialized populations and individuals from Indian cohorts.

Where do you seek scientific inspiration?

My scientific inspiration has been the degree to which each of these three studies have complemented each other. Each of these studies was performed on distinct cohorts of individuals with completely different objectives and approaches using independent lines of investigation. It was really inspiring to see how the results seemed to fit in like parts of a jigsaw puzzle.

How do you intend to help Indian science improve?

There are several clinical and public health applications of the above findings from the Indian perspective. The first is with respect to clinical diagnostics and identifying population-level susceptibilities to different diseases. Disease-gut-microbiome association studies provide insights on the gut microbial species that are altered in a given disease. These insights can then be used to devise classifiers that can diagnose a given disease as well as identify sub-population-level susceptibilities to different diseases, that too using a strategy as simple as sequencing the microbial DNA from one’s stool samples. However, the challenge arises because the gut microbiome also varies across individuals of various strata and consequently the disease-linked gut microbiome alterations are likely to vary. Similarly, specific sub-populations may be susceptible (or immune) to certain diseases like Inflammatory bowel diseases (IBD), Type-2 diabetes (T2D), non-alcoholic fatty liver disease (NAFLD) and colorectal cancer (CRC), etc. All these diseases have certain microbial basis. Unfortunately, a majority of disease-gut-microbiome alteration studies have focussed on individuals residing in industrialized/western societies (Figure 4B). Similar studies on Indian sub=populations, are still limited or on small study cohorts. The same observation holds for aging. Almost all aging-microbiome studies have focused on western populations. One of my future directions is to work and address this knowledge gap.

The second perspective pertains to the consequences of sudden life-style transitions on the gut microbiome. Of special interest on this aspect is our recent investigation of Irish Travellers [5]. The findings of the study have immense implications for informing public health initiatives. Irish Travellers are an ethnic minority who lead a traditionally nomadic lifestyle, with large families living in close confinement and proximity to domesticated animals. Notably, despite leading a traditional, marginalized life-style, he incidence of several inflammation-linked diseases in Irish Travellers has been surprisingly low. There has been constant pressure from the legislation forcing the community to abandon their traditional lifestyle and move to settled housing. The implications of these legislative policies on the health of these Travellers was never investigated in detail. Our study identified that the gut microbiome of the Irish Travellers was distinct and characterized by the abundance of a specific guild of “putatively” therapeutic and anti-inflammatory microbes, similar to that found in other geographically distinct non-industrialized societies like the Hadjas (Tanzania), Fijians, Peruvians and Mongolians. However, increased adoption of a settled lifestyle leads to a gradual decline in the abundances of these species and an emergence of a microbiome that is increasingly susceptible to non-communicable diseases. The findings suggest that enforced imposition of life-style changes in ethnic minorities without the introduction of appropriate health-restoration initiatives can lead to deterioration of health status with an increased susceptibility to non-communicable inflammatory diseases. Importantly, the story of the Irish Travellers has clear reflections in India. Increased migration from rural villages to urban slums, increased adoption of a westernized calorie-rich diet amongst the current generation of individuals have serious implications that need to be investigated from the perspective of informing public health agencies. Pursuing investigations on these lines within the Indian sub-populations is one of my future objectives.

Another aspect that needs to be investigated is the therapeutic effect of the traditional Indian diet. As noted previously in this narrative, most of the healthy dietary regimes have certain common properties, like increased consumption of vegetables, legumes, whole meal cereals and fish, all of which also constitute a major fraction of the traditional Indian diet. Additionally, the Indian diet is also characterized by an increased consumption of fermented food products which have distinct probiotic properties. However, there are distinct region-specific flavors. Intervention studies on region-specific healthy dietary regimes need to be performed in population cohorts across different locations to identify components that are consistently associated with a good microbiome and better health and subsequently promote these as therapeutic cost-effective population-level dietary initiatives.

References (*: Joint first author)

  1. Ghosh TS, Das M, Jeffery IB, et al. Adjusting for age improves identification of gut microbiome alterations in multiple diseases. Elife 2020; 9:e50240.
  2. Chng KR*, Ghosh TS*, Tan YH*, et al. Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in gut. Nature Ecol Evol. 2020; 4(9):1256-1267.
  3. Ghosh TS*, Rampelli S*, Jeffery IB*, et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut. 2020; 69(7):1218-1228.
  4. Shanahan F, Ghosh TS, O’Toole PW. The Healthy Microbiome – What Is the Definition of a Healthy Gut Microbiome?. Gastroenterology. 2020; S0016-5085(20)35508-6.
  5. Keohane DM*, Ghosh TS*, Jeffery IB, Molloy MG, O’Toole PW, Shanahan F. Microbiome and health implications for ethnic minorities after enforced lifestyle changes. Nature Medicine. 2020; 26(7):1089-1095. The accompanying editorial to this publication (published in Nature Medicine) is available at:

Edited by: Pragya Gupta

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