Human Microbiome, Health and Diet

Human Microbiome, Health and Diet

Human Microbiome, Health and Diet


There is the intricate relationship between the gut microbiome, diet, and human health. The human gut microbiome is a diverse ecosystem of microorganisms residing within the gastrointestinal tract that have a significant impact on various aspects of health, including immune system metabolism. Consuming a diverse range of foods promotes a diverse microbiome. Dietary components, such as fibers, carbohydrates, fats, and proteins, play a pivotal role in shaping the microbiome. The microbiome has a significant impact on metabolic processes and energy extraction from food.The microbiome,s fermentation of dietary components, resulting in the production of short- chain fatty acids (SCFAs). Probiotics and prebiotics supporting a healthy microbiome by nourishing beneficial microorganisms. The microbiome plays a crucial role in regulating and maintaining immune system, nutrient absorption, in the production of enzymes and organic acids. Dysbiosis is an imbalance in the microbiome that can result from dietary factors, can lead to autoimmune diseases. Imbalances in the microbiome are linked to conditions such as obesity, cancer and Autism spectrum disorders (metabolic disorders) .Diets high in processed foods and low in fiber can disrupt the balance of beneficial and harmful microorganisms. Personalized nutrition, tailored to an individual’s health status and microbiome composition, is vital for optimizing health and preventing diseases.

The human gut microbiome is a vast and intricate community of microorganisms that inhabits the gastrointestinal tract. The microbiome of the gastrointestinal tract usually constitutes around 200–300 distinct species, and at the strain level, these are largely exclusive to the individual human host.1 These microorganisms play a pivotal role in human health and are integral to the body’s normal physiological functions. It is often referred to as the “last organ”2 because it plays a crucial role in various bodily functions, including digestion, immunity, and metabolism. The gut microbiome is

considered an organ because it functions as a complex system that interacts with the host organism and other organs to maintain overall health. These microorganisms play a pivotal role in human health and are integral to the body’s normal physiological functions. The relationship between the gut microbiome, diet, and health is intricate and bidirectional. Diet influences the composition and activity of the microbiome, while the microbiome, in turn, influences how the body processes and extracts nutrients from food. This connection has far-reaching implications for human health.

Human gut microbiome

In 1988, Whipps and colleagues provided the first definition of the term microbiome. They define the “microbiome” as a combination of the words “micro” means “small” and “biome” means “life”, given name to a “distinct microbial community” thrives in a “well-defined environment with specific physio-chemical properties” serving as “active stage.”3 This term microbiome encompasses the entirety of the ecosystem incorporating microorganisms that naturally live in our body like bacteria, archaea, as well as viruses, along with their genomes (genes) and ambient environment.4
The collection of bacteria, viruses, fungus, and other microorganisms that live in the gastrointestinal tract of animals, especially humans, is known as the gut microbiome. Gut microbiome contributing to overall health and homeostasis.


The gut microbiome is a complex ecosystem that harbors a vast array of microorganisms, creating a diverse and dynamic environment within the gastrointestinal tract. These microorganisms include bacteria, viruses, fungi, archaea, and other microbes. The majority of the gut microbiota comprises bacteria, with thousands of different species identified. The diversity of these microorganisms is influenced by factors such as genetics, diet, age, and environmental exposures. Variations in composition and abundance is influenced by factors such as host physiology, immune responses, ecological processes, host genetics, environmental exposure, ethnicity, and diet.The pH and gut transit time are two important aspects of the gut environment that are influenced by diet.The composition of the microbiota can be greatly impacted by variations in the diet of the three primary macronutrients: lipids,

proteins, and carbohydrates. In the gut, the three main bacterial phyla are Firmicutes , Bacteroidetes and Actinobacteria. These bacteria possess enzymes that can degrade complex dietary substrates.

  • Firmicutes are Involved in the breakdown of complex carbohydrates and fermentation, influencing energy metabolism.
  • Bacteroidetes are Specialized in the digestion of complex polysaccharides, contributing to short-chain fatty acid production such as acetate, propionate, and butyrate.
  • Some species of Actinobacteria aid in breaking down tough plant fibers and play a role in nutrient absorption.
  • Gut microbes influence the expression of host genes related to nutrient absorption, promote the uptake of essential nutrients.

The Role of Macronutrients in Shaping Microbial Composition

(Impact of diet)

A diverse diet is crucial for fostering a healthy gut microbiome as it provides a wide range of nutrients that support the growth and maintenance of diverse microbial populations. A variety of plant-based foods, fibers, and nutrients positively impact microbial diversity and contribute to overall gut health.A well-balanced intake of macronutrients, including proteins, fats, and carbohydrates, supports microbial diversity


Every day, about 40 g of dietary carbohydrates that have eluded host enzyme digestion make their way to the colon. The three primary groups are oligosaccharides, non-starch polysaccharides (NSP), and resistant starches (RS), while other mono- and di-saccharides, such sugar alcohols, may also enter the colon. Interestingly, there is direct proof that altering the kind and/or quantity of carbohydrates in adult human volunteers during times up to four weeks has a significant and quick impact on the composition of the gut microbiota and its metabolic products. Additionally, there is

circumstantial evidence that habitual death could eventually have significant effects on the composition of the microbiota.

Resistant starch (RS) and non-starch polysaccharides (NSP)

There are four recognized types of resistant bounce( RS1 – RS4) that are consumed within our diet that resist degradation in the small intestine. Different types of RS affect the bacterial composition. Starch is a complex polysaccharide conforming of a mixture of amylose(, 1- 4 linked glucose) and amylopectin, a branched polymer composed of amylose chains, (1- 6 cross-linked) to an amylose backbone. The relative proportion of amylose and amylopectin also affects the capability of bacterial species to use different types of starch for growth. A range of catalytic conditioning are needed for effective starch breakdown, including amylases, pullulanases and amylopullulanases( which retain both conditioning) .In a mortal salutary intervention study one bacterial group, nearly affiliated to R. bromii, increased nearly twofold when diet switched from normal to RS fortified diets


Approximately 12-18 g of protein reach the human colon daily, comprising of residual dietary protein and enzymes secreted in the small intestine. The proportion of residual dietary protein in the colon (around 10% of ingested protein) depends on the amount and kind of protein consumed. The colon is an active site of protein turnover which provides nitrogen for the growth of saccharolytic bacteria and amino acids for fermentation by asaccharolytic species . The predominant proteolytic bacteria identified in human faeces are Bacteroides species (especially the B. fragilis group ) and also Clostridium perfringens, propionibacteria, streptococci, bacilli and staphylococci . Fermentation of amino acids as an energy source occurs in the distal colon where carbohydrate sources are depleted and the luminal pH is near neutral. Amongst faecal bacteria Bacteroides species possess very strong peptidase activity and also predominate when the pH is around pH as in the distal colon. Furthermore, several bacterial groups preferably ferment amino acids and possess only weak saccharolytic activity such as some fusobacteria , eubacteria and clostridia .


Dietary fat is mostly absorbed in the human small intestine, but a recent study showed that 7% of 13 Clabelled dietary fatty acids were excreted in stool . Few studies have investigated the effect of dietary fat on human microbiota. Consumption of a high fat (HF) diet compared to a low fat (LF) diet significantly reduced faecal short chain fatty acid concentrations, including butyrate concentrations and bifidobacteria counts However, in order to create energy equivalent diets, the high fat diet was low in carbohydrate whilst the low fat diet was significantly higher in digestible carbohydrate and fibre. As carbohydrate composition has a significant effect on both microbial composition and activity, so it is not clear in such human studies whether the crucial dietary factor affecting microbiota composition and metabolism is the elevated fat or reduced carbohydrate content.

Fermentation by the gut microbiome

Protein fermentation results in a more diverse metabolite profile compared to carbohydrate fermentation. The main pathway of amino acid fermentation in the human colon is deamination, leading to the production of SCFA and ammonia . About 30% of substrate is converted to the major SCFA acetate, propionate and butyrate and the branched chain fatty acids (BCFA) isobu- tyrate, 2-methylbutyrate and isovalerate. These BCFA are mainly formed from the branched-chain amino acids valine, isoleucine and leucine, respectively and are often used as faecal markers for protein fermentation

Probiotics and prebiotics

Probiotics. These are live bacteria found in certain foods or supplements. They can provide numerous health benefits. . Fermented foods contain live beneficial bacteria,

promoting a balanced gut microbiome. Including items like yogurt, kefir, sauerkraut, and kimchi introduces probiotics that support gut health.Probiotics play important roles through different mechanism in the host body.
Multiple mechanisms are rated to probiotic, the importance of any given mechanism will depend on many factors. For example, in an inflamed intestine, the ability to downregulate inflammatory mediators and increase epithelial barrier function might be most important, whereas the ability to increase short-chain , fatty acids (SCFAs) and hydration in the colon could be more important to normalizing intestinal motility.The historic concept of “colonization resistance”, the situation whereby native gut microbiota occupy with its host tissues to exclude infection by potential pathogens (resident or invading), is another mechanism attributed result from to probiotics”

Production of organic acids.

Probiotic species belonging to the Lactobacillus and Bifidobacterium genera produce lactic and acetic acids as primary end products of carbohydrate metabolism. These organic acids when produced in situ can lower luminal pH and discourage the growth of pathogens

Modulation of cell-mediated and humoral immune functions

Some probiotics have been shown to increase phagocytosis or natural killer cell activity and interact directly with dendritic cells . Some also demonstrate the ability to upregulate antibody secretion translating into improved defences against pathogens . Probiotic strains can increase levels of anti-inflammatory cytokines such as TNF with implications for abating colon cancer and colitis.
Interaction with gut microbiata

Probiotic strains can interact with the gut microbiota through competition for nutrients, antagonism, cross feeding and support of microbiota stability”. Many probiotic strains are antagonistic toward other microorganisms, in part due to saccharolytic metabolism, which produces organic acids, but also by production of bacteriocins. These antimicrobial compounds can be active against pathogens at many sites including the human urinary tract and the gut of humans and animals.
Production of enzymes.

Microbial enzymes such as ẞ-galactosidase and bile salt hydrolases, which are pro- duced and delivered by some probiotic strains, improve lactose digestion and blood lipid profiles in humans, respectively.


These substances come from types of carbs (mostly fiber) that humans can’t digest. The beneficial bacteria in your gut eat this fiber. Fermented foods contain live beneficial bacteria, promoting a balanced gut microbiome. Including items like yogurt, kefir, sauerkraut, and kimchi introduces probiotics
Prebiotics are “selectively fermented ingredients that allow specific changes”, both in the composition and/or activity in the gastrointestinal microflora that confer benefits upon host well-being and health” and have routinely been screened for their ability to selectively promote bifidobacteria. Many studies, therefore, have shown increases in bifidobacteria following dietary supplementation with fructans and more recently with galacto- oligosaccharides
Immune modulation.

Although the exact mechanisms are unclear, there is evidence that prebiotic intervention can reduce type 2 T helper responses and therefore affect allergy.
Increased mineral absorption.

Since most absorption of minerals takes place by active transport mechanisms in the small intestine, scavenging calcium could make a substantial positive contribution to health.
Fermentation of prebiotics leads to production of SCFA, which reduces luminal pH. This drop in pH can increase calcium solubility, thereby providing a greater driving force for passive uptake. A problem with proving this process is that many calcium salts in supplements and food have pH-dependent solubility and limited availability, and depending on the starting pH, the solubility of calcium can actually increase with increasing pH.Studies have shown that consumption by young adolescents of a mixture of FOS and inulin or GOS can result in marked increases in absorption and calcium mineralized into bone. Such early intervention could reduce the incidence of osteoporosis later in life. This hypothesis is supported by data from animal models, but long-term studies in humans are lacking.
Defence against pathogens.

Although mechanistically challenging to establish in humans in vivo, pathogen defence can be investigated in vitro using model sys-tems.

As noted for probiotics, production of organic acids through prebiotic administration and propagation of beneficial bacteria will result in a reduction in luminal pH, inhibiting growth of pathogens. Establishment of a stable population of commensal microorganisms will reduce nutrient availability for invading micro- organisms, inhibiting colonization. In studies of elderly individuals, 10 weeks of daily galacto-oligosaccharide (GOS) consumption induced increases in immune func- tion, notably enhanced phagocytic activity and activity of natural killer cells


Dysbiosis is a key term in human microbiome research, especially when microbiome patterns are associated with disease states
dysbiosis refers to an imbalance or disruption in the composition and function of the gut microbiome. In the last decade, a number of studies have documented significant changes in the structure of microbial communities in patients and mouse models of inflammatory bowel diseases (IBD) such as Crohn’s and ulcerative colitis , diabetes), asthma), allergies and even autism .Given the emerging importance of the microbiota to host development, it is speculated that these observed changes in microbial composition are contributing factors to the initiation and/or persistence of many of these diseases.
Obesity is a metabolic disorder involving an excess amount of body fat storage that has been considered to be caused by an imbalance of energy, with low energy expenditure and increasing caloric intake. However, recent evidence suggests that obesity is a more complicated disease associated with intestinal dysbiosis in both mice and humans. Certain microbiota signature seems to be associated with the development of obesity. In obese individuals, there is an overall decrease in bacterial diversity in the intestines. High fats diet are shown to alter the microbiota composition. The changes in the microbiota observed in obesity are believed to cause various effects that could promote chronic inflammation-associated obesity.
The obese microbiota signature shows an altered ratio of Bacteroidetes and Firmicutes, which contain members that produce short-chain fatty acids (SCFAs).

Individuals have a more disproportionate ratio of these bacteria. The amount of Bacteroidetes seems to be important in obesity since obese individuals on a caloric- restricted diet with a loss in body weight show that there is an increased ratio of Bacteroidetes species in the intestinal microbiota. In obese individuals, the levels of SCFAs are significantly decreased compared with lean individuals. The decrease of SCFAs may be due to increased SCFA absorption and the altered composition of intestinal microbiota, which shows a decrease in butyrate-producing bacteria, which would cause less SCFA production. SCFAs are believed to inhibit the accumulation of fat in adipose tissue, so a decreased level is thought to contribute to obesity

Autism Spectrum Disorders

Autism spectrum disorders (ASD), are a group of disorders that include autism and Asperger’s syndrome that are characterized by social and communication deficits, repetitive behaviors, and sometimes, cognitive delays.35 The exact cause of ASD is still largely unknown; however, there are strong implications that intestinal dysbiosis may play a role in the pathogenesis of ASD, particularly in autism. This link between ASD and dysbiosis is strengthened by various studies indicating that the gut microbiota and its metabolites seem to affect the central nervous system via the gut–brain axis, which may communicate to the central nervous system through neural, endocrine, and immune pathways to influence brain functions and altered behavior


Intestinal dysbiosis has also been linked to colorectal cancer( CRC) , which is the third most common cancer and second leading cause of cancer death (both sexes combined) in the United States according to the American Cancer Society. CRC has several risk factors, including IBD, obesity, diabetes, and a diet consisting of high fat and protein, all of which also are linked to intestinal dysbiosis. This suggests that dysbiosis may also play a key role in CRC pathogenesis
Addressing dysbiosis involves restoring a healthy balance to the gut microbiome. It can be restored by
Introducing beneficial bacteria through probiotic supplements or fermented foods.

consuming prebiotic-rich foods, such as fiber, supports the growth of beneficial bacteria in the gut.
Adopting a balanced and diverse diet that includes a variety of fruits, vegetables, whole grains, and lean proteins can positively impact the gut microbiome.
: Unnecessary or prolonged use of antibiotics can disrupt the balance of the gut microbiome, so their use should be minimized.

Personalized Nutrition

An approach to diet and health known as “personalized nutrition” adjusts dietary interventions and suggestions to each person’s particular needs. This personalization considers variables like heredity, way of life, health, and (of growing significance) the composition of a person’s gut microbiota. Personalized nutrition aims to promote optimal health outcomes, illness prevention, and overall well-being by offering an array of nutritional guidance tailored to each individual’s unique biological composition.


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1 Cell Host & Microbe 19 June 2023 Clémence Frioux Rebecca Ansorge Falk Hildebrand,

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4 JR Marchesi, J Ravel Microbiome, 2015,,5