Physiological functions of gut microbiome.
Obesity is a worldwide pandemic causing increased morbidity/mortality and high cost for the society. Management of obesity requires multidisciplinary approaches including diet, food supplement, exercise, behavior change, drug, medical device, gut microbiome manipulation, and surgery. Over the past two decades, there has been a growing awareness of the importance of gut microbiome in human health and disease. Profound changes affecting the diversity and the abundance of gut microbiome are associated with several disorders including obesity. A decrease in microbiome diversity and an increase in the ratio of Firmicutes-to-Bacteroidetes phyla have been reported in obese subjects. The gut microbiome can be manipulated to change the host metabolism and manage obesity. Potential interventions include diet (e.g., low calories, low fat, and high fiber), prebiotics (e.g., inulin, lactulose, and resistant starch), probiotics (e.g., yogurt, cheese, and milk), synbiotics (combination of prebiotics and probiotics), bariatric surgery (e.g., Roux-en-Y gastric bypass), and fecal microbiota transplantation (through colonoscopy, esophagogastroduodenoscopy, orogastric tube, or oral capsule). A better understanding of the interactions between different diets and gut microbiome should help the development of new guidelines for the prevention and management of obesity.
- gut microbiome
- weight management
Obesity is excess body weight for a given height, defined by a body mass index (BMI) ≥ 30 kg/m2. In some Asian countries (e.g., Japan), the threshold to define obesity is 25 kg/m2. The main cause of obesity is an imbalance between energy intake and energy expenditure. Obesity is a worldwide pandemic associated with increased morbidity/mortality and high cost for the society. The prevalence of obesity is increasing exponentially. The number of adult subjects with obesity is around 700 million worldwide. Near 4 million subjects die each year from the consequences of obesity. The annual cost of obesity is more than $2 trillion [1, 2, 3].
Management of obesity requires multidisciplinary approaches including diet, food supplement, exercise, behavior change, drug, medical device, gut microbiome manipulation, and surgery [1, 4, 5, 6, 7, 8, 9]. The annual obesity treatment market is around $6 billion.
The human intestine harbors a complex and diverse microbial ecosystem referred to as gut microbiome [10, 11, 12, 13, 14]. This rich community of microorganisms has co-evolved in a symbiotic relationship with humans. Its diversity is influenced by several factors including host genetics, mode of birth, age, gender, pregnancy, BMI, diet, medications, and surgery [12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]. The understanding of the gut microbiome evolves at a rapid pace, but the practical application of this knowledge is still in its infancy. The gut microbiome is essential for the maintenance of human health. It is involved in protection against pathogens and regulation of immune system and metabolism . Profound changes affecting the diversity and the abundance of gut microbiome (dysbiosis) are associated with several disorders including obesity . The prevention and management of obesity may benefit from manipulation of gut microbiome.
2. Gut microbiome description and composition
Gut microbiome is a complex community of microorganisms living in the digestive tract, mainly in the colon (Figure 1). Variable pH and oxygen concentration affect the abundance of gut microbiome across the gastrointestinal tract. Gut microbiome represents up to 60% of the dry mass of feces (biomass around 1.5 kg), has more cells than host somatic cells and at least 100 times more genes than human genome [10, 11, 12, 13, 14].
Gut microbiome is established within the few first years of life and contains up to 100 trillion microbes, mainly bacteria (more than 1,000 species) but also fungi, protozoa, archaea, and viruses. The taxonomic ranking of gut microbiome includes species, genera, families, orders, classes, and phyla. Most of the species belong to Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia phyla. The predominant phyla (90%) are Firmicutes (e.g., Ruminococcus and Lactobacillus genera) and Bacteroidetes (e.g., Bacteroides and Prevotella genera). Three enterotypes with functional differences have been defined based on variation in the level of genera: Enterotype 1 (Bacteroides), Enterotype 2 (Prevotella), and Enterotype 3 (Ruminococcus).
3. Gut microbiome projects
There are two major gut microbiome projects: European Megagenomics of the Human Intestinal Tract and US Human Microbiome Project . For gut microbiome studies, multiple fecal collections of the same subject are recommended. The assessments are DNA-based methods (16S rDNA sequencing, whole genome shotgun sequencing) (Figure 2) [32, 34, 35]. The challenges in the assessments of gut microbiome are due to the diversity and the inter/intra-individual variability caused by different factors such as age and diet.
4. Gut microbiome metabolism
4.1 Nutrition sources
The sources for nutrition of gut microbiome are ingested dietary components (carbohydrate, protein, lipid) and host-derived components (shed epithelial cells, mucus).
Several metabolites are produced by gut microbiome. They include short-chain fatty acids (following carbohydrate fermentation), phenolic substances (following protein fermentation), and vitamins (vitamin B, vitamin K).
5. Gut microbiome changes
Gut microbiome is diverse, varies between individuals, and can fluctuate over time. Western gut microbiome has less species than non-Western gut microbiome.
In addition to several pathological conditions that can alter gut microbiome composition, multiple factors are responsible for the changes in gut microbiome (Figure 3) [12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31].
5.1 Host genetics
There are possible relations between host genetic profile and gut microbiome composition, but additional studies are needed for a better understanding of these relations .
5.2 Mode of birth
Mode of birth has an important influence on gut microbiome composition [12, 16]. With vaginal delivery, infants are colonized by maternal vaginal bacteria (dominated by Lactobacillus and Prevotella genera) while following C-section delivery, infants are colonized by maternal skin bacteria (dominated by Staphylococcus, Corynebacterium, and Propionibacterium genera).
Age is associated with important changes in gut microbiome [12, 17]. The changes occur mainly before 20 and after 70 years. The diet plays a significant role. In preterm infants, there is a predominance of Proteobacteria phylum. There are marked changes in infants. The choice of diet after birth (breast milk or formula milk) affects the colonization process in the newborn. With age, the introduction of solid food from 2 years and the production of sex hormones from puberty (to menopause in females) bring additional richness and complexity to gut microbiome. There is a relative stability of gut microbiome between 20 and 70 years (predominance of Firmicutes phylum). In elderly subjects, Bacteroidetes phylum is predominant.
Elevated levels of estrogen and progesterone observed during pregnancy have important impact on gut microbiome [12, 16, 19]. The changes are characterized by a decrease in richness of gut microbiome, a higher abundance of Proteobacteria and Actinobacteria phyla, a decrease in Faecalibacterium genus, and an increase in Firmicutes-to-Bacteroidetes phyla ratio.
BMI is associated with gut microbiome composition particularly in women . Bacteroidetes phylum is less abundant in subjects with high BMI. The role of estrogen has been proposed.
Diet has an important influence on gut microbiome composition [20, 21, 22, 23, 24, 25]. However, there is a high interindividual variability. A diet high in fat (≥ 55% of total macronutrients) is associated with increased Firmicutes and Proteobacteria phyla and decreased Bacteroidetes phylum while a diet rich in fiber (≥ 30 g/day) has the opposite effect. The changes in gut microbiome (composition and functionality) induced by diet can be observed as early as 2 days. However, major changes in gut microbiome require long-term change in dietary habits.
Important differences in gut microbiome have been reported in children between Europe and rural African village of Burkina Faso (polysaccharide-rich diet) with Firmicutes-to-Bacteroidetes phyla ratios of 2.8 and 0.5, respectively .
Diet may also contribute to the seasonal variations of gut microbiome likely due to different availability of fresh produce containing complex carbohydrates .
Several medications (e.g., antibiotics, nonsteroidal anti-inflammatory drugs, proton pump inhibitors, and metformin) affect gut microbiome [28, 29, 30]. The use of antibiotics is associated with increased Firmicutes phylum, with higher sensitivity in infants.
The impact of prebiotics and probiotics on gut microbiome is presented in Section 8.
Since colon is the main reservoir of gut microbiome, surgical removal of colon may affect gut microbiome . Indeed, right hemicolectomy for colorectal cancer has been reported to be associated with a decrease in diversity and richness of gut microbiome.
The impact of bariatric surgery on gut microbiome is presented in Section 8.
6. Gut microbiome functions
|Function of gut microbiome||Mechanism and target|
|Protection||Killing or inhibiting unwanted organisms competing for nutrients|
|Immune system||Influencing production of cytokines and antibodies|
|Metabolism||Regulating energy homeostasis, producing short-chain fatty acids and vitamins, impacting glycemic control, interacting with incretins, regulating metabolism of lipids and bone|
6.1 Protection against pathogens
Gut microbiome can protect against pathogens by killing or inhibiting unwanted organisms (e.g., Clostridium difficile genera) that are competing for nutrients.
6.2 Regulation of immune system
Gut microbiome regulates immune system by influencing the production of cytokines and antibodies.
6.3 Regulation of metabolism
Gut microbiome is involved in several metabolic processes. These processes include regulation of energy homeostasis and body weight, production of short-chain fatty acids (following fermentation of nondigestible fibers) and vitamins (vitamins B, vitamin K) [32, 36], glycemic control [37, 38], interaction with incretins , and metabolism of lipids  and bone .
7. Gut microbiome in diseases
Dysbiosis is observed in several medical conditions including obesity, malnutrition, type 2 diabetes, inflammatory bowel diseases, neurological disorders, and cancer [33, 42, 43, 44, 45, 46, 47, 48]. The dysbiosis can be the cause and/or the consequence of these diseases.
Gut microbiome influences drug pharmacokinetics and bioavailability, and thus, affects the efficacy and safety of several drugs used to treat diseases .
8. Gut microbiome and obesity
8.1 Gut microbiome composition in obesity
Although there are some conflicting data, most studies have reported that in obesity, there is a lower gut microbiome diversity, a higher abundance of Firmicutes phylum, a lower abundance of Bacteroidetes phylum, and a higher Firmicutes-to-Bacteroidetes phyla ratio [33, 42, 43, 44, 45]. There is also a higher abundance of Lactobacillus (genus belonging to Firmicutes phylum).
According to most studies, the low-grade inflammation stimulated by lipopolysaccharide production is the prime mechanism by which gut microbiome induces obesity .
8.2 Gut microbiome in obesity management
Diet is an important factor for the manipulation of gut microbiome and management of obesity. The amount of daily caloric intake and the content of food significantly affect gut microbiome but with high interindividual variability [20, 21, 51]. A diet that is low in calories, low in fat (< 20% of total macronutrients), and high in fiber (≥ 30 g/day) has a favorable effect on gut microbiome (increase in richness, decrease in Firmicutes-to-Bacteroidetes phyla ratio) and weight control (weight loss).
Prebiotics are chemicals (nondigestible food ingredients) inducing growth and/or activity of bacteria [50, 52]. Prebiotics must be able to resist gastric acidity, resist enzymatic hydrolysis, resist absorption in the upper gastrointestinal tract, and be fermentable by the gut microbiome. Examples are inulin, lactulose, and resistant starch. Prebiotics can be found in many foods (e.g., leek, asparagus, onion, and soybean).
By modulating gut microbiome and lowering the production of lipopolysaccharide, prebiotics have the potential to manage obesity. In a double-blind, placebo-controlled clinical study, administration of oligofructose-enriched inulin (8 g/day) to overweight/obese children for 16 weeks caused a significant increase in Bifidobacterium (genus belonging to Actinobacteria phylum) and significantly slowed the body weight gain compared with placebo .
Probiotics are nonpathogenic living microorganisms with direct or indirect effect on gut microbiome [50, 54, 55]. Products containing probiotics should be tested for safety risks before marketing. Probiotics can be found in several foods (e.g., yogurt, cheese, and milk).
Probiotics can manage obesity by reducing the production of lipopolysaccharide through an impact on gut microbiome. In a double-blind, placebo-controlled clinical study, administration of fermented milk containing Lactobacillus gasseri species (LG2055) to overweight/obese adults for 12 weeks caused a significant decrease in body weight .
Synbiotics are combination of prebiotics and probiotics. They have the potential to induce more effects on gut microbiome and body weight than prebiotics or probiotics alone.
8.2.5 Bariatric surgery
Bariatric surgery can modify gut microbiome and further affect body weight [57, 58]. The mechanisms include reduced caloric intake, reduced gastric emptying, and alterations in gastric acid production and bile acids.
8.2.6 Fecal microbiota transplantation
Fecal microbiota transplantation, which consists of transfer of feces from a healthy donor to a recipient, is an exciting therapy with important potential. It can modify gut microbiome for the purpose of obesity management [59, 60]. The addition of healthy stool can be done through colonoscopy, orogastric tube, esophagogastroduodenoscopy, or oral capsule. It is important to carefully select and screen the donor to avoid risk of infection, aggravation of obesity, or other complications [61, 62].
Available clinical data are very preliminary and limited. Several studies are ongoing. There is no regulatory guidance for the use of fecal microbiota transplantation in the management of obesity.
8.2.7 Cost of gut microbiome manipulation
Cost of gut microbiome manipulation in obesity management is reported in Table 3.
|Tool for gut microbiome manipulation||Description|
|Diet||Low calories, low fat, high fiber|
|Prebiotics||Inulin, lactulose, resistant starch|
|Probiotics||Yogurt, cheese, milk|
|Synbiotics||Combination of prebiotics and probiotics|
|Bariatric surgery||Roux-en-Y gastric bypass|
|Fecal microbiota transplantation||Addition of healthy stool|
|Tool for gut microbiome manipulation||Average cost (range)|
|Diet||Cost of food|
|Bariatric surgery (Roux-en-Y gastric bypass)||$23,000 ($20,000–$30,000)|
|Fecal microbiota transplantation||$1,800 ($1,600–$2,000) + cost of administration/dose|
9. Clinical study design to assess gut microbiome in obesity
Well-designed clinical studies are urgently needed to better understand the interactions between obesity/obesity treatment and gut microbiome.
Several factors affect the quality of weight-loss studies aimed to assess gut microbiome. A well-calculated sample size allowing subgroup analysis is a key factor. Relevant stratification factors (e.g., race, age, gender, BMI, diet, and medications) at randomization will make the study more informative. Any underestimation of these stratification factors, as it has been the case in several clinical studies, especially in relation to diet and medications, may lead to misleading and conflicting results. The duration of the clinical studies has to be sufficient to allow both short-term and long-term/follow-up assessments. Adequate adjustments should be made during the statistical analysis.
10. Ideal gut microbiome
An ideal gut microbiome should have high diversity. At the level of phyla, the ideal gut microbiome should have low Firmicutes phylum and high Bacteroidetes phylum with a Firmicutes-to-Bacteroidetes phyla ratio < 1.0. At the level of genera, the ideal gut microbiome should be rich in Prevotella genus.
The recommended diet to reach the above objectives is a diet adequate in calories (adjusted to the activity), low in fat (< 20% of total macronutrients), and rich in fiber (≥ 30 g/day).
Gut microbiome influences normal physiology and susceptibility to diseases. Profound changes affecting the diversity and the abundance of gut microbiome are associated with obesity. A decrease in microbiome diversity and an increase in the ratio of Firmicutes-to-Bacteroidetes phyla have been reported in obese subjects.
Gut microbiome can be manipulated to change the host metabolism and manage obesity. Potential interventions include diet, prebiotics, probiotics, synbiotics, bariatric surgery, and fecal microbiota transplantation.
A better understanding of the interactions between different diets and gut microbiome should help the development of new guidelines for feeding humans to prevent or manage obesity.
Conflict of interest
The author received honorarium for consultancy from Gelesis, Inc.