Handbook- Diseases and Symptoms

Obesity

Firmicutes and Bacteroidetes are two dominant bacterial phyla in the human gut microbiome and play a key role in energy metabolism and obesity development. Individuals with obesity often exhibit a higher Firmicutes-to-Bacteroidetes ratio compared to lean individuals. Firmicutes are efficient at breaking down complex carbohydrates into short-chain fatty acids (SCFAs), such as butyrate, acetate, and propionate, which are then absorbed by the host. This enhanced caloric extraction from the diet can contribute to increased energy harvest and fat storage.

Bacteroidetes, on the other hand, are less efficient at fermenting polysaccharides and are associated with leaner body types. A shift in the balance toward Firmicutes may promote low-grade inflammation, insulin resistance, and increased fat accumulation, all of which are factors in obesity. Diet plays a significant role in shaping this microbial balance; high-fat, low-fiber diets tend to favor Firmicutes proliferation.

Type 2 -Diabetes

Specific gut microbes such as Clostridium coccoides, Atopobium species, Prevotella species, and Lactobacillus species play distinct roles in the development of type 2 diabetes (T2D) through their impact on metabolism, inflammation, and gut barrier function.

Clostridium coccoides, a group within the Firmicutes phylum, is known for producing short-chain fatty acids (SCFAs) like butyrate, which support gut health and reduce inflammation. However, some studies have shown reduced abundance of butyrate-producing Clostridium coccoides in T2D, potentially contributing to impaired gut barrier integrity and metabolic dysregulation.

Atopobium species, part of the Actinobacteria phylum, have been associated with inflammation and metabolic disturbances in some studies. Their overrepresentation may contribute to increased gut permeability and endotoxemia, triggering insulin resistance.

Prevotella species, which ferment dietary fibers into SCFAs, are linked to both protective and harmful effects depending on the host’s diet and health status. In T2D, an increased abundance of certain Prevotella strains has been associated with pro-inflammatory pathways and glucose intolerance.

Lactobacillus species are commonly considered beneficial; however, certain strains have been found in higher abundance in T2D patients. Their role is strain-specific—some may promote glucose regulation, while others might contribute to dysbiosis and metabolic imbalance.

Hypertension

The gut microbes Lactobacillus, Prevotella, Clostridium, and Akkermansia influence hypertension through their effects on inflammation, metabolism, and vascular health. Lactobacillus species are often beneficial, producing bioactive peptides that help regulate blood pressure by inhibiting angiotensin-converting enzyme (ACE). Prevotella species can promote inflammation and have been associated with increased blood pressure in some populations. Clostridium species include both beneficial SCFA-producing strains and harmful ones linked to inflammation and gut barrier dysfunction. Akkermansia muciniphila supports gut integrity and reduces inflammation, and its reduced abundance is often observed in hypertensive individuals. Modulating these microbes may offer new strategies for blood pressure control.

Irritable Bowel Syndrome

In irritable bowel syndrome (IBS), specific gut microbes like Bacteroides, Prevotella, Lactobacillus, Clostridium, and Methanobrevibacter influence gut function and symptoms. Bacteroides and Prevotella are involved in carbohydrate fermentation; their imbalance may lead to gas production and bloating. Lactobacillus species, though typically beneficial, are often increased in IBS and may exacerbate symptoms in some cases. Clostridium species include both beneficial and harmful strains—some produce toxins or promote inflammation. Methanobrevibacter smithii, a methane-producing archaeon, is linked to constipation-predominant IBS due to its role in slowing intestinal transit. Overall, microbial imbalance contributes to altered motility, sensitivity, and inflammation in IBS.

CKD

In chronic kidney disease (CKD), gut microbes like Enterobacteriaceae, Clostridium, Lactobacillus, Bacteroides, and Akkermansia play significant roles. Enterobacteriaceae are often elevated in CKD and contribute to the production of uremic toxins like indoxyl sulfate and p-cresyl sulfate, which worsen kidney function. Some Clostridium species also produce harmful metabolites, while others may support gut health. Lactobacillus can have protective effects by reducing inflammation and enhancing gut barrier integrity. Bacteroides contribute to both beneficial SCFA production and toxin generation, depending on the species. Akkermansia muciniphila supports mucosal integrity and may help reduce systemic inflammation, potentially slowing CKD progression.

Colorectal Cancer

In colorectal cancer (CRC), specific gut microbes contribute to tumor initiation and progression. Fusobacterium nucleatum promotes inflammation, suppresses immune responses, and enhances tumor cell proliferation. Bacteroides fragilis, particularly enterotoxigenic strains, produce toxins that disrupt epithelial barriers and trigger chronic inflammation. Certain Escherichia coli strains carry the pks genomic island, producing colibactin, a genotoxin that induces DNA damage. Peptostreptococcus species are enriched in CRC tissues and may support a pro-tumor microenvironment through immune modulation. Clostridium species, while diverse, include some that produce harmful metabolites or toxins, contributing to mucosal damage and carcinogenesis. These microbes collectively drive inflammation and genomic instability in CRC.

Depression

In depression, Eggerthella and Coprococcus play contrasting roles. Eggerthella is often increased in individuals with depression and is linked to inflammation and impaired gut barrier function, which may contribute to neuroinflammation and mood disturbances. In contrast, Coprococcus is typically reduced in depressed individuals. It is a butyrate-producing genus associated with anti-inflammatory effects and enhanced gut-brain communication. Lower levels of Coprococcus may negatively impact serotonin production and emotional regulation, contributing to depressive symptoms.

Atherosclerosis

Chlamydia pneumoniae, Porphyromonas gingivalis, and Helicobacter pylori are pathogenic microbes implicated in the development of atherosclerosis through inflammatory and immune-mediated mechanisms. Chlamydia pneumoniae has been detected in atherosclerotic plaques and may contribute to vascular inflammation by infecting endothelial cells and promoting immune activation. Porphyromonas gingivalis, a key pathogen in periodontal disease, can enter the bloodstream, triggering systemic inflammation and endothelial dysfunction, both of which accelerate plaque formation. Helicobacter pylori infection is associated with chronic inflammation and increased oxidative stress, which can damage blood vessels and promote atherogenesis. These microbes contribute to a pro-atherogenic environment, linking infection and cardiovascular risk.

Rheumatoid arthritis

In rheumatoid arthritis (RA), alterations in the gut microbiome play a significant role in disease onset and progression. Faecalibacterium prausnitzii, a beneficial butyrate-producing bacterium, is often reduced in RA patients, contributing to inflammation due to its anti-inflammatory properties. Glaesserella parasuis, typically an animal pathogen, may contribute to immune activation when present in humans. Porphyromonas gingivalis, linked to periodontal disease, can trigger autoimmune responses through citrullination of proteins, a key process in RA pathogenesis. Segatella (Prevotella) copri is frequently enriched in early RA and associated with increased inflammation and immune dysregulation. Leyella stercorea and Ligilactobacillus salivarius are less studied but may influence gut immune interactions and inflammation. Bacteroidaceae family members show variable roles; some contribute to immune modulation, while others may promote inflammation. Overall, dysbiosis involving these microbes can disrupt gut barrier function, trigger immune responses, and promote systemic inflammation, contributing to RA development and severity.

Stomach Pain

In stomach pain, gut microbes such as Bifidobacterium, Blautia, Streptococcus, Prevotella, and Lacticaseibacillus rhamnosus play varying roles. Bifidobacterium and Lacticaseibacillus rhamnosus are beneficial probiotics that support gut barrier integrity, reduce inflammation, and help alleviate symptoms like bloating and discomfort. Blautia, a short-chain fatty acid producer, generally supports gut health, though its imbalance may contribute to dysbiosis. Some Streptococcus species, especially when overgrown, can produce excess lactic acid and cause irritation or discomfort. Prevotella species are involved in carbohydrate fermentation and gas production, which may lead to bloating and pain in sensitive individuals. Their balance is key to symptom relief.

Flatulence and Bloating

In flatulence and bloating, specific gut microbes play key roles through gas production and fermentation. Bilophila wadsworthia produces hydrogen sulfide, a gas contributing to odor and gut discomfort. Bacteroides ovatus ferments complex carbohydrates, leading to gas buildup and bloating in some individuals. Bifidobacteriales are generally beneficial, aiding digestion, but their fermentation can also produce gas. Blautia helps produce short-chain fatty acids and may support gut balance, though overgrowth may contribute to bloating. Some Clostridium species generate gas and toxins, aggravating symptoms. Phascolarctobacterium consumes fermentation byproducts, potentially reducing bloating, but its imbalance may disrupt this protective role.

Constipation

In constipation, gut microbes influence motility, fermentation, and intestinal health. Desulfovibrionaceae produce hydrogen sulfide, which can impair gut motility and contribute to constipation. Bifidobacterium and Lactobacillus are beneficial probiotics that promote bowel regularity by enhancing gut barrier function and producing lactic acid, which stimulates peristalsis. Roseburia intestinalis and Coprococcus are butyrate-producing bacteria that support gut health and motility; their reduction is linked to slower transit. Butyricimonas also produces butyrate, aiding stool softening and colon function. An imbalance or reduction in these beneficial microbes can lead to harder stools, slower bowel movements, and increased risk of chronic constipation.

Diarrhea

In diarrhea, certain gut microbes can disrupt intestinal balance and promote fluid loss. Bacteroides fragilis, especially enterotoxigenic strains, produce toxins that increase intestinal permeability and fluid secretion. Escherichia, particularly pathogenic E. coli strains, can cause inflammation and water loss through toxin production. Streptococcus species, when overgrown, may ferment sugars excessively, producing gas and acids that irritate the gut. Fusobacterium mortiferum is linked to gut inflammation and may exacerbate diarrheal conditions. In contrast, Bifidobacterium pseudocatenulatum is a beneficial species that supports gut health, reduces inflammation, and may help restore balance and reduce the severity or duration of diarrhea.