Intestinal microbiota is the most abundant (and the most important) microbial network of our body with trillions and trillions of microorganisms (not yet all identified), but let us remember that there are other microbiotas, including oral, vaginal, skin, or respiratory ones. They serve as a control of the health of the respective local organ. Much more challenging is to understand which microbial clusters or groups are helpful or harmful to our body as well as their communication between the different microbial ecosystems and the human cell’s hardware.” – Prof. Lorenzo Drago

Here listed are the main bacterial groups involved in the health and diseases of the human gut processes:

Bacterial phyla present in the gut microbiota

Bacterial phyla are the major lineages of the domain bacteria. In the gut, these include:

Main bacterial phyla in the gut microbiota


Firmicutes are one of the most abundant phyla together with Bacteridetes and play a significant role in the relationship between gut bacteria and human health. Many of the members of this phylum break down carbohydrates in the gut that can’t be digested by the body’s enzymes, such as dietary fiber and resistant starch. Members of the Firmicutes phylum are Lactobacilli, Faecalibacterium with probiotic activity by producing also health-promoting short-chain fatty acid and butyrate. But inside this phylum, there are some pathogenic species, such as Clostridium perfringens or Clostridium difficile (types of bacteria that causes gastrointestinal infections), Staphylococcus aureus, which is a common cause of some serious infections, and other opportunistic gram-positive bacteria.

Sulphate Reducing Bacteria are also produced by Firmicutes, and Proteobacteriae phylum. This group produces hydrogen sulfide (H2S) via the metabolism of sulfur-containing compounds such as mucins and amino acids, which is considered highly toxic outside the tightly regulated physiological range. The phylum is involved in many metabolic, enzymatic, hormonal processes, mineral absorption, and its balance is considered pivotal for the intestinal and other organs’ well-being.

Source: Firmicutes: Microbiome and Metabolome in Diagnosis, Therapy, and other Strategic Applications, 2019.


The phylum includes Gram-negative, non-spore-forming, anaerobic or aerobic, and rod-shaped. Many Bacteroidetes are good friends of our body by participating in some essential metabolic conversions, such as degradation of proteins or complex sugar polymers. Bacteroidetes phylum contains also opportunistic pathogens, such as Bacteroides fragilis and Porphyromonas. The balance of Bacteroidetes may have negative or positive consequences for the host. As members of polysaccharide-degrading consortia, they contribute to the release of energy from dietary fiber and starch, and they are likely to be a major source of propionate; however, they are also involved in the release of toxic products from protein breakdown.

Members of this group have some activities that may help to suppress inflammation, but they also have the potential to promote inflammation. Disbalance of Bacteroidetes is actually assigned to obesity and to Inflammatory bowel diseases, such as Chron’s Disease and Ulcerative Colitis, which brings to overexpression of microbial proteases and hydrolases. The over presentation of endotoxin LPS by this gram-negative group may also have an important role in the inflammation, both oxidative and metabolic processes.

Source: Bacteroidetes: Encyclopedia of Food Microbiology (Second Edition), 2014.


The phylum includes the majority of Gram-negative bacteria with a variety of several pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia, Legionellales, and other non-pathogenic bacteria responsible for nitrogen fixation. The family of Enterobacteriaceae is the main representative of this phylum and is commonly present in our gut in a balanced amount.

This group of bacteria is involved in many denitrifying and nitrate reduction processes thanks to the periplasmic nitrate reductase (Nap), the copper-containing nitrite reductase (Cu-Nir), the cytochrome c oxidase NO reductase (cNor), and the nitrous oxidoreductase (Nos) activities. The disbalance of the phylum is considered particularly important in many diseases.

Source: Proteobacteria: Microbiome and Metabolome in Diagnosis, Therapy, and other Strategic Applications, 2019.


Actinobacteria include mostly Gram-positive bacteria with three important main families: Bifidobacteriaceae, Coriobacteraceae, and Corynebacteriaceae. The vast majority of Actinobacteria are important saprophytes capable of breaking down a wide range of plant and animal debris in the process of decomposition. This phylum includes the Streptomyces and Micromonospora group, which are recognized as the producers of many bioactive metabolites that are useful to humans as antimicrobials, enzyme inhibitors, and gut balance control substances (signaling molecules, and immunomodulators).

One of the most important genera belonging to Actinobacteria is Bifidobacterium. The list of the positive effects of Bifidobacteria (which includes 100 different species at least) is very wide: regulation of intestinal microbial homeostasis, inhibition of harmful and opportunistic bacteria, modulation of immune responses, repression of carcinogenic compounds, production of vitamins, bioconversion of dietary compounds into bioactive molecules, reduction of endotoxin LPS in the intestine. It is also involved in the improvement of Ulcerative Colitis remission and Irritable Bowel Syndrome (IBS) FODMAP diet management.

Source: Actinobacteria: Encyclopedia of Microbiology (Third Edition), 2009.


Cyanobacteria are Gram-negative bacteria, which includes five types of toxin producers and other useful bacteria well recognized for their ecologically important phototrophic characteristics. They are defined by their ability to carry out oxygenic photosynthesis (water-oxidizing, oxygen-evolving, plant-like photosynthesis). Until modern techniques for sequencing nucleic acids became available, many of these microorganisms were unknown.

Cyanobacteria are now found in the gut microbiome and advances in sequencing technology have made it possible to study the evolution and properties of these microbes, including their impact on human health. They provide, with the Melainabacteria group, also to synthesize several B and K vitamins in the human gut, which suggests that these bacteria are beneficial to their host because, in addition to aiding with the digestion of plant fibers, they are also a source of vitamins.

Source: Cyanobacteria: eLife, 2013; Biology of the Nitrogen Cycle, 2007.

Pro-inflammatory bacteria

Bacteria known to be pro-inflammatory, cause inflammation include:

  • Acinetobacter
  • Clostridium
  • Turicibacter
  • Haemophilus
  • Helicobacter
  • Klebsiella
  • Escherichia
  • Prevotella
  • Salmonella
  • Streptococcus
  • Sutterella
  • Alistipes

Pro-inflammatory bacteria in the gut microbiota


Acinetobacter genus is ubiquitous Gram-negative coccobacillus and nonmotile. Many Acinetobacter species resemble saprophytic pseudomonads and other Gram-negative non fermentative organisms in their ability to utilize a wide range of organic compounds as sole sources of carbon and energy. Rectal colonization of Acinetobacter comprises the risk of ‘translocation’ phenomenon (transfer from gut to form infected sites in lungs or other organs).

Acinetobacter spp. is opportunistic in healthcare and home care settings. The rate of colonization with Acinetobacter spp. of the skin, oral mucosa, and gastrointestinal tract increases rapidly after admission to the hospital and particularly to intensive care units (ICUs).

Source: Acinetobacter: Microbiology of Waterborne Diseases (Second Edition), 2014.


Clostridium is a genus of a group of strictly anaerobic Gram-positive bacteria, which have the ability to produce a special type of dormant cell, the endospore. Around 100 Clostridium species have been discovered and some of them are responsible for human diseases due to the formation of toxins.

The abundance in the gastrointestinal tract is considered a negative outcome, only Clostridium clusters XIVa and IV possess some beneficial attributes (they are significantly low in Inflammatory Bowel Disease (IBD) patients). Clostridium difficile in the gut may produce several toxins, some of the cytotoxic (types A and B).

Source: Clostridium: Encyclopedia of Microbiology (Third Edition), 2009.


Turicibacter is a genus in the Firmicutes phylum commonly found in the gut. Its role is controversial. It is involved in host lipid and steroid metabolism. Its abundance is inversely correlated with exercise, Chron’s Disease, tryptophane/serotonin metabolism, but not in autoimmune disease.

It is known only one spore-forming species, Turicibacter sanguinis. The presence in the gut of Turicibacter is important when its abundance is not excessive.

Source: T. A. Auchtung et al. Genome Announc. 2016.


Haemophilus genus is a very small rod-shaped bacteria belonging to Pasteurellaceae (Proteobacteria). All species of Haemophilus are strict opportunistic pathogens occurring in the respiratory tracts of warm-blooded animals, including humans, and in certain cold-blooded animals.

Although the presence of Haemophilus in gut microbiota still remains unknown, the abundance of this genus has been recently related to schizophrenia/depression and to several inflammatory effects (i.e. gastroenteritis, peritonitis).

Source: Haemophilus: Mosby’s Guide to Women’s Health, 2007.


Members of the genus Helicobacter (Proteobacteria phylum) colonize the stomach (gastric species), liver (enterohepatic species), and the intestine. The release of urease by the gastric Helicobacter species, such as H. pylori, generates ammonia to neutralize the gastric mucosal niche to a pH of 6–7 and it is considered a survival mechanism.

Helicobacter causes diarrheal illness, and it is associated with peptic ulcer disease being considered also a risk factor for gastric cancer.  Helicobacter is part of the gastrointestinal tract and its abundance may produce inflammatory adhesins, cytotoxic enzymes, and enterotoxins.

Source: Helicobacter pylori and Other Gastric Helicobacter Species. John E. Bennett MD, in Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases, 2020.


Klebsiella is a non-spore-forming, non-motile, facultative anaerobic Gram-negative straight rod genus, belonging to the Proteobacteria phylum. Klebsiella microorganisms are found commonly in the environment, but they also can asymptomatically colonize the human nasopharynx and gastrointestinal tract, and, less frequently, other sites.

High gastrointestinal colonization of Klebsiella may precede abdominal infections, increasing the risk of abdominal infection up to sevenfold as well as the colonization rates in hospitalized patients. Klebsiella genus as fermentative bacteria may metabolize glucose with the production of acid and gas.

Source: Klebsiella: Reference Module in Biomedical Sciences, 2021.


Escherichia genus belongs to the Enterobacteriaceae family (Proteobacteria phylum), a group of gram-negative bacilli responsible for a broad range of infections in humans and in animals. Both acid and gas are formed from fermentable carbohydrates. Only some sugars, as inositol, are not utilized, and adonitol is used by only one species.

Lactose is rapidly fermented by many members by producing a high amount of acids and gas. Like many Enterobacteriaceae, Escherichia can influence the inflammatory status by the large number of LPS (lipopolysaccharide toxin) on its external membrane and cell wall.

Source: Encyclopedia of Food Microbiology (Second Edition), 2014.


Prevotella genus (Bacteroidetes phylum) includes Gram-negative rods commonly associated with oral and gut human colonization. This genus has the ability to hydrolyze xylans and pectins and to utilize breakdown products from plant cell-wall degradation. The genus is considered to have an important role in the metabolism of protein and peptides since many strains are actively proteolytic and possess a characteristic dipeptidyl peptidase activity.

Prevotella species are implicated in chronic sinusitis, middle ear infections, brain abscesses, intraabdominal abscesses, and recently with some autoimmune diseases. Virulence mechanisms include an attachment to the mucosa, immune system evasion, production of proteases, and increased production of virulence factors when the microorganism transition from commensal to pathogen occurs.

Source: Prevotella: Encyclopedia of Food Microbiology (Second Edition), 2014.


Salmonella genus includes many facultative anaerobes species. They are catalase positive, oxidase negative and glucose, mannitol, and sorbitol fermenting with the production of acids or acids and gas. Only S. arizonae is able to ferment lactose, which is an exception rather than the rule. As a group, Salmonella is able to ferment sucrose, but rarely adonitol and overall do not form indole. They make up a core group of the Enterobacteriaceae family and are considered an important cause of foodborne disease in humans and a significant cause of morbidity, mortality, and economic loss throughout the world.

Some serovars (nowadays more than 2500 differents) can colonize regularly the intestine. Illness can range from mild to severe gastroenteritis, and in some people, the invasive disease can be fatal. Long-term sequelae such as reactive arthritis and irritable bowel syndrome have also been described as negative outcomes and consequences of salmonellosis.

Source: Salmonella: International Encyclopedia of Public Health (Second Edition), 2017.


Streptococcus genus belongs to the Micrococcaceae family (Phylum Firmicutes), and consists of 104 recognized species, commensal and pathogenic as well. Species of Streptococci can be defined using the Lancefield grouping scheme, a serotyping classification. Group A Streptococcus (GAS) includes Streptococcus pyogenes: GAS is estimated to cause 240,000 foodborne illnesses annually.

Other Streptococcus groups have also been observed to occasionally result in foodborne illnesses. Symptoms of illness are significantly different than the majority of foodborne illnesses since illness does not include gastroenteritis but more commonly a sore throat; complications include acute rheumatic fever and kidney inflammation. Streptococcus is considered an inflammatory cluster causing also septicemia, endocarditis, pneumonia, and many tissues infections.

Source: Streptococcus: Advances in Applied Microbiology, 2014.


Sutterella is a genus of Gram-negative, anaerobic, non-spore-forming bacteria of the family Sutterellaceae (Phylum Proteobacteria). Members of the genus Sutterella are widely prevalent commensals with mild pro-inflammatory capacity in the human gastrointestinal tract. However, the increase of Sutterella is related to many disorders of intestinal flora and intestinal inflammations.

Sutterella is also related to gut dysbiosis and neurological disorders, such as Autism, Down syndrome, or other autoimmune and inflammatory diseases, such as IBD. LPS per-production due to the increase of genus Sutterella in the gut may be considered the main pathogenic factor of the inflammatory properties.

Source: Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella spp. Frontiers Microbiology, 2016.


Alistipes is a relatively new genus of bacteria isolated primarily from medical clinical samples. Although present at a low rate compared to other genus members of the Bacteroidetes phylum in the gut, its abundance is considered relevant in gut dysbiosis and disease. According to the taxonomy database at The National Center for Biotechnology Information, the genus consists of 13 species.

All species of Alistipes were found to produce sulfonolipids, which are considered to have inflammatory capabilities. The genus Alistipes has emerging implications in many inflammatory processes, colon cancer, and mental health. Gut dysbiosis with an abundance of Alistipes in the feces seems to play also a role in other metabolic diseases, e.g., in non-alcoholic steatohepatitis, hepatic encephalopathy, and liver fibrosis.

Source: The genus Alistipes: Front. Immunol. 2020.