We cover the gut microbiome and its impact on overall health

The upper gastrointestinal tract microbiome, proteobacteria and gut health

Proteobacteria is a large phylum of bacteria that includes a wide range of species. Proteobacteria are Gram-negative bacteria, and are found in many different environments, including the human body. They can be part of the microbiome of various areas, such as the mouth, gut, and skin. Some species of Proteobacteria are beneficial and play a role in maintaining health, while others can cause infections or other health problems.

The human GI tract is composed of multiple different organs and can be divided into the upper and lower GI tract. The upper GI tract refers to the mouth, oesophagus, stomach, duodenum, jejunum, and ileum, while the colon, rectum, and anus make up the lower GI tract. Important physiologic conditions like pH, bile content, and transit time vary along the GI tract and contribute to distinct microbial communities inhabiting the upper and lower GI tract. However due to the crosstalk between the microbiota of each region, the microbiota of upper GI tract influences the microbiota of lower GI and ultimately the human health.

Oral Cavity

The oral cavity is the mouth. It includes the lips, teeth, gums, tongue, and other structures that are involved in chewing, and swallowing. In the oral microbiome, Proteobacteria may be present in small numbers and may include species from the genera Neisseria, Haemophilus, and Moraxella, along with other phyla like Firmicutes, Bacteroidetes, Actinobacteria, Spirochaetes, and Fusobacteria. Overgrowths of Proteobacteria in the oral microbiome may be associated with oral health problems. For example, certain species of Proteobacteria have been linked to the development of periodontal disease, a condition that affects the gums and can lead to tooth loss.  Imbalances in oral microbiome may be also involved in the development and progression of certain gastrointestinal (GI) diseases such as inflammatory bowel disease (IBD) and colorectal cancer.

Dietary components may influence the oral microbiome, including Proteobacteria. For example, a diet that is high in fermentable carbohydrates, such as sugar and refined grains, may promote the growth of harmful bacteria in the mouth, including Proteobacteria, which can increase the risk of dental cavities and gum disease. On the other hand, a diet that is high in fiber, such as vegetables, fruits, and whole grains, may promote the growth of beneficial bacteria in the mouth and help to maintain a healthy oral microbiome. Prebiotics like beta-methyl-d-galactoside, N-acetyl-d-mannosamine, Nitrate, short-chain galacto-oligosaccharides, long-chain fructo-oligosaccharides, and glutamine can help in getting eubiosis in oral microbiome.


The oesophagus is a tube that connects the mouth to the stomach, and it is responsible for transporting food and liquids from the mouth to the stomach. The oesophagus is a relatively sterile environment, due to the low pH and the lack of nutrients that support microbial growth.  The oesophageal microbiome is influenced by several factors, including diet, medications, and overall health. The normal oesophageal microbiome is a bacterial community dominated by Gram-positive bacteria from the Firmicutes phylum or Streptococcus at the genus level.  Proteobacteria may be present in small numbers and may include species from the genera Neisseria and Haemophilus.

There is some evidence that changes in the abundance of Proteobacteria in the oesophageal microbiome may be associated with certain diseases and conditions. For example, studies have found that people with Barrett's oesophagus, a condition in which the normal tissue lining the oesophagus is replaced by tissue that is like the lining of the intestine, have a higher abundance of Proteobacteria in their oesophageal microbiome compared to people without the condition. Oesophageal composition appears to be independent of proton-pump inhibitor use or gender. Oesophageal microbiota of patients with gastro oesophageal reflux disease (GERD), bronchiolitis obliterans (BO) have diminished bacterial count of all genera except Campylobacter, i.e. a proteobacteria.

Increasing fiber intake was significantly associated with increasing relative abundance of Firmicutes and decreasing relative abundance of Gram-negative bacteria overall. Low fiber intake was associated with increased relative abundance of several Gram-negative bacteria, including PrevotellaNeisseria, and Eikenella. Isomaltooligosaccharides have been demonstrated to increase the number of gram-positive flora, especially Bifidobacterium and lactobacillus spp. Prebiotics, including Maltosyl-isomaltooligosaccharide (MIMO), are aimed at improving gram-positive/gram-negative ratio in the oesophagus. Use of probiotics like Lactobacillus and Bifidobacterium to has been shown to decrease GERD symptoms


The stomach microbiome is the community of microorganisms that inhabit the stomach. The stomach has a highly acidic environment, with a pH that can range from 1.5 to 3.5. This low pH helps to kill off many types of bacteria, and as a result, the stomach is typically colonized by only a few species of bacteria. These bacteria are often from the genera Helicobacter, Lactobacillus, and Streptococcus. The stomach microbiome is influenced by several factors like switching to a high-fat diet, including a decrease in Bacteroidetes and an increase in both Firmicutes and Proteobacteria. Helicobacter pylori (H. pylori) is a type of proteobacteria that can infect the stomach and cause inflammation (gastritis), abdominal pain, nausea, and bloating, and can increase the risk of certain conditions, such as peptic ulcer disease and gastric cancer. Bifidobacterium spp., Clostridium coccoides and Clostridium leptum were also reduced in H. pylori-negative gerbils. The reason for these observations is unclear, a possible explanation is that H. pylori induced inflammation induces gastric atrophy and reduces the parietal cell mass, resulting in elevation of gastric pH, which predisposes to the colonization of environmental microbiota. In patients with abundant H. pylori, a greater number of bacteria belonged to the phylum Proteobacteria and the gastric microbiomes yielded lower overall diversity. When looking at the gut microbiome of individuals with H. pylori, there is increased abundance of Succinivibrio, Coriobacteriaceae, Enterococcaceae, and Rikenellaceae.

Small Intestine

The small intestine consists of the duodenum, jejunum, and the ileum and is the location where most nutrient digestion and absorption occur. The duodenum is the portion of the small intestine where the food bolus enters from the stomach, and bile salts from the gallbladder along with pancreatic enzymes start digestion. The intestinal epithelium of the jejunum and ileum is then responsible for nutrient absorption. The small intestine is dominated by rapidly dividing facultative anaerobes such as Proteobacteria and Lactobacillales. The duodenum harbours similar genera as the stomach (Bacillales incertae sedis, Streptococcaceae, Enterobacteraceae, Leptorichiaeceae, Veillonellaceae, and Pseudomonadaceae). The terminal ileum exhibited a composition closer to that of the colon (Clostridiaceae, Lachnospiraceae, Peptostreptococcaceae, Ruminococcaceae, Enterobacteriaceae, and Bacteroidaceae). Small intestine bacterial overgrowth (SIBO) is a condition in which there is an excessive number of bacteria in the small intestine. In SIBO, there may be an overgrowth of Proteobacteria which includes species from the genera Escherichia, Salmonella, and Vibrio. Monoprobiotics with well characterized strains like Sacharomyces boulardii may have a favourable role in preventing the progression of SIBO symptoms. Mindful eating, defined as appropriate breaks between meals, including the omission of snacking, might be a key element in the prevention and treatment of SIBO.


  1. Kahana, Doron D., and Timothy Van Natta. "Mucosa-related Gastropathology: The upper gastrointestinal tract and the microbiome." Esophageal and Gastric Disorders in Infancy and Childhood. Springer, Berlin, Heidelberg, 2017. 1447-1462.
  2. Ruan, Wenly, et al. "Healthy human gastrointestinal microbiome: composition and function after a decade of exploration." Digestive diseases and sciences 65.3 (2020): 695-705.
  3. Nardone, Gerardo, Debora Compare, and Alba Rocco. "A microbiota-centric view of diseases of the upper gastrointestinal tract." The Lancet Gastroenterology & Hepatology 2.4 (2017): 298-312.
  4. Maitre, Yoann et al. “Pre and Probiotics Involved in the Modulation of Oral Bacterial Species: New Therapeutic Leads in Mental Disorders?.” Microorganisms vol. 9,7 1450. 6 Jul. 2021, doi:10.3390/microorganisms9071450





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