Introduction

The human body is home to a vast array of microbial communities, and among the most versatile is the phylum Pseudomonadota (formerly known as Proteobacteria). This diverse group of bacteria inhabits nearly every niche of the human body, from the respiratory tract to the skin and the gastrointestinal system. While many members of this phylum coexist peacefully as commensals, others can act as opportunistic pathogens when the host's microbial balance is disrupted.

Through the lens of metagenomics and shotgun sequencing, scientists are now uncovering how the abundance and functional potential of Pseudomonadota influence our overall health. Understanding the delicate balance of this phylum is key to recognizing the transition from a healthy state to dysbiosis, where microbial imbalances may be associated with various inflammatory conditions.

Location of Microbe

Distribution Across Body Ecosystems

Skin: Pseudomonadota are present as part of the diverse skin microbiota, contributing to the overall microbial diversity of the cutaneous surface.

Nasal: In the nasal cavity, this phylum serves as a component of the frontline defense, though its prevalence can shift in systemic disorders like sickle cell disease.

Respiratory: Within the pulmonary system, including the lungs and bronchial branches, Pseudomonadota are detected as part of the resident microbial community that helps regulate lung homeostasis.

Urinary: This phylum is identified within the urinary tract, where its presence is monitored in the context of urogenital health and potential opportunistic colonization.

Ocular: Pseudomonadota are found in the ocular ecosystem, contributing to the low-biomass microbial community of the eye.

Ear: In the ear canal and associated tissues, these bacteria are part of the normal flora that maintains the local ecosystem.

Behavior During Dysbiosis

Microbial Shifts and Ecosystem Imbalance

Skin: Dysbiosis often manifests as a loss of diversity, where certain Pseudomonadota may expand and disrupt the skin's protective barrier integrity.

Nasal: In children with sickle cell disease, there is a documented higher prevalence of Pseudomonadota, including pathobionts like Klebsiella pneumoniae and Yersinia enterocolitica.

Respiratory: Imbalances in the lung microbiota, including shifts in Pseudomonadota abundance, are associated with respiratory diseases and a decline in lung homeostasis.

Urinary: An overgrowth of this phylum in the urinary tract is often associated with inflammatory signaling and a breakdown of the mucosal barrier.

Ocular: Shifts in ocular Pseudomonadota abundance are linked to changes in the local immune environment and potential opportunistic infections.

Ear: Dysbiosis in the ear ecosystem may involve the expansion of opportunistic strains that trigger local inflammatory responses.

Disease Associations

Impact Across Ecosystems

Respiratory and Nasal Ecosystems: In the nasal cavity, an increased prevalence of Pseudomonadota species is associated with pediatric sickle cell disease, potentially increasing susceptibility to pneumonia or sinusitis. In the lungs, dysbiosis of the pulmonary microbiome is associated with conditions such as community-acquired pneumonia and chronic obstructive pulmonary disease (COPD).

Gastrointestinal and Biliary Ecosystems: Although primarily located in other niches, Pseudomonadota shifts in the gut are associated with colorectal cancer (CRC), where they appear significantly elevated in stage III CRC. In the biliary system, they are a dominant phylum in benign biliary diseases, but their relative abundance may decrease in patients with cholangiocarcinoma compared to benign cases.

Systemic and Other Associations: In the oral cavity, a decreasing trend of Pseudomonadota is observed in patients with acute ischemic stroke (AIS) and transient ischemic attack (TIA). Furthermore, the overgrowth of intestinal Pseudomonadota is strongly associated with recurrent Clostridioides difficile infection (rCDI) and the presence of antimicrobial resistance genes (ARGs).

Foods Supporting Healthy Balance

Maintaining a healthy microbial balance involves supporting the growth of beneficial anaerobes that provide colonization resistance against the overgrowth of opportunistic Pseudomonadota. Dietary fiber is a primary driver of this balance, as it is fermented by beneficial bacteria into short-chain fatty acids (SCFAs) like butyrate, which support gut barrier integrity and modulate inflammatory signaling.

Specific prebiotic interventions, such as Maitake mushroom extract (rich in $\beta$-glucans), have been shown in vitro to positively modulate reconstructed human gut microbiota. When combined with probiotics like Lactiplantibacillus plantarum and Bifidobacterium animalis, these extracts promote a tolerogenic microenvironment and the production of beneficial metabolites like lactate and propionate. Additionally, reducing the intake of artificial sweeteners, such as acesulfame K, may help prevent microbiome disturbances associated with metabolic stress and weight gain.

Actionable Insights

Strategies for Microbial Management

• Prioritize Fiber-Rich Foods: Increase intake of diverse plant fibers to support SCFA production, which helps keep opportunistic Pseudomonadota in check.
• Consider Prebiotic Support: Incorporate foods like Maitake mushrooms to encourage a balanced, anti-inflammatory microbial environment.
• Limit Artificial Sweeteners: Be mindful of artificial sweeteners that may be associated with oral and systemic microbiome disturbances.
• Respiratory Hygiene: For those with systemic conditions like sickle cell disease, maintain strict nasal and respiratory hygiene to reduce the risk of pathobiont expansion.
• Urinary Health: Maintain adequate hydration and hygiene practices to support the integrity of the urinary tract ecosystem and prevent opportunistic colonization.
• Monitor Antibiotic Use: Use antibiotics only when necessary, as they can deplete commensal anaerobes and lead to an overgrowth of antimicrobial-resistant Pseudomonadota.

Conclusion

The Pseudomonadota phylum represents a complex and dynamic component of the human microbiome. Its impact on health is highly dependent on the specific strain and the ecological niche it occupies. In the nasal and respiratory tracts, its balance is critical for preventing infections; in the gut, its overgrowth is often a marker of dysbiosis and antimicrobial resistance; and in the biliary system, it plays a role in distinguishing between benign and malignant states. By focusing on microbial diversity and supporting the host's natural barriers through diet and hygiene, we can maintain this versatile phylum in a commensal state, ensuring the overall stability of the human microbial ecosystem.

Scientific Sources

• Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients - PMC12503293
• Roles of Gut Microbiota and Associated Metabolites in Clostridioides difficile Infection - PMC12182954
• A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection - PMC10506460
• Dysbiosis of Bile Microbiota in Cholangiocarcinoma Patients - PMC11855699
• Altered nasal and oral microbiomes define pediatric sickle cell disease - PMC12188711