Introduction

The human body is home to a vast and complex array of microorganisms, and among the most influential is the phylum Bacillota (formerly known as Firmicutes). As one of the primary phylogenetic categories dominating the human microbiome, Bacillota plays a fundamental role in maintaining physiological balance, from nutrient metabolism to immune regulation.

Understanding the abundance and behavior of Bacillota is essential for grasping the overall state of the gut ecosystem. Because this phylum encompasses a diverse range of species—some providing critical health benefits and others acting as opportunistic pathogens—their impact is highly dependent on the specific niche and the surrounding microbial community.

Location of Microbe

Bacillota are widely distributed across various human biological niches, adapting their functional potential to meet the requirements of different ecosystems.

Gut

In the gastrointestinal tract, Bacillota are among the most dominant bacteria, residing throughout the GI tract from the stomach to the rectum, including the mucosa-associated layers.

Oral

Within the oral cavity, Bacillota are prevalent in the saliva and oral biofilms, where they contribute to the complex microbial networks of the mouth.

Vaginal

Bacillota are also present within the vaginal ecosystem, contributing to the overall microbial diversity of this niche.

Behavior During Dysbiosis

Gut

In the gut, dysbiosis can manifest as significant shifts in Bacillota abundance. For example, acute depletion occurs following bowel-preparation for colonoscopies, with repopulation aligning with fiber intake. In other contexts, such as HIV-1 infection, geographic-specific alterations in Bacillota are observed, which may contribute to neurocognitive and affective disruptions through the brain-gut-microbiota axis.

Oral

Oral dysbiosis is characterized by shifts in the relative abundance of Bacillota. In patients with acute ischemic stroke (AIS) or transient ischemic attack (TIA), there is a statistically significant increase in Bacillota abundance within the saliva, coinciding with increased genus richness and a shift toward a pro-inflammatory microbial community.

Vaginal

Dysbiosis in the vaginal ecosystem involves an imbalance in the relative abundance of Bacillota, which can disrupt the local microbial homeostasis and impact the host-microbe interaction.

Disease Associations

Gut Ecosystem

Metabolic Disorders and Obesity

The ratio of Bacillota to Bacteroidota is frequently associated with obesity and metabolic syndrome. An increased ratio is often observed in overweight individuals and is linked to enhanced energy harvest from the diet. Specifically, certain genera within Bacillota, such as Megamonas, are positively correlated with obesity severity and may promote endometrial cancer progression by enhancing lipid absorption and inducing hyperestrogenemia.

Neurocognitive and Affective Disorders

Alterations in Bacillota abundance are associated with the neurocognitive impairments (NCI), apathy, and depression observed in individuals living with HIV-1. These changes may underlie deficits in serotonin and γ-aminobutyric acid (GABA) neurotransmission, illustrating the influence of the gut-brain axis on mental well-being.

Acute Lung Injury (ALI)

Following cardiopulmonary bypass surgery, patients who develop acute lung injury exhibit a significant increase in Bacillota. This shift is associated with the enrichment of genera such as Streptococcus and Enterococcus, suggesting a link between gut dysbiosis and the gut-lung axis in post-surgical complications.

Oral Ecosystem

Cerebrovascular Events

Increased abundance of Bacillota in the saliva is associated with acute ischemic stroke and transient ischemic attack. This microbial shift is linked to higher genus richness and the enrichment of pathways related to cardiovascular diseases and inflammation, potentially acting as a non-invasive biomarker for stroke risk.

Vaginal Ecosystem

Microbial Imbalance

Shifts in Bacillota abundance within the vaginal niche are associated with various states of dysbiosis, which can compromise the integrity of the vaginal barrier and increase susceptibility to opportunistic infections.

Foods Supporting Healthy Balance

Maintaining a healthy balance of Bacillota, particularly the beneficial butyrate-producing species, is largely driven by dietary patterns that support high microbial diversity and the production of short-chain fatty acids (SCFAs).

High-Fiber Intake

Dietary fiber is critical for the maintenance and repopulation of Bacillota. Increased fiber consumption is associated with improved therapeutic responses in cancer immunotherapy and is essential for the recovery of the microbiome following clinical procedures like colonoscopies. Specifically, fiber supports the growth of SCFA-producing bacteria such as Faecalibacterium prausnitzii.

Phytochemicals and Specific Vegetables

The consumption of tomatoes has been shown to influence the Bacillota/Bacteroidota ratio, helping to maintain a more favorable profile and increasing overall phylum-level alpha-diversity. This suggests that specific phytochemicals can prevent the unwanted increase of Bacillota associated with obesity.

Prebiotics and Fasting Protocols

Prebiotics such as inulin and trans-galactooligosaccharides (B-GOS) stimulate beneficial groups and can inhibit pro-inflammatory signaling. Additionally, early time-restricted eating (eTRE) combined with energy restriction has been associated with a decrease in Bacillota during follow-up, potentially aiding in the management of obesity and improving fasting glucose and blood pressure.

Actionable Insights

General Microbiome Management

• Prioritize Fiber: Increase intake of diverse plant-based fibers to support the growth of beneficial Bacillota and ensure the production of anti-inflammatory SCFAs.
• Implement Time-Restricted Eating: Consider an early eating window (e.g., 8:00 AM to 4:00 PM) to promote lasting shifts in the microbiome associated with better metabolic health.
• Post-Procedure Nutrition: After bowel-cleansing procedures like colonoscopies, focus on immediate fiber-rich nutrition to accelerate the repopulation of depleted Bacillota.
• Incorporate Phytochemicals: Regularly consume vegetables like tomatoes to help maintain a healthy Bacteroidota-to-Bacillota ratio.

Oral Health and Hygiene

• Maintain Oral Diversity: Be mindful that excessive use of antimicrobial mouthwashes (e.g., chlorhexidine) can create selection pressure, leading to the development of resistant Bacillota strains.
• Monitor Oral-Gut Connection: Recognize that oral dysbiosis can be associated with systemic inflammation; maintaining a balanced oral microbiome may support overall vascular health.

Vaginal Health

• Support Ecosystem Stability: Maintain vaginal health through a balanced approach to hygiene, avoiding harsh chemicals that may trigger dysbiosis and alter the abundance of the Bacillota phylum.

Conclusion

The phylum Bacillota is a cornerstone of the human microbiome, playing a dual role as both a provider of essential health benefits and a marker of certain disease states. In the gut, they are vital for SCFA production and metabolic regulation; in the oral cavity, they contribute to the complex biofilm structure; and in the vaginal tract, they help maintain ecosystem stability.

It is crucial to understand that the impact of Bacillota depends entirely on the specific strain and the niche context. While an increase in this phylum can be associated with obesity or systemic inflammation in some individuals, other Bacillota members are indispensable for immune modulation and gut barrier integrity. Achieving a healthy microbiome is not about the total elimination or maximization of one phylum, but about fostering a diverse and balanced ecosystem tailored to the individual's health needs.