Which Microorganisms Colonize the Respiratory Tract?

The human respiratory system hosts a wide array of microorganisms, including bacteria, fungi, and viruses. These microbial communities, known as the microbiota, are an integral part of respiratory health. The composition of these communities is not uniform, as it varies significantly between the upper and lower sections of the respiratory system. Each area presents a unique habitat for different types of microbes.

Microorganisms of the Upper Respiratory Tract

The upper respiratory tract (URT), which includes the nasal passages, sinuses, and pharynx, is in constant communication with the outside world. This exposure results in a densely populated and diverse microbial community. Common bacterial inhabitants include genera such as Staphylococcus, Corynebacterium, and viridans group Streptococci in the nasal passages. The oropharynx, the part of the throat behind the mouth, contains many of these same bacteria but also includes species of Prevotella, Fusobacterium, and Haemophilus.

Fungi, particularly Candida species, are also present in the oropharynx as part of its normal mycobiome. Many healthy individuals can carry potential pathogens like Streptococcus and Neisseria without any symptoms. The initial colonization of the nasopharynx in infants is influenced by microbes from the mother, with genera like Moraxella, Corynebacterium, and Dolosigranulum being predominant early in life. In toddlers, especially those in daycare, it is common to find colonization by Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis.

This diverse URT microbiota is beneficial, helping to prime the immune system.

Microbial Inhabitants of the Lower Respiratory Tract

In contrast to the upper airways, the lower respiratory tract (LRT) is much less populated. This region, consisting of the trachea, bronchi, and the alveoli of the lungs, was once believed to be sterile. Modern molecular techniques have revealed that the LRT has its own sparse and distinct microbial population, kept in check by host defense mechanisms. A primary defense is the mucociliary escalator, where a layer of mucus traps microbes and cilia propel it toward the pharynx to be swallowed.

The LRT is also protected by immune cells called alveolar macrophages, which engulf microbes, and by secreted antibodies and antimicrobial peptides. Despite these defenses, a small number of bacteria are consistently found in the healthy LRT, including Prevotella, Veillonella, Streptococcus, and Pseudomonas. These organisms are thought to arrive through microaspiration, the inhalation of tiny droplets from the oropharynx. Whether these microbes constitute a stable community or are transient visitors is a subject of ongoing research.

Resident Microbes Versus Pathogenic Invaders

The relationship between the respiratory tract and its microbial inhabitants ranges from harmless coexistence to active disease. Many organisms that colonize the system are commensals, meaning they reside there without causing harm. Some resident microbes are beneficial by preventing the establishment of more dangerous organisms, a concept known as colonization resistance.

A distinction exists between these residents and pathogens, which are microbes capable of causing illness. Many respiratory infections are caused by opportunistic pathogens. These are organisms, such as Streptococcus pneumoniae or Haemophilus influenzae, that can be harmless colonizers but cause infection if host defenses are weakened or the microbial community is disrupted.

For example, Staphylococcus aureus colonizes the upper respiratory tract of about one-third of adults. While often harmless, this colonization is a known risk factor for developing serious infections like pneumonia, especially in hospitalized patients. The clinical picture helps distinguish between colonization and infection, as a child colonized with Group A Streptococcus without a sore throat may not require treatment.

Influences on Respiratory Tract Colonization

The specific makeup of an individual’s respiratory microbiota is not static and is shaped by a variety of internal and external factors. Host genetics and the status of the immune system play a role in managing these microbial communities.

Environmental exposures also significantly influence the microbiota. For example, living in overcrowded conditions or attending a childcare center can lead to earlier colonization by certain bacteria in infants and toddlers. Lifestyle choices have an impact, as smoking is known to alter the microbial balance.

The use of medications, particularly antibiotics, can disrupt the normal flora, potentially allowing for the overgrowth of resistant organisms. Underlying health conditions can also dramatically shift the respiratory ecosystem. Chronic diseases like asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis are associated with distinct changes in the lung microbiome.

In a hospital setting, the use of a ventilator is a high-risk factor for altering the LRT microbiota, potentially leading to pneumonia. These shifts, known as dysbiosis, can reduce the protective effects of the normal flora and increase susceptibility to infection.