Microbiota and Allergy

Introduction

The prevalence of allergic diseases has increased over recent decades. These conditions negatively affect patients’ quality of life and impose additional financial burdens on both patients and healthcare systems. Epidemiological studies indicate that reduced exposure to environmental bacteria during early life is associated with an increased risk of developing allergic diseases and asthma in adulthood. Conversely, individuals living in environments where they are exposed to a wide variety of microorganisms have a lower risk of developing allergic diseases [1].

The human microbiome encompasses all microorganisms living inside and on the surface of the human body and their interactions with the environment. The microbiome may be regarded as a new organ system because it influences human health and disease development [2]. The term microbiome refers to the collective genomes of microorganisms within a particular habitat, whereas microbiota describes the ecological community of commensal, symbiotic, and pathogenic microorganisms residing within and on the surface of a multicellular organism.

The microbiota consists of bacteria, viruses, fungi, and protozoa. Changes in the composition of the human microbiota are associated with an increased susceptibility to inflammatory conditions, including allergic diseases, asthma, inflammatory bowel disease, obesity, and other disorders. The microbiota is also believed to influence nervous system development and mental health [3].

We therefore live in a microbial world. Microorganisms were among the earliest forms of life on Earth and currently account for the largest proportion of biomass. Because individual microorganisms have difficulty surviving independently in nature, they form complex, highly developed communities adapted to the environments they colonize [4].

The human microbiota consists of microorganisms inhabiting the gastrointestinal tract, respiratory tract, skin, and other parts of the body.

Gut Microbiota

The intestinal epithelium, mucosal immune system, and bacterial and nonbacterial flora form a dynamic morphological and functional system responsible for maintaining local intestinal integrity and barrier function in the host.

The human intestine contains approximately 500 species of microorganisms, which account for around 1.5 kg of an average person's body weight. Microbial cells outnumber human body cells by approximately 10 to 1, while the microbial genome encodes 100–1,000 times more genetic information than the host genome [5].

The relationship between the host and the microbiota is mutually beneficial and involves the immune system. The gut microbiota benefits from the stable environment and nutrients provided by the intestine, while the host receives products of bacterial fermentation of substances it cannot digest independently.

For example, dietary fiber is broken down into short-chain fatty acids, primarily acetate, propionate, and butyrate, which provide approximately 10% of our energy requirements. The microbiota also produces vitamins K and B12 and protects against potential pathogens, which are eliminated through competition with beneficial intestinal microorganisms [4].

The development of the gut microbiota during the first years of life is a dynamic process. This period is also critical for the development and maturation of the intestine and immune system.

The development of the infant gut microbiota is influenced by perinatal exposure to microorganisms, gestational age, mode of delivery, host genetics, breastfeeding, and, in older children, antibiotic treatment and diet [2].

The first bacteria to colonize the newborn intestine and the gradual transition toward a stable, mature ecosystem play a central role in establishing host–microbiota interactions necessary for optimal symbiosis. This early colonization may also have a substantial influence on future health [4].

The composition of the microbiota changes considerably during two stages of early childhood: from birth until the introduction of complementary feeding and from the introduction of complementary foods until adulthood, depending on dietary diversity.

The first bacterial species to colonize the newborn intestine are facultative anaerobes, including Staphylococcus, Streptococcus, Enterococcus, and Enterobacter spp. These bacteria create an anaerobic environment that allows obligate anaerobes, such as Bifidobacterium, Bacteroides, Clostridium, and Eubacterium spp., to grow and become dominant after the first 1–2 weeks of life [4].

For many years, it was believed that the fetus developed in a sterile environment and that newborns were born without microorganisms. According to more recent molecular studies, interactions with microorganisms begin before birth, meaning that newborns already carry microorganisms acquired from their mothers during pregnancy.

A unique placental microbiome has recently been identified [6]. Its composition resembles the oral microbiome found in supragingival dental plaque and on the surface of the tongue rather than the microbiome of feces or the vagina.

It is therefore considered likely that bacteria reach the placenta through the bloodstream from the oral cavity rather than ascending from the vagina or entering through fecal contamination [6, 7].

The mode of delivery, whether vaginal birth or cesarean section, plays an important role in the development of the gut microbiota.

Newborns and infants delivered by cesarean section have a gut microbiota characterized by lower bacterial abundance and diversity, fewer beneficial bacteria, and more potentially pathogenic microorganisms. In contrast, infants born vaginally have a more diverse microbiota.

Vaginally delivered newborns have higher levels of bacteria belonging to the Actinobacteria, Bacteroidetes, and Bifidobacteria groups [8].

Vaginal seeding, in which newborns delivered by cesarean section are exposed to their mother's vaginal secretions after birth, may help restore microbial balance [9].

Whether a cesarean section was medically necessary or performed electively, without rupture of the fetal membranes, may also influence the microbiota [7].

Through changes in the microbiota, cesarean delivery increases the risk of allergic diseases later in childhood. However, it has been suggested that the underlying medical condition necessitating the cesarean section may itself be the primary cause of the increased allergy risk [1].

Furthermore, a recent study found that six weeks after birth, the composition of the infant microbiota depended on the body site and maternal factors rather than the mode of delivery [10].

The first six weeks of life are particularly important and are considered a critical period, or window of opportunity, during which an infant's susceptibility to allergies and asthma may be determined [1].

After birth, the first microorganisms are acquired from the mother's microbiota, including vaginal, fecal, breast milk, oral, and skin microorganisms, as well as from the surrounding environment.

Breast milk is an important source of microbiota. This is supported by the finding that bacterial strains present in breast milk can also be detected in the feces of breastfed infants.

These bacteria migrate from the maternal intestine to the mammary glands through the mesenteric lymph nodes and may thereby induce immunological tolerance to these microorganisms.

Another possible route by which microorganisms enter the mammary glands is through contact with the mother's skin and/or the infant's mouth.

The microbiota of breastfed infants is dominated by bifidobacteria and contains fewer Clostridium species [4, 11]. In contrast, formula-fed infants have a more diverse microbiota that more closely resembles that of adults.

Premature infants and those delivered by cesarean section have a lower diversity of Bifidobacterium species and slower intestinal colonization than full-term infants born vaginally [4].

Breastfeeding promotes the establishment and adaptation of specific bifidobacterial subspecies in the intestine, depending on the composition of oligosaccharides in breast milk. This composition varies between breastfeeding mothers and is not characteristic of infant formula.

Therefore, not only microbial diversity but also the appropriate composition of the microbiota and its ability to adapt to the host's needs are important.

Although breastfeeding benefits infant health and is associated with reduced infection-related morbidity and mortality, higher intelligence, and a potentially lower risk of obesity and diabetes mellitus, its effectiveness in reducing the risk of allergic diseases has not been established. Methodological limitations make it difficult to interpret the results of many clinical studies [1].

The structure of the infant gut microbiota is unstable and characterized by limited diversity.

The introduction of the first solid foods into the diet at 4–6 months of age has a substantial effect on the gut microbiota [4].

Some evidence suggests that microbiota changes associated with the introduction of solid foods are not clearly apparent while the child continues to receive breast milk.

It is believed that discontinuation of breastfeeding may have a greater influence on the transition toward an adult-type microbiota than the introduction of solid foods itself [12].

The infant-type microbiota, dominated by bifidobacteria, is gradually replaced by an adult-type microbiota, in which Bacteroides spp. and Clostridium clusters IV and XIV predominate.

Factors influencing bacterial colonization of the intestine also affect the development of the microbiota after solid foods are introduced.

Feeding infants formula without prebiotics promotes the early development of adult-type microbial diversity.

As children consume an increasingly varied diet, the abundance and diversity of Bacteroidetes and Firmicutes gradually increase to adult levels, while Bifidobacterium usually remains relatively limited [4].

The microbiota continues to develop with age and generally stabilizes by approximately 3–5 years of age [4, 13].

In healthy adults, the microbiota is stable and unique to each individual, although it shares a common core with that of other people.

The microbiota may change and become destabilized again in older age.

Although adults have relatively low levels of Bifidobacterium, these bacteria remain important for metabolism.

With aging, Bifidobacterium levels decline significantly. Together with other changes and increased microbial instability, this reduction is associated with decreased resistance to infections [4].

Human diet influences the diversity of the gut microbiota, which in turn affects the immune system both directly and indirectly.

Although intestinal bacteria can communicate directly with the central nervous system through the vagus nerve, recent findings in gut microbiota and neuropsychiatric research indicate that most communication occurs through the immune system [7, 14].

The foods we consume also influence gut microbiota health.

Fresh foods contain their own microbiome of nonpathogenic bacteria, such as Lactobacillus plantarum found on fruits and vegetables, which can suppress allergic reactions.

For these immunobiotics to exert their effects, it is important that they remain alive.

Furthermore, animal experiments have demonstrated that L. plantarum derived from human foods can influence brain function and behavior.

Processed foods contain substantial amounts of protein and lipid oxidation products that directly affect the gut microbiota. Artificial sweeteners, emulsifiers, and phthalates may have similar effects [7].

The loss of gut microbial diversity associated with a Western-style diet promotes mechanisms that disrupt the gastrointestinal biofilm and intestinal barrier, resulting in increased intestinal permeability, commonly referred to as "leaky gut."

This allows endotoxins to penetrate the intestinal barrier, triggering a low-grade inflammatory immune response associated with metabolic and behavioral changes [15].

The interaction between the gut microbiota and dietary phytochemicals derived from plant-based foods is bidirectional. This relationship promotes microbial diversity and reduces oxidative stress and inflammation [16].

In addition to diet, antibiotic use also affects the gut microbiota, and these effects may persist for a long time [17].

Evidence suggests that even a one-week course of antibiotics can alter the gut microbiota for up to three years [18].

Children treated with antibiotics before three months of age have a statistically higher incidence of atopic diseases. However, upper respiratory tract infections may also contribute to this association [19].

The Role of the Gut Microbiota

According to Hippocrates, all diseases begin in the gut. The gastrointestinal mucosa and its microbiota play an important role in protecting the body. The widely accepted hygiene hypothesis suggests that insufficient exposure to microorganisms and infections during childhood suppresses the development of natural immunity and promotes chronic diseases. More recently, this theory has been supplemented by the microflora hypothesis, which emphasizes the role of the microbiota during infancy as a potential factor contributing to immune dysregulation and allergic diseases [20].

It is believed that a so-called window of opportunity exists, defined as a critical period during the neonatal stage when environmental factors influence the maturation of the immune system and tissues, thereby affecting susceptibility to immune-mediated and other diseases in adulthood [21].

One possible explanation for the involvement of the gut microbiota in the development of allergic diseases is its important role in establishing mucosal immunological tolerance. In addition, the gut microbiota may influence the balance between Th1 and Th2 lymphocytes [2, 19].

Impaired regulatory T-cell function and an enhanced immune response against the body's own microbiota may help explain the development of asthma and diseases associated with modern lifestyles, including inflammatory bowel disease, obesity, and diabetes.

The importance of the endogenous microbiota is supported by a positive correlation between environmental factors affecting the gut microbiota, such as antibiotic use and cesarean delivery, and the development of allergic diseases [4].

It is known that the gut microbiota regulates the presence and function of invariant natural killer T cells in mice. These cells control both commensal and pathogenic microbiota and play an important role in the development of eosinophilic esophagitis [13].

The gut microbiota may regulate immunoglobulin E (IgE) production in mice during early life, while microbial dysbiosis may predispose individuals to IgE-mediated allergic diseases.

In germ-free mice, levels of all antibody isotypes, particularly immunoglobulin A (IgA) and immunoglobulin G1 (IgG1), are reduced. These levels can be normalized by introducing the normal microbiota of adult mice.

Furthermore, germ-free mice and mice with low microbial diversity have elevated serum IgE levels, associated with increased IgE binding to mast cells and a greater likelihood of developing systemic anaphylaxis.

Only colonization with a conventional microbiota during the first four weeks after birth can normalize IgE levels in adult mice.

A correlation has also been identified between specific bacterial species in infant stool samples and IgE-associated food allergy [13].

Food allergen sensitization at one year of age has been associated with changes in the microbiota occurring between three and 12 months of life.

Infants with positive skin prick tests indicating food sensitization had higher levels of Enterobacteria and lower levels of Bacteroides than infants with negative skin prick tests [22].

The stool microbiota of infants with food allergies shows a relative abundance of Clostridium cluster I, Anaerobacter, and Firmicutes, but lower levels of Bacteroides and Clostridium cluster XVIII [19].

Changes in the gut microbiota not only have local effects but also influence respiratory responses and are associated with the development of asthma [23].

Lower levels of Bifidobacterium adolescentis have been identified in stool samples from allergic adults with long-standing asthma.

In patients with atopic dermatitis, a dysbiotic gut microbiota, intestinal inflammation, and impaired epithelial barrier function may contribute to a Th2-type immune response to allergens in the skin [19].

Interestingly, the gut microbiota is important not only in the development of allergic and inflammatory diseases but also in mental health.

A healthy microbiota is necessary for maintaining a healthy nervous system. Increasing evidence suggests that the gut microbiota acts as a regulator of nervous system function, influencing neurological development, stress responses, anxiety, appetite, and circadian rhythms.

Bowel cleansing or other disturbances of the microbiota have been associated with psychiatric disorders [24, 25].

Respiratory Tract Microbiota

For many years, the lungs were considered sterile. However, approximately 2,000 bacterial genomes have been identified in the upper lung lobes of healthy individuals, while Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria predominate in the nose and nasopharynx [2].

The microbiota of the lower respiratory tract resembles that of the oropharynx. Most bacteria are believed to enter the lungs through migration from the oral cavity or through microaspiration.

Bacteria isolated from the bronchoalveolar lavage fluid of healthy lungs are similar to those found in the mouth. Bacteria characteristic of the nasal cavity are not typically found in healthy lungs.

Other bacteria present in the lower respiratory tract, including Prevotella, Veillonella, and Streptococcus spp., are likely inhaled and may colonize the bronchi of healthy individuals.

The composition of the respiratory microbiome is determined by the balance between bacteria entering through microaspiration and inhalation and those removed through coughing, mucociliary clearance, and innate and adaptive immune responses.

Other factors influencing the microbiome affect the growth of particular bacterial species, including oxygen availability, pH, blood perfusion, and the presence of inflammatory cells and nutrients [26].

Evidence suggests that the intestinal and pulmonary mucosa are interconnected through what is known as the gut–lung axis.

This relationship has been demonstrated in mice. When intestinal bacteria were eliminated, mice developed more severe pneumonia, whereas restoration of the microbiota reduced disease severity.

Stimulation of the respiratory tract with lipopolysaccharides also induces changes in the gut microbiota.

However, evidence regarding the gut–lung axis in humans remains limited [26].

Not only changes in the gut microbiota but also respiratory tract dysbiosis may be associated with allergic diseases, particularly asthma.

Proteobacteria, especially Haemophilus spp., are detected more frequently in the lungs of adults and children with asthma than in healthy controls, who have higher levels of Bacteroidetes.

Children with asthma also have substantially higher bacterial loads in their lungs than healthy children.

Among children with asthma whose bronchial reactivity decreased significantly after antibiotic treatment, greater respiratory microbial diversity was observed [2, 23, 26].

The nasopharyngeal microbiota of infants consists of six major bacterial genera: Haemophilus, Streptococcus, Moraxella, Staphylococcus, Alloiococcus, and Corynebacterium. These microorganisms persist into later childhood and adulthood.

However, the composition of the nasopharyngeal microbiota changes with age.

In healthy infants, the nasopharynx is initially colonized by Staphylococcus or Corynebacterium, which are subsequently replaced by Moraxella or Alloiococcus.

Further research is needed to determine whether early changes in the microbiota are associated with the subsequent development of allergic diseases.

It is known that nasopharyngeal and respiratory tract colonization by Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae in newborns is strongly associated with recurrent wheezing and childhood asthma.

Staphylococcus aureus may also be a risk factor for asthma development in children and young adults, but not in older adults.

In studies examining the nasopharyngeal microbiota of adults with asthma, Streptococcus pneumoniae infection was associated with asthma exacerbations [27].

Changes in the respiratory tract microbiota have also been identified in patients with chronic rhinosinusitis [27, 28].

Skin Microbiota

The skin is inhabited by numerous microorganisms, including bacteria, fungi, viruses, and mites. Most of these microorganisms are harmless and provide protective benefits.

Interestingly, molecular genetic studies have demonstrated that the skin microbiota may extend into the subepidermal layer even in healthy skin [29].

Microbial colonization of the skin begins at birth. Lactobacilli predominate on neonatal skin, while four major bacterial phyla subsequently become established: Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria.

The composition of each individual's skin microbiota is highly heterogeneous and depends on the specific microenvironment of different skin regions.

Three main types of skin microenvironments have been identified, each with a characteristic microbiota:

• Sebaceous areas, dominated by Propionibacterium spp. and Staphylococcus spp.
• Moist areas, dominated by Corynebacterium, with Staphylococcus spp. also present.
• Dry areas, characterized by mixed bacterial populations, particularly β-Proteobacteria and Flavobacteriales.

The microbiota may change in response to alterations in the local microenvironment, as well as depending on health status, age, sex, behavior, occupation, and environmental conditions [30].

Environmental factors such as clothing, topical and systemic antibiotic use, cosmetics, soaps, emollients, and other skincare products may influence the skin microbiota.

High temperatures and humidity, characteristic of warm and humid climates, are associated with a broader range of skin bacteria, while Gram-negative bacteria predominate on dry skin [29].

Among the Firmicutes, Staphylococcus epidermidis accounts for more than 90% of all aerobic skin bacteria. It has anti-inflammatory properties, helps maintain skin barrier function, and prevents colonization by pathogenic strains of Staphylococcus aureus and other potentially harmful microorganisms.

These protective effects are mediated through the production of antibacterial peptides (bacteriocins), immunomodulatory properties that suppress proinflammatory cytokine production, and stimulation of tight junction protein production through activation of keratinocytes and other immune cells.

Furthermore, the skin microbiota plays an important role in the maturation and regulation of keratinocytes [30].

Interactions between microorganisms within the skin microbiota are essential for the development of cutaneous immunity.

Evidence suggests that, in patients with atopic dermatitis, skin microorganisms may influence the entire immune system and alter cutaneous immune activity.

Elevated IgE levels in patients with atopic dermatitis may be associated not only with allergy or atopy but may also reflect an abnormal immune response to the normal skin microbiota [29].

In addition, patients with atopic dermatitis have reduced skin microbial diversity, with the lowest diversity observed in areas affected by skin lesions.

The abundance of Malassezia spp. decreases substantially, while various non-Malassezia fungi are detected.

The skin also shows increased colonization by Staphylococcus aureus, accompanied by a reduction in other bacterial species, including Propionibacterium [31, 32].

Animal studies indicate that the skin microbiota may be a driving factor in the development of atopic dermatitis [31].

During the treatment of atopic dermatitis, the skin microbiota can recover. For example, following phototherapy, microbial diversity increases…

Neringa Stirbienė, MD, Allergist and Clinical Immunologist¹, and Laura Malinauskienė, Associate Professor²

¹ Clinic of Children's Diseases, Faculty of Medicine, Vilnius University

² Clinic of Chest Diseases, Immunology and Allergology, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University

Continued in Internistas, supplement Allergy. Asthma. Immunology, 2018.