Asthma is a common, complex, and heterogeneous disease characterized by chronic airway inflammation and remodeling of the small airway structure. It can lead to serious limitations in the lives of patients by disrupting routine activities [1]. Many allergenic (house dust mites, cockroach residues, molds) and non-allergenic (viruses, cigarette smoke, cold air, exercise) factors trigger asthma [2]. In the last few decades, microorganisms have been increasingly recognized to impact the clinical course of asthma, with inducing airway inflammation and the host immune response [3,4].

Although studies of asthma have focused on the most common pathogens, the neglected fungi or parasite sources are also likely to have a significant impact on the disease. Pneumocystis jirovecii, initially considered as a protozoon, was later identified as a fungus in the Ascomycota order [5]. P. jirovecii that may lead to fatal P. jirovecii pneumonia (PJP) in immunocompromised patients and is associated with an allergic-type reaction in the lung [6]. Recently, its impact on the asthmatic patients has been further emphasized [7,8].

In addition, Cryptosporidium, which is an intracellular protozoan pathogen and predominantly causes intestinal diseases, is also capable of infecting the respiratory tract [9]. Cryptosporidium oocysts transmitted by droplet inhalation usually cause severe infections with an inflammation in the respiratory tract [10,11]. However, respiratory cryptosporidiosis is often neglected, especially in immunocompromised and asthma patients.

In addition, since the role of intestinal parasite infections in allergy is of great interest, parasites have been investigated in patients with asthma, atopy, allergic rhinitis, and urticaria [12]. However, there is no data on the association between intestinal Cryptosporidium spp and asthma. Therefore, there is a lack in studies addressing the incidence of Cryptosporidium spp. in the samples of asthmatic patients.

Little is known about the prevalence and impact of P. jirovecii and Cryptosporidium spp., which infect or colonize the respiratory tract, in patients of asthma. Investigating these neglected eukaryotes will further assist the elucidation of asthma pathogenesis and severity. Hence, in this study, we investigated P. jirovecii, and Cryptosporidium spp., by both PCR and conventional methods, in stool and sputum samples obtained from asthma patients and healthy individuals.