All of the microorganisms such as bacteria, archaea, virus, yeast and parasite living inside and outside our body are called microbiota. Each region has different microbiota such as gastrointestinal (GI), skin, oropharyngeal, genitourinary and respiratory. While the human body consists of 1013 cells, it contains 1014 microorganisms [1]. The genome of all these microorganisms in the body is called microbiome, it is at least 100 times larger than the human genome and contains eight million different genes [2]. Thousands of bacterial and fungal species have been identified with the Human Microbiome Project, which was initiated in 2007 by the US National Institute of Health in order to understand the diversity of microorganisms associated with humans and to determine how the microbiome changes in health and disease. Therefore, it is important to define the intestinal environment as an ecosystem in which biological and biochemical interactions occur at various organizational levels between parasites, microbial communities and the host immune response. The diversity of microbiota differs in every person, this is caused by many reasons such as our modern lifestyle (psychological, physical stress, etc.), nutrition, diabetes, allergy, immune system, drug use and various diseases [3,4].

The human gut is a highly complex ecosystem with a large microbial community. The gastrointestinal system (GIS) microbiota stands out because it contains a community of about 100 trillion microorganisms weighing two kilograms that live with us. The most important part of this diversity is anaerobic bacteria including Bacteroides and Firmicutes [5]. In fact, categorization has been suggested due to the predominant intestinal bacterial species, enterotype I Bacteroides, enterotype II Prevotella and enterotype III are classified as Ruminococcus dominant cluster [6]. Microbiota plays an effective role in many factors such as digestion and absorption, vitamin production, regulation of fat storage, stimulation and regeneration of intestinal epithelial cells, body defense, intercellular communication, and also contributes to the development and maturation of the immune system [7,8]. As a result, the imbalance between the intestinal microbiota and the human body or the changes in the microbial composition cause deterioration of health and various diseases.

Many health problems such as autoimmune diseases, diabetes, cardiovascular diseases, depression and obesity, become common nowadays, may be caused by imbalances in the gut microbiota. In fact, various pathological conditions such as Crohn's disease (CD) and ulcerative colitis (UC) have been associated with the gut microbiota. Chronic inflammation of the intestinal mucosa in inflammatory bowel disease (IBD) has also been shown to be associated with changes in microbial community structure and function, termed "dysbiosis" [9]. Thus, the gut health of the individual provides information about our overall health (Fig.1).

Members of microbiota and parasites are living in the human body for centuries. Today, more than 15 different protozoa genera belonging to different groups such as amoebozoa, flagellata, ciliata, stramenopiles and apicomplexan live commensally in the human gastrointestinal tract [10]. Since the parasite needs a host to survive, it is inevitable that it encounters and interacts with microbiota members when settles in the human body [11]. Microbiota can change the survival, reproduction and virulence of the parasite, as well as the parasites can be effective in the reduction or proliferation of microbiota elements [12]. Host health and homeostasis are affected directly or indirectly as a result of disruptions between microbial and parasite communities. Intestinal microbiomes are also known to modulate host susceptibility to infectious pathogens, particularly intestinal parasites, by influencing the development and maturation of immune responses [13]. In recent years, the role, benefit and relationship of microbiota on human health, disease and treatment success have begun to be understood more clearly.

In recent years, there has been increasing interest in the role, benefit, and impact of the microbiota-parasite relationship on human health. In this study, microbiota changes resulting from parasite interactions and their effects on the host were reviewed (Table 1).