The gut microbiome constitutes a highly complex ecosystem in which bacteria are the most prominent components. Around 70% of primary colonization of the gut microbiota is maternal in origin [1], and the first 1000 days of life are crucial for the development of the intestinal microbiota [2]. Despite its early formation, the gut microbiota is highly dynamic and dependent on host-associated confounding factors such as age, diet, antibiotics, lifestyle, and environmental conditions [3,4]. Alterations in gut microbiota have been described in people with different types of allergy, including cow's milk allergy (CMA) [5][6][7].

The role of the microbiome in the molecular mechanisms underlying allergy has become highly relevant in recent years. Studies are increasingly suggesting that altered composition of the microbiota, or dysbiosis, may result in local and systemic alteration of the immune response to specific allergens. In this regard, a link has been established between lung microbiota and respiratory allergy, between skin microbiota and atopic dermatitis, and between gut microbiota and food allergy. The composition of the human microbiota is dynamic and depends on host-associated factors such as diet, diseases, and lifestyle. Omics are the techniques of choice for the analysis and understanding of the microbiota. Microbiota analysis techniques have advanced considerably in recent decades, and the need for multiple approaches to explore and comprehend multifactorial diseases, including allergy, has increased. Thus, more and more studies are proposing mechanisms for intervention in the microbiota. In this review, we present the latest advances with respect to the human microbiota in the literature, focusing on the intestinal, cutaneous, and respiratory microbiota. We discuss the relationship between the microbiome and the immune system, with emphasis on allergic diseases. Finally, we discuss the main technologies for the study of the microbiome and interventions targeting the microbiota for prevention of allergy.