Wheat is one of the world’s most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. With the world’s growing population and the climate change, there is a constant need to improve crops such as wheat and their environment for a sustainable agriculture management and feeding the population. Different studies demonstrated that different tissues/organs of the crop and different genotypes could harbor specific microbes. These microbes could have neutral, negative or positive effects on plants which makes it very important to understand their roles and benefits to improve the quality and yield production of wheat. An important question is to assess to what extent different genotypes, environments and their interactions affect the bacterial communities and which is the role of bacteria in plant resilience to environmental/nutritional stresses. The objective herein is to unravel rhizobiota and endophytic bacterial colonization in diverse wheat genotypes using metagenomics and evaluation of different locations and varietal effects on microbiota compositions. Hence, 30 highly diverse wheat genotypes (T. aestivum, T. durum, T. dicoccoides, T. dicoccum, T. monococcum and triticale) have been sown in three biological replicates in two fields in northern and southern Italy, followed by a minimum-tillage management, and a total of 800 samples (rhizosphere and endophytic samples) have been collected from two developmental stages (first node and beginning of ripening). Purification of genomic DNA from soil and root samples was carried out using protocols based on the QIAGEN DNeasy PowerSoil Pro kit and DNeasy Plant Mini Kit, respectively. Furthermore, 16S rRNA high-throughput amplicon sequencing (V3-V4 hypervariable regions) was carried on a NovaSeq 6000 using 250-bp paired-end reads to explore bacterial communities in soil rhizosphere and root endosphere. Raw reads will be analysed using QIIME (v.2.9.1), available publicly at http://qiime2.org/ and preliminary results reported.