Diet may influence the gut microbiota and subsequently affect the host's health. Recent developments in methods analyzing the composition and function of the gut microbiota allow a deeper understanding of diet-gut microbiota relationships. A state-of-the-art methodology, shotgun metagenomics sequencing, offers a higher taxonomic resolution of the gut microbiota at the bacterial species and strain levels, and more accurate information regarding the functional potential of gut microbiota. Here, the available evidence on the relationship between diet and gut microbiota was critically reviewed, focusing on results emerging from recent metagenomics sequencing studies applied in randomized controlled trials and observational studies. The PubMed and Embase databases were used to search publications between January 2011 and September 2023. Thus far, the number of studies is limited, and the study designs and methods utilized have been variable. Nevertheless, the cumulative evidence from interventions relates to dietary fiber as a modifier of bacterial species, such as Anaerostipes hadrus and Faecalibacterium prausnitzii. Furthermore, observational studies have detected associations between different dietary patterns and food groups with certain microbial species. Utilization of metagenomics sequencing is becoming more common and will undoubtedly provide further insights into diet-gut microbiota relationships at the species level as well as their functional pathways in the near future. For reproducible results and to draw reliable conclusions across various studies on diet-gut microbiota relationships, there is a need for harmonization of the study designs and standardized ways of reporting.