The role of gut microbiota in the pathogenesis and disease course of IBD continues to gain increasing scientific interest. This review highlights important advances in the field via collation and discussion of relevant publications between April 2021 and March 2022. A literature search was performed using the PubMed online database and the following search terms: inflammatory bowel disease(s) (IBD); ulcerative colitis; Crohn’s disease; microbiome OR microbiota. Exclusion criteria included non-English language publications, narrative reviews, case reports and case series containing less than 5 patients. 1180 articles were initially identified. Duplicates were excluded and abstracts imported into an online systematic review platform (www.rayyan.ai). Abstracts were screened by one of four independent reviewers to ensure relevance. Abstracts of equivocal importance were flagged for second independent review. Human studies and novel, high-quality and methodologically robust animal models demonstrating important therapeutic or mechanistic insight were selected. 287/1180 (24%) were included with only highlights chosen for discussion. Selected papers were divided into one of seven subheadings: pathophysiology, genetics, therapy, FMT, diet and prebiotics, paediatrics and the mycobiome. Whilst we discuss a number of important advances, there remains a need for further, prospective, controlled and preferably human, research that better defines the bidirectional relationship between the gut microbiota and the pathogenesis, disease course and treatment responsiveness of IBD.