BackgroundPatients with depression exhibit significant gut microbiota dysbiosis; however, visualized studies into dysbiosis-related microbial signatures in depression remain limited. To identify characteristic differential genera in depressed individuals, this study adopted a knowledge graph–based visualization analysis to clarify the associations between intestinal microbial dysbiosis and depression.MethodsA search strategy was constructed and literature searches were conducted in 7 databases, including Web of Science, PubMed, Scopus, Cochrane Library, CNKI, Wanfang Database and VIP Net (VIP). The search cutoff date was April 1, 2026. The included literature was strictly screened according to the PRISMA guidelines. EndNote 25 was used to sort and trace the literature meeting the inclusion criteria. GRADE system, Cochrane ROB2.0, and JBI scale were used for quality evaluation and evidence grading of RCTs and cross-sectional studies.ResultsA total of 159 valid studies from 21 countries were ultimately included, involving 25310 patients with depression. The bacterial community taxa predominantly consisted of Bacillota, Bacteroidota, and Actinomycetota, among which Bacillota was overwhelmingly dominant. Ascomycota predominated within the fungal community. For bacteria, 73 genera including Faecalibacterium and Butyricicoccus, alongside 66 species such as Levilactobacillus brevis and Bifidobacterium animalis, exhibited depleted abundances. Such reductions were linked to diminished production of butyrate-producing commensal beneficial bacteria. 43 genera (e.g., Escherichia and Coprobacillus) and 21 species (including Escherichia-Shigella and Clostridium bolteae) belonging to pro-inflammatory and pathogenic microbes showed elevated levels. 25 genera represented bidirectionally altered taxa with both increased and decreased abundances, exemplified by Bifidobacterium and Bacteroides. Regarding fungi, 16 taxa including Aureobasidium and Saccharomyces cerevisiae boulardii were less abundant, whereas 10 taxa such as Candida and Saccharomyces had higher abundances.ConclusionDysbiosis in patients with depression was characterized by markedly decreased abundances of protective microbes including Faecalibacterium and Aureobasidium, accompanied by concurrent enrichment of pathogenic bacteria such as Escherichia and Candida in the gut. Taxa exhibiting bidirectional abundance shifts may be affected by confounders including age and gender, which requires further high quality clinical validation. Targeted modulation of disrupted microbiota, development of strain-specific biologics, and species-level profiling of microbial variations will enhance the therapeutic benefits of microecological preparations for depression adjuvant treatment.