A systematic search of the Web of Science Core Collection (WoSCC) and Scopus databases was performed on September 14, 2025, to collect publications related to GM research in FBDs.

The WoSCC search formula was: TS = ((gut OR intestine OR bowel OR gastrointestine OR colon OR intestinal OR colorectal OR gastrointestinal OR enteric) AND (microbiome* OR microbiota* OR microbe* OR bacteria* OR microflora OR flora)) AND TS = (“functional bowel disorder*” OR “functional bowel disease*” OR “irritable bowel syndrome*” OR “irritable colon syndrome*” OR IBS OR “functional constipat*” OR “chronic idiopathic constipat*” OR “functional diarrh*” OR “functional abdominal bloat*” OR “functional abdominal distent*” OR “unspecified functional bowel disorder*” OR “opioid-induced constipat*”) (Note: The detailed search formulas for the Scopus database are provided in Supplementary material 1).

The search strategies are detailed in Figure 1. The literature retrieved from WoSCC was downloaded as full records with cited references and saved in plain text format. The literature obtained from Scopus was similarly downloaded as full records with cited references and saved in CSV format. In addition, relevant clinical trial data were retrieved from the PubMed database, and the detailed search strategy is provided in Supplementary material 1. Results of clinical trials were exported in PubMed format.

Given the differences in data formats between WoSCC and Scopus, merging datasets would result in data loss. Consequently, both databases were analyzed independently to preserve completeness and ensure reliability. Due to the superior data quality and citation precision of WoSCC, this dataset served as the primary focus of subsequent analyses, while results from Scopus were used for cross-validation.

Data visualization and bibliometric analyses were performed with the following software: (1) Annual publication trends were summarized using Microsoft Excel 2016. (2) Comprehensive bibliometric analysis was carried out in R software (version 4.5.1) employing the bibliometrix package (25). (3) Collaboration networks, co-citation maps, and keyword co-occurrence networks were constructed and visualized using VOSviewer (version 1.6.20) (26). (4) Citation burst detection was conducted with CiteSpace (version 6.4.1) (27). To enhance accuracy, two independent researchers conducted data extraction and verification.

The parameters in VOSviewer were standardized as follows: (1) In co-authorship network analysis, a minimum of ≥20 publications was required for countries and ≥15 for institutions. (2) In source co-citation analysis, each journal needed to have at least ≥500 citations. (3) In keyword co-occurrence analysis, the minimum keyword frequency was set at ≥30 for the WoSCC database and ≥80 for the Scopus database. To enhance analytical specificity, generic terms such as “gut microbiota” and “functional bowel disorders,” along with their synonyms, were excluded from the dataset. Information on journal impact factor (IF) was retrieved from the 2024 Journal Citation Reports (JCR).

In total, 3,740 publications concerning GM in FBDs were identified from WoSCC. As illustrated in Figure 2A, annual publications show an overall upward trajectory over the past decade. The annual publication output demonstrated distinct phases: a period of gradual growth from 2016 to 2019 was followed by a rapid surge from 2019 to 2022. Subsequently, the number of publications stabilized at a high level with some fluctuation from 2022 to 2024. As of the search date (September 14, 2025), 337 articles had already been published within the year, further driving the growth of literature in this field. Similarly, 2,839 records were identified from Scopus, showing a broadly similar publication trend (Figure 2B). The annual publication trends in both databases reflect the expanding global attention to the role of GM in FBDs.

The distribution of corresponding authors’ countries revealed that China (n = 896) led in publications, followed by the United States (n = 607), Italy (n = 287), the United Kingdom (n = 149), and Australia (n = 140). Despite its dominant publication volume, China exhibited relatively limited international collaboration (Figure 2C; Table 2). In contrast, the United States exhibited the most extensive international collaboration network, linking closely with European and Asia-Pacific countries (Figure 3A). Institutional collaboration analysis (Figure 3B; Table 3) identified the Mayo Clinic (n = 102) and University College Cork (n = 91) as the primary research centers and hubs of international cooperation. The results from Scopus supported these findings, showing consistent patterns in inter-country and inter-institutional collaboration (Figures 3C,D).

To determine the most influential journals in research on GM in FBDs, publication and citation metrics were analyzed using the bibliometrix package in R software. The results were visualized with the ggplot2 package.

A total of 3,740 articles from 886 journals were identified from the WoSCC dataset (see Supplementary material 2 for detailed information). In terms of publication output (Table 4; Figure 4A), Nutrients (n = 197, IF = 5.0) had the highest number of publications, followed by Neurogastroenterology and Motility (n = 104, IF = 2.9), Frontiers in Microbiology (n = 94, IF = 4.5), Gut Microbes (n = 64, IF = 11.0), and International Journal of Molecular Sciences (n = 64, IF = 4.9). In terms of citation frequency (Table 5; Figure 4B), Gastroenterology ranked first (n = 15,143, IF = 25.1), followed by Gut (n = 10,657, IF = 25.8), American Journal of Gastroenterology (n = 8,676, IF = 7.6), Alimentary Pharmacology and Therapeutics (n = 7,166, IF = 6.7), and Neurogastroenterology and Motility (n = 6,864, IF = 2.9). As shown in Figure 5, the co-citation analysis indicated that Gastroenterology, Gut, and American Journal of Gastroenterology are central collaborative hubs in this field, exerting substantial influence. These results indicate that journals with higher impact factors generally publish a smaller number of studies in this domain, underscoring the necessity to strengthen the methodological depth, analytical rigor, and overall quality of research in this area. We also identified 2,839 articles from 883 academic journals from the Scopus dataset (see Supplementary material 3 for detailed information). The journals with higher publication volumes largely align with the findings from the analysis of data sourced from WOSCC.

To identify influential papers and frontier research trends, we employed CiteSpace to detect the 25 references exhibiting the most significant citation bursts from the WoSCC dataset (Figure 6). The titles and DOIs of these references are presented in Supplementary material 4.

Notably, the three references with the strongest citation bursts were: (1) “Worldwide Prevalence and Burden of Functional Gastrointestinal Disorders, Results of Rome Foundation Global Study (strength: 53.43);” (2) “Intestinal microbiota in functional bowel disorders: a Rome foundation report (strength: 44.89);” (3) “Bowel Disorders (strength: 39.61).” Furthermore, the three most recent bursts representing frontier research corresponded to the following publications: (1) “Global prevalence of irritable bowel syndrome according to Rome III or IV criteria: a systematic review and meta-analysis;” (2) “British Society of Gastroenterology guidelines on the management of irritable bowel syndrome;” (3) “Global burden of irritable bowel syndrome: trends, predictions and risk factors.”

The citation bursts analysis identified three primary research areas: (1) the mechanistic link of the gut-brain axis in FBD development; (2) distinct GM profiles associated with subtypes of IBS; and (3) the regulation of FBD symptoms by GM through dietary intervention.

Keyword co-occurrence analysis reveals major research themes. In this study we identified 10,407 keywords from the WoSCC dataset using VOSviewer. Table 6 presents the top 20 high-frequency keywords with “probiotics” (n = 711) “double-blind” (n = 611) “short-chain fatty acids” (n = 358)“inflammation” (n = 351) “gut-brain axis” (n = 336) and “quality of life” (n = 321) ranking at the forefront. Further analysis of keywords with an occurrence frequency of ≥30 resulted in 165 keywords from which a keyword clustering map was generated (Figure 7A). The clustering analysis revealed five major research hotspots as follows: (1) The neuroimmune mechanism of GM regulation of FBDs via the gut-brain axis (red dots) including 59 keywords. In this cluster “gut-brain axis” serves as the central concept with many related keywords such as “short-chain fatty acids,” “butyrate,” and “serotonin” that are key signaling molecules in this axis. Play a crucial role in the communication between the gut and the brain. Keywords like “immune activation,” “cytokines,” and “oxidative stress” suggest that changes in the GM may lead to immune dysregulation. The inclusion of “depression,” “visceral hypersensitivity,” and “intestinal barrier” highlights the bidirectional regulation between the gut and the brain as well as the neuroimmune mechanisms involved. (2) Dietary interventions on GM metabolic activity and symptom management in FBDs (green dots) including 46 keywords. This cluster includes keywords such as “low-FODMAP diet” and “gluten-free diet,” which represent specific dietary interventions aimed at managing FBDs. Keywords like “fermentation,” “hydrogen,” and “methane” highlight the role of dietary interventions in modulating the metabolic activity of the GM. The research also emphasizes factors like “quality of life,” “reduces symptoms,” and “nutrition,” underscoring the potential of diet to improve patient outcomes and alleviate symptoms. Collectively these keywords outline a research paradigm that links specific dietary inputs to microbial metabolic outputs ultimately aiming for symptom relief and improved quality of life in FBDs management. (3) Evidence-based investigations into the roles of probiotics and prebiotics in FBDs (blue dots) including 26 keywords. This cluster highlights keywords such as “probiotics,” “prebiotics,” and “health,” underscoring the role of probiotics and prebiotics in improving gut health in FBDs. Keywords like “efficacy,” “impact,” and “safety” indicate that the research focuses on evaluating the efficacy and safety of these interventions. Keywords such as “systematic review,” “meta-analysis,” and “double-blind” reflect that the research primarily centers on validating the application of probiotics and prebiotics in FBDs management through clinical trials and systematic reviews emphasizing their reliability as therapeutic tools. (4) The clinical application and therapeutic efficacy of probiotics and fecal microbiota transplantation (FMT) in FBDs management (yellow dots) including 25 keywords. This cluster includes keywords such as “fecal microbiota transplantation,” “saccharomyces-boulardii,” and “lactic acid bacteria,” which indicate the therapeutic potential of probiotics and FMT in managing FBDs. Keywords like “dysbiosis,” “ulcerative colitis,” and “antibiotic-associated diarrhea” highlight the connection between GM imbalance and gastrointestinal diseases. Keywords such as “randomized controlled-trial,” “placebo-controlled trial,” and “prevention” emphasize the clinical validation and effectiveness of these therapies. Overall, these keywords underscore the therapeutic potential of probiotics and FMT in restoring GM balance and improving FBDs symptoms. (5) Comparative analysis of GM diversity between healthy individuals and patients with FBDs (purple dots) including 9 keywords. This cluster includes keywords such as “healthy controls,” “molecular analysis,” and “identification,” highlighting the approach of comparative studies and molecular identification to reveal differences in the GM between healthy individuals and patients with FBDs. Keywords like “fecal microbiota,” “Bifidobacterium,” and “diversity” underscore the distinctions in the GM between healthy individuals and those with FBDs. These keywords suggest that analyzing microbiota diversity is a crucial tool for understanding the pathophysiological mechanisms of FBDs. All keywords corresponding to these five clusters are listed in Supplementary material 5.

Additionally, 16,619 keywords were identified from the Scopus dataset. Table 6 presents the top 20 high-frequency keywords with an occurrence frequency of ≥457. Further screening identified 168 keywords with an occurrence frequency of ≥80, and a keyword clustering map was drawn (Figure 7B). Currently, research on GM and FBDs focuses on four key hotspots: (1) the role of GM imbalance in the pathophysiology of FBDs (red dots); (2) the management of FBD symptoms to improve quality of life through GM intervention (green dots); (3) multi-omics Insights into GM characteristics in FBD Patients (blue dots); and (4) the impact of the low FODMAP diet on GM and FBD symptoms (yellow dots). All keywords corresponding to these four clusters are listed in Supplementary material 6.

To identify evolving research trends and future directions, we employed the bibliometrix package in R software to analyze topical trends based on the WoSCC dataset (Figure 8A). The analysis reveals a clear thematic evolution over time. From 2016 to 2018, the field was primarily dedicated to the fundamental exploration of the gut-brain axis and the role of GM in the pathophysiology of FBDs, based primarily on basic and animal studies. The period from 2019 to 2021 was marked by advancements in research methods, particularly the increasing prominence of placebo-controlled trials and randomized controlled trials, which significantly enhanced the rigor and scientific quality of studies. Meanwhile, the connection between GM and the immune system emerged as a key research direction. Between 2022 and 2023, research extended to multi-omics and metabolomic analyses, highlighting microbial metabolism, intestinal function, and disease subtype differentiation. Since 2024, research has entered a stage of interdisciplinary integration and clinical standardization, emphasizing diagnostic criteria, bioinformatics, and precision-based microbiota interventions. Building on this foundation, future research is expected to place greater emphasis on early warning mechanisms for disease, effects of GM interventions across different populations, and more precise treatment strategies. Furthermore, the same topic trend analysis conducted on the Scopus dataset was broadly consistent with the WoSCC results (Figure 8B).

To further confirm these future research trends and highlight the latest advancements in the field, we reviewed 337 papers published in 2025 from the WoSCC dataset (see Supplementary material 7 for detailed information). The findings from this recent research confirm that GM studies related to FBDs are increasingly focusing on clinical applications and precision medicine. Key developments include the use of multi-omics techniques for advancing diagnostic biomarkers and an enhanced understanding of brain-gut interactions, particularly the neuroimmune mechanisms involved. Moreover, as the role of GM in specific FBD subtypes continues to attract attention, personalized interventions tailored to individual microbiota profiles are becoming more prominent.

Overall, the field has gradually shifted from early pathological and clinical observations to a balance between mechanism exploration and clinical application, with future research moving toward precision, evidence-based approaches, and interdisciplinary integration.

To gain a more holistic understanding of current focal points, we integrated results from citation bursts, keyword frequency, keyword clusters, and thematic evolution. The results demonstrate that the research hotspots in this area cluster around three principal directions, as follows: (1) the mechanisms by which GM influences FBDs via the gut-brain axis, involving a complex network encompassing the nervous, immune, and endocrine pathways; (2) variations in the composition and metabolites of GM among different subtypes of FBDs, which drive research into biomarkers for precise diagnosis and targeted therapy; and (3) intervention strategies for treating FBDs through the modulation of GM, particularly via specific dietary patterns, probiotics, prebiotics, and FMT.

A total of 57 clinical trials were retrieved from the PubMed database (see Supplementary material 8 for detailed information). These studies can be categorized into three major research themes: (1) the role of core metabolites of the GM in symptom regulation in FBDs; (2) the clinical application of integrated GM-modulating strategies in FBDs; and (3) the impact of specific GM abnormalities in FBDs and the application of precision interventions.

Between 2016 and 2025, the study identified 3,740 publications in WoSCC and 2,839 articles indexed in Scopus. As the general information obtained from the two databases was highly consistent, the analysis is presented based on the WoSCC dataset. From 2016 to 2025, publications addressing GM in FBDs exhibited an overall upward trend, underscoring the increasing attention devoted to GM’s role in FBDs.

Among the countries contributing to this field, China led in publication output, with substantial contributions also observed from the United States, Italy, the United Kingdom, and Australia. Notably, despite China’s leading output, the United States exhibited more extensive international collaboration. Within the top 20 publishing institutions, five were based in the United States and five in China, with the remaining institutions located in Australia and several European countries. The absence of a single dominant institution, together with this wide geographic distribution, reflects a highly competitive yet collaborative global research landscape. Encouraging broader international collaboration in future studies will be essential for improving the generalizability and overall impact of research findings.

Journal analysis showed that the 3,740 publications were distributed across 886 journals. Journals such as Nutrients, Neurogastroenterology and Motility, Frontiers in Microbiology, Gut Microbes, and International Journal of Molecular Sciences had higher publication volumes and made substantial contributions. High-impact journals such as Gastroenterology and Gut were highly cited but published fewer papers in this field. The results suggest that these journals are crucial platforms for advancing scientific knowledge on GM in FBDs.

By integrating multiple analytical approaches, such as citation burst, keyword frequency, keyword clusters, and thematic evolution, this study elucidated the key research domains within GM research in FBDs. The findings indicate that current cutting-edge studies and newly emerging focal points in this field primarily concentrate on three main thematic domains. First, the mechanism by which GM influences FBDs via the gut-brain axis. Second, variations in the composition and metabolites of GM among different subtypes of FBDs. Finally, intervention strategies for treating FBDs through the modulation of GM.

This study comprehensively evaluated 57 clinical trials and clarified the key trends and key areas of focus in current clinical research on the GM in FBDs: (1) Symptom regulation by SCFAs in FBDs. Clinical evidence indicates that levels of SCFAs in patients with FBDs, particularly butyrate levels, are closely associated with the severity of gastrointestinal symptoms (75). For example, increased butyrate levels are significantly correlated with symptom improvement in patients with FBDs, suggesting that butyrate may exert therapeutic effects by enhancing epithelial barrier integrity and modulating local immune responses (76). Further studies have demonstrated that enrichment of butyrate-producing bacteria effectively alleviates abdominal pain in patients with IBS-D (77). (2) Probiotic-centered combination therapy as a strategy for modulating the GM in FBDs. Probiotics used in combination with other therapeutic approaches or as multi-strain formulations can exert synergistic effects and provide more sustained clinical benefits than single-strain probiotics. For instance, probiotic supplementation has been shown to mitigate the reduction in Bifidobacterium induced by a LFD, thereby helping maintain microbial diversity (78). In addition, multi-strain formulations have been demonstrated to alter GM composition and improve clinical symptoms (79, 80). A compound preparation containing Lactobacillus, Bifidobacterium, xylo-oligosaccharides, and dietary fiber has been reported to significantly improve defecation perception in patients with FC, accompanied by a decreased proportion of Bacillota and an increased proportion of Bacteroidota in the GM (78). Collectively, these studies indicate that probiotics and their combined interventions have broad clinical application potential in FBDs. (3) Impact of specific GM abnormalities in FBDs and microbiota-targeted therapy. Evidence suggests that a Clostridium-enriched GM can induce diarrhea in patients with IBS-D by disrupting bile acid metabolism, indicating that pathogenic or dysbiotic microbial overgrowth may represent one of the etiological factors underlying FBDs (81). Moreover, patients with FBDs frequently exhibit small intestinal bacterial overgrowth, and interventions specifically targeting this defined microbial abnormality have been shown to effectively alleviate related gastrointestinal symptoms, thereby underscoring the clinical value of precision-targeted, microbiota-based therapeutic strategies for FBDs (82, 83).

This bibliometric and visualization-based assessment offers an extensive and systematic perspective on research trends and hotspots, yet it also carries several inherent limitations. First, the literature search was confined to the WoSCC and Scopus databases, which offer comprehensive coverage of high-quality publications and are considered ideal sources for bibliometric analysis (84, 85), but relevant studies indexed in other databases may still have been overlooked. Second, this study included only English-language publications, potentially excluding valuable studies published in other languages. Additionally, bibliometric analyses as a methodological constraint cannot serve as complete alternatives to systematic reviews, as they are unable to evaluate the quality and outcomes of individual studies. Finally, low citation counts typically indicate limited impact on the field, so we focus more on highly cited articles to analyze hotspots and trends, but citation metrics are inherently time-dependent, which may disadvantage more recent publications (86). While this study has limitations, its findings remain robust and credible, offering a comprehensive summary and a solid foundation for future investigations in this area.