The gut microbiome dysbiosis and regulation by fecal microbiota transplantation: umbrella review

Background Gut microbiome dysbiosis has been implicated in various gastrointestinal and extra-gastrointestinal diseases, but evidence on the efficacy and safety of fecal microbiota transplantation (FMT) for therapeutic indications remains unclear. Methods The gutMDisorder database was used to summarize the associations between gut microbiome dysbiosis and diseases. We performed an umbrella review of published meta-analyses to determine the evidence synthesis on the efficacy and safety of FMT in treating various diseases. Our study was registered in PROSPERO (CRD42022301226). Results Gut microbiome dysbiosis was associated with 117 gastrointestinal and extra-gastrointestinal. Colorectal cancer was associated with 92 dysbiosis. Dysbiosis involving Firmicutes (phylum) was associated with 34 diseases. We identified 62 published meta-analyses of FMT. FMT was found to be effective for 13 diseases, with a 95.56% cure rate (95% CI: 93.88–97.05%) for recurrent Chloridoids difficile infection (rCDI). Evidence was high quality for rCDI and moderate to high quality for ulcerative colitis and Crohn’s disease but low to very low quality for other diseases. Conclusion Gut microbiome dysbiosis may be implicated in numerous diseases. Substantial evidence suggests FMT improves clinical outcomes for certain indications, but evidence quality varies greatly depending on the specific indication, route of administration, frequency of instillation, fecal preparation, and donor type. This variability should inform clinical, policy, and implementation decisions regarding FMT.


Introduction
Gut microbes, including commensal and pathogenic microbes, colonize in the gastrointestinal (GI) tract and significantly affect gut homeostasis and host health by producing various metabolites that influence the gut barrier and immunity (Guarner and Malagelada, 2003).Pathogenic or commensal microbes are frequently associated with disease development and progression (Guarner and Malagelada, 2003).Under normal conditions, gut microbes co-exist symbiotically with the host, maintain a dynamic balance, and play major roles in metabolism, nutrition, protection, immune regulation, hematopoiesis, anti-inflammation and anti-tumor functions (Guarner and Malagelada, 2003).However, when this balance is disrupted, normal bodily functions become impaired and GI and extra-GI diseases can emerge, including recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), Crohn's disease (CD), obesity and metabolic syndrome, among others (Borody and Khoruts, 2011;Allegretti et al., 2019;Lloyd-Price et al., 2019).Several databases catalog associations between the gut microbiome and disease but data analysis and visualization remain limited (Janssens et al., 2018;Cheng et al., 2020).Elucidating complex links between the gut microbiome and disease could enable novel therapies.
Fecal microbiota transplantation (FMT), which restores microbiome diversity and function by transferring screened feces from healthy donors to patient GI tracts, is gaining popularity for research and clinical use (Allegretti et al., 2019;Oka and Sartor, 2020;van der Lelie et al., 2021;Sorbara and Pamer, 2022).Numerous metaanalyses have examined FMT for specific diseases and subgroups (Allegretti et al., 2019;Green et al., 2020), but no study has quantitatively synthesized efficacy and safety across research or evaluated evidence quality and strength.
We aimed to systematically review relationships between gut microbiome dysbiosis and diseases and determine evidence on FMT efficacy and safety for various indications.

Database analysis
We used gutMDisorder (Jun 10, 2019, v1.0), a database cataloging relationships between diseases and the gut microbiome in humans, to examine associations (Cheng et al., 2020).The gutMDisorder contains 2,263 curated relationships between 579 gut microbes and 123 disorders as well as 77 interventions presented for humans.Each entry in the gutMDisorder database contains detailed information about an association, including the intestinal microbe, disorder name, intervention measures, and experimental technology.As the first manually curated resource for annotating gut microbiota functions, gutMDisorder enables the exploration of novel microbiota functions by leveraging previous computational methods and tools for predicting molecular functions (Cheng et al., 2020).Compared to other databases, gutMDisorder aggregates literature data from more sources and contains more detailed information, fulfilling the requirements of this study regarding data volume and information completeness.We analyzed and visualized these complex associations to identify key microbes linked to human diseases.For data collection, cluster analysis, and graphing code, we used Microsoft Excel (Microsoft Corporation, Redmond, WA, United States).In analyzing disease and dysbiosis in the database, we excluded post-intervention changes in microbes and only analyzed microbes directly related to the diseases.We generated graphs using ChiPlot, Origin 2021 (Origin Lab, Northampton) and Adobe Illustrator CS6 (Adobe, San Jose, CA, United States).

Umbrella review
We searched ClinicalTrials.govfor ongoing FMT trials and conducted an umbrella review following Cochrane living review guidelines (Elliott et al., 2017;Hunt et al., 2018).An umbrella review provides an overview of evidence from systematic reviews and metaanalyses; a living review is continually updated (Aromataris et al., 2015;Neuenschwander et al., 2019;Zhang et al., 2020).As FMT develops, new evidence could emerge affecting findings, so we will update our review.We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) 2020 guideline (Page et al., 2021;Gates et al., 2022) and registered our protocol (CRD42022301226).

Search strategy and selection criteria
We searched MEDLINE via PubMed, Embase, Cochrane Database of Systematic Reviews, Web of Science, China National Knowledge Infrastructure, Chinese Biomedical Literature Database and Wanfang Database for meta-analyses of randomized clinical trials (RCTs) or observational studies on FMT through October 2021, updating in June 2022 without language restrictions.We searched reference lists of identified studies (Appendix 1).
Studies were eligible if: (1) study design: meta-analyses of RCTs and/or observational studies; (2) participants: any condition or subtype of the disease; (3) intervention: FMT by any route of administration, donor type, infusion frequency or bacterial fluid status; and (4) outcomes: clinical remission, response or adverse events.We excluded: (1) systematic reviews without meta-analysis; (2) pre/probiotic research; and (3) animal research.

Study selection
After eliminating duplicates, two reviewers independently screened the titles and abstracts and the full texts.Disagreements were resolved by consensus or appeal to a senior reviewer.We recorded reasons for exclusion.

Data extraction
Two reviewers extracted data independently and a third checked accuracy.For each study, we extracted: (1) characteristics: author, publication year, country, disease, studies, participants, age, sex, follow-up, adverse events; and (2) FMT details: participants, outcome measures including relative risk (RR), odds ratio (OR), mean difference (MD), weighted mean difference (WMD) and standardized mean difference (SMD), and heterogeneity (I 2 , P).

Quality assessment
Two reviewers independently assessed meta-analysis quality using A Measurement Tool to Assess Systematic Reviews (AMSTAR-2) (16 items; Shea et al., 2017).We used the Grading of Recommendations Assessment Development and Evaluation (GRADE) approach to assess evidence quality as high, moderate, low or very low (Guyatt et al., 2011).

Data synthesis
We synthesized data from the most recent meta-analysis for each disease, estimating heterogeneity (I 2 > 50%, p < 0.10).If no remission rate was reported, we used another outcome.We chose the study with the highest number of RCTs or cohort studies if two or more studies for the same disease category and outcome were published within the same 24-month period.If two or more studies published in the same period had the same number of RCTs or cohort studies, we included the study with the highest AMSTAR-2 score.When both cohort studies and case series were included in a meta-analysis, and subgroup analysis was stratified by study design, the cohort design sub-analysis was selected for inclusion in the summary forest plots.We summarized subgroup analyses by administration route, donor type, frequency or bacterial fluid status.

Search results
We conducted a systematic search of gutMDisorder, trial registers and databases, identifying 1,474 microbe-disorder associations for analysis and 370 trial registrations for data visualization (Figure 1).Our umbrella review yielded 2,576 publications, of which 62 metaanalyses (Supplementary Table S1) met inclusion criteria.

Registered clinical trials using fecal microbiota transplantation
Analysis of 370 registered clinical trial entries presented an overview of FMT used for treating various digestive and non-digestive diseases since 2008 (Figure 5). Figure 5A showed the number of registered trials per year (red) and the cumulative total number (green). Figure 5C

Study characteristics and quality assessment
We identified 62 meta-analyses examining FMT for clinical outcomes (Supplementary Table S1 in details).Excluding duplicates left 13 conditions (Figure 5B): CDI (n = 24), UC (n = 14), IBD (n = 6), IBS (n = 4), CD (n = 3), AMR (n = 2), obesity (n = 1), metabolic syndrome (n = 1), functional gut disorders (n = 1), psychiatric outcomes (n = 1), chronic pouchitis (n = 1), functional constipation (n = 1) and GVHD (n = 1).We utilized an evidence mapping approach to visually present the reported efficacy, safety, and recurrence outcomes of FMT across 20 disease conditions after screening (Figure 6).In the map, the bubble size represents sample size, the emoji denotes evidence quality rating, and color ranging from red to yellow to green indicates the degree of FMT treatment efficacy on diseases, corresponding to the effect size values.Detailed outcome measures are shown in forest plots .Subgroup analyses (route of administration, frequency of instillation, fecal preparation, and donor type) and more information are presented in Supplementary Table S2.
The quality scores of included studies were presented in Supplementary Table S1.GRADE evidence ratings for each outcome were displayed in forest plots (Figures 7-10).Overall, the evidence was high quality for CDI and moderate to high quality for UC and CD, but low to very low quality for other diseases.

Psychiatric outcomes
Although the gut-brain axis suggests microbes could affect the central nervous system and neurological diseases, no meta-analysis has explored the clinical efficacy of FMT for these conditions.Available studies evaluating psychiatric outcomes have focused on patients with IBS.For the Fatigue Assessment Scale mental health subscale at 1 month, patients receiving 30 g of FMT vs. placebo showed significant improvement (MD, −1.9; 95% CI, −2.7 to −1.1; low; Figure 9).Similarly, significance was seen at 3 months for patients receiving 60 g of FMT vs. placebo (MD, −2.3; 95% CI, −3.1 to −1.5; low; Figure 9; Green et al., 2020).Anxiety and depression symptoms measured using the Hospital Anxiety and Depression Scale did not differ significantly (Green et al., 2020).

Functional constipation
Combined FMT and laxative therapy was more effective than laxatives alone for improving total effective rate (RR, 1.35; 95% CI, Top 10 gut microbes dysbioses and their associated diseases.The tree trunks denote the microbes and the leaves present the diseases related to dysbioses of each microbe.The inner circle heatmap indicates the taxonomic classification of the microbes, and the outer circle heatmap reveals the over-and under-abundance of particular microbes for each disease cluster.Full radial dendrograms were in Supplementary Figure S2.Microbe names use hyphens in place of spaces. Frontiers in Microbiology 07 frontiersin.orgEvent rates (efficacy) of fecal microbiota transplantation in the treatment of various diseases.95%

Graft versus host disease
The overall response rate was 64.4% (54/87), including 43.7% complete response and 20.7% partial response.Clostridioides emerged as the species with the greatest value for preventing graft versus host disease recurrence.Most patients had no major complications after FMT (Hm et al., 2021).

Extra-gastrointestinal diseases
Obesity and metabolic syndrome FMT was consistently associated with beneficial changes in earlystage (2-6 weeks) hemoglobin A1c (MD, −1.69 mmol/L; 95% CI, −2.81 to −0.56; low) and early-stage high-density lipoprotein cholesterol (MD, 0.09 mmol/L; 95% CI, 0.02-0.15;low; Figure 9; Proença et al., 2020).FMT was associated with lower early-stage fasting glucose, early-stage triglycerides, early-stage total cholesterol, and Homeostatic Model Assessment for Insulin Resistance score but did not reach significance (Proença et al., 2020).Similarly, FMT was associated with beneficial changes in late-stage (12 weeks) hemoglobin A1c, late-stage low-density lipoprotein cholesterol, late-stage high-density lipoprotein cholesterol, and late-stage triglycerides but did not reach significance (Proença et al., 2020).FMT also seemed associated with beneficial changes in early-stage body mass index, late-stage body mass index reduction, and late-stage hip width reduction but did not reach significance (Proença et al., 2020).
Some patients decolonizing AMR bacteria experienced mild, temporary symptoms like vomiting, diarrhea, abdominal cramps, and bloating (Tavoukjian, 2019).During 6 months of follow-up, four of 18 patients were recolonized, a few spontaneously decolonized, and six died of underlying disease.
For patients with metabolic syndrome and obesity, RCTs found FMT to be safe (Proença et al., 2020).No severe adverse events were reported.

Principal findings
Previous studies showed gut microbiota relate to disease progression.Carding et al. summarized previous studies elucidating some disease-associated gut microbiota dysbioses (Carding et al., 2015).We have built on this work by summarizing a larger body of current evidence, expanding microbe-disease associations, and identifying key microbes implicated across multiple studies.In 2008, Jia et al. proposed strategies targeting gut microbes, pioneering rationale (Jia et al., 2008).Since then, microbial-targeted therapeutics (MMT) emerged, e.g., FMT, prebiotics, biologics, microbiomeinspired biotherapeutics.Many published studies have examined gut microbiome dysbiosis in disease and the efficacy and safety of FMT for various diseases.In this database analysis, we analyzed associations between 117 gastrointestinal and extra-gastrointestinal diseases and 479 gut microbes.Researchers could use these results to determine disease-microbiota associations and identify key pathogenic bacteria at different taxonomic levels.
In this umbrella review, we identified high-quality meta-analyses assessing FMT for 13 diseases.For rCDI, FMT had high-quality evidence of benefit.However, evidence was very low quality for primary CDI.For IBD, evidence was moderate quality overall, high or moderate for UC, moderate to low or very low for CD, and very low for chronic pouchitis.Low-quality evidence supported FMT for IBD-related CDI and IBS.Low-quality evidence supported FMT for decolonizing AMR bacteria.FMT may help obesity and metabolic syndrome, but evidence was low or very low quality.
In a recent study (Martinez et al., 2022), Hospitalized elderly individuals with CDI had significantly lower abundances of Lachnospiraceae, Ruminococcaceae, Blautia spp., Prevotella spp., Dialister spp., Bifidobacterium spp., Roseburia spp., Anaerostipes spp., Faecalibacterium spp., and Coprococcus spp.compared with healthy controls, and higher Enterococcaceae and Enterococcus spp.Some microbial alterations from this study were observed to be consistent with our radial dendrogram.FMT restores bile acid metabolism and colonic bile acid composition, creating an unfavorable environment for Clostridioides difficile spore germination and facilitating rCDI recovery (Weingarden et al., 2014;Brown et al., 2018).The inflammatory to noninflammatory fatty acid ratio decreased, and total fatty acids normalized (Brown et al., 2018).FMT was associated with normalized fecal microbiota and restored alpha diversity (Kelly et al., 2016).Given the current evidence, we recommend FMT be used mainly for CDI patients, especially those with recurrent CDI who stand to benefit the most.This application is endorsed by current guidelines (Appendix 6 showed the current clinical practice guidelines and consensus on FMT).European guideline recommended FMT or bezlotoxumab for rCDI in addition to antibiotics (weak, moderate).However, a multidisciplinary risk assessment was mandatory for FMT, and the preparation and screening of the products should be standardized (weak, moderate;Van Prehn et al., 2021).United Kingdom guideline recommend FMT for rCDI and potential other indications, specifying patient selection, donor screening, preparation, administration, follow-up, and service configuration (strong; Mullish et al., 2018).United Kingdom guideline included an antibiotic strategy for CDI that supported FMT for CDI treating in adults, young people, and children (≥72 h) in community and hospital settings (National Institute for Health and Care Excellence, 2021).United States guideline recommended FMT for multiple rCDI recurrences after appropriate antibiotics (adults: strong, moderate; children: weak, very low; McDonald et al., 2018).We found fresh FMT with multiple infusions via colonoscopy most effective for rCDI.Frozen (−20°C or − 70°C) and lyophilized FMT can also work.Bowel cleansing and aerobic processing may improve outcomes.
For IBD, reduced alpha diversity and dysbiosis are found in active disease.Decreased facultative anaerobes like E. coli and increased obligate anaerobes like Faecalibacterium prausnitzii occur in CD (Lloyd-Price et al., 2019).Ruminococcus torques and Ruminococcus gnavus decreased in CD and UC dysbiosis, respectively (Lloyd-Price et al., 2019).For UC, lower gastrointestinal FMT and higher total stool dosage were associated with greater clinical remission.Further study should examine pediatric and adult patients, single or repeated infusions, fresh or frozen FMT, and antibiotics before FMT.For CD, fresh upper gastrointestinal FMT without antibiotics pretreatment may achieve better clinical remission but needs confirmation.
For IBS, especially diarrhea-predominant IBS, decreased Lactobacillus, Bifidobacterium, and F. prausnitzii occur (Liu et al., 2017).After FMT, symptoms improved and the gut microbiome repaired over time (Holvoet et al., 2021).FMT may help IBS but further study should examine routes of administration, donor types, infusion frequency, FMT types, and long-term use.
A trial found FMT significantly decreased AMR bacteria abundance for 2 months, indicating donor engraftment extent directly related to decreased fecal antimicrobial resistance gene carriage (Isgut et al., 2021).FMT was considered to decolonize regimens targeting multidrug-resistant Gram-negative bacteria (Tacconelli et al., 2019).However, guideline argued insufficient evidence to recommend for or against FMT.
For other conditions, evidence is insufficient to recommend for or against FMT.Further study should examine FMT routes of administration, donor types, infusion frequency, and FMT types for clinical use.
Our findings align with and build upon those from several current studies.Borody and Khoruts (2011) proposed FMT may be beneficial

Potential mechanisms
Multiple mechanisms interact to cause disease and its progression.For many diseases, dysbiosis is an important etiology.Healthy donor feces contain species-rich microbiomes, viromes and mycobiomes that increase diversity, enhance microbial networks and core microbiota, treating symptoms (Jalanka et al., 2016).
Recent studies (Hanssen et al., 2021;De Vos et al., 2022;Lam et al., 2022;Leonardi et al., 2022) suggest seven key mechanisms by which FMT may modify human and microbial physiology (Figure 11): A. FMT can rapidly restore normal diversity and enhance microbial networks and core microbes in dysbiosis (Jalanka et al., 2016).B. In CDI, sterile fecal filtrate (containing viruses, metabolites, not bacteria) achieved remission, showing gut viruses' significance (Ott et al., 2017).Recent studies used sterile feces and fecal viral transplantation to study roles in obesity, diabetes, bacterial overgrowth, necrotizing enterocolitis, post-antibiotic dysbiosis (Lam et al., 2022).C. Reducing Candida albicans may improve CDI/IBD outcomes with FMT (Lam et al., 2022).Changes in the gut mycobiome were associated with symptom improvement in IBS/GVHD (Lam et al., 2022).Mucosaassociated fungi activate mucosal immunity (Leonardi et al., 2022).D. FMT alters microbial metabolites acting on hosts (e.g., liver/ immune cell metabolism; Hanssen et al., 2021).Metabolites may be from new or existing bacteria.E. Microbial metabolites interact with host cells, activating/inhibiting signaling and health.Bacterial metabolites include short-chain fatty acids (nourishing intestine, altering permeability), peptidoglycan, lipopolysaccharides (De Vos et al., 2022).F. By altering metabolites, antigens, or other mechanisms, FMT influences the host immune response.G. Gut microbiomes connect with organs/systems through structure/metabolites, possibly altering tissue metabolism (GUT-X axies).FMT changes microbiomes, affecting these potential axies.The concept of "GUT-X axies" outlining putative interactions between the gut microbiota and distal organs/ systems mediated through structural motifs or bioactive metabolites was formulated based on pertinent publications identified in our PubMed search.This acts as a provisional framework delineating putative microbiota-organ interplay that warrants further verification and interrogation through empirical research to develop additional axies.

Limitations
This review has some limitations.First, some findings relied on observational studies or small studies, introducing bias and heterogeneity risks and limiting evidence quality.Also, FMT parameters (e.g., delivery route, donor type, dosing frequency, commensal preparation) for non-CDI indications need refinement.Finally, ClinicalTrials.govlists numerous ongoing FMT studies across diseases; as new evidence emerges, it may alter our conclusions.We will update this review to incorporate impactful new findings when published.

Conclusion
In summary, gut dysbiosis associates with at least 117 gastrointestinal and extra-gastrointestinal diseases.FMT provides a new modality to reshape the gut microbiome, virome, mycobiome and metabolome, benefitting patients with said diseases.Meta-analyses suggest FMT efficacy and safety in clinical practice, but higher-quality evidence is needed to strengthen recommendations.
Future research should explore gut-disease causality, measure dysbiosis, identify disease mechanisms and FMT's molecular effects.Improving FMT standardization, innovation and delivery will enhance its efficacy, safety and indications.However, large, rigorous studies are still needed to support expanded use.
Several avenues remain unexplored: (1) Determine if dysbiosis causes or results from certain diseases.New techniques can quantify dysbiosis and its disease-specific nature.(2) Identify disease-associated microbes and FMT's mechanisms of action.This can illuminate new therapeutic targets and applications (Chen et al., 2022;Lloréns-Rico et al., 2022).(3) Optimize FMT preparation, delivery and dosing through standardization and innovation.Engineered bacterial groups or bacteriophage-based therapy with more precise delivery and control can be developed through FMT (Yang et al., 2022;Airola et al., 2023).Engineered bacteria combined with gut bacteria and functional magnetic nanoparticles provide new ideas for precise regulation of gut bacteria.Using external magnetic field control, engineered bacteria can be successfully and precisely aggregated and colonized in the gut.The external magnetic field also can control the gene expression of the engineered bacteria to remotely regulate genetic functions.This enables more precise and convenient control of engineered bacterial functions.(4) Conduct large RCTs and prospective studies on FMT for complex, non-CDI diseases.Robust evidence will enable guideline recommendations and insurance coverage.(5) Integrate multi-omics datasets to capture the gut microbiome's immense complexity.Mapping genomes, metabolites and the host interactome may transform disease understanding and precision editing of the gut microbiota.

FIGURE 1
FIGURE 1Flow diagram depicting results for inclusion.

FIGURE 2
FIGURE 2Top 5 diseases and their associated gut microbes dysbioses.The tree trunks represent the diseases while the leaves show the specific microbial dysbioses linked to each disease.The inner circle heatmap indicates the taxonomic classification of the microbes, and the outer circle heatmap reveals the over-and under-abundance of particular microbes for each disease cluster.Full radial dendrograms were in Supplementary FigureS1.Microbe names use hyphens in place of spaces.

FIGURE 4
FIGURE 4 Radial bar charts showing relative abundances of key microbes grouped by taxonomic classification.Microbe names use hyphens in place of spaces.(A) Fhylum; (B) Class; (C) Order; (D) Family; (E) Genus; (F) Species; (G) No rank.

FIGURE 5
FIGURE 5 Registered clinical trials using fecal microbiota transplantation for 114 digestive or non-digestive diseases from 2008 to 2022.(A) Number of trials (red) and cumulative total (green) per year.(B) 13 conditions from 62 meta-analyses.(C) 19 cancer-related conditions.FMT has been applied not only to treat gastrointestinal cancers themselves, but also cancers of other organ systems and gastrointestinal side effects arising from other cancer treatments.(D) 53 non-digestive conditions.(E) 42 digestive conditions.

FIGURE 6
FIGURE 6Evidence mapping of reported efficacy, safety and recurrence outcomes of fecal microbiota transplantation in treating various diseases.CDI, Clostridioides difficile infection; CDAD, Clostridioides difficile-associated diarrhea; IBD, inflammatory bowel disease.GRADE, Grading of Recommendations Assessment Development and Evaluation.