1 Introduction
In the past two decades, a series of pioneering technologies, notably microbiome sequencing, multi-omics integration, and fecal microbiota transplantation (FMT), have enabled insights into the composition and functions of the gut microbiome. Accumulating clinical and mechanistic evidence reveals the key role of the microbiome in human health and disease [
1–
3]. Therefore, microbiomes have been explored as a target for disease diagnosis, treatment, and prevention, which constitute the core goals of microbiota medicine [
4,
5]. Nowadays, significant medical translation advances have been achieved in the microbiota medicine area, especially for therapeutics targeting microbiome modulation [
6]. Microbiome modulation with novel modalities has been investigated for an increasing number of dysbiosis-related diseases, including infections [
7–
11], inflammatory diseases [
12–
14], metabolic diseases [
15–
17], autoimmune diseases [
18,
19], and cancers [
20–
22]. The technologies for modulating gut microbiome have promoted in-depth basic mechanistic research and directly revealed relationships between microbiome and diseases, which provides more evidence for microbiome-based diagnostic biomarkers and therapeutics. Meanwhile, developing microbiome-based diagnostic and therapeutic technologies involving diseases from different human body systems requires a new discipline that breaks the barriers of the existing clinical medical discipline classification system. The implementation of microbiota medicine as an independent clinical medical discipline will provide an ideal platform for the conduction of integrative medical microbiome research, the translation of technologies, and the cultivation of talents [
5]. This review, covering the searches till January 2026, aims to summarize the evidence and advances in the indications, therapeutic modalities, diagnostic evidence, discipline frameworks of microbiota medicine, and future perspectives in this field.
2 Indications of Microbiota Medicine
The most effective and direct evidence of humans using microbial materials to treat diseases is FMT [
23]. Fecal therapy as a medical technique has been recorded in medical history for at least 1700 years, dating back to ancient China. Initially, it was used to treat food poisoning, diarrhea, and fever [
23,
24]. In the past decades, FMT, defined as the infusion of fecal microbiota from a healthy donor to a recipient to treat dysbiosis-related diseases, has been a research focus in the biomedicine and clinical medicine field [
25,
26]. FMT is a safe and effective treatment for recurrent
Clostridioides difficile infection (rCDI) and has been recommended by international guidelines for this indication [
27,
28]. Based on the success of FMT in rCDI and its potential to restore altered gut microbiota, FMT has been investigated in a wide range of diseases related to gut dysbiosis. The effectiveness of FMT has been described in 85 diseases which can be categorized into eight types including infections, gut diseases, microbiota-gut-liver axis, microbiota-gut-brain axis, metabolic diseases, oncology, hematological diseases, and other diseases [
29]. In addition, the application of FMT in several new indications has been reported recently. In 2023, Lu et al. first reported the beneficial effects of washed microbiota transplantation (WMT), the improved methodology of FMT based on the automatic washing process [
30], on amyotrophic lateral sclerosis (ALS), which is a systemic disorder that involves dysfunction of multiple organs [
31]. Yang et al. subsequently reported the rescue effect of FMT via the mid-gut tube on ALS with respiratory failure in a case report including two patients [
32]. In a Phase 2 randomized controlled trial (RCT), Tian et al. performed a 3-cycle FMTs/placebo in patients with progressive supranuclear palsy-Richardson's syndrome (PSP-RS) [
33], which is a progressive and devastating neurodegenerative disease that is also the most common atypical Parkinsonism [
34]. The FMT group showed significantly decreased PSP rating scale (PSPRS) scores and improved symptoms of constipation, depression, and anxiety compared with the placebo group [
33]. In a case-control study, Zhong et al. demonstrated that WMT treatment is associated with reduced liver fat accumulation in patients with metabolic-associated fatty liver disease (MAFLD) [
35]. The "farthest" (from gut to peripheral nervous system) example is the use of FMT to treat distal symmetric polyneuropathy (DSPN) [
36]. The proof-of-concept RCT demonstrated that transplantation of gut microbiota from healthy donors effectively improves nerve function and neuropathic symptoms in patients with DSPN [
36]. As of January 2026, more than 400 active or ongoing clinical trials have been registered on ClinicalTrials.gov investigating the effectiveness of FMT across a wide range of diseases. Apart from the therapeutic effectiveness on specific diseases, microbiome modulation-based treatments can be an important part of the prevention and treatment framework of radiation injury from war or accident [
37]. The history and evolution of indications of microbiota medicine were summarized in Figure 1.
3 Therapeutic Modalities of Microbiota Medicine
The success of FMT against CDI has sparked interest among physicians, researchers, patients, and biomedicine companies in gut microbiome-targeted therapeutics. However, the actual application of FMT is far lower than expected, and the number of patients who should benefit from FMT is far from the theoretical number of beneficiaries [
5]. The limitations of FMT may help explain its restricted adoption beyond rCDI. The challenges span five key domains: safety, ethics, regulation, product standardization, and therapeutic efficacy [
38]. Safety concerns extend beyond common, self-limiting adverse events (e.g., abdominal discomfort and diarrhea) to include rare but serious risks, such as transmission of multidrug-resistant (MDR) organisms or unexpected pathobionts [
39,
40]. Ethically, the field faces unresolved issues regarding donor screening frameworks, long-term recipient follow-up, and the commodification of human microbiota. Regulatory policies remain highly fragmented. The U.S. Food and Drug Administration (FDA) classified FMT as an investigational drug, thereby mandating an investigational new drug (IND) application for clinical use. But following concerted advocacy from researchers, clinicians, and patients, the FDA exempted the specific indication of rCDI from the IND requirement while maintaining the investigational drug framework for other applications [
41]. The European Medicines Agency (EMA) has designated FMT as a substance of human origin (SoHO) under the new EU SoHO Regulation (2024/1938), which permits broader clinical applications in member states adopting this framework, and is still formulating dedicated guidelines for microbiota-based therapies [
42]. Australia's Therapeutic Goods Administration (TGA) categorized FMT as a biological product, and the Therapeutic Goods Order No. 105 (TGO 105), which commenced in 2021, established legally binding requirements for the quality, safety, and efficacy of FMT products [
43]. Consequently, FMT products need approval from TGA to be included in the Australian Register of Therapeutic Goods (ARTG) for routine use, and manufacturers and producers are also required to be approved by TGA and additionally to operate in compliance with good manufacturing practices (GMP). In the Chinese mainland, FMT was formally incorporated into the National Technical Specifications for Medical Service Items in 2023 as a licensed medical technology, permitting clinical applications without restriction on indications in principle [
44]. However, no FMT product has yet been approved as a drug by the National Medical Products Administration (NMPA) in China, as such approval requires a regulatory pathway distinct from the medical technology framework. Other countries mostly have integrated FMT for rCDI into routine clinical practice under local hospital governance, without centralized product approval [
45]. The comparison of regulatory frameworks for FMT is listed in Table 1. Beyond these governance and safety hurdles, poor availability and lack of standardization persist as major logistical barriers. Furthermore, efficacy data for noninfectious diseases remain inconsistent, tempering clinical enthusiasm.
In this context, a range of novel microbiome-based therapeutic modalities have been developed to enable safer, more consistent, and targeted modulation of the gut ecosystem. These include microbiota consortia, bacteriophages, engineered probiotics, microbiota-derived metabolites, antimicrobial peptides (AMPs), and oncolytic bacteria and viruses. Beyond gut-targeted approaches, emerging technologies are also being explored to modulate the microbiome at distal sites and to enable repeated microbiota transplantation in a controlled manner. A comparative summary of different therapeutic modalities in microbiota medicine is listed in Table 2.
3.1 Microbiota Consortia
Microbiota consortia consisting of the full microbiome or selected bacteria have been designed to overcome the poor availability and reproducibility of FMT since 2016 [
46,
47]. Investigations into microbiota consortia are predominantly focused on the treatment of CDI, given the satisfactory efficacy of FMT in this regard.
RBX2660 (REBYOTA, Rebiotix, USA), consisting of fecal microbiota prepared from screened human feces and delivered via enema, is the first U.S. FDA-approved live biotherapeutic product for the prevention of rCDI. In a Phase 3 RCT including 267 patients, a single RBX2660 enema exhibited superior efficacy to placebo in preventing rCDI at 8-week follow-up (70.6% vs. 57.5%, estimated treatment effect 13.1%; posterior probability of superiority 0.991) [
47].
Two oral lyophilized full microbiota-based consortia for rCDI are under evaluation to make the products more user-friendly than frozen enemas, as they do not need refrigerated storage. A Phase 1 trial of 30 patients who were divided into three groups and treated with different dosages of oral lyophilized RBX7455 demonstrated that the RBX7455 was able to prevent rCDI in 80%–100% of patients at Week 8, depending on the dosage used and without serious adverse events (SAEs) [
48]. Despite the limited sample size and pilot study design, the preliminary data are interesting in showing the potential of this user-friendly product for the prevention of rCDI. CP101 (Finch Therapeutics, USA) is another oral lyophilized microbiota consortium composed of the full microbiome. In a Phase 2 RCT including 198 patients, the CP101 demonstrated its superiority to placebo in preventing rCDI in Week 8 (74.5% vs. 61.5%,
p < 0.05) [
49]. The CP101 arm exhibited significantly higher alpha diversity, which was sustained over time compared to the placebo arm. However, a Phase 3 trial of CP101 was stopped prematurely due to slow enrollment, financial pressures, and strategic shifts.
Several microbiota consortia, composed of selected bacterial strains, have been designed and are currently under evaluation. Unlike full microbiota-based products, these consortia aim to specifically target pathogenic bacteria and reduce the risk of transmitting pathogenic or antibiotic-resistant microbes [
39,
50]. SER-109 (VOWST, Seres Therapeutics, USA) is an oral microbiome consortium composed of purified
Firmicutes spores, which are expected to reduce the abundance of antibiotic-resistant bacteria [
51,
52]. In a Phase 3 trial (NCT03183128) including 182 patients with three or more episodes of CDI, SER-109 showed superiority over placebo in preventing rCDI (8-week recurrence rate of 12% vs. 40%,
p < 0.001) [
46]. In 2022, SER-109 was granted a biologics license by the FDA for the prevention of rCDI. Subsequent analysis revealed the pharmacological effects of SER-109 on patients, including changes in microbial composition and key bioactive metabolites, and validated its function in producing these
C. difficile-inhibiting metabolites in vitro [
53]. VE303 (Vedanta Biosciences, USA) is an oral bacterial consortium of eight strains of purified commensal
Clostridia [
54]. In a dose-finding Phase 2 RCT, high-dose (8.0 × 10
9 colony-forming units, CFUs) but not low-dose VE303 (1.6 × 10
9 CFUs) was more effective than placebo for the prevention of CDI at week 8 (86% vs. 73% vs. 55%, respectively;
p = 0.006 for high-dose vs. placebo) [
55].
Although several microbiota consortia are being investigated for diseases beyond CDI, positive reports in non-CDI indications remain scarce. Rather than repurposing CDI-derived formulations for other conditions, a more promising strategy may be to design disease-specific consortia. Machine learning, based on multi-cohort metagenomic datasets, might offer a powerful approach to identify candidate bacterial strains and enable the targeted development of consortia formulas [
56].
3.2 Bacteriophages
Bacteriophages, also known informally as phages, are viruses that infect and replicate within bacteria and archaea. Human guts harbor abundant phages, with estimates ranging from 10
8 to 10
10 phage particles per gram of human feces [
57,
58]. A recent study demonstrated that a large number of phages for specific commensal gut bacteria can be isolated and cultured from the human gut [
59]. Phages were considered the cure for bacterial infections before the discovery of antibiotics [
60]. However, after the discovery of antibacterial compounds such as penicillin and the subsequent success of the antibiotic era, the therapeutic uses of phages were largely disregarded [
61]. More recently, the rise in MDR bacterial infections, such as
Klebsiella pneumoniae infection, has brought bacteriophage therapy to the forefront. Unlike antibiotics, bacteriophages offer high specificity, can reduce side effects, and present a different resistance profile that may be managed through co-evolution and combination therapy [
62]. Federici et al. conducted a proof-of-concept study in inflammatory bowel disease (IBD) animal models, demonstrating the feasibility of oral administration of
K.
pneumoniae-targeting phages to avoid bacterial resistance and inhibit pathogenic bacteria for ulcerative colitis (UC) [
63]. Two salvage therapy reports demonstrated the clinical efficacy of the combination of antibiotics with bacteriophage in MDR wounds and urinary tract infections (UTI) [
64,
65]. Nevertheless, only a few small RCTs, primarily in Phase 1/2, have been conducted to use bacteriophages in treating bacterial infections [
66–
68]. Jault et al. conducted an RCT comparing phages against
Pseudomonas aeruginosa with topical antibiotics in patients with burn wounds. However, this study stopped early due to the insufficient efficacy of phages, which was attributed to stability issues [
68]. Saker et al. conducted an RCT assessing the efficacy of oral coliphages in acute bacterial diarrhea, but the phages failed to achieve intestinal amplification and to improve diarrhea outcome, possibly due to insufficient phage coverage and too low
Escherichia coli pathogen titers requiring higher oral phage doses [
67]. The above findings suggest the current challenges and areas for improvement in the application of bacteriophages for bacterial infections, including matching bacteria with effective bacteriophages, pre-testing of stability, selection of routes of administration, and optimal dosage [
69,
70].
3.3 Engineered Probiotics
Engineered probiotics are regarded as the next generation of live biotherapeutics that can be genetically modified to target specific diseases [
71]. The engineering of probiotics has become easier with the development of synthetic biology [
71]. Accumulating animal studies have revealed the therapeutic potential of engineered probiotics in the treatment of cancers [
72–
75], infections [
76–
78], metabolic diseases [
79–
81], and inflammation [
82–
85]. Nevertheless, limited research progress on engineered probiotics has been under investigation in clinical trials [
71].
Lactobacillus lactis was the first genetically engineered microorganism investigated in clinical trials as a vehicle for the secretion of immunomodulatory molecules.
L.
lactis engineered (AG019) was used as monotherapy for the oral delivery of human proinsulin and interleukin-10 (IL-10) to attenuate the autoinflammation in recent-onset type 1 diabetes mellitus (T1DM) in an open-label phase 1b study (NCT03751007). Patients treated with the monotherapy of AG109 showed stabilized metabolic variables for up to 6 months (C-peptide and insulin use) or 12 months (HbA1c) [
86]. In Phase 2a RCT, the combination therapy of AG019 and teplizumab led to stabilized or improved insulin secretion and immune tolerance [
86]. However, a Phase 2 trial in which
L. lactis released human trefoil factor 1 to treat oral mucosal inflammation was terminated due to poor efficacy (NCT03234465).
E. coli Nissle 1917 is another engineered probiotic investigated in clinical trials. In a Phase 1/2a RCT, the
E. coli Nissle 1917, designed as SYNB1618, was tested to consume phenylalanine (Phe) in patients with phenylketonuria (PKU) [
87]. The results showed that SYNB1618 was able to consume Phe and convert it to nontoxic metabolites in a dose-responsive manner with good safety and tolerability [
87]. However, a further Phase 3 RCT on
E. coli Nissle 1917 (SYNB1934) for PKU was terminated due to poor efficacy (NCT05764239).
Clostridium butyricum encapsulated as CBM588 was demonstrated to improve the objective response rate (ORR) and progression-free survival (PFS) of approved immunotherapy in renal cell carcinoma (RCC) in a Phase 1 trial (NCT05122546) [
88]. A Phase 3 trial, NCT07383441, which is designed to compare the effect of adding this biotherapy to immunotherapy in treating RCC patients, is estimated to start in June 2026.
The clinical translation of engineered probiotics remains constrained by a confluence of technology, safety, and regulation. Foremost among technical factors are the low viability and poor efficiency in practice [
89]. A wide range of novel technologies, including encapsulation strategies, synthetic biology design, and targeted delivery systems, are under active development to enhance the therapeutic performance [
89,
90]. Beyond efficacy concern, safety and biocontamination constitute major regulatory and ethical barriers to the clinical adoption of these genetically modified organisms. The uncertainties (e.g., environmental escape, horizontal gene transfer to commensal microbiota, long-term health effects of sustained colonization, and host immune response to engineered strains or their products) necessitate rigorous preclinical assessment [
90].
However, the absence of approved probiotic "drugs" or "medicines" cannot be attributed solely to technical or safety limitations. A more fundamental explanation lies in economic and commercial considerations. Numerous probiotic products are currently marketed as medical foods or food supplements. These regulatory categories do not require rigorous clinical trials, pre-market approval, or post-marketing surveillance mandated for live biotherapeutic products (LBPs) [
91]. This pathway offers strategic advantages, including faster time-to-market, substantially lower development and manufacturing costs, more flexible regulatory oversight, and broader consumer access. Consequently, the vast majority of probiotic products remain outside the drug regulatory framework, positioned instead as dietary supplements or probiotic foods. Importantly, the quality of clinical evidence remains subject to scrutiny even within these less stringent categories [
91]. VSL#3, one of the most extensively studied multi-strain probiotic formulations, was removed from the National Health Service (NHS) prescribing formularies due to the lack of robust clinical evidence in 2018.
3.4 Microbial Metabolites
Microbial metabolites are a range of small soluble bioactive molecules produced, modulated, or degraded by the microbiome [
92]. Certain classes of microbial metabolites, including short-chain fatty acids (SCFAs) and bile acids, are mostly beneficial to the host [
93]. Different end-products of microbial tryptophan metabolism can be either beneficial or harmful [
94,
95]. Others, such as some amino acid derivatives or trimethylamine-oxide (TMAO), are noxious and associated with the contribution to disease pathogenesis [
96]. Supplementation or modulation of microbial metabolites was regarded as a therapeutic modality of microbiota medicine, which was recently termed postbiotic treatment [
97]. A recent consensus statement by the International Scientific Association of Probiotics and Prebiotics (ISAPP) defined a postbiotic as a "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host" [
98]. Although the effects of postbiotics on the microbiota might be temporary, they could still have an important mechanistic role, including modulating microbiota indirectly [
99,
100], mitigating antibiotic-induced microbiome injury [
101], enhancing epithelial barrier function [
102], modulating immune responses [
103,
104] and systemic metabolism [
105,
106], and signaling via the nervous system [
107,
108].
SCFAs are organic acids composed of less than six carbons in their carbon chain, with representatives including acetate (C2), propionate (C3), and butyrate (C4) [
109]. SCFAs have several beneficial effects on human health, including promoting the integrity and permeability of the gut barrier and affecting innate and adaptive immunity [
110]. Based on the anti-inflammatory immune modulation effects of SCFAs in colitis [
111], an RCT investigating the efficacy of SCFA enema for distal UC indicated that more patients with UC improved, though the difference was statistically nonsignificant (33% vs. 20%,
p = 0.14) [
112]. Similarly, in a pilot RCT, the administration of microencapsulated butyrate did not show significant improvement in clinical activity in patients with IBD, though the enrichment of SCFA-producing bacteria was observed [
113]. On the other hand, Groot et al. conducted an RCT using oral butyrate to treat patients with T1DM and found that the administration of butyrate did not result in any significant changes in adaptive or innate immunity or in glucose and lipid metabolism despite the increase in the levels of fecal butyrate and propionate [
114]. The current evidence suggests limited clinical efficacy of local or oral administration of SCFA, but the observed enrichments in fecal SCFA and SCFA-producing bacteria might provide more insights to enhance the efficacy of SCFA. The specific promising efficacy of SCFA enema in patients with short active episodes of distal UC suggests that prolonged contact with rectal mucosa seems to be necessary for therapeutic benefit [
112].
Apart from direct supplementation, applying prebiotics (i.e., complex carbohydrates, resistant starches, or dietary fibers) to promote bacterial metabolism of SCFA is another way to increase the SCFA concentration. In a placebo-controlled trial, supplementation with 3 months of inulin-type fructans had no significant impact on the body mass index (BMI) and waist/hip ratio in obese women but led to an increase in
Bifidobacterium and
Faecalibacterium prausnitzii [
115]. In another RCT, 14 days of intake of fructooligosaccharides (FOS) and galactooligosaccharides (GOS) led to increased
Bifidobacterium but decreased butyrate-producing bacteria and adverse effects on glucose metabolism [
116]. In addition, in patients with type 2 diabetes mellitus (T2DM), dietary fibers can promote a select group of SCFA-producing strains, leading to a subset of these individuals having improved glucose regulation in line with elevated levels of glucagon-like peptide-1 (GLP-1) [
117]. Therefore, investigations on personalized prebiotic intervention based on gut microbiota might be the future direction.
3.5 AMPs
AMPs are small molecular peptides that typically consist of less than 100 amino acid residues [
118,
119]. AMPs are produced by a broad spectrum of organisms, including microorganisms, plants, insects, and vertebrates [
120]. Animal AMPs play a crucial role in the innate immune system and are known for their broad-spectrum antimicrobial activity [
121]. On the contrary, bacterial AMPs, known as bacteriocins, often demonstrate a limited spectrum of antimicrobial activity, particularly targeting bacteria that share a phylogenetic relationship with the bacteriocin-producing bacteria [
122]. In addition, AMPs are associated with lower susceptibility to resistance development in pathogens and stronger phylogenetic barriers within bacteria to prevent the horizontal transfer of resistance genes [
123] compared to small molecular antibiotics, rendering them potential agents against MDR bacterial infections [
124]. The above properties render AMPs particularly interesting compounds for translational applications as novel therapeutics for microbiome modulation [
125]. Currently, in addition to a few AMPs that have been approved by the FDA for clinical treatment [
125], a variety of AMPs have been assessed in clinical trials for different indications, including atopic dermatitis (AD) [
126], nasal infection [
127], methicillin-resistant
Staphylococcus aureus (MRSA) infection [
128], CDI [
128], diabetic foot ulcers [
128], epidermal wounds [
129], etc. On the other hand, the human microbiome encodes numerous AMPs [
130–
132]. Ma et al. identified a set of AMPs from the human gut microbiome with > 80% of which hold antibacterial activity by machine learning models [
133]. King et al. found more than 200 AMPs from genomes of species colonizing skin, gut, urogenital tract, mouth, and trachea, 70 of which were synthesized and expressed in
E. coli and 23 could be purified and functionally characterized [
130]. The above findings bring insights into the investigation of AMPs from the human microbiome and the therapeutic potential of targeting AMPs for microbiome modulation [
134,
135].
3.6 Oncolytic Bacteria and Viruses
The origins of oncolytic bacteria date back to early observations of infections leading to tumor regression by Dr. William Coley in the late 19th century [
136]. He observed that some cancer patients experienced tumor shrinkage following bacterial infections, prompting the use of live bacteria like
Streptococcus pyogenes in cancer treatment [
137,
138]. This concept evolved into the development of genetically modified strains, which are designed to target and destroy cancer cells selectively. Currently, oncolytic bacteria include species of
Klebsiella,
Listeria,
Mycobacteria,
Streptococcus/Serratia (Coley's Toxin),
Proteus,
Salmonella, and
Clostridium.
Clostridium novyi, which lyses tumors through direct embedding lipase and/or secreting exotoxin, has been proven to have excellent antitumor capability in clinical trials. An attenuated strain
C. novyi-NT (lacking alpha-toxin) was evaluated in a Phase 1 study (NCT01924689) for treatment-refractory solid tumors. Forty-two percent of 24 patients treated with a single intratumoral injection had tumor destruction from
C. novyi-NT germination in the injected lesions. Forty-one percent of 22 valuable patients showed a decreased size of the injected tumor, and 86% had stable disease as the best response [
139]. However, its toxicity suggested the exploration of multiple dosing and multiple injections. The following Phase 1b study (NCT03435952) reported the safety and synergistic effects of the combination of
C. novyi-NT with the immune checkpoint inhibitor pembrolizumab in advanced tumors. Of 16 patients, most AEs were Grade 1 or 2, and Grade 3 dose-limiting toxicity (DLT) was observed in one patient. Six patients experienced SAEs, including one treatment-related SAE linked to
C. novyi-NT. The combination study revealed an ORR of 25%, and most patients had stable disease (only one experienced progressive disease) [
140]. Though these trials implicated the promising prospects of oncolytic bacteria for treating solid tumors, studies in larger scale are required to advance it to later stages.
Oncolytic virotherapy is an innovative cancer treatment strategy that harnesses the selective ability of viruses to infect and kill cancer cells while sparing normal tissue. Oncolytic virotherapy is well recognized as a type of immunotherapy, the mechanisms of which include induction of direct cytotoxicity in cancer cells and elicitation of the immune-mediated antitumor response by stimulating the patient's immune system [
141]. Recent clinical trials have highlighted the potential of oncolytic viruses (OVs), including herpes simplex virus (HSV), vaccinia virus (VV), Newcastle disease virus (NDV), vesicular stomatitis virus (VSV), and Coxsackievirus, as transformative agents in cancer therapy. Talimogene laherparepvec (T-VEC), an HSV-1-based oncolytic therapy, has been approved by the U.S. FDA for melanoma since 2015. Recently, it was evaluated in combination with neoadjuvant chemotherapy (NAC) in a Phase 2 trial (NCT02779855) for triple-negative breast cancer. The study reported a 45.9% complete response rate (RCB0) and a 65% combined RCB0-1 rate, with no recurrences in RCB0-1 patients and a 2-year disease-free survival rate of 89%, suggesting that T-VEC enhances NAC efficacy [
142]. Another promising HSV-based OV, CAN-3110, was evaluated in Phase 1 trial (NCT03152318) in 41 patients with recurrent glioblastoma. Engineered with a nestin promoter-regulated
ICP34.5 gene, CAN-3110 showed preferential replication in tumors, no dose-limiting toxicities, and also potential in enhancing immune responses, especially in HSV1-seropositive patients, which highlights its promise for treating immunotherapy-resistant cancers [
143]. In addition to HSV, VV is another promising oncolytic virus that has been investigated in clinical trials recently. A phase Ⅰ/Ⅱ trial assessed the safety and efficacy of pexastimogene devacirepvec (PexaVec) combined with durvalumab and tremelimumab in chemotherapy-refractory mismatch repair proficient metastatic colorectal cancer (CRC). The combination treatment was safe and tolerable, showing common toxicities like fever and chills, and a median PFS of 2.3 months [
144]. A recent Phase 1 clinical trial (Chinese Clinical Trial Registry of WHO, ChiCTR2000031980) assessed the feasibility of a recombinant NDV with porcine
α1, 3GT gene (NDV-GT) in 20 patients with relapsed/refractory metastatic cancer. The intravenous treatment of NDV-GT resulted in a high disease control rate (DCR) of 90% without significant toxicity or virus shedding, indicating its potential application against various solid tumors [
145]. VSV and Coxsackievirus also showed promise in Phase 1 trials for lymphoma and in Phase 1b and Phase 2 trials for skin malignancies [
146–
149]. Despite the advances in clinical trials, translating oncolytic virotherapy to clinical practice faces challenges related to safety, efficacy, and regulatory complexities. Future directions in this area include integrating gene-editing technologies, improving biomarker-driven patient selection, and combining with next-generation immunotherapies, which require ongoing collaboration among researchers, clinicians, and regulatory bodies [
141].
3.7 Microbiota Transplantation Beyond the Gut
In addition to the gut microbiota, microbiota inhabiting in/on other parts of the human body also play an important role in human health and disease, such as vaginal microbiota [
150,
151] and skin microbiota [
152–
154]. The dysbiosis in vaginal microbiota has been associated with a range of adverse health outcomes including bacterial vaginosis (BV) [
155], sexually transmitted infections (e.g., human immunodeficiency virus (HIV) [
156] and human papillomavirus (HPV) [
157]), nonsexually transmitted infections (e.g., UTI [
158], pelvic inflammatory disease [PID] [
159], and preterm delivery [
160]), and in vitro fertilization during female infertility [
161]. The dysbiosis in skin microbiota has been associated with a range of skin diseases, such as common acne [
162–
164] and AD [
165–
168].
The promising results from studies of FMT for gut dysbiosis-related diseases have motivated the investigation of vaginal microbiota transplantation (VMT) and skin microbiota transplantation. An exploratory study tested the use of VMT from healthy donors as a therapeutic alternative for patients suffering from symptomatic, intractable, and recurrent BV [
169]. Four of five (80%) patients achieved long-term remission during the 5–21 months of follow-up after VMT, and the microbiome analysis indicated the reconstitution of a
Lactobacillus-dominated vaginal microbiome [
169]. VMT has also been investigated in some pilot studies for microbiota restoration in cesarean-born infants [
170–
172]. In RCT including 68 cesarean-delivered infants, Zhou et al. found that the transfer of mothers' vaginal microbiota to cesarean-born infants is likely safe with an AE rate of 12.5% vs. 13.9% (
p > 0.999) in the VMT group and control group, respectively. The VMT group exhibits improved neurodevelopmental scores and faster maturation of gut microbiota than the control group [
172]. On the other hand, the transfer of commensal skin microbiota for AD has been investigated. A small open-label Phase 1/2 study demonstrated that the transfer of commensal
Roseomonas mucosa from healthy individuals to patients with AD is associated with significant decreases in disease severity, topical steroid requirement, and
S. aureus burden [
173]. In Phase 1 RCT, autologous coagulase-negative
Staphylococcus (CoNS) was used to treat
S. aureus in patients with AD [
174]. The results showed that the use of autologous CoNs is associated with a 99.2% reduction in
S. aureus colonization and improved local Eczema Area and Severity Index scores [
174]. However, another Phase 1 RCT transferring the
Staphylococcus hominis A9 (ShA9) isolated from healthy individuals' skin to patients with AD indicated that 1 week of topical ShA9 treatment was not associated with a significant change in the eczema severity compared to the placebo group, whereas a significant decrease in
S. aureus and increased ShA9 DNA were seen [
175]. Further transcriptional analysis indicated that participants whose
S. aureus was not killed by ShA9 remained sensitive to the inhibition of toxin production, suggesting that longer therapy is needed to observe clinical improvement [
175].
3.8 Mechanism and Technology-Guided Potential Therapeutic Modalities in Microbiota Medicine
Host–microbiome interactions are fundamental to both human physiology and pathology. Elucidating the precise mechanisms underlying these interactions provides the cornerstone for developing targeted therapeutic modalities in microbiota medicine. Several recent studies that elucidate the mechanism of involvement of microbiota in disease prognosis, drug responses, and adjunctive therapy have provided important research directions from mechanism to intervention in microbiota medicine.
Bacteria are well-known residents in human tumors, first reported more than 100 years ago. Whether the presence of bacteria is advantageous to the tumors or to the bacteria themselves is still being elucidated [
176]. A recent study has demonstrated that intratumor bacteria are not passive bystanders but active contributors to metastatic spread. For instance, intracellular bacteria carried by circulating tumor cells enhance cellular survival during metastasis by reorganizing the host actin cytoskeleton, thereby increasing resistance to fluid shear stress [
177]. This mechanistic insight informs a novel therapeutic modality: targeting pro-metastatic intratumor bacteria. Developing localized, bacterium-specific interventions (e.g., bacteriophage) could inhibit metastasis while minimizing disruption to the commensal microbiome.
A significant translational challenge in microbiota medicine is identifying functional microbial activities that directly affect the host's drug metabolism. Traditional sequence-based approaches struggle to identify microbial enzymes with functions similar to host enzymes, known as isozymes, owing to a lack of sequence conservation between the microbial and host counterparts [
178]. Wang et al. [
179] created an activity-based screening platform and found that the bacterial isozyme dipeptidyl peptidase 4 (mDPP4), mainly produced by
Bacteroides spp., plays an important role in the various responses to sitagliptin in patients with T2DM. This mechanistic discovery guided the development of a selective small-molecule inhibitor, daurisoline-d4, which specifically targets mDPP4 and improves glucose metabolism in preclinical models [
179]. This work exemplifies a mechanism-guided modality using the precision inhibition of a specific microbial enzyme to enhance drug efficacy.
The mechanistic understanding that commensal bacteria can systemically regulate host immunity has unlocked a powerful therapeutic modality: engineered live biotherapeutics. A recent study has shown that specific gut bacteria, such as
Lactobacillus johnsonii, and their metabolites can enhance the efficacy of cancer immunotherapy by modulating CD8
+ T-cell activity [
180]. This mechanism has inspired the development of microbial adjuvants designed to overcome immunotherapy resistance. Furthermore, the intrinsic tumor-targeting capability of certain commensal strains, like
Lactobacillus plantarum, has been harnessed to create precision drug-delivery systems [
181]. By engineering these bacteria to locally release chemotherapeutic agents, enhanced tumor suppression with reduced systemic toxicity was achieved in animal models [
181]. The translation potential of this modality is substantial, representing a shift from broad ecological modulation towards programmable, mechanism-driven microbial therapeutics.
The development of next-generation living therapeutics is being propelled by a convergence of advanced engineering disciplines. One of its core lies in the application of synthetic biology toolkits, which enable the rational and feasible design of engineered biologics [
182]. A prime example is the creation of sophisticated probiotics and artificial microbial consortia. Furthermore, by integrating metabolic engineering with multi-omics insights, engineered artificial microbial consortia can be precisely tailored to modulate dysbiotic microbiome and address specific disease mechanisms, moving beyond single-strain approaches [
183].
Simultaneously, nanotechnology has emerged as a powerful strategy to overcome fundamental delivery challenges, raising the field of microbiota-based nanotherapeutics. Although predominantly demonstrated in preclinical cancer models, the core strategies are broadly applicable. Research focuses on several key approaches: enhancing chemotherapy or immunotherapy efficacy via nanoparticles co-delivered with live microbes [
181,
184–
186] and enabling novel modalities like nanoparticle-assisted delivery of engineered microbes for photodynamic therapy [
187,
188]. Illustrative preclinical examples highlight the potential of this convergence. In CRC, employing a prebiotic nanoparticle as a carrier for the chemotherapeutic capecitabine (CAP) dramatically improved its tumor inhibition rate from 5.29% to 71.78% [
184]. In another strategy, oral treatment with polyphenol-based supraparticles attached to
E. coli Nissle 1917 in the enteritis mouse model dramatically enhanced bacterial survival rate, and when combined with chemotherapy, yielded a 2.35-fold greater tumor regression than chemotherapy alone [
186]. Importantly, the potential applications of microbiota-based nanotherapeutics extend beyond oncology. Early research indicates promise for managing chronic liver diseases, which are often linked to gut–liver axis dysfunction [
189]. However, significant translational gaps remain. The mechanisms underlying the detoxification of nanomaterials by the gut microbiota, along with their long-term biological impacts, have not been fully explored. Further investigations, such as standardized nanoparticle processing, synthesis, and precise control over properties like shape and size, are critical for clinical advancement [
190].
In parallel, to navigate this complexity and accelerate personalized medicine, artificial intelligence (AI), particularly machine learning, provides indispensable support. These computational tools are essential for analyzing intricate multi-omics datasets, identifying predictive biomarkers, optimizing therapeutic designs, and forecasting individual patient responses to microbiome-targeted interventions [
191,
192]. Despite considerable promise, the clinical translation of AI-driven strategies confronts critical hurdles. The model performance is heavily constrained by the quality, size, and diversity of training data, whereas pronounced interindividual variability of microbiomes leaves substantial challenges to models' generalizability across different populations [
191–
193]. Nevertheless, the convergence of AI with complementary technologies, such as single-cell sequencing and multi-omics platforms, holds significant potential to propel the translation of microbiome research into precise, scalable, and personalized clinical strategies.
3.9 Delivery Routes of Microbiome Modulation
The safety, efficacy, and cost of microbiome modulation depend not only on the therapeutic modality itself but also on the route of administration [
194]. The common routes of microbiome modulation can be divided into three categories, including upper gastrointestinal (GI) tract, mid-gut, and lower GI tract. As the lower GI tract is colonized with the highest microbial numbers [
195], microbiome modulation by delivering microbiota and medications into the lower GI tract has been widely used in dysbiosis-related diseases [
8,
10,
13,
196,
197]. The routes of the lower GI tract commonly include enema, colonoscopy, and colonic transendoscopic enteral tubing (TET). The enema has been used in patients with rCDI [
7] and UC [
12,
13], pediatric patients [
198], and critically ill patients [
199]. The simple and repeatable enema can be considered if no other routes are available, especially for patients with lesions limited to the sigmoid colon and rectum. However, a recent meta-analysis showed that the efficacy of FMT by enema for CDI is inferior to that by colonoscopy [
200]. Although colonoscopy enables examination and biopsy for the whole colon, it can only be used for a single delivery.
Colonic TET is an interventional intestinal therapeutic procedure first reported in 2015 [
201]. Colonic TET facilitates three major applications in clinical practice and research: (1) delivering microbiota and medications into the lower GI tract frequently and timely [
202,
203]; (2) drainage and decompression for colonic perforation [
204] and ileocolic obstruction [
205,
206]; and (3) obtaining gut microbial samples regardless of defecation time [
207]. Several cohort studies have reported the application of colonic TET as a delivery route of multiple FMTs for CDI [
208], IBD [
203,
209,
210], irritable bowel syndrome (IBS) [
211], autism spectrum disorder (ASD) [
212,
213], etc. Colonic TET has also shown its specific advantages for the delivery of fecal microbiota in pediatric patients with a 100% success rate and a 70% parents' preference [
212]. Recently, two case reports reported the application of colonic TET in rescuing endoscopy-associated perforation [
204] and management of intestinal obstruction [
205], respectively. In 2021, Liu et al. first demonstrated the circadian rhythms in the composition and function of the human gut microbiome based on obtaining ileocecal microbiota samples in situ through a colonic TET [
207]. The colonic TET is considered a useful tool for microbiota medicine both in clinical practice and research as it is a two-way route for delivery and suction. Physicians or researchers can deliver the microbiota or medications of microbiome modulation into the gut and obtain specimens back in real time to explore dynamic microbial changes or pharmacomicrobiomics in situ. In addition, colonic TET facilitating multiple delivery of microbiota or other medication is a useful tool for microbiome-mediated immune training. The microbiome plays a critical role in the training and development of major components of the host's innate and adaptive immune system [
214]. Microbiome-mediated immune training is implicated in the progress of microbiome modulation for chronic immune-mediated diseases (e.g., IBD) [
215], which is supported by the efficacy of the step-up FMT strategy in patients with IBD [
210,
216,
217]. The step-up FMT strategy consists of three steps: step one is single FMT, step two is multiple FMTs, and step three is the combination of FMT and standard medications (i.e., steroids and immune agents) [
217]. Liu et al. demonstrated that the factor of multiple courses of FMT is independently associated with the long-term response in patients with UC [
218]. Ding et al. conducted a pooled analysis including two clinical trials on FMT for UC and found the promising efficacy of the combination of FMT and immune agents in patients with UC [
210].
4 Diagnostic Evidence of Microbiota Medicine
Large-scale assessments of the gut microbiome–disease associations by multi-omics technologies have revealed the existence of disease-specific and shared gut microbial signatures [
219–
221], which enable the use of disease-specific gut microbial signatures as biomarkers for disease diagnosis (Figure 2).
4.1 Microbiome-Based Diagnostic Tools for CRC
Numerous studies have demonstrated that gut dysbiosis is typically an early event in colorectal tumorigenesis, and consistent unique patterns by enrichment of some pathogenic bacteria (e.g.,
Fusobacterium nucleatum [
Fn], enterotoxigenic
Bacteroides fragilis, etc.) in CRC are observed. Metagenomic sequencing data from both single-cohort and multi-cohorts have shown the potential of these signatures to discriminate CRC from those without cancers with high accuracy (area under the curve (AUC) > 90%) [
222–
224]. Due to the high cost and complex analysis procedure of metagenomic sequencing, for translational applications in clinical settings, convenient and cost-effective tests (e.g., quantitative PCR (qPCR)) involving only the optimal bacteria are preferable.
Fn is a well-known pathogenic bacterium enriched in the stool and mucosal samples of patients with CRC [
225,
226]. It is also the most reported bacterial marker for discriminating CRC from those without cancer [
227–
230]. In a case-control study, Liang et al. demonstrated that the single bacterial marker
Fn tested by duplex-qPCR can discriminate CRC from healthy controls with an AUC of 0.87 [
227]. Similarly, Wong found that the single bacterial marker
Fn tested by qPCR can achieve an AUC of 0.86 in discriminating CRC from healthy controls [
228]. The diagnostic performance of the single
Fn can be improved to an AUC of 0.95 when combined with the fecal immunochemical test (FIT) [
228]. The
Fn can also be combined with three or four other species to achieve an improved diagnostic accuracy. A bacterial marker panel combining
Fn,
Clostridium hathewayi (
Ch),
Bacteroides clarus (
Bc), and
m7 resulted in a superior AUC of 0.89 and outperformed
Fn alone [
227]. Guo et al. tested the ratio of
Fn to
Faecalibacterium prausnitzii (
Fp) and
Bifidobacterium (
Bb) by qPCR, yielding an AUC of 0.94 for CRC diagnosis [
231]. The enrichment of
Fn in the precancerous lesions of CRC (i.e., adenoma) has also been observed [
228,
230,
232], whereas single
Fn can yield an AUC of 0.57–0.62 for discriminating colorectal adenoma from healthy controls [
228,
230], which is reasonable as
Fn mainly works for discriminating CRC. In a case-control study, Liang et al. found a novel bacterial gene marker from
Lachnoclostridium named
m3 [
230]. The single bacterial marker
m3 tested by qPCR showed improved diagnostic performance in detecting colorectal adenoma compared to that of
Fn (AUC being 0.68 vs. 0.62) [
230]. In addition, the combination of
Fn,
m3,
Ch,and
Bc as a panel showed promising diagnostic performance in the detection of CRC (AUC of 0.91) and adenoma (AUC of 0.66) [
230]. The combination of the panel of four bacterial markers and FIT achieved a sensitivity of 93.8% and 47.1% for CRC and adenoma, respectively, which was superior to the widely used stool test FIT, which showed 67.3% sensitivity for CRC and 23.3% sensitivity for advanced precancerous lesions [
230]. The superior sensitivity of the bacterial marker panel to FIT indicates its potential as a noninvasive biomarker for CRC diagnosis and screening [
233]. Recently, in a prospective multicenter cohort study, individual bacterial gene marker
m3 tested by qPCR could significantly discriminate CRC and advanced adenoma (AA) from normal controls, with an AUC of 0.701 and 0.604, respectively [
234]. In addition to the diagnostic perspective, in a case-control study, the combination of three bacterial markers (
Fn,
m3,and
Ch) tested by qPCR has shown high accuracy for predicting adenoma recurrence, yielding an AUC of 0.95, with 90% of sensitivity and 87% of specificity [
232]. The bacterial marker panel has been translated as a commercial product named M3CRC test (G-niib, Hong Kong, China) for the diagnosis and surveillance of colorectal neoplasia, which is available in Hong Kong, China. Preliminary data from a prospective, multicenter study showed that M3CRC is more sensitive than FIT in detecting colorectal advanced neoplasia (CRC and AA) [
235]. On the other hand, a comparative cost-effectiveness modeling study conducted economic evaluations of CRC screening based on FIT, M3CRC test, and colonoscopy [
236]. Although FIT was identified as the most cost-effective strategy in the prevention and management of CRC with the lowest incremental cost-effectiveness ratio (ICER), the utilization of M3CRC biomarkers was reported to result in smaller total loss of cancer-related life-years, a higher number and proportion of CRC cases prevented, and more life-years saved compared to FIT [
236]. Cheaper total costs per life-year saved and higher compliance rates were achieved by the M3CRC test compared to the other two methods, demonstrating its cost-effectiveness as a primary screening test [
236]. Although M3CRC shows potential in terms of diagnostic performance and cost-effectiveness, it still faces challenges before entering clinical applications, such as population suitability, stronger evidence of cost-effectiveness analysis, and policy approvals from other regions.
4.2 Microbiome-Based Diagnostic Tools for Other Diseases
Emerging sequencing data have also revealed the disease-specific signatures in IBD [
237–
239], whereas the use of microbiome markers for the diagnosis of IBD is still in the exploratory stage. Kang et al. profiled the microbiota signatures in patients with UC or Crohn's disease (CD) and used a machine-learning model, achieving an AUC of 0.97 among UC and healthy individuals and an AUC of 0.92 among UC and CD patients [
238]. Despite the high accuracy achieved, it might be difficult to use the machine learning of sequencing data in clinical practice. For translational applications, the qPCR approach has also been used in the investigation of bacterial markers for IBD. Zheng et al. developed a multiplex droplet digital PCR (ddPCR) test targeting selected IBD-associated bacterial species, which showed better performance than fecal calprotectin in discriminating IBD from controls [
240]. However, the evidence of microbial biomarkers in diagnosing IBD is much less than that for CRC, and no consistent disease-specific microbial biomarkers have been investigated in clinical trials [
241]. The complex pathogenesis of IBD and the ambiguous role of gut microbiome might be the explanation [
242].
The validated relevance between ASD and microbiome in pre-clinical studies indicates its potential role as a biomarker in ASD diagnosis. Alterations in gut microbiome have been demonstrated as a potential detection to predict ASD progress [
243], such as
Parasutterella and
Alloprevotella [
244]. In a recent correlation analysis based on 16S rRNA gene sequencing data using recursive ensemble feature selection (REFS), 26 specific intestinal bacterial taxa were identified for distinguishing ASD patients from controls with a high AUC of 0.816, and the cross-validation in two independent cohorts resulted in an AUC of 0.748 and 0.74 [
245]. Another study identified a fecal microbial panel including five bacterial taxa, two viral metagenome-assembled genomes (MAGs), and 43 bacterial MAGs with excellent discrimination performance in the discovery cohort (AUC of 0.886) and independent validation cohort (AUC of 0.734) [
246]. Besides, another study identified a panel of bacterial genomic structural variations (SVs) consisting of 11 variable SVs (v-SVs), 5 deletion SVs (d-SVs), and 9 bacterial species, achieving an AUC of 0.791 (v-SVs), 0.752 (d-SVs), and 0.723 (bacteria) in distinguishing ASD children from neurotypical children, respectively. Compared with panels using pure SVs or bacteria alone, the mixture integrating both SVs and bacterial species demonstrated improved diagnostic performance, with AUCs of 0.858 and 0.811 in the discovery and validation cohorts, respectively [
247]. An integrative multi-omics analysis uncovered the mechanistic interactions between gut microbiota and the ASD process (e.g., bacterial metaproteins, associated metabolites, and host proteome), supporting its biomarker role in early diagnosis [
248]. Meanwhile, the disparities of oral microbiota were investigated to identify the potential biomarkers of ASD early detection based on 16S rRNA sequencing data. A total of 11 discriminatory species were validated for the ASD diagnostic capability with an AUC of 0.937, sensitivity of 0.778, and specificity of 0.857, and the cross-validation achieved the accuracy of 0.813 [
249]. Recently, Su et al. conducted integrated analyses on metagenomic sequencing data from 1627 samples and identified 14 archaea, 51 bacteria, 7 fungi, 18 viruses, 27 microbial genes, and 12 metabolic pathways altered in children with ASD. The combination of multikingdom and functional markers achieved a high diagnostic accuracy with an AUC of 0.91 for distinguishing ASD [
250]. Its translated result, "AI-Powered Multikingdom Microbial Biomarkers Technology" MSX Metagenie for ASD detection in children, received Breakthrough Device Designation from the FDA, and a pilot project in Hong Kong, China was scheduled in January 2026. Another observational research GEMMA (NCT04271774) focused on standardized sampling, metabolomics, and multi-center validation cohorts, but lacked broadly validated, prospective diagnostic tests for clinical use. Compared to the current diagnostic criteria of ASD complicated by multifactorial interference (e.g., the subjectivity and susceptibility of behavioral assessment, heterogeneous phenotypes, and co-occurring disorders [
251]), microbiome-based diagnosis offers a promising noninvasive tool for the objective and quantifiable early stage detection.
Early diagnosis of esophageal adenocarcinoma (EAC) has also been described as one application of microbiome diagnostic biomarkers. Combining machine learning, a novel diagnostic panel based on circulating microbial DNA achieved an AUC of 0.93 in the training cohort and demonstrated robustness in independent testing cohorts (AUC of 0.91 and 0.88 for EAC and high-grade dysplasia, respectively) [
252].
Although microbiome-based diagnostic tools hold promises for early detection and personalized medicine, their translation into routine clinical practice faces several substantial hurdles. First, the standardization of sample collection and processing remains a critical challenge, as variations in collection methods, storage conditions, and DNA/RNA extraction protocols can drastically alter microbial profiles and compromise reproducibility across different centers [
253,
254]. Second, the complexity of data analysis presents a barrier: interpreting high-dimensional, multi-omics data require specialized bioinformatics expertise, and the lack of universal analytical pipelines makes it difficult to compare results or establish definitive diagnostic thresholds [
255–
257]. Most importantly, robust clinical validation of diagnostic accuracy is often lacking. Many proposed microbial biomarkers originate from exploratory, case-control studies and have not been prospectively validated in large, diverse cohorts. Overcoming these challenges will require concerted efforts to establish international standards, develop user-friendly analytical platforms, and conduct rigorous, multi-center clinical trials to move biomarkers from promising associations to validated diagnostic tools.
5 Framework, Meaning, and Challenges of Microbiota Medicine as a Discipline
Over the past few decades, microbiota medicine has accumulated evidence that breaks traditional disciplinary boundaries. Microbiota medicine was established as a discipline within clinical medicine in 2023. This development of microbiota medicine stemmed from four key favorable conditions [
5]. First, a series of concepts, including metagenomics, metabolomics, viromics, and phageomics, has been widely used in life science research. Second, related conceptual networks have emerged from these concepts to facilitate understanding of microbiota-based prevention, diagnosis, and treatment, as well as to characterize specific physiological axes, such as the gut–brain, gut–liver, and gut–lung axes. Third, microbiota-based knowledge and concepts can be verified by clinical practice, such as the thousands of years of continued application of FMT, the great changes in the spectrum of human disease in recent decades, and the health problems in the post-antibiotic era. Fourth, specific technologies have been developed for research, education, and clinical application in microbiota medicine to promote the advancement of clinical medicine, such as WMT [
30], repeated microbiota transplantation via colonic TET [
258], spore-based microbiota consortium therapeutics [
46], bacteriophage consortia therapy [
63], and dietary fiber treatments [
117].
Microbiota medicine is defined as a branch of clinical medicine that investigates the fundamental theories and diagnostic/therapeutic technologies regarding microbiota–host interactions, aiming to facilitate disease diagnosis, treatment, and prevention, as well as to advance clinical medical education[
5]. The subdisciplines of microbiota medicine include basic microbiota technology, clinical microbiota treatment technology, and microbiota medicine management (Figure 3). The main task of basic microbiota technology is to carry out microbiota laboratory technical services, research, and education around clinical needs, such as donor recruitment, microbiota preparation, component analysis, technical quality control, safety evaluation, microbiota diagnosis, engineering technology, and pathophysiological mechanisms of dysbiosis-related diseases [
5]. The main task of clinical microbiota treatment technology is to carry out microbiota treatment services, research, and education directly for patients, such as decision-making, endoscopic intervention for microbiota-based diagnosis and treatment, and microbial community component treatment. The main task of microbiota medicine management is to carry out services, research, and education on healthcare policies, professional talent training, and cost-effectiveness analysis of microbiome-based diagnosis and treatment technologies [
5].
The interdisciplinary nature of microbiota medicine enables multi-dimensional research and clinical practice, covering fundamental host–microbiome interactions, microbiome-based diagnostics, therapeutic technologies (e.g., WMT, selected microbiota transplantation [SMT], and bacteriophage therapy), multi-system disease management, human microbiota preservation, lifelong nutritional strategies, antimicrobial stewardship, microbiome–immune and microbiome–tumor interactions, as well as healthcare policy and education. The development of transfusion medicine serves as a fitting reference for this emerging field, as both share a similar trajectory. Transfusion medicine evolved from a basic technique into an independent clinical discipline through key technological advances, and FMT, the core technology of microbiota medicine, is following a parallel course, with foundational milestones such as the establishment of national technical standards for washed microbiota preparation providing the necessary groundwork for its recognition as an independent discipline. [
259].
With the development of microbiome technologies, researchers should take more factors into account because microbiome-based diagnosis and treatment technologies, like technologies in other fields, are susceptible to distortion, misapplication, and methodological inconsistencies during their development, thereby hindering the progress of microbiota medicine [
5]. On the one hand, given the profit-driven nature of biotechnological innovation and the entrenched interests of industry stakeholders, unregulated commercialization of microbiota-based diagnostics and therapeutics in competitive markets risks distorting technological progress. Such misaligned incentives not only undermine scientific integrity but also invite punitive regulatory interventions. On the other hand, the translation of microbiome technologies from bench-side hype to widespread clinical adoption often proceeds without adequate theoretical grounding, robust technological iteration, or supportive regulatory frameworks. This evidence-deficit gap fosters aberrant developmental trajectories that diverge from—and sometimes actively contradict—genuine clinical needs. Fortunately, owing to its interdisciplinary nature, microbiota medicine holds substantial importance for the advancement of both technology and medicine. The development of microbiota disciplines is a strategic investment in the development of new technologies that emerge in an endless stream and form a technological ecology. Driven by the fundamental human impulse for discovery, an expanding community of physicians, scientists, and even investigators in extreme environments, from aerospace to deep-earth research, continue to generate innovations that advance both technology and medicine. These converging efforts ultimately underscore a unifying insight: the gut microbiome stands at the center of microbiota medicine.
While establishing microbiota medicine as a discipline was illustrated in China, its establishment as a global discipline must adapt to different healthcare systems. In Western healthcare systems marked by entrenched subspecialization, the principal challenge lies in bridging siloed disciplines—a fragmentation increasingly untenable as antimicrobial resistance escalates, underscoring the imperative for microbiome-integrated therapeutic strategies. A practical first step could be forming interdisciplinary teams or conducting shared clinical consultations in which microbiota-focused clinicians and scientists collaborate closely with established departments. This approach is especially useful in several key specialties, such as gastroenterology, where microbiome research is already helping us better understand and treat various gut disorders (e.g., IBS, IBD, etc.) [
12,
13,
260,
261]; infectious diseases, where it offers new ways to tackle antibiotic resistance [
262]; oncology, where microbiome modulation may improve cancer immunotherapy and reduce side effects [
21,
263]; and endocrinology, where it provides a new perspective on metabolic diseases such as diabetes [
17] and obesity [
264]. Sustainable integration will depend not only on developing standardized diagnostic protocols and evidence-based therapeutic guidelines recognized across specialties but also on advancing targeted interventions, such as next-generation antimicrobials and phage therapy, to address the dual challenge of drug resistance and microbiome disruption. Furthermore, dedicated training pathways must be established to equip future practitioners with both specialty-specific knowledge and system-level expertise in microbiome science.
5.1 Research Standardization Facilitating Clinical Translation
Regarding the complexity of microbiota, limited pre-clinical models and knowledge, and absent regulations, the clinical translation of microbiome research is obstructed due to the challenges of producing reliable, reproducible, and comparable results. The growing demands of translating microbiome-based tools into clinical diagnosis and therapeutics raised an urgent requirement for standardized guidelines or recommendations supporting researchers and clinicians to preclude practical variations for further clinical translation and regulatory framework establishment (Table 3).
In 2015, Sinha et al. initiated the Microbiome Quality Control (MBQC) project to improve the meaningfulness of comparing results in independent microbiome studies by identifying variation sources and magnitudes. Their work established baselines for variation quantification and assessment frameworks for control strategies [
265]. Another project for standardization is Human Microbiome Action (2021–2024), an European Union (EU)-funded coordination focusing on improving the coherence and harmony in microbiome studies for researchers, public health, and industry. After the project completion, the European Microbiome Centers Consortium (EMCC) was created as an institutional network, facilitating clinical translation, healthcare, and regulations of microbiome research. Other recent projects mostly concern the consistency of more detailed practical guidelines. Strengthening The Organization and Reporting of Microbiome Studies (STORMS) provided a rigorous, transparent, and updated checklist supporting the clear, organized, and efficient study description, peer review, and interpretation [
270]. This checklist has been applied in some observational [
274] and analysis [
275] studies. In 2024, Zhang et al. initiated a project aiming to develop a preferred reporting items for the microbiotherapy (PRIM) checklist for oncology studies, which identified that only 39.3% of oncology studies met all reporting criteria, with culture-based microbiotherapy outperforming nonculture-based studies. PRIM 2024 consisted of 10 statements and 18 points to enhance the consistent reporting of microbiotherapy in clinical research, improving the evaluation and implementation of findings [
271]. Another international consensus statement in 2025 developed comprehensive guidelines covering ethical, organizational, and technical recommendations for research, commercialization, and clinical implementation of microbiome testing [
272]. Meanwhile, the International Human Microbiome Standards (IHMS) coordinated the standardization of operating, sequencing, and analysis procedures and protocols to optimize data quality and comparability [
258]. Similar to EMCC in Europe, the Clinical-Based Human Microbiome Research and Development Project (cHMP) in 2025 is a more regional guideline in the Republic of Korea, underscoring the methodology of standardization to improve the integrity, fidelity, and reproducibility of the results for potential applications [
273]. The 2025 CHINAGUT Conference produced two guideline documents. Wang et al. provided 30 scientific recommendations tailored to the regulatory and clinical landscape of probiotic science, the food industry, LBPs, and FMT in China [
276]. Zhang et al. established standardized principles and practice guidelines for FMT and LBP implementation, organized into 15 key statements from a more international perspective [
277]. These statements proposed integrating microbiota medicine into the education system and promoting multidisciplinary collaboration for managing dysbiosis‑related diseases [
277]. In summary, these recent consensuses provide relatively complete frameworks for governing the trial protocol for future research from the pre-clinical stage to the interventional trial, whereas other guidelines underpin more detailed procedures, covering laboratory protocols (e.g., EMCC and IHMS), data analysis (e.g., IHMS and cHMP), and reporting (e.g., STORMS and cHMP) [
270–
273]. The application of technical and reporting standard operating procedures (SOPs) within clinical standards serves as a practical framework to overcome some existing obstacles.
Despite these advancements in standardization, there are some scientific and practical hurdles remaining unresolved in clinical translation. One of the main restrictions is inter- and intra-individual variability. Interindividual variability driven by diet, lifestyle, age, geography, genetics, and environmental exposure remains a major barrier to microbiome composition [
269,
278–
280]. Meanwhile, high day-to-day microbiome variation is reported within individuals, but this intra-individual variation is much smaller than the dissimilarity between individuals [
281]. Another critical gap is the limited cross-cohort generalization introduced by technical biases [
282]. Although the standardization projects provide some practical guidelines, all the suggestions are intrinsically conceptual or technical and cannot be applied to a GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach [
272]. Consensus-based rather than evidence-grade methodologies also limit the impact of these guidelines. Additionally, due to the regional limitation of these consensuses, establishing globally robust reliability and repeatability remains a considerable undertaking. CHINAGUT recommendations, while regionally impactful and comprehensive, remain predominantly confined to specialized academic centers in China [
276,
277]. The absence of long-term data on safety outcomes is also one of the key concerns of clinical translation, for which the longitudinal studies are advocated for priority in the consensus statement initiated by Human Microbiome Action [
269]. Notwithstanding persistent challenges, the establishment and widespread implementation of standardization frameworks provide an essential foundation for advancing the successful clinical translation of microbiome research.
5.2 Integrative Strategies for Personalized Microbiota Modulation
The advancement of microbiota medicine is intrinsically aligned with the paradigm of personalized or precision medicine. Moving beyond generic, one-size-fits-all interventions, the field is progressively focusing on tailoring therapeutic strategies to the individual patient's unique microbial and host profile. This personalized approach integrates multi-dimensional data: baseline microbiota composition and functional analysis (e.g., presence/absence of key taxa and metabolic pathway activity) identifies specific dysbiosis patterns or therapeutic targets; host genetic factors (e.g., immune-related gene variants) can predict inflammatory responses or adhesion receptor availability for probiotics; and clinical phenotypes or metabolomic profiles provide context on disease severity, metabolic status, and actual functional output of the host–microbiome interaction. By synthesizing this information, clinicians and researchers can rationally design interventions to optimize efficacy and safety, such as selecting specific probiotic strains, prebiotics, or dietary regimens to augment deficient functions, or choosing targeted antimicrobials to suppress pathobionts. To advance personalized microbiome modulation, we need integrated diagnostic platforms and decision-support algorithms that translate complex personal data into dynamic, personalized treatment plans. The goal thus shifts from generic microbiome manipulation towards restoring an individual's unique ecological balance for sustained health.
6 Future Perspective
The translation of microbiome insights into clinical practice and the establishment of microbiota medicine as a formal discipline are contingent upon actively solving several fundamental challenges. The field must move beyond correlation to establish causality, ensuring that microbial biomarkers are reproducible across diverse populations to create reliable diagnostics. A central puzzle remains the stark efficacy gap between the consistent efficacy of FMT for CDI and its variable outcomes in other conditions. Furthermore, next-generation therapeutics such as engineered live biotherapeutics and phages face formidable regulatory and safety hurdles. In addition to the diagnostic and therapeutic applications, accumulating evidence indicates that microbiota conveys prognostic significance in various cancers, although these studies remain investigational and await further validation [
283–
285].
In this context, the integration of AI and machine learning can be crucial to the efficient interpretation of big datasets to discover key bacteria, metabolites, and other bacterial derivatives [
133,
286,
287], thereby advancing precision medicine. Facing various dazzling advancements in therapeutic modalities of microbiota medicine, physicians, researchers, biomedical companies, and patients have their own responsibilities to find their way forward. For physicians and researchers, microbiome modulation therapeutics targeting microbiota-related physiological function pathways rather than the general composition might be easier to succeed. High-quality trials investigating novel or improved microbiome-based therapeutics, technologies, and diagnostic tools are warranted. Biomedical companies play a dual role in microbiota medicine research. It can provide sponsor support for research and promote the implementation of translational research, but it is also associated with market-driven, selective results reporting. Patients can be exposed to a variety of microbiome modulation plans from doctors or commercial advertisements. Education will help patients understand microbiota medicine and will affect their judgment and acceptance of microbiome modulation therapeutics [
288]. The establishment of microbiota medicine as a discipline in clinical medicine incorporates the fundamental concepts and technologies of microbiome and medicine within the framework of disease diagnosis, treatment, and prevention, while also emphasizing sustainability principles. The increasing need for effective disease management acts as a driving force for the development of microbiota medicine, with education playing a crucial role in ensuring its continuous development. The time is ripe to officially recognize microbiota medicine as a new branch within modern clinical medicine and to improve its organizational framework following medical standards, thereby promoting the structured evolution of its principles, methodologies, and educational endeavors. Governmental entities and academic establishments (such as association of microbiota medicine) should prioritize the development of microbiota medicine, as this initiative will enhance the United Nations' sustainable development goals.
© 2026 The Author(s). Microbiota Medicine Research published by John Wiley & Sons Australia, Ltd on behalf of Higher Education Press.
PDF
(2280KB)
