Pharmacomicrobiomics in precision cancer therapy: bench to bedside

The burgeoning field of pharmacomicrobiomics offers promising insights into the intricate interplay between the microbiome and cancer, shaping responses to diverse treatment modalities. This review aims to analyze the molecular mechanisms underlying interactions between distinct microbiota types and cancer, as well as their influence on treatment outcomes. We explore how the microbiome impacts antitumor immunity, and response to chemotherapy, immunotherapy, and radiation therapy, unveiling its multifaceted roles in cancer progression and therapy resistance. Moreover, we discuss the challenges hindering the development of microbiome-based interventions in cancer therapy, including standardization, validation, and clinical translation. By synthesizing clinical evidence, we underscore the transformative potential of harnessing pharmacomicrobiomics in guiding cancer treatment decisions, paving the way for improved patient outcomes in clinical practice.


Introduction
Precision medicine, or personalized therapy, is a rapidly evolving trend in modern healthcare, tailoring treatment to individual patients by selecting the right drug, at the right dose and at the right time based on their specific cellular, molecular, and genetic characteristics.This approach optimizes treatment effectiveness while minimizing the risk of adverse drug reactions (ADRs).Among therapeutic fields, cancer treatment has seen particularly swift advancements in precision medicine due to its typical characteristics such as the highly heterogeneous nature of tumors, substantial variability in drug response among individuals, and the significant side effects associated with cancer therapies (1).Additionally, the high costs of treatment and the invaluable cost of life opportunities necessitate precise treatment protocols without room for trial and error.Biomarkers used to predict treatment response and disease prognosis not only aid in selecting appropriate drugs for patients but also drive innovation in drug development, reducing time and costs for clinical trials and substantially increasing success rates (2).
To date, the most extensively utilized biomarker in personalized cancer therapy is the somatic mutations found in tumors.These mutations assist in identifying patients who are likely to respond favorably to targeted therapy and immunotherapy.Furthermore, the distinctive germline mutations present in individual patients significantly influence the pharmacokinetics and pharmacodynamics of chemotherapy, enabling the prediction of those at risk of experiencing severe ADRs (3,4).As a result, pharmacogenomics has emerged as a rapidly advancing field, essential for integrating personalized cancer therapy into clinical practice.However, clinical studies and trials have indicated that pharmacogenomic biomarkers only partially account for the inter-individual variation in drug response (3,5).Therefore, to fully leverage the benefits of personalized therapy for patients, additional research is necessary to investigate other types of biomarkers that can help elucidate the differences among individual patients with impacts on treatment response.
Although the role of human microbiome in health and various diseases, including cancer, has been known for a long time, the concept of Pharmacomicrobiomics only emerged around 2010 as an extension of Pharmacogenomics (6).The human microbiome refers to the community of microorganisms residing in specific body environments, with the gut microbiome being the first and most extensively studied (7).However, nowadays, increasing attention is being paid to the important role of microbiota in other body environments such as the skin microbiome, vaginal microbiome … and even more recently, microbiota discovered within the microenvironments of tumors (6).Pharmacomicrobiomics is a field that investigates the interaction between individual's microbiomes and drug response to understand how the composition and activity of these microorganisms influence the pharmacokinetics and pharmacodynamics of various medications (8 ).Pharmacomicrobiomics explores how differences in the microbiome among individuals can affect drug metabolism, efficacy, and toxicity, ultimately influencing an individual's response to treatment.This field has implications for personalized medicine, as it may help optimize drug therapy by considering an individual's microbiome profile.
There have been numerous studies on the role of various human microbiomes in tumorigenesis and progression across different cancer types (9)(10)(11)(12)(13)(14).However, only in recent years have scientists begun to explore the influence of the microbiome on cancer treatment response (15).With the increasing demand for the rapid adoption of personalized medicine in cancer therapy to prolong survival and improve the quality of life of patients, pharmacomicrobiomics may contribute vital biomarkers to enhance the translation of precision medicine into clinical practice.This review analyzes the molecular mechanisms of interaction between different microbiome types and tumors, as well as their response to various cancer treatment modalities.It also analyzes the challenges to consider in developing this application direction, proposes potential solutions to benefit patients, and ultimately provides clinical evidence for the advancement of pharmacomicrobiomics in practice.2 The role of microbiome in cancer

The microbiota dysbiosis in cancer development and progression
There is compelling evidence indicating a correlation between various types of human microbiomes and different types of cancer (16).Among these, the gut microbiome has been the first and most extensively studied.It is well-documented that the gut microbiome influences systemic metabolic balance and immune function, thus playing a significant role in the tumorigenesis and progression of various cancer types, from gastrointestinal cancers to breast or lung cancer (Table 1).Additionally, changes in the bacterial ecosystem on the skin, which is the body's largest organ, also have implications for breast health and the risk of developing breast cancer (10).Reduced alpha diversity within the oral microbiome could potentially correlate with an elevated likelihood of developing lung cancer, offering a potential indicator for predicting lung cancer risk (11).In particular, recent discoveries regarding the existence of intratumoral microbiota also underscore their significant influence on tumor development, invasion, and metastasis (12,56).
Numerous studies have revealed that tumors can interact with various components within the body as well as metabolisms (57), such as platelets (58), circulating tumor cells (CTCs) (59), exosomes (60), and modify these components to serve the tumor's growth.Similarly, an important mechanism explaining the causal relationship between the human microbiome and cancer development is the interplay between microbiota and tumor cells, leading to significant alterations in the composition and function of microbiomes in cancer patients.The dysbiosis in various microbiota has been observed in cancer patients with changed variability of ecosystems compared to healthy people.Fusobacterium nucleatum and Parvimonas micra were found to be more prevalent, while Clostridia and Bacteroidia decreased in the gut of colorectal cancer (CRC) patients (61).Additionally, Lactococcus and Fusobacteria exhibited higher abundance, whereas Pseudomonas and Escherichia-Shigella were downregulated in CRC tissues compared to adjacent non-cancerous ones (62, 63).Likewise, the gut microbiota of cervical cancer patients exhibited notable variations in the abundance of seven genera, namely Escherichia-Shigella, Roseburia, Succinivibrio, Lachnoclostridium, Lachnospiraceae_UCG-004, Dorea, and Pseudomonas (30).
Reprogrammed ecosystems were also identified in cancer patients beyond the gastrointestinal tract, involving other different microbiota.Cervical cancer exhibits the greatest diversity in vaginal microbiota, with the enrichment of Ralstonia,Lactobacillus, Gardnerella, Sneathia and Prevotella.Similarly, Gardnerella, Prevotella, and Sneathia exhibit higher prevalence within the HPV-positive cervical intraepithelial neoplasia (CIN) group.In Metabolic reprogramming: The gut microbiome alterations observed in individuals with CRC are linked to changes in the serum metabolome. ( CRC Human cell and mouse model. The capability of pks+ E. coli to create colibactin (DNA adducts) in mammalian cells and mice provides further evidence supporting colibactin's role in cancer development or progression.
Genome instability:DNA double-strand breaks (DSBs) by producing colibactin, a small-molecule genotoxin that causes alkylation of DNA through an unusual electrophilic cyclopropane mechanism.
LC LC patients and healthy volunteers.
The abundance of 232 operational taxonomic units (OTUs) showed significant differences between the Healthy control and Lung cancer groups.

LC
Early-stage LC patients and healthy individuals.
Species more abundant in the cancer group were primarily from the Bacteroides and Proteobacteria phyla.Conversely, species exhibiting a significant decrease in the cancer group were mainly from the Firmicutes and Actinobacteria phyla.

Metabolic reprogramming:
The cancer group exhibited enrichment in pathways associated with cellular antigens, steroid biosynthesis, ubiquitin system, transcription-related proteins, bile secretion, and fatty acid elongation in mitochondria.On the other hand, pathways related to bacterial motility proteins, bacterial chemotaxis, flavone and flavonol biosynthesis, apoptosis, and G protein-coupled receptors showed a decrease in the cancer group. ( LC LC patients and healthy controls.
Healthy controls exhibited a higher abundance of the bacterial phylum Actinobacteria and the genus Bifidobacterium, whereas patients with LC demonstrated elevated levels of Enterococcus.
A notable decline in the normal function of the gut microbiome was observed in LC patients.

Metabolic reprogramming:
There was a significant decline in the functional abundance spectrum, including 24 gut microbiota metabolic pathways in LC patients.This decline included a reduction of more than 80% in the expression of functional proteins involved in chromatin structure and dynamics, as well as RNA processing and modification.Conversely, there was an increase of over 10% in protein expression levels related to extracellular structures in the metabolic functions associated with LC patients.
LC LC patients and healthy controls.
The LC group had elevated levels of Bacteroides, Veillonella, and Fusobacterium, but lower levels of Escherichia-Shigella, Kluyvera, Fecalibacterium, Enterobacter, and Dialister compared to the healthy control group.In patients with cervical cancer (CC), there was a notably higher proportion of the Proteobacteria phylum.Seven genera exhibited significant differences in relative abundance between CC and controls, including Escherichia-Shigella, Roseburia, Pseudomonas, Lachnoclostridium, Lachnospiraceae_UCG-004, Dorea, and Succinivibrio.

Inflamation:
Bacterial microbiome-induced tumorigenesis is believed to be associated with an inflammatory response mediated by MAMP and their activation of PRRs.This activation induces the transcription of antibacterial proteins through an intracellular signaling cascade in the host epithelial cell.Additionally, pro-inflammatory cytokines such as IL-17, TNF-a, and IFN-g were upregulated.Metabolic reprogramming: The gut microbiota play a role in modulating the enterohepatic circulation of estrogens, which circulate to exert effects on target organs like the breast and uterine cervix.In prostate cancer cases, a higher relative abundance of Bacteroides massiliensis was observed compared to controls.Faecalibacterium prausnitzii and Eubacterium rectalie had a higher relative abundance among controls.

Metabolic reprogramming:
Faecalibacterium prausnitzii plays a crucial role in the metabolism of acetic acid, which can subsequently be converted into butyric acid.Butyric acid, the most abundant short-chain fatty acid (SCFA) in the colon, is recognized for its anti-tumor activities, primarily characterized by inducing apoptosis and diminishing proliferation.Additionally, a deficiency of F. prausnitzii has been observed in patients with Crohn's disease. ( LiC NAFLD patients and healthy subjects. In the gut microbiota of healthy subjects, five genera, including Alistipes and Prevotella, were significantly more abundant compared to Non-alcoholic fatty liver disease (NAFLD) patients.Conversely, NAFLD patients showed increased levels of Escherichia, Anaerobacter, Lactobacillus, and Streptococcus in their gut microbiota compared to healthy subjects.

Inflamation:
The dysbiosis of the gut microbiota, along with gut microbiota-mediated inflammation of the intestinal mucosa, was evident in NAFLD patients.This inflammatory response was characterized by decreased numbers of CD4+ and CD8+ T lymphocytes and increased levels of TNF-a, IL-6, and IFN-g in the NAFLD group compared to the healthy group.These factors, along with the related impairment in mucosal immune function, play a significant role in the pathogenesis of NAFLD. (32)

Melanoma
Patients with melanoma and healthy volunteers.
Patients diagnosed with melanoma exhibited a higher relative abundance of Fusobacterium compared to the control group.
In early-stage melanoma, there was an increased alpha diversity and a higher abundance of the genus Roseburia compared to the control group.
Inflamation: Regulating the immune system.
( In the faecal microbiota of MeLiM piglets, Bacteroides, Fusobacterium, and Escherichia-Shigella were found to be associated.
membrane transport pathways, potentially contributing to increased intestinal permeability and alterations in the intestinal mucosal barrier.

LC LUAD and LUSC patients.
There were significant differences in gene expression and microbial abundance associated with recurrence and metastasis between LUAD and LUSC.In LUSC, the bacterial community associated with recurrence and metastasis (RM) exhibited lower richness compared to non-RM cases.There were significant correlations between host genes and tissue microbes in LUSC, while such host-tissue microbe interactions were rare in LUAD.

Metabolic reprogramming:
A set of pathways was identified that showed an association with specific tissue microbiome composition in LUSC.These pathways primarily involved various metabolic and metabolism-related enzymes, some of which have been previously implicated in LC, including drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450, and steroid hormone biosynthesis. ( PaC Mouse model and cell lines.
Tumor microbiome was abundant in anaerobic Bacteroidales in hypoxic and immunosuppressive tumors.

Sustaining proliferative signaling:
The homotrimeric form of Collagen Type 1 (Col1 a1/a1/a1) derived from pancreatic cancer cells has been demonstrated to facilitate oncogenic signaling via DDR1 and integrin a3b1.This process results in an increased abundance of Bacteroidales within the intratumoral microbiome. ( CRC Tissue from the tumors of CRC patients.
In CRC tumors, Fusobacterium and Bacteroides emerge as the most dominant genera.

Invasion and metastasis: CRC cells infected with Fusobacterium nucleatum
showcase heightened invasiveness into their surrounding environment.These infected cells attract myeloid cells to the bacterial niches, accelerating migration rates significantly.This process is mediated through various signaling pathways crucial for cancer metastasis, including extracellular matrix remodeling and modulation of cell adhesion and migration via ERK1 and ERK2.
(48) CRC CRC cell lines.CRC cell lines infected with Fusobacterium nucleatum formed larger tumors, more rapidly in nude mice compared to uninfected cells.
Inflammation: Several inflammatory factors, including interleukin 17F, interleukin 21, interleukin 22, and MIP3A, were significantly increased in the serum of mice given Fusobacterium nucleatum.Invasion and metastasis: Fusobacterium nucleatum activates Toll-like receptor 4 signaling to MYD88, leading to activation of the nuclear factor-kB and increased expression of miR21; this miRNA reduces levels of the RAS GTPase RASA1.Patients with both high amount of tissue F.nucleatum DNA and miR21 demonstrated a higher risk for poor outcomes.
CRC, GC CRC and GC patients.
In CRC, Fusobacterium, Bacteroides, and Ruminococcus were found to be highly enriched.
Genome instability: DNA repair-associated microbiota were observed in CRC, including mismatch repair, DNA repair, and recombination proteins and DNA replication proteins.

Metabolic reprogramming:
The microbiotas in GC were associated with central carbon and amino acid metabolism pathways, such as glyoxylate and dicarboxylate metabolism, and glycine/serine/ threonine metabolism.
GC GC patients.The abundance of Helicobacter was observed to be increased in non-tumor tissues, while the abundance of Lactobacillus, Streptococcus, Bacteroides, Prevotella, and six additional genera was increased in tumor tissues.

Metabolic reprogramming:
The differences in metabolome profiles between GC tumor and matched non-tumor tissues may be attributed, in part, to the collective activities of Helicobacter, Lactobacillus, and other bacteria.These activities are believed to influence GC carcinogenesis and progression.Frontiers in Immunology frontiersin.orgcontrast, Gardnerella and Prevotella are more prevalent in the HPVpositive non-CIN group (38).
The significance of microbiota variation in tumorigenesis is evident when comparing the microbiome across healthy tissue, precancerous lesions, and malignant tissues.A transitional microbial dysbiosis is observed from healthy skin to pre-malignant actinic keratosis (AK) and further to squamous cell carcinoma (SCC), marked by an elevated presence of the pathobiont Staphylococcus aureus, surpassing the commensal Cutibacterium acnes in SCC (44).In a recent study, Bacteroides, Trueperella, Staphylococcus, Streptococcus, and Fusobacterium were found to be notably more abundant in the microbiome of melanoma tissue, while Corynebacterium 1, Clostridium sensu stricto 1, and Lactobacillus were identified as the genera exhibiting significantly higher levels in the microbiome of healthy skin (46).Furthermore, there is a significant differentiation in the microbial enrichment of microbiome between patients at various stages of cancer (33).The well-documented heterogeneity of tumor cells and the tumor microenvironment extends beyond diversity at the cellular and molecular levels to include microbial clusters forming micro niches with varying species composition and quantities within a tumor mass.This specific distribution of clusters has been reported with multiple types of tumors, from skin cancer to CRC or gastric cancer (48, 50).

Reprogrammed microbiota impact cancer hallmarks
Not only limited to changes in microbial composition, in the cancer state, there are significant alterations in the functions of microorganisms, especially in metabolism, generating metabolites that favor the hallmarks of cancer cells (Table 1).The toxin produced by enterotoxigenic Bacteroides fragilis (ETBF), known as B. fragilis toxin (BFT), is implicated in colitis and prompts a procancerous inflammatory response.This inflammation, driven by Stat3 and T helper type 17 (T(H)17) cells, contributes to colonic hyperplasia and the development of tumors (64).Similarly, through the Stat3 pathway and interleukin-17-positive (IL-17+) gd T-cells axis, the oral microbiota found in periodontitis, particularly with a dominant presence of Porphyromonas, has been implicated in the promotion of oral SCC (39).The homotrimeric form of Collagen Type 1, comprising three a1 chains, derived from pancreatic cancer cells, has been shown to facilitate oncogenic signaling via Discoidin domain receptor 1 and integrin a3b1.This signaling pathway promotes cancer cell proliferation and the formation of tumor organoids.Additionally, it leads to an increased abundance of Bacteroidales within the intratumoral microbiome (47).
Angiogenesis is another important hallmark, essentially contributing to the growth of tumors.There is ample evidence  (67).In recent years, advancements in nextgeneration sequencing (NGS) technology have facilitated the exploration of interactions between metagenomics across diverse microbiomes and the host genome.In a case-control study, a correlation was discovered between the colon microbiota and specific mutations and genome stability in CRC tumors.This study revealed that the presence of the Kirsten rat sarcoma virus (KRAS) mutant type was positively linked to Faecalibacterium while inversely associated with the presence of Bifidobacterium (18).A characteristic of cancer cells leading to recurrence and treatment failure is their ability to metastasize and invade surrounding tissues.The role of gut microbiota in the dissemination, survival, and colonization of metastatic cancer cells has long been recognized through numerous studies across various cancer types (68).Recently, along with the discovery of microbiota residing within tumors, their significant role in tumor migration and metastasis has been unveiled.Research conducted on a murine model of spontaneous breast tumors revealed that during the process of metastatic colonization, bacteria residing within the tumor were transported by CTCs.These bacteria played a role in enhancing the survival of host cells by increasing their resistance to fluid shear stress during the metastasizing process through the reorganization of the actin cytoskeleton.Additionally, the direct administration of certain bacterial strains, such as Staphylococcus and Lactobacillus, isolated from the microbiota of breast tumors, promoted metastasis in experimental tumor models.Conversely, when breast intratumor bacteria were depleted, there was a significant reduction in lung metastasis (52).CRC cells infected with F. nucleatum exhibit enhanced invasiveness into their surrounding environment and attract myeloid cells to the bacterial niches.This process accelerates migration rates significantly by mediating various signaling pathways crucial for cancer metastasis, including extracellular matrix remodeling and modulation of cell adhesion and migration via ERK1 and ERK2 (48).

Reprogrammed microbiota modifies the host immune system
The characteristic changes in microbiota composition in cancer patients can result in alterations of the composition and functions of immune cells including T-cells, natural killer (NK) cells, dendritic cells (DCs), and macrophages, implicated in antitumor immunity.A comparative analysis of intraepithelial lymphocytes in CRC tissue versus healthy colonic tissue revealed a reduction in gd T-cells and resident memory T-cells within cancerous tissue.These populations exhibited a regulatory CD39-expressing phenotype in the cancer microenvironment.Moreover, distinct patterns of T-cell proliferative responses to various commensal bacteria were observed in CRC patients, while B cell memory responses to certain bacteria/yeast were notably elevated.This increase in B cell memory responses was accompanied by higher proportions of circulating effector memory B cells, transitional B cells, and plasmablasts (69).
The influence of microbiota on lymphocyte populations is partially attributed to the modulation of antigen presentation cells through microbiota metabolites.Specifically, butyrate, a short-chain fatty acid (SCFA) metabolite produced by microbiota, has been shown to hinder DCs presentation of tumor-associated antigens.Consequently, this impediment affects the infiltration of T-CD8+ cells in an IFN-g-dependent manner.Therefore, the depletion of butyrate-producing strains in the gut microbiota through vancomycin treatment has been observed to enhance the antitumor response to radiotherapy (70).Likewise, phytosphingosine, a metabolite derived from the gut microbiota, can increase the expression of HLA class I on cancer cells.This sensitizes the cells to targeted antigen-specific cytotoxic T lymphocyte destruction, both in vitro and within living organisms, thereby enhancing the efficacy of immuno checkpoint inhibitor (ICI) treatments (71).
Besides altering the antigen-presenting function of immune cells, microbiota also has the capability to influence the production of pro-inflammatory cytokines like interleukin-12 (IL-12) and IFNg.These cytokines play crucial roles in activating and enhancing the function of cytotoxic T-cells and NK cells (72,73).Apart from the systemic immune modulation exerted by gut microbiota, the intratumoral microbiota plays a role in shaping the immune profile within the tumor microenvironment.In oral SCC, an enrichment of genera such as Capnocytophaga, Fusobacterium, and Treponema correlated with the presence of effector subsets of tumor-infiltrating lymphocytes and the associated gene expression involved in the recruitment of B cells and T-cells.This enrichment ultimately leads to immunosuppressive effects within the tumor microenvironment (74).
Fascinatingly, the microbiota not only can interact with tumors to modulate immune responses toward decreased tumor surveillance, but it can also interact with therapeutic drugs to alter the immune system in a synergistic antitumor direction.A recent study revealed that ICI induces the movement of specific native gut bacteria into secondary lymphoid organs and subcutaneous melanoma tumors.Specifically, ICI prompts the restructuring of lymph nodes and activation of DCs, facilitating the migration of a specific subgroup of gut bacteria to extraintestinal tissues.This migration promotes optimal antitumor T-cell responses in both the tumor-draining lymph nodes (TDLNs) and the primary tumor.Furthermore, antibiotic treatment leads to reduced translocation of gut microbiota into mesenteric lymph nodes (MLNs) and TDLNs, resulting in weakened DCs and effector CD8+ T-cell responses, as well as diminished responses to ICI.These findings offer opportunities for leveraging microbiota in a beneficial direction for treatment (75).
Immune checkpoint molecules, such as programmed cell death protein 1 (PD-1), Programmed Death Ligand 1 (PD-L1), and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), play pivotal roles in regulating T-cell responses.Research indicates that certain microbial species and their metabolites can influence the expression of these checkpoint molecules, thereby impacting T-cell activation and facilitating immune evasion by tumors.A study examining the urogenital microbial community in bladder cancer patients revealed an increased presence of Leptotrichia, Roseomonas, and Propionibacterium, along with a reduction in certain bacterial genera, such as Prevotella and Massilia, among those exhibiting PD-L1 expression on cancerous tissues compared to those who tested negative for PD-L1 expression (76).Similarly, Veillonella dispar was prevalent in the lung microbiome of lung cancer patients exhibiting high PD-L1 expression, whereas the abundance of Neisseria was notably elevated in patients with low PD-L1 expression.Consequently, V. dispar predominated in the group of patients showing a positive response, whereas Haemophilus influenzae and Neisseria perflava were prevalent in the non-responder group (77) Overall, the molecular intricacies governing the interplay between the microbiome and antitumor immunity encompass complex interactions among microbial elements, host immune cells, and the tumor microenvironment.Grasping these mechanisms is imperative for devising microbiome-centered interventions aimed at bolstering antitumor immune responses and refining cancer treatment outcomes.

The impact of microbiota on cancer treatment
Given the crucial role in tumor formation, development, metastasis, and host immunity, microbiota can exert significant influences on patients' responses to cancer treatment modalities, including both therapeutic efficacy and toxicity.Among these therapies, the most extensively investigated area with compelling evidence supporting the role of microbiota is the field of immunotherapy -the latest cancer treatment method that has made remarkable advances in clinical application.Additionally, microbiota also affect response to other cancer therapies, suggesting perspectives of interventions to achieve precision medicines (Figure 1).

Microbiota and immunotherapy response
In precision medicine, the most important aspect is to identify biomarkers for the stratification of patient groups to select The interplays between microbiomes and tumors affecting responses to cancer treatment modalities.Together with the enhanced alpha diversity, the enrichment of g-Blautia has been suggested as a potential predictor of responders to ICI with longer progression-free survival (PFS) in patients with non-small cell lung cancer (NSCLC) (81).Interestingly, Sarfaty et al. not only identified cancer type-specific microbiome signatures to distinguish between favorable responders and nonresponders but also observed certain similarities in the microbiome signatures of non-responders across three different cancer types including lung, urothelial, and melanoma.This suggests the potential utility of these signatures as common pharmacomicrobiomic biomarkers (82).Despite the treatment efficacy advantages of such an advanced therapeutic modality, ICI, like other cancer treatment regimens, also have unintended effects, notably immune-related adverse events (irAEs), which can impact treatment response and patient adherence.Among melanoma patients, responders experiencing irAEs from grade 2 in the Common Terminology Criteria for Adverse Events (CTCAE) exhibited a predominance of Bacteroides plebeius and Bacteroides coprophilus in their gut microbiota, while those without irAEs showed an enrichment of Eubacterium siraeum (83).Apart from alterations in gut microbiota, there is also a distinction in the skin microbiome among melanoma patients experiencing cutaneous irAEs following ICI treatment.This is characterized by an increase in Staphylococci and Proteobacteria, whereas patients without irAEs exhibited enrichment in anaerobic Eubacteriales (84).Identifying predictors of irAEs can aid in mitigating severe ADRs and preventing patient suffering.
Beyond merely identifying differences in microbiota between patient groups responding and not responding to immunotherapies, scientists can actively modify treatment responses by intervening in the microbiota.In vivo experiments have shown that transplanting fecal material from patients who respond to treatment with an abundance of Bifidobacterium longum, Collinsella aerofaciens, and Enterococcus faecium into germ-free mice could result in enhanced tumor control, increased T-cell responses, and improved efficacy of anti-PD-L1 therapy (85).Conversely, mice that received fecal transplants from patients with poor responsiveness exhibited elevated frequencies of regulatory CD4 +FoxP3+ T-cells and CD4+IL-17+ T-cells in the spleen.This indicates compromised host immune responses, ultimately resulting in the failure of ICI treatment (79).A thorough study on improving the gut microbiota to finetune cancer immunotherapy shows that certain bacteria in the gut are very important in determining the immune responses linked to CTLA-4 checkpoint blocking therapy.By regulating the gut flora, this understanding has the potential to enhance the therapeutic effectiveness of ICI and potentially reduce its immune-mediated toxicity (86).
In addition to impacting gut microbiota through fecal transplantation, skin bacteria can be genetically modified to induce changes in systemic anti-cancer immune responses.A recent study revealed that modifying the skin bacterium Staphylococcus epidermidis to express tumor antigens could enhance highly specific adaptive immune responses mediated by T-cells, leading to significant improvements in melanoma i m m u n o t h e r a p y e ffi c a c y (8 7 ) .A dd it i o n a l l y , a m o r e straightforward approach to modulate gut microbiota and thus modify the response to ICI treatment is through dietary interventions.Melanoma patients who consumed a diet rich in dietary fiber experienced significantly extended PFS while undergoing ICI treatment.Conversely, mice fed a low-fiber diet exhibited poor responsiveness to anti-PD1 therapy, characterized by a reduced frequency of interferon-g-positive cytotoxic T-cells in the tumor microenvironment (88).

Microbiota and chemotherapy response
In addition to its impact on immunotherapy, the microbiota plays a significant role in influencing the effectiveness of other treatments such as chemotherapy, whose response relies heavily on pharmacokinetics and pharmacodynamics (Figure 2).Like many other therapeutic groups, the bioavailability of chemotherapy agents is determined by hepatic metabolic enzymes and transporters, including the cytochrome P450 superfamily, which is responsible for metabolizing a majority of medications.Research has shown that alterations in gut microbiota can affect the expression of key pharmacokinetic proteins like CYP3A1, UGT1A1, and P-glycoprotein (P-gp) in the liver.Specifically, changes in the composition of gut microbiota have been observed to impact the metabolism and bioavailability of drugs like cyclosporine.For instance, higher levels of Alloprevolleta and Oscillospiraceae UCG 005 have been associated with reduced bioavailability of cyclosporin, while increased levels of Parasutterella and the Eubacterium xylanophilum group have been linked to increased bioavailability (89).Previously, only the biotransformation processes of drugs by human hepatic enzymes were known.However, recent studies have shown that enzymes from the intestinal microbiota also participate in drug metabolism reactions, significantly affecting the plasma concentration of drugs and their metabolite as well as the drug's elimination half-life (90,91).Consequently, this impacts the efficacy and toxicity of the treatment.This is particularly significant for drugs with a narrow therapeutic window such as chemotherapies.
Similar to immunotherapies, there exists a significant disparity in both the composition and abundance of microorganisms within the gut microbiota between patients who respond favorably to chemotherapy and those who do not, across various types of cancer.This contrast has been observed in locally advanced rectal cancer patients, where intestinal microbes associated with butyrate production, such as Roseburia, Dorea, and Anaerostipes, were found to be more prevalent in responders to neoadjuvant chemotherapy, whereas Coriobacteriaceae and Fusobacterium were more prevalent in nonresponders.A set of ten predictors, including Dorea, Anaerostipes, and Streptococcus, was identified for the stratification of responders, achieving an area under the curve value of up to 93.57% (92).
The favorable efficacy of chemotherapies is associated with some specific microbiota-derived metabolites, suggesting their utility as solutions to enhance the benefit of such a popular The impact of gut microbiome on efficacy and toxicity of chemotherapy (created with BioRender.com).
cancer therapy.The microbiota-derived tryptophan metabolite, indole-3-acetic acid (3-IAA) which plays a crucial role in the autophagy process of cancer cells was found in higher concentrations in pancreatic cancer patients who positively responded to treatment.Studies have shown that interventions such as fecal microbiota transplantation, short-term dietary adjustments focusing on tryptophan, and oral administration of 3-IAA enhance the effectiveness of chemotherapy in humanized murine models of pancreatic cancer.Furthermore, a significant correlation between the levels of 3-IAA and the chemotherapy's efficacy has been observed in two separate cohorts of patients with pancreatic ductal adenocarcinoma (PDAC) (93).By utilizing machine learning models incorporating both drug response and microbiota data, Hermida et al. demonstrated that the microbiota profile emerges as a superior predictor of clinical outcomes when compared to clinical variables across seven distinct cancer types, including chemotherapy treatments for bladder urothelial carcinoma, docetaxel treatment for breast invasive carcinoma and sarcoma, as well as various treatments for stomach adenocarcinoma (94).
Not only can the microbiota profile predict the efficacy of chemotherapies, but it can also help anticipate specific ADRs caused by chemotherapy agents.In acute lymphoblastic leukemia (ALL), the initial gut microbiome composition, marked by an abundance of Proteobacteria, served as a predictive factor for febrile neutropenia following chemotherapy.Notably, a prevalence of Enterococcaceae was associated with a significantly higher likelihood of experiencing subsequent febrile neutropenia and diarrheal ADRs.Additionally, the dominance of Streptococcaceae predicted a remarkably increased risk of subsequent diarrheal adverse events (95).Similarly, the presence of Bacteroides and Blautia2 in the gut microbiota of rectal cancer patients could predict ADRs such as fatigue, sleep disturbance, or depression following chemotherapy with an accuracy of 74% (96).Also in rectal cancer cases, dynamic changes observed in the tumor microbiome throughout and following chemoradiation therapy were associated with drug-related toxicity.Specifically, patients who experienced heightened toxicity by week 5 displayed elevated relative counts of Clostridia, Actinobacteria, and Clostridiales at the outset of treatment (97).

Microbiota and radiotherapy response
Radiotherapy stands as a crucial cancer treatment modality with interindividual variations in therapeutic effectiveness and toxicity.Among its most significant antitumor mechanisms is the stimulation of both innate and adaptive immunity.Consequently, the microbiota, which exerts profound influences on the host immune system, can significantly influence therapeutic outcomes.The intricate relationship between intestinal microbiota and postradiation immune responses in mouse models of breast cancer and melanoma has been uncovered.While the exclusion of gut fungi enhanced the anti-tumor effects of radiation, the use of antibiotics to deplete bacteria diminished responsiveness, leading to the proliferation of commensal fungi.Moreover, the expression level of intratumoral Dectin-1, a key innate fungal sensor was essential for the impact of commensal fungi in mice undergoing radiation therapy and could predict survival rates in breast cancer (98).
Butyrate, a common metabolite produced by intestinal bacteria, is renowned for its impact on immune function.Recent research using murine models has revealed a negative correlation between the abundance of butyrate-producing gut bacteria and anticancer responses to radiation.Butyrate inhibited STING-activated type I IFN expression in DCs by blocking TBK1 and IRF3 phosphorylation.This inhibition abolished radiation-induced tumor-specific cytotoxic T-cell immune responses, without directly shielding CRC and melanoma cells from radiation.These results underscore the potential of selectively targeting butyrate-producing microbiota as a novel therapeutic approach to enhance tumor radiation sensitivity (99).The contribution of gut microbiota via the STING pathway to antitumor immune responses has also been observed in both hepatocellular carcinoma (HCC) patients and experimental HCC models (100).
Radiation therapeutic response is not solely influenced by the gut microbiome.A recent investigation using CRC mouse models revealed that modifications in oral microbiota led to shifts in bacterial makeup within CRC tumors while leaving adjacent peritumor tissues unaffected.Notably, the migration of Fusobacterium nucleatum from the oral cavity to the CRC site was observed, hindering the effectiveness of radiotherapy and impacting prognosis.The administration of metronidazole successfully countered the detrimental effects of oral microbiome alterations on CRC radiotherapy outcomes.Furthermore, the oral microbiota was found to correlate with radiation-induced intestinal damage through its influence on intestinal microbial communities (101).
One drawback of radiotherapy is the emergence of undesired side effects affecting various organs in the body, such as toxicity to the digestive or nervous systems.Around 90% of cancer patients undergoing pelvic radiotherapy experience gastrointestinal (GI) toxicity, including symptoms like bloody diarrhea and gastritis, with many linked to gut dysbiosis.Hence, the gut microbiome, pivotal in regulating digestive function, significantly influences gastrointestinal ADRs to radiation.In a preclinical investigation, radiation-induced damage to intestinal villi height and mucosal thickness was observed, along with induced neural inflammation and cell death (102).Intriguingly, altering the gut microbiota effectively mitigated toxicity in both the gastrointestinal and neural systems, suggesting a key to the challenge of radiotherapy.A study conducted on gynecologic cancer patients yielded similar findings, demonstrating that modifying the vaginal microbiota resulted in changes to radiation-induced vaginal toxicities, including pain, dyspareunia, and sexual dysfunction (103).

Perspectives for microbiometargeted solutions to improve cancer treatment outcomes
Understanding the significant influence of the various microbiota on the development, metastasis, and response to treatment of tumors not only allows the use of microbiome components as biomarkers for selecting appropriate treatment methods, achieving high efficacy with minimized toxicity but also opens perspectives for intervening to alter the microbiome to bring about favorable outcomes for cancer patients.The advantages of microbiome-targeted interventions lie in their high feasibility, as they do not require overly advanced, costly methods, are minimally invasive, have fewer long-term systemic side effects, and are nonirreversible for patients.Another particularly notable aspect is that interventions targeting the microbiome can be personalized according to the unique microbiome characteristics of each patient.Additionally, microbiome-targeted interventions can be combined with various therapeutic modalities in a personalized manner to maximize benefits for patients.The followings are primary strategies for microbiome interventions.

Diet and supplementbased interventions
Substantial evidence highlights significant differences in microbiota composition, beneficial/pathogenic microbe abundance, and metabolite profiles between healthy individuals and cancer patients, as well as among cancer patients with varied treatment responses (63).Consequently, modifying dietary habits to promote beneficial microbe growth and diminish harmful ones can positively influence treatment outcomes in cancer patients.Recognized as pivotal components of cancer precision medicine, diet, and supplement-based interventions target specific dietary factors and nutritional supplements to optimize treatment efficacy.For example, embracing a diet abundant in fiber, fruits, vegetables, and fermented foods fosters a diverse and healthy microbiota.Additionally, a proactive approach to microbiome influence involves supplementing beneficial microbes and their substrates through microbiome modulators such as probiotics, prebiotics, and postbiotics to elicit desired effects.This notion finds support in numerous clinical studies across diverse cancer types (Table 2).
Despite increasing interest in these interventions, challenges persist regarding standardization, efficacy, and safety (149).Additionally, some contrary findings have been reported, in which, probiotics use compromised the efficacy of ICIs in cancer patients (150).Therefore, rigorous clinical trials are indispensable to assess the efficacy and safety of diet approaches, establish optimal dosages and formulations, and ascertain their compatibility with conventional cancer therapies.Furthermore, personalized strategies are imperative to tailor diet and supplement interventions to individual patient characteristics, including cancer type, stage, genetic profile, and lifestyle factors.

Fecal microbiota transplantation
Bacteriotherapy, which involves utilizing microbes or their byproducts to treat illnesses, encompasses various approaches.Alongside supplementing specific microbes through probiotics, Fecal Microbiota Transplantation (FMT) is emerging as a promising method to utilize the gut microbiome's potential to modulate therapeutic responses and enhance patient outcomes.FMT entails transferring fecal material from a healthy or therapeutically responsive donor into the gastrointestinal tract of a patient to restore or manipulate the microbiota composition (151).According to a Europe-wide survey conducted in 2019, 31 FMT centers across 17 countries performed a total of 1,874 procedures.However, the sole officially approved indication for FMT remains Clostridioides difficile infection (152).
Despite accumulating evidence demonstrating the potential benefits of FMT in enhancing outcomes of cancer treatment in experimental models, its application in cancer patients is currently limited to research and clinical trials (Table 3).Often integrated with other therapeutic approaches, some of these trials have shown promising results, suggesting a potential avenue for effective cancer treatment.FMT has been demonstrated to enhance the efficacy of immunotherapy by bolstering anti-tumor immune responses in CRC and melanoma (156,195).Additionally, FMT has proven effective in mitigating treatment-related toxicities, such as chemotherapy-induced gastrointestinal symptoms (194).In particular, several clinical studies have demonstrated the efficacy of FMT in treating Gastrointestinal Acute Graft-versus-Host Disease (GI-aGvHD), a severe and potentially life-threatening complication arising from Allogeneic Stem Cell Transplantation (allo-SCT), an advanced therapeutic approach utilized in the management of hematologic malignancies.
However, challenges and considerations accompany the implementation of FMT in cancer treatment.These include standardizing donor selection and screening procedures, optimizing FMT protocols, determining optimal timing and dosing, and managing potential risks such as infection transmission and immune-related adverse events.That is the reason why FMT has not been approved for use in clinical setting, except for Clostridioides difficile infection, in European countries.Despite these challenges, FMT represents a promising avenue for precision oncology, offering a personalized and microbiome-based approach to cancer therapy.Further research is necessary to elucidate the mechanisms of action, optimize treatment protocols, and identify patient subgroups most likely to benefit from FMT.Overall, FMT holds potential as an innovative strategy to complement existing cancer treatment modalities and improve outcomes for cancer patients.

Antibiotic-based interventions for microbiome
Antibiotics, traditionally used to combat bacterial infections, have garnered attention for their potential to influence cancer treatment responses through modulation of the microbiome through both preclinical and clinical research (196).Despite promising findings in preclinical research indicating potential benefits of antibiotics in enhancing treatment efficacy and reducing adverse reactions in cancer therapy, clinical studies across diverse cancer types consistently demonstrate that antibiotic usage before or during treatment is associated with worsened outcomes, notably in immunotherapy (Table 4).These observations suggest an additional strategy for regulating microbiota in cancer precision medicine through the selective use of antibiotics given the requirement for thorough research for the appropriate antibiotic.Targeting harmful microbes with antibiotics to manipulate microbial communities can optimize treatment   responses and reduce adverse effects.However, careful consideration, especially in antibiotic dosage is necessary to avoid disturbing the beneficial microbiota, leading to clinical complications (209) and the danger of antibiotic resistance (210).

Modulation of other local microbiotas beyond the gut
Local interventions targeting microbiotas beyond the gut microbiota are emerging as promising strategies in cancer precision therapy, aiming to harness the influence of various microbial communities on tumor biology and treatment responses.While much attention has been focused on the gut microbiota, other microbiotas throughout the body, including those in the oral cavity, skin, respiratory tract, urogenital tract, and tumor microenvironment, also play significant roles in cancer development and treatment.
Research has revealed the intricate interactions between these microbiotas and cancer, highlighting their potential as therapeutic targets for precision therapy (15,16).Local interventions seek to modulate the composition and function of these microbiotas to enhance treatment efficacy, reduce treatment-related toxicities, and improve patient outcomes.These interventions encompass a range of approaches, including probiotics, prebiotics, antibiotics, microbial metabolites, targeted therapies, and physical interventions.
In the oral cavity, interventions targeting the oral microbiota, such as mouthwash formulations containing probiotics or antimicrobial agents, hold promise for preventing oral mucositis and reducing the risk of secondary infections in patients undergoing radiation therapy or chemotherapy for head and neck cancers (101).Similarly, interventions targeting the skin microbiota may involve topical applications of probiotic formulations or antimicrobial agents to alleviate radiation-induced dermatitis and enhance wound healing in patients with skin cancers (52,87).
In the respiratory tract, interventions may include inhalation therapies with probiotics or antimicrobial agents to improve treatment responses and reduce the risk of respiratory infections in patients with lung cancers (211).Likewise, interventions targeting the urogenital microbiota may involve the use of vaginal probiotics or antimicrobial agents to prevent urinary tract infections and enhance treatment tolerability in patients with genitourinary cancers (76,212).
Moreover, interventions targeting the tumor microenvironment may encompass immunomodulatory therapies, such as ICI or adoptive cell therapies, aimed at modulating the local immune response and tumor growth in various cancer types.Additionally, microbial-based therapies, such as oncolytic viruses or bacteria engineered to target tumors, offer novel strategies for directly targeting tumor cells and modulating the tumor microenvironment (213).
Despite the potential benefits of local interventions on non-gut microbiotas for cancer precision therapy, challenges exist in their implementation and optimization.These include the need for further research to elucidate the complex interactions between microbiotas and cancer, as well as the development of targeted and personalized interventions tailored to individual patient characteristics and tumor biology.

Conclusion
The field of pharmacomicrobiomics holds immense promise for revolutionizing precision cancer therapy by leveraging the intricate interplay between the microbiome and drug response.From preclinical investigations elucidating molecular mechanisms to clinical trials evaluating patient outcomes, advancements in this field offer unprecedented opportunities to optimize treatment strategies tailored to individual patients.By harnessing the potential of pharmacomicrobiomics, we can enhance treatment efficacy, minimize adverse effects, and ultimately improve patient outcomes in the era of precision oncology.However, challenges such as standardization, validation, and clinical translation remain, underscoring the need for continued research and collaborative efforts across disciplines.
of specific bacterial strains, including Staphylococcus and Lactobacillus, isolated from the microbiota of breast tumors, was shown to promote metastasis in experimental tumor models.Invasion and metastasis:During metastatic colonization, intratumor bacteria carried by circulating tumor cells played a role in promoting hostcell survival.This was achieved by enhancing resistance to fluid shear stress through the reorganization of the actin cytoskeleton.(52) (Continued) Le Ngoc et al. 10.3389/fimmu.2024.1428420 In the context of CTLA4 blockade therapy, heightened concentrations of butyrate and propionate in the bloodstream correlate with treatment resistance and an increased proportion of Treg cells.Mouse studies reveal that butyrate impeded the CTLA-4-induced elevation of CD80/CD86 expression on DCs and ICOS expression on T-cells, along with the buildup of tumor-specific T-cells and memory T-cells.In patients, elevated blood butyrate levels mitigated the ipilimumab-induced accumulation of memory and ICOS + CD4 + T-cells and IL-2 production, suggesting that SCFA restricts the efficacy of anti-CTLA-4 therapies (78).

FIGURE 2
FIGURE 2 antibiotics during ICI markedly diminished the effectiveness of treatment (204) NA CT Disruption of the microbiome caused by antibiotics exacerbated chemotherapy-induced diarrhea.(205) PaC CT Incorporating antibiotics into first-line gemcitabine chemotherapy regimens could potentially enhance outcomes.(206) OC CT Treatment with antibiotics was linked to reduced PFS and OS (207) NSCLC ICI The utilization of antibiotics within 21 days before and after the initiation of anti-PD-1 treatment significantly decreased OS and PFS (208) NA, Not avaiable; GC, Gastrointestinal cancer; LiC, Liver cancer; OC, Ovarian cancer; PaC, Pancreatobiliary cancer; NSCLC, Non-Small Cell Lung Cancer; RC, Renal cancer; RT, Radiotherapy; CT, Chemotherapy; Immuno-checkpoint inhibitor, IC.

TABLE 1 Continued
-In experiments with mice and in laboratory studies, lithocholic acid (LCA), a secondary bile acid, decreased cancer cell proliferation and VEGF production, as well as reduced the aggressiveness and metastatic potential of primary tumors.-BC patients reduced abundance of baiH in Clostridium sordelli, Pseudomonas putida, and Staphylococcus aureus.In early-stage BC patients, a more significant decline in the abundance of baiH in Bacteroides thetaiotaomicron and Pseudomonas putida was observed.. Metabolic reprogramming: Comparing all patients to healthy controls, BC patients had lower levels of baiH in Clostridium sordelli, Staphylococcus haemolyticus, Escherichia coli, and Pseudomonas putida, aligning with decreased Lithocholic acid (LCA), a bacterial metabolite.In the early stages of BC, there was a notable decrease in LCA biosynthesis and levels, suggesting a potential role for this pathway in human disease through the activation of the TGR5 receptor.

TABLE 1 Continued
the relationship between microbiomes at various locations in the body, from the gut to ocular microbiota, and the process of neovascularization (65, 66).The immortality of tumor cells is originated from the capability to resist apoptosis.On the other hand, apoptosis can be impacted by metabolites from certain taxa in various microbiota.P. anaerobius, found in abundance in Across various cancer types, species from the Proteobacteria and Firmicutes phyla were predominant in the detected bacterial sequences.However, the Proteobacteria to Firmicutes (P/F) ratio varied among different tumor types.Taxa from the Actinobacteria phylum, particularly the Corynebacteriaceae and Micrococcaceae families, were prevalent in nongastrointestinal tumors like breast, lung, and ovarian cancer.Fusobacterium nucleatum, previously linked to enrichment in colorectal tumors, was also identified in breast and pancreatic tumor cohorts.AK, actinic keratosis; BC, Breast cancer; Bft, Bacteroides fragilis toxin; CC, Cervical cancer; CRC, Colorectal cancer; EAC, Esophageal adenocarcinoma; EC, Esophageal Cancer; EO-CRC, Earlyonset CRC; ER, Endocrine receptor; ESCC, Esophageal squamous cell carcinoma; GC, Gastrointestinal cancer; IL-6, Interleukin-6; LC, Lung cancer; LiC, Liver cancer; LO-CRC, late-onset CRC; LUAD, Lung adenocarcinoma; LUSC, Lung squamous cell carcinoma; MAMP, Microorganism-associated molecular patterns; NLR, Neutrophil-to-lymphocyte ratio; OSCC, Oral squamous cell carcinoma; OTUs, Operational taxonomic units; PaC, Pancreatobiliary cancer; PLR, Platelet-to-lymphocyte ratio; PRRs, Pattern recognition receptors; PC, Prostate Cancer; RM, Recurrence or metastasis; sCTLA-4, Soluble cytotoxic T lymphocyte associated antigen-4.demonstrating Le Ngoc et al. 10.3389/fimmu.2024.1428420Frontiers in Immunology frontiersin.orgappropriate drugs for each group.Although some molecular biomarkers have been applied in personalized medicine with immunotherapies, their true effectiveness in clinical practice remains controversial, requiring supplementation or support from other types of biomarkers.Significant variations in the composition of gut microbiota have been observed between patients who respond favorably to ICI and non-responders across a range of different cancer types.Responding melanoma patients exhibited notably higher alpha diversity, along with a relative abundance of Ruminococcaceae bacteria.Intriguingly, metagenomic analysis revealed an enrichment of amino acid biosynthesis in responders, thereby contributing to enhanced immunity characterized by increased infiltration of CD4+ and CD8+ T-cells (79).Likewise, an analysis of gut microbiota utilizing 16S ribosomal RNA sequencing revealed increased alpha diversity among responders to ICI and CTLA-4 inhibitors across various cancer types.The microbiota composition of responders resembled that of healthy individuals.Additionally, certain bacteria, including Prevotella copri and Faecalibacterium prausnitzii, were linked to a favorable treatment outcome (80).

TABLE 3
Application of fecal microbiota transplantation in cancer clinical settings.

TABLE 4
Microbiota-mediated impacts of antibiotics on anti-cancer treatment.presence of gut bacteria responsible for producing butyrate and amplified the body's immune response against tumors when combined with ionizing radiation (IR).