Gut microbiome-based strategies for HIV prevention and therapy, current challenges and future prospects

Abstract

The gut microbiome has become a primary controller of host immunity as well as the pathogenesis of human immunodeficiency virus (HIV) infection. Commensal microbes in healthy persons keep the intestinal and other body barriers intact and regulate mucosal and systemic immune responses and generate metabolites, including short-chain fatty acids and indole derivatives that suppress inflammation and stimulate epithelial healing. These functions are impaired by HIV infection via depletion of gut CD4 + T cells, damage caused to epithelium, microbial translocation, and microbiota disruption. In this review article, we summarize recent studies suggesting that a balanced microbiome can mitigate HIV susceptibility and progression by preserving mucosal defenses, limiting systemic immune activation, and generating antiviral compounds. Other interventions, including probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation (FMT), have been trialed with mixed outcomes in most cases, showing small but significant changes in the gut microbial composition and/or inflammatory markers. Current evidence highlights the potential of microbiome-targeted strategies to support HIV management; however, substantial gaps remain. Future research should focus on defining protective microbial signatures, developing next-generation live biotherapeutics, exploring metabolite-based therapies, and conducting large, mechanistically driven clinical trials. Harnessing the microbiome’s protective functions could offer novel approaches to reducing HIV transmission, mitigating inflammation, and improving immune reconstitution in infected individuals.

Introduction

A multitude of host-associated bacteria thought to affect viral infections, and the makeup of commensal microorganisms influences the development of viral diseases [1]. The gut microbiota and HIV infection are two other areas where this is true [2]. HIV infection results in immunological activation, persistent inflammation, and microbial translocation, undermining the gut barrier [3]. However, alterations to the intestinal barrier substantially influence the development of other age-related, metabolic, immunological, and chronic diseases, including AIDS [4, 5]. Intestinal permeability alters microbiota composition, allowing greater penetration of pathogens or the diffusion of extra bacteria and tiny chemicals into the bloodstream [6]. The gut barrier is affected by these bacterial alterations [7]. The most adverse outcome: these alterations disturb the delicate equilibrium of the gut’s commensal flora. Certain bacteria may pose a danger, but others can counteract or propagate viruses. The buildup of harmful or pro-inflammatory microorganisms is more likely. Consequently, much research has been undertaken to ascertain techniques for avoiding HIV-related illnesses, including (a) controlling the populations of certain microorganisms or (b) managing the microbiota to diminish dangerous bacteria and enhance healthy ones. Despite the fluctuating impact of environmental and dietary factors, it is crucial to examine the gut microbiota of HIV affected individuals [8].

Gut bacteria

The gut microbiota has mostly been examined concerning bacteria. These bacteria, especially those residing in the intestines, have been extensively researched. Analysis of gut microbiota in cross-sectional datasets of diseased and healthy persons indicates that individuals with HIV possess a different bacterial microbiome relative to those without the virus. Both individuals are present [9, 10]. Edda et al. identified the gut microbiota of People living with HIV (PLH) as unique. Pathogenic taxa far exceed commensal species in comparison to PLH. An excess of some gut bacteria, such as Prevotella, may be the primary cause of inflammation [11]. Evidence mostly indicates variations in the variety of microbes, a lessening in beneficial symbiotic bacteria, and an escalation in potent dangerous bacteria as the principal symptoms of gut microbiota changes in PLH [12]. In diverse demographic patterns indicate significant alterations in gut microbiota attributable to the specific characteristics of HIV. The primary characteristics linked with these disparities include sexual orientation, the length and type of antiretroviral therapy (ART), and immunological response status. Research indicates that an infant’s gastrointestinal microbiome may be significantly influenced by the mother’s HIV status [9]. Researchers often examine several cohorts to ascertain the role of gut microorganisms in HIV [13]. Wu et al.‘s study illustrates that the composition of gut microbiota differs between HIV-positive and HIV-negative individuals, due to gut dysbiosis associated with HIV infection [5]. The findings suggest that gut microbiota may serve as a potential therapeutic target for the prevention and therapy of HIV-related conditions. This is equally pertinent to fungi and viruses. Accurately identifying relevant species of gut-residing bacteria, fungi, or viruses continues to pose a considerable problem for researchers in this domain [5].

Gut fungi

The second most significant parameter is fungal mass, influencing gut microbiota composition, behind bacterial bulk. Fungal infections significantly contribute to morbidity and mortality in immunodeficient infected individuals [14]. Fungi have a substantial role in opportunistic infections in patients with HIV, especially those who are immunocompromised [5]. A decline in immunological function is a hallmark of HIV infection. As a result, gut fungi, which are becoming more common illnesses, have attracted significant attention. However, there has only been a limited amount of research done thus far on gut fungus in HIV-infected individuals [15]. Wu et al. [5] found that people with HIV had a different gut fungus diversity than HIV-negative individuals. People with HIV showed both a change in fungal composition and an enhancement in the gut variety of fungi. Yin et al. [1] indicated that the gut mycobiome in patients solely infected with HIV differed from that of healthy persons and those co-infected with HIV and HCV. They came to the conclusion that reciprocal limitation changed the dominant fungus and aided in the spread of illness. These findings clarify the correlation between variations in gut fungi and the spread of HIV illness, hence facilitating the identification of key gut fungi as shown in Table 1 [1].

Table 1.

Summarizes reported changes in gut fungal microbiota among people with HIV, highlighting differences in diversity and abundance across infection status, co-infection, and ART treatment compared to healthy controls

Gut microbiota	Study comparison	Diversity	Abundance	Reference
Fungi	HIV mono-infected vs. Healthy controls	In HIV cases, Eurotiomycetes levels were higher, while Saccharomycetes were lower	Among genera, Aspergillus dominated in healthy participants, whereas Candida was more prevalent in HIV cases. Additionally, HIV patients showed enrichment of Schwanniomyces, Preussia, and Leotiomycetes (including Thelebolales, Thelebolaceae, and Thelebolus), while Agaricomycetes were reduced	[1]
Fungi	HIV/HCV co-infected vs. HIV mono-infected vs. Healthy controls	The fungal diversity in co-infected (HIV/HCV) patients was reduced compared to HIV-only cases, but overall similar to healthy individuals	Overall fungal abundance decreased in the co-infected group. Compared with HIV mono-infected cases, co-infected cases showed lower Schwanniomyces and Thelebolus	[1]
Fungi	ART-treated HIV + vs. HIV- healthy controls	Overall diversity remained relatively unchanged between groups	Fungal abundance was higher in ART-treated patients. At the phylum level, Ascomycota and Basidiomycota were more prominent in healthy individuals, whereas Mucoromycota and Chytridiomycota appeared specifically in ART-treated cases. At the genus level, Penicillium was more frequent in controls, while Candida was enriched in ART patients	[16]
Fungi	HIV+ patients vs. HIV- participants	HIV-positive individuals had greater overall fungal diversity	In HIV cases, Microsporum was elevated, while Cystobasidium and Rhodotorula were reduced compared to controls	[5]

Gut viruses

Juvenile bacteriophages form a gut viral community [17]. A multitude of eukaryotic DNA and RNA viruses reside in the human gastrointestinal tract; nevertheless, bacteriophages are the dominating organisms [18]. It is believed that 83% to 95% of the body’s HIV-infected cells reside in the gastrointestinal tract, promoting the virus’s propagation throughout the body. Herpesviruses are not the only pathogens shown to survive in human intestines for prolonged periods [19]. This include eukaryotic adenoviruses, microviridae bacteriophages, and crAs-like viruses found in prokaryotes [20]. Similar research on gastrointestinal bacteria has shown that viruses may survive for a minimum of 10 years [21]. In the context of HIV, gastrointestinal viruses have garnered considerable interest. The gut viromes of most individuals show little fluctuation; however patients with inflammatory bowel disease or other chronic infectious illnesses may experience significant changes [20]. Recently, researchers investigated the processes behind the HIV gut virome. Investigators from Washington University School of Medicine in St. Louis identified several new viruses inside the gut microbiome of persons infected with HIV [19]. The researchers posited that alterations in the viral makeup of the intestines could correlate with the emergence of severe immunodeficiency in HIV patients [22, 23]. Patients with AIDS and consequent immunodeficiency have been associated with a higher prevalence of gastrointestinal viruses compared to those with strong immunological responses [19]. Mitigating the transmission of pathogenic bacteria and viruses in the intestines may reduce stress on the gastrointestinal tract and, consequently, the difficulties encountered by individuals with chronic HIV infection, as articulated by Edward Mallinckrodt. Adenoviruses , linked to AIDS and subsequent immunodeficiency, may cause illness due to their ability to proliferate as enteropathogens [19]. They also proposed that some viruses, such as adenoviruses, may specifically target certain organs [24]. t [25]. A novel virus, designated as a phage-type virus, is evolving, despite the potential harm viruses inflict on the cells they invade. These viruses not only infect bacteria but also live with them, and some generate genes that augment the lifespan of the host cells. Additional research is necessary to determine if gut viromes have advantageous or harmful impacts. The functions of gut microbiota are shown in Table 2 [16, 26].

Table 2.

Key functions of gut microbiota [27]

Function Type	Main Roles
Neurological	Regulates both the enteric and central nervous systems by influencing neurotransmitter and neurotrophic factor production, turnover, and activity; helps preserve intestinal barrier and tight junction integrity; modulates sensory nerve pathways; microbial metabolites support immune balance in the gut
Metabolic	Breaks down dietary fibers through fermentation; produces short-chain fatty acids (SCFAs); participates in amino acid and protein metabolism; assists in bile salt conversion and nutrient processing
Structural	Maintains intestinal architecture by regulating tight junctions, supporting mucus layer function, promoting crypt and villus formation, and enhancing villi blood vessel development
Protective	Enhances nutritional uptake, strengthens intestinal barrier, stimulates immune responses, and promotes secretion of antimicrobial peptides (AMPs)

Gut microbiota in immune homeostasis

The gut microbiome acts as a key regulator of mucosal immunity and systemic homeostasis. A balanced microbiota competes with pathogens for ecological niches and stimulates the development of immune tissues [28]. Commensal organisms produce SCFAs (acetate, propionate, butyrate) by fermenting fiber; these metabolites reinforce tight junctions, serve as energy for colonocytes, and modulate immune cell function [29]. Moreover, IgA repertoire on gut is determined by microbial antigens and metabolites, which facilitate responses by antibodies against pathogens within the lumen [30]. Animals that do not harbor this microbiome (germ-free animals) are prone to infection, have poorly developed gut-associated lymphoid tissues, low intraepithelial lymphocytes, and IgA [31], emphasizing the symbiotic value of the intestinal flora. Infection early in HIV causes disruption of this symbiosis. Th17 and Th22 cells which regulate bacterial communities are rapidly depleted and CD4 + activated T cells which are activated in gut-associated lymphoid tissue (GALT) are the exclusive targets of infection by the virus [32]. The death of such cells results in malfunction of the microbial sensing and impaired epithelial barriers. As a result of this, the intestines become more permeable and luminal microbes or their products (e.g., lipopolysaccharide, LPS) find their way into the blood [33]. It results in systemic immune activation, increasing a process of inflammation, which contributes to another instability of the gut barrier and disrupts the microbiome. It is important to note that such effects are usually inhibited by the healthy microbiome: it controls the GALT homeostasis and prevents the microbial translocation and long-term immune activity [34]. This protective role is however lost when dysbiosis happens in case of HIV infection. Therefore, prevention or treatment of HIV-pathogenesis may be effective through the maintenance or replacement of a positive gut microbiota. It has been established that there are several specific pathways through which microbes or their products reverse HIV-related damage [35]. These are the strengthening of the epithelial integrity, regulation of the inflammatory processes and even the direct impact on the viral replication [36].

Mechanistic pathways of microbiome-mediated protection

Barrier integrity and microbial translocation

The key role of the gut microbiome is the maintenance of both the physical and immunologic protection of the intestinal mucosa [37]. Commensal bacteria stimulate mucus, tight junction proteins as well as maintenance of immune cells that block the barrier. As an example, Bifidobacteria, which are normal inhabitants of the intestines, have been demonstrated to shield the mucosal integrity: they are capable of inhibiting the development of epithelial defects and translocation of microbes [38]. This is not the case in HIV infection where the levels of Bifidobacteria tend to be depleted hence aiding in barrier leakiness. On the other hand, experimental evidence suggests that addition of good bacteria is assistive in restoration of gut barrier function. When Lactobacillus-containing probiotics were administered in the gut of SIV-infected macaques (a primate model of HIV), the gut epithelial cells were repaired [39], implicating that probiotic microbes have the potential to stimulate the process of mucosal healing despite additively changing the overall microbiota composition [40]. The gut microbial communities also control the optimal populations of important immune cells that protect the barrier. Th17 and IL-22-secreting cells (generated by innate lymphoid cells and Th22 cells) secrete the cytokines that promote epithelial cell turnover and release antimicrobial peptides [41]. Microbial metabolites particularly tryptophan-derived indoles used to stimulate IL-22 release by innate lymphocytes promote the barrier [42]. Producibility of these indole metabolites is compromised in the microbiota of progressive HIV infection. This loss can increase epithelial damage: lack of indole-AhR (aryl hydrocarbon receptor) signaling causes the weakening of IL-22 + cells and makes the epithelium more prone to the destruction and growth of opportunistic pathogens. Conversely, a healthy gut is facilitated to produce IL-22- inducing metabolites by microorganisms to aid mucosa defense [43]. These results suggest that there is a feedback mechanism in that HIV-mediated dysbiosis diminishes the microbial aid of the barrier, which enhances translocation and immune activation. On the other hand, a healthy microbiome containing Bifidobacteria, indole-forming bacteria ensures the health of epithelia and prevents translocation [44]. The aim of the microbiome-based therapies (diet, prebiotics, probiotics, FMT) is to restore this balance to the protective barrier [45].

Anti-inflammatory effects and immune modulation

Gut microbes also regulate inflammation. A dysbiotic microbiota in HIV often shows enrichment of pro-inflammatory Gram-negative bacteria (e.g. Prevotella, Proteobacteria) and depletion of anti-inflammatory taxa (e.g. Faecalibacterium, Roseburia) [46, 47]. These dysbiotic shifts are associated with elevated circulating LPS and inflammatory cytokines. In contrast, certain commensals produce metabolites that buffer inflammation [48]. For example, members of the Succinivibrionaceae and Erysipelotrichaceae families can “mop up” pro-inflammatory molecules and accumulate antiviral compounds [49]. In practice, higher abundance of Erysipelotrichaceae has been linked to lower HIV acquisition risk in a human genetic study, consistent with its anti-inflammatory reputation. Erysipelotrichaceae (and related taxa) may produce metabolites or secondary bile acids that dampen immune activation and perhaps directly inhibit HIV replication. Short-chain fatty acids (SCFAs) are among the key anti-inflammatory mediators derived from microbes [50]. Butyrate in particular plays a central role in regulating immune homeostasis in the gut. Butyrate provides energy to colonic epithelial cells, promotes regulatory T cell differentiation, and inhibits NF-κB–mediated inflammatory signaling. In treated and untreated HIV patients, many butyrate-producing Firmicutes (e.g. Roseburia, Coprococcus, Faecalibacterium) are consistently reduced [50]. This loss correlates with lower fecal butyrate levels and with higher markers of immune activation. Notably, in HIV-infected individuals, levels of the butyrate producer Roseburia intestinalis inversely correlate with microbial translocation and immune activation. In vitro, adding butyrate to peripheral blood T cells from people with HIV suppresses their activation and reduces HIV replication [51]. Thus, depletion of SCFA-producing microbes removes a key anti-inflammatory brake in HIV [52]. Restoring these taxa (for example via dietary fiber or fecal transplant) could enhance colonic production of butyrate and related SCFAs, thereby reducing inflammation [53]. Other microbial metabolites also exert systemic immunomodulatory effects. Microbiota-derived kynurenine (a tryptophan catabolite) is elevated in HIV and is immunosuppressive: high kynurenine/tryptophan ratios in plasma predict poor CD4 recovery and vascular inflammation [54]. Bacteria that can catabolize tryptophan via indoleamine 2,3-dioxygenase–like enzymes are enriched in HIV patients. Increased kynurenine skews the Th17/Treg balance toward regulation and impairs mucosal immunity [55]. Conversely, pathways that shunt tryptophan into anti-inflammatory indoles (e.g. indole-3-propionate) rather than kynurenine would be protective [56]. Microbiome-targeted interventions (such as probiotics) might be designed to favor indole production, thus supporting IL-22^+ cells and limiting Th17 loss. Overall, by modulating systemic cytokine levels, T cell polarization, and innate immune signaling, the microbiome shapes the environment in which HIV must replicate [57]. A community rich in anti-inflammatory metabolites and regulatory cues should in principle limit the CD4^+ T cell activation and turnover that fuel HIV expansion as shown in Fig. 1 [58].

Fig. 1.

Illustration of HIV-induced gut dysbiosis and barrier dysfunction. HIV infection causes bacterial overgrowth, epithelial barrier disruption, and reduced antimicrobial peptide (AMP) production, leading to microbial translocation and chronic inflammation. These changes drive CD4⁺ T cell depletion, enhanced viral replication, and progression from healthy gut to AIDS

Direct antiviral effects of microbiome-derived factors

Beyond shaping immunity, some microbiota-derived substances may have direct anti-HIV activity. For example, lactic acid produced by lactobacilli has been shown in vitro to inactivate viruses [59]. Although most studies have focused on vaginal lactobacilli and HIV, similar principles may apply in the gut: a low pH and bacteriocin production by commensal bacteria can create an environment hostile to pathogens [60]. In line with this, the increase of bacteria that “accumulate antiviral compounds” suggests that certain taxa may secrete small molecules or peptides that inhibit viral replication. Experimental data support this idea: as noted, exogenous butyrate directly reduced HIV replication in cell culture [61]. It is plausible that other SCFAs or tryptophan metabolites similarly alter host cell susceptibility to HIV or interfere with viral transcription. In addition, the IgA antibodies whose repertoire is shaped by the gut microbiota may neutralize HIV virions in the gut lumen, preventing further infection of target cells. the gut microbiome contributes to defense against HIV by (1) maintaining the epithelial barrier and preventing microbial translocation, (2) producing anti-inflammatory metabolites (SCFAs, indoles, etc.) that regulate immune activation, (3) supporting protective T cell subsets (Th17/Th22) and innate lymphoid cells, and (4) potentially generating direct antiviral factors that limit HIV replication [62]. Disruption of these mechanisms by dysbiosis may explain why HIV infection often leads to unchecked inflammation [63]. Therefore, interventions aimed at bolstering the “protective” microbiome functions could reduce HIV susceptibility or disease severity. The gut microbiota in HIV infected are shown in Table 3 [64].

Table 3.

Outlines recent evidence on gut microbiota composition across various HIV-infected groups

Gut Microbiota	Study Group/Comparison	Diversity	Abundance (Main Findings)	References
Bacteria	Sero-converters (SC) before HIV-1 infection vs. HIV-1 negative controls (NC)	—	SC before infection: Families Succinivibrionaceae, S24-7, Mogibacteriaceae, Coriobacteriaceae	[12]
Bacteria (MSM)	(1) SC with HIV-1 progressing to AIDS within 5 years vs. (2) SC remaining AIDS-free > 10 years without ART	—	Group 1: Family Prevotellaceae, Victivallaceae increased; Species Bacteroides fragilis, Eubacterium cylindroides enriched	[12]
Bacteria (Maternal & Infant)	Mothers with HIV vs. HIV-negative mothers	No major differences	HIV+ mothers: Reduced Lactobacillus	[13]
Bacteria (Unspecified group)	High viremia vs. viral suppression	—	High viremia: Ruminococcus 2, Succinivibrio increased. Viral suppression: Intestinibacter decreased	[11]
	Before vs. after ART (longitudinal analysis)	No significant changes	No significant changes	[11]
	Immunological responders (IR) vs. non-responders (INR)	—	IRs: Faecalibacterium reduced; Alistipes increased	—
	HIV + vs. HIV- individuals	HIV+ showed reduced diversity	HIV+: At phylum level → Fusobacteria higher, Firmicutes lower. At genus level → Fusobacterium, Prevotella 9 enriched, while Faecalibacterium, Alistipes, Akkermansia, Ruminococcaceae UCG-014 depleted	[5]

Microbiome composition and HIV susceptibility

Observational studies have identified specific bacterial signatures that correlate with HIV susceptibility and progression [12]. In one prospective analysis of men who have sex with men (MSM), individuals who later acquired HIV (“seroconverters”) already had higher gut abundances of taxa such as Succinivibrionaceae, Coriobacteriaceae, and Erysipelotrichaceae, and lower levels of Bacteroidaceae, Akkermansia, and certain Bacteroides species, compared to HIV-negative controls [65]. These alterations were present months before infection and were accompanied by elevated plasma levels of sCD14, sCD163, IL-6, and LPS-binding protein (markers of microbial translocation and immune activation) [66]. This suggests that pre-existing gut dysbiosis, even in the absence of HIV, may increase the likelihood of viral acquisition by creating a pro-inflammatory milieu [66, 67]. A separate Mendelian randomization study used human genetics to infer causality and found that certain gut families (e.g. Ruminococcaceae, Subdoligranulum) were associated with higher HIV risk, whereas Erysipelotrichaceae and Methanobrevibacter appeared protective [68]. While MR analysis cannot reveal mechanisms, it supports the idea that microbiome composition influences HIV susceptibility. Together, these data suggest that a microbiome that is both abundant in Bacteroidaceae (e.g. Bacteroides fragilis), Akkermansia and butyrate producers may help prevent infection, whereas a microbiome dominated by pro-inflammatory taxa (Prevotella, Proteobacteria, etc.) could be the predisposing factor to infection [69]. The underlying causative relationships are still under study, but the patterns are in line with established interactions of the microbiome and immune system: e.g. Bacteroides fragilis has the potential to stimulate regulatory T cells through its polysaccharide A, which reduces inflammation and Prevotella is capable of stimulating IL-17 and IL-17 stimulation. Therefore, the differences in microbial composition are reflected as specific states of immune [70, 71].

Microbiome‑associated determinants of HIV acquisition

HIV and SIV produce extreme depletion of gut CD4 + T cells, particularly those that produce critical cytokines IL-17 and IL-22 that are obligatory to preserve gut barrier competence and enlist protective immune cells [72]. This loss compromises the structural and immunological capabilities of the intestinal mucosa, causing more microbial translocation and inflammation. These alterations are also connected with changes in the composition of gut microbiomes, which indicates a two-way interaction between dysbiosis and immune dysfunction in HIV/SIV [73].

Recent evidence suggests that the makeup of the microbiome can affect HIV infection. Vaginal microbiomes that are not dominated by Lactobacillus species increase women’s risk of contracting HIV, and in men who have sex with men (MSM), certain gut microbial signatures, such as Prevotella dominance, are linked with increased risk of HIV. Longitudinal studies indicate that those who eventually seroconvert have unique microbiome characteristics and increased systemic inflammation before infection. There is further experimental animal evidence that antibiotic-induced dysbiosis predisposes rectal SIV, although this is apparently caused more by dysbiosis-induced changes in mucosal immunity than by individual microbial taxa [74]. Therefore, the host immune responses that are influenced by the microbiome, and not individual bacteria themselves, might mediate susceptibility to HIV infection [75].

Microbiome-based interventions

Given the microbiome’s influence on HIV pathogenesis, a number of interventions have been tested to manipulate gut flora and its metabolic output [76]. These include probiotics (live microbial supplements), prebiotics (non-digestible substrates that feed beneficial microbes), synbiotics (combinations of both), and fecal microbiota transplantation (FMT) [77]. A conceptual framework shows that these strategies seek to enrich “protective” taxa and functions, for example, boosting SCFA production or replenishing depleted genera as shown in Fig. 2 [78].

Fig. 2.

Schematic representation of gut–liver axis involvement in fibrosis during HIV infection. HIV impairs the gut epithelial barrier, allowing translocation of microbiome products into the portal system. These microbial products reach the liver via the portal vein, where they activate toll-like receptors (TLRs) on hepatic stellate cells (HSCs) and Kupffer cells, triggering inflammation, hepatocyte injury, and progression to fibrosis

Probiotics and synbiotics

Probiotics are the most widely studied microbial therapies in HIV. Common formulations include Lactobacillus spp., Bifidobacterium spp., or the yeast Saccharomyces boulardii. Early uncontrolled studies hinted that probiotics could reduce gut permeability and improve CD4 recovery [79]. For instance, an RCT in Spain found that 12-week supplementation with S. boulardii in ART-treated patients significantly lowered plasma markers of microbial translocation (lipopolysaccharide-binding protein, LBP) and inflammation (IL-6) compared to placebo [80]. These results indicate that probiotics have the potential to partially reinstate gut barrier functioning as well as attenuate systemic immune activation. A second North American trial (Visbiome study) demonstrated that high-potency probiotic mixture in a very mild decrease Gammaproteobacteria levels but no improvement of crucial markers of inflammation. Even these promising signs do not make bigger controlled studies any less disappointing [79, 81]. The PROMALTIA trial gave a synbiotic cocktail (prebiotic oligofructose plus S. boulardii and omega-3s) to patients starting ART with advanced disease; after 12 weeks there was no added benefit on CD4 recovery or gut integrity beyond ART alone [82]. Pooled with other studies, it was also noted in the PROOV-IT study that there was no effect on Visbiome (Lactobacilli/Bifidobacteria mix) on immunologic outcomes in immunologically non-responding individuals on suppressive ART [82]. These mixed results reflect several challenges. Conventional probiotics often fail to stably engraft in the gut and typically do not alter the resident microbiota composition long-term. Indeed, most studies saw only transient shifts in taxa after probiotic use [83]. In addition, the strains and doses used vary widely across studies, making it hard to draw firm conclusions [84]. Overall, current evidence does not support routine use of existing probiotic products to control inflammation or enhance immune recovery in HIV. Nonetheless, the concept remains promising: more recent efforts focus on next-generation probiotics or live biotherapeutic products (LBPs) – defined consortia or engineered strains derived from healthy gut microbiota – that are tailored to precise immunologic goals [84, 85]. Such products, once developed, may provide more robust and durable colonization, and could be administered alone or in combination with dietary therapies [86].

Prebiotics and dietary modulation

Prebiotics are fermentable fibers or oligosaccharides that selectively stimulate beneficial bacteria. By enhancing the growth of SCFA-producers (e.g. Faecalibacterium, Lachnospira) and Bifidobacteria, prebiotics can increase production of butyrate and other protective metabolites. In one study of ART-treated patients receiving prebiotic supplements, the abundance of Faecalibacterium prausnitzii (a major butyrate producer) rose, correlating strongly with fecal butyrate levels [86, 87]. Such increases in butyrate-producers are associated with improved gut barrier markers. However, as with probiotics, clinical trials of prebiotics in HIV have been limited and varied; many small studies have found only partial or inconsistent improvements in dysbiosis or inflammation [88]. Dietary interventions more broadly have been explored. A Mediterranean-style diet (rich in fiber, polyphenols, and healthy fats) was tested in a randomized trial of HIV patients, with results showing increases in beneficial bacteria and reduced markers of immune activation (though the trial was small) [89]. In general, diets high in fruits, vegetables, and whole grains tend to promote gut diversity and SCFA production, whereas Western diets (high fat/sugar) can exacerbate dysbiosis [73]. Thus, nutritional guidance is often suggested as a supportive therapy for people with HIV, although definitive evidence of reduced HIV risk is lacking [90].

Fecal microbiota transplantation (FMT)

FMT involves transfer of a whole microbial community from a healthy donor into the patient’s gut. It has been remarkably effective for Clostridioides difficile infection, and it is being investigated for HIV [91]. The logic is that FMT could replace a dysbiotic microbiota with a diverse, resilient one that restores protective functions. In animal models of HIV (SIV-infected macaques), experimental FMT has shown intriguing benefits [92]. A single study showed that antibiotic conditioning and thereafter FMT upsurged the frequency of IL-17 and IF 22-producing lymphocytes in the intestine and lowered the activation of CD4 T cells, whereas there was scanty clinical SIV marker alterations [93]. These results indicate that despite having no effect on the level of the viral load, FMT is able to promote mucosal immunity and possibly enhance the barrier. There is early and positive evidence of FMT in HIV trials on humans. Small pilot studies in ART-treated patients (all virologically suppressed) have demonstrated that repeated FMT (via colonoscopy or oral capsules) is safe and can transiently increase gut microbial diversity and donor strains. For example, a weekly oral FMT regimen over 8 weeks led to significant engraftment of butyrate-producing taxa and a drop in intestinal fatty acid–binding protein (IFABP, a marker of gut epithelial damage) [91]. These changes hint at reduced gut injury and inflammation. The effects, however, often wane over months unless the patient receives multiple or high-dose FMTs [94, 95]. Not all subjects respond equally – those with very low diversity at baseline tend to show greater donor engraftment, – suggesting patient selection will be important. Importantly, no safety signals (beyond mild GI symptoms) have emerged in HIV FMT trials to date, but systematic studies are needed [92]. Given the complexity of HIV-associated dysbiosis, FMT may be more effective when combined with other therapies (e.g. temporary antibiotics or prebiotics) to help the donor microbes establish. Future trials are aiming to determine if FMT can sustainably reduce systemic inflammation or improve immune reconstitution in HIV [85].

Postbiotics and next-generation therapeutics

Beyond whole microbes, interest is growing in postbiotics (microbial metabolites or components) and tailored live biotherapeutic products. For example, given the importance of butyrate, researchers have considered directly supplementing this SCFA or its precursors [96]. In SIV macaques on ART, oral tributyrin (a prodrug of butyrate) was tested but showed only minimal effect on residual inflammation [97]. One reason may be rapid absorption or metabolic conversion before reaching the colon [98]. Another approach is to administer butyrate-producing bacteria (next-generation probiotics) in high numbers. Indeed, patients with HIV have notably lower levels of Roseburia intestinalis and other butyrate-producers, which correlates with higher immune activation. In vitro, adding butyrate to immune cells from such patients reduced HIV replication, underscoring its regulatory potential [99]. Thus, delivering either the metabolite or its microbial producers is an appealing strategy. Other candidate postbiotics include indole-3-propionate and other AhR ligands derived from tryptophan metabolism, which could promote IL-22 production and barrier defense [83]. Formulations of bacterially derived peptides or polysaccharides (similar to Bacteroides fragilis PSA) might be explored to bias the immune response. Advances in synthetic biology now allow design of LBPs: defined cocktails of gut bacteria engineered to perform specific functions (for example, secrete anti-inflammatory cytokines or HIV-binding proteins) [100]. These approaches are at an early stage in HIV research, but analogous products have been developed for other conditions [101]. In all these interventions, the ultimate goal is to restore the biochemical and immunologic environment of a healthy gut – abundant SCFAs, intact mucus/IgA layer, regulatory immune tone, which should make the host more resistant to HIV [102].

Current limitations and future directions

Despite promising concepts, the field faces significant limitations. Most human studies to date are cross-sectional or small trials; causality is hard to prove. Observational microbiome surveys are confounded by many variables: diet, geography, sexual behavior, ART regimen, co-infections, and more [89]. For instance, many reported shifts (e.g. Prevotella enrichment) reflect lifestyle or cohort differences rather than HIV per se. Even sophisticated analyses have sometimes found only subtle microbiome differences when controlling for confounders [93]. Mechanistic studies in humans are few as shown in Table 4.

Table 4.

Summarizes the major barriers in microbiome-HIV research, outlining specific challenges and potential strategies to overcome them

Research Barrier	Specific Challenge	Proposed Solution
Complexity of microbial interactions	Hard to distinguish causation from correlation in microbial relationships	Foster multidisciplinary research using advanced computational modeling combined with experimental verification
Incomplete definition of a healthy microbiota	No clear agreement on what constitutes a “healthy” microbiome, with wide variation across populations	Establish standardized criteria for microbiome studies through international collaborations
Individual variability in microbiome	Differences among individuals make standardization difficult	Emphasize personalized approaches and conduct large-scale population-based studies
Confounding effects of sexual practices	Difficult to separate HIV-related effects from those linked to sexual behavior	Design controlled studies that specifically assess the influence of sexual practices
Confounding effects of geographical and dietary factors	Regional and dietary diversity complicates generalization of results	Incorporate cross-cultural comparisons and diverse dietary backgrounds in research
Interactions with ART	Antiretroviral therapy affects the microbiome differently depending on regimen	Carry out systematic studies on ART–microbiome relationships with standardized treatment protocols
Limited longitudinal data	Lack of long-term monitoring hampers evaluation of safety and effectiveness	Implement long-term study frameworks with extended follow-up after treatment
Ethical and clinical trial constraints in tissue studies	Invasive sampling raises ethical and logistical challenges	Develop innovative, noninvasive methods to study microbial activity in tissues
Lack of standardized methodologies	Variations in techniques hinder consistency, especially in proteomics and metabolomics	Create universal research protocols supported by collaborative method development
Technological and analytical challenges	Current tools have limitations in capturing the microbiome complexity, and data analysis is difficult	Invest in cutting-edge technologies and strengthen collaborations with computational scientists
Generalizability of findings	Microbiome variation makes it difficult to apply results across populations	Conduct multicenter studies with participants from diverse backgrounds
Interdisciplinary integration	Coordinating across different fields can be challenging	Build structured interdisciplinary programs and shared collaborative platforms
Funding and resource allocation	Insufficient financial support and competing priorities	Promote stronger advocacy for funding and diversify sources of financial support

It highlights methodological, biological, and ethical constraints, along with proposed solutions for advancing future studies

It is difficult to directly observe the impact of specific bacterial functions on HIV outcomes. Animal models (SIV-infected macaques) have been informative but do not fully replicate human HIV infection and microbiome diversity [103]. Gnotobiotic mouse models or in vitro gut-on-a-chip systems may help dissect cause–effect but lack certain human immunological components. Intervention trials have been heterogeneous. Probiotics and prebiotics come in many formulations, making comparisons hard [104, 105]. FMT studies have only enrolled a handful of patients; the optimal dosing regimen and donor selection remain unresolved. On the mechanistic front, key questions persist. Exactly which microbial metabolites are most critical [105], While SCFAs and indoles have been implicated, many other pathways are unexplored (e.g. bile acid metabolism, peptidoglycan sensing, fungal/viral components of the microbiome). The role of non-bacterial microbiome (fungi, bacteriophages) in HIV defense is virtually unknown. Furthermore, individual responses to microbiome-targeted therapies vary: host genetics, immune status, and baseline microbiome all influence engraftment and effect [106].

Future research must address these gaps. Large longitudinal cohort studies are needed to track the microbiome from HIV exposure through infection and treatment, to identify causal microbiota–HIV links. Metagenomic and metabolomic profiling should be combined with immune phenotyping to pinpoint protective versus harmful functions [107]. The development of multi-omics and machine learning can show microbial fingerprints indicating susceptibility or response to treatment. Interventional trials are supposed to shift to a rational design. Human microbiome information should also inform next-generation probiotics (LBPs): e.g., HIV-uninfected individuals strains that are best at mucosal immunomodulation [108]. Attention is being given to design of defined microbial consortia (cocktails of cultured human symbionts) and no single ones. Individualized treatment (adoption of donor stool that suits the patient in FMT, or customization of prebiotics according to the diet) can enhance uniformity [109]. Purified butyrate analogs (e.g. indole derivatives) and postbiotic therapies, which would avoid the variability of live microbes, would need careful dosing studies. Lastly, human clinical trials need to strictly evaluate the outcomes that extend the microbiome composition: gut permeability tests, immune activation consortia, viral store size, etc [110]. It will be essential to identify whether or not interventions with microbiomes have the potential to really change the trajectory of HIV, such as by seeding reservoirs during acute infection or improving ART immune restoration. It is only through that kind of mechanistic and clinical research that the potential of microbiome in terms of HIV defense is achieved to the fullest [111]. There is an increasing literature on the active role of the gut microbiome in the defense against HIV in its host. A healthy microbiome can reduce HIV pathogenesis by promoting intestinal barrier integrity, immune activation regulation, and antiviral metabolic synthesis [112]. Microbiome-based treatments (probiotics, prebiotics, FMT, etc.) have the potential to supplement these natural defenses. Nonetheless, existing data are still primitive and, at times, inconsistent, which is why more systematic, mechanistic researches are necessary. This next step will be achieved through combined efforts across microbiology, immunology, and clinical HIV research to come up with validated microbiome-targeted HIV prevention and treatment strategies [74, 113, 114].

Conclusion

The last ten years have brought a lot of enlightenment on the role of the gut microbiome in the HIV infections that the paradigm has shifted the outlook and instead of looking at the microbiota as a bystander, it is being considered as an active member of the immune system. Diverse and balanced microbiome allows the maintenance of integrity of the barrier, regulation of inflammation, and direct antiviral activity, thus providing a less favorable environment to HIV infection and the progression of the disease. On the other hand, dysbiosis and depletion of useful metabolites enhance immune response and contribute to the maintenance of viruses. Although the use of microbiomes as disease-modifying interventions (e.g. probiotics, prebiotics, FMT, etc.) were demonstrating promise, their clinical effectiveness remained low due to inconsistency of effects and methodological concerns. In the future, studies should focus on the mechanistic understanding, rational structure of the microbial consortia and metabolomic and immunologic data combination to design interventions. The gut microbiome has potential to become a therapeutic focus together with antiretroviral therapy, as well as treating the enduring problems of immune activation, reservoir maintenance, and long-term health in HIV-positive people, through the careful design of studies that enable it to be a therapeutic focus. The gastrointestinal tract is a complex microbiome with metabolic and immunologic activities being essential to the well-being of the host. In a healthy person, the intestinal microbiota (or about 10 14 organisms representing hundreds of species) has a complex set of functions, including the metabolic assistance of the intestinal mucosal surface and fine-tuning of the immune system. As an illustration, commensal bacteria break down dietary fibers into short-chain fatty acids (SCFAs) that provide energy to enterocytes and provide a signal to immune cells, and plasma cells present in the gut secrete IgA which combats luminal microbes and viruses. These host microbiome relations contribute to the sustenance of the integrity of the gut barrier and regulated mucosal immune setting. The infection with human immunodeficiency virus (HIV) infection significantly disrupts this system: HIV quickly infects (GALT), eliminates CD4. + T cells (particularly Th17/Th22 varieties) and makes the mucosa damage and translocate microbes. The outcome is persistent systemic inflammation as well as immune activation, which enhances disease development. There is mounting evidence that a healthy gut microbiome may neutralize such outcomes and an HIV susceptibility/pathogenesis, through multiple mechanistic routes. The review will first consider the most recent evidence (within the last 5–10 years) of the ability of gut microbes to protect against HIV in humans, and then consider interventions, probiotics, prebiotics, dietary modification, and fecal microbiota transplantation (FMT) intervention designed to harness these effects. We also address the existing constraints as well as the future research initiatives in this nascent area.

Author contributions

A.Z. wrote the text and performed the formal analysis; N.A. and M.Y.S. curated the data. A.M.A. handled the conceptualization and writing edits.

Funding

This study was funded by the Deanship of Research and Graduate Studies at King Khalid University through Large Research Project under grant number RGP2/497/46.

Data availability

No datasets were generated or analysed during the current study.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.