The Gut–Iron–Immune Axis in Severe Anaemia and Bacteraemia

1. Introduction

Severe anaemia, characterised by critically low haemoglobin concentrations or red blood cell (RBC) mass [1], remains a major cause of hospitalisation and mortality among young children and women of reproductive age globally [2,3]. The burden is disproportionately high in sub-Saharan Africa, where severe anaemia affects up to 14% of community-based children, and accounts for 9 to 40% of paediatric hospital admissions with febrile illness [4,5,6]. In this region, severe anaemia is driven by complex and often overlapping aetiologies, including infections, haemoglobinopathies, and nutritional deficiencies [2,3]. Beyond its direct clinical consequences, severe anaemia is associated with an increased risk of invasive bacterial infections, particularly those caused by enteric pathogens such as non-typhoidal Salmonella (NTS) and Escherichia coli [6,7]. Although the biological mechanisms underlying this association remain incompletely understood, disruption of iron homeostasis, impaired immunity, and gut dysfunction have emerged as important contributors [8,9].

The gut represents a plausible interface linking severe anaemia with enteric pathogens. Under physiological conditions, the gut microbiome regulates nutrient metabolism, epithelial barrier integrity, mucosal immunity, and colonisation resistance against enteric pathogens [10,11,12]. Emerging evidence suggests that severe anaemia disrupts these processes through tissue hypoxia, dysregulated iron homeostasis, compromised barrier integrity, and impaired immune function (Figure 1). These changes may promote gut dysbiosis, characterised by reduced microbial diversity, depletion of beneficial commensals, expansion of pathobionts, altered microbial metabolism, impaired mucosal barrier function, and increased microbial translocation and virulence [13,14,15,16]. Conversely, gut dysbiosis may further exacerbate anaemia by impairing iron absorption and utilisation, disrupting micronutrient metabolism, promoting intestinal and systemic inflammation, and compromising barrier integrity [10,17,18]. Invasive bacterial infection may further exacerbate anaemia through inflammation-driven iron sequestration, haemolysis, bone marrow suppression, and sepsis-mediated eryptosis [19,20,21]. Together, these interactions support a self-reinforcing cycle linking severe anaemia, gut dysfunction and invasive bacterial infection. In high-burden settings, this cycle is likely to be modified by contextual factors including undernutrition, malaria, environmental enteric dysfunction (EED), and host genetic variation, which are factors that influence both anaemia susceptibility and gut microbial ecology [22,23,24].

In this Review, we propose that disruption of the gut-iron-immune axis represents a unifying biological framework linking severe anaemia to invasive bacterial infection. We synthesise current evidence on the bidirectional biological mechanisms linking severe anaemia, iron homeostasis, and the gut microbiome; examine how these interactions contribute to susceptibility to invasive bacterial disease; and discuss priorities for future mechanistic and translational research.

2. The Gut Microbiome in Health

The gut microbiome is a complex and spatially heterogeneous intestinal ecosystem comprising bacteria, archaea, viruses, fungi and protozoa [12,25]. Its microbial component, the gut microbiota, consists of approximately 10¹³–10¹⁴ microbial cells in the adult human gut, with the highest microbial densities in the colon [26,27]. The gut microbiota has co-evolved with the host to form a dynamic mutualistic ecosystem [28,29]. Although microbial composition varies considerably between individual and over time, bacterial communities typically span approximately 50 phyla and are dominated by Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) [12,30].

Functionally, the gut microbiota regulates host nutrient metabolism, iron homeostasis, immune function, and intestinal barrier integrity [11,22,23]. One of the principal metabolic functions of the gut microbiota is the fermentation of dietary fibre into short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate [18]. These metabolites support epithelial energy metabolism, modulate mucosal and systemic immune responses, strengthen barrier integrity, and lower luminal pH [18,31]. The microbiota also converts primary bile acids, amino acids, and dietary phytochemicals into bioactive metabolites that regulate epithelial regeneration, antimicrobial peptide production, and mucosal immune tolerance [32,33]. In addition, the gut microbiota synthesises vitamin K and several B vitamins including folate, vitamin B6, and vitamin B12 [17]. Folate and vitamin B12 are required for DNA synthesis and proliferation of erythroid precursors, while vitamin B6 acts as a cofactor in haem biosynthesis [34,35].

Beyond these metabolic functions, the gut microbiota is an important regulator of iron homeostasis influencing luminal iron availability, intestinal iron absorption, and systemic iron-regulatory pathways [10]. Microbial metabolism increases iron solubility by lowering luminal pH through SCFA production, potentially enhancing intestinal iron absorption [36,37,38]. Iron availability, in turn, shapes the intestinal ecological landscape and host-pathogen interactions. Many enteric bacteria, particularly members of Enterobacteriaceae, produce high affinity siderophores that scavenge ferric iron from the intestinal microenvironment [39,40], providing a competitive advantage under iron-limited conditions [41]. Conversely, host proteins such as hepcidin, transferrin, lactoferrin, and lipocalin-2 restrict microbial access to iron while maintaining systemic iron homeostasis, a process termed nutritional immunity [42]. The gut microbiota also contributes to the production of hepcidin [43,44], the principal iron regulatory hormone [45].

These metabolic activities are closely integrated with maintenance of intestinal barrier integrity and mucosal immunity. The intestinal barrier comprises a single layer of epithelial cells reinforced by tight junctions, a mucus layer, antimicrobial peptides, secretory IgA, and specialised resident immune cells [46,47,48]. Continuous crosstalk between the microbiota, epithelial cells, and resident immune cells coordinates intestinal homeostasis and immune surveillance, tolerance, and protection [48,49]. Through interactions with the host’s pattern-recognition receptors, microbiota’s microbial-associated molecular patterns support the development, maturation, and function of both mucosal and systemic immune cells [11].

Together, these metabolic, barrier, and immune functions of a healthy microbiota maintain colonisation resistance (Figure 2). Resident commensals suppress expansion of enteric pathogens through competition for nutrients and ecological niches, production of antimicrobial metabolites, maintenance of luminal oxygen and pH, and sequestration of essential micronutrients, particularly iron [50]. Loss of colonisation resistance promotes expansion of enteric pathobionts, increasing the risk of microbial translocation and invasive bacterial infection.

3. Severe Anaemia and the Gut Microbiota

Severe anaemia and the gut microbiota are linked through complex bidirectional interactions Experimental studies demonstrate that disruption of the gut microbiota, including through broad-spectrum antibiotic exposure, impairs haematopoiesis and exacerbates anaemia [51]. In contrast, direct evidence in humans remains sparse and is largely derived from aa small number of observational studies in patients with chronic kidney disease or Crohn’s disease [52,53]. Mendelian randomisation analyses, conducted predominantly in populations of European ancestry, provide preliminary evidence supporting a potentially causal relationship between specific microbial taxa, including Ruminococcus, Desulfovibrio, and Roseburia, and increased susceptibility to iron deficiency anaemia (IDA) [54,55,56,57]. However, these findings may not be generalisable to populations in sub-Saharan Africa where gut microbial composition, diet, and infectious disease burden differs substantially. Thus, whether the gut microbiota similarly contributes to severe anaemia pathogenesis in African children remains unknown.

Conversely, accumulating evidence indicates that severe anaemia is associated with remodelling of the intestinal ecosystem. Experimental studies demonstrate that severe anaemia compromises intestinal barrier integrity through hypoxia-induced epithelial injury, intestinal inflammation, and reduced expression of tight-junction proteins, including zonula occludens-1 [15,16]. These changes are likely to alter the intestinal microenvironment, promoting microbial dysbiosis and weakening colonisation resistance. Consistent with this, studies in young children and preterm infants report a dysbiotic microbial profile characterised by reduced microbial diversity, depletion of beneficial commensals, and expansion of enteric pathobionts [13,58,59,60]. The extent of these alterations appears to increase with anaemia severity. For example, among preterm infants in the United States, increasing anaemia severity was associated with progressive depletion of Bacillota and enrichment of Pseudomonadota [13]. Despite marked differences in underlying aetiology, broadly similar microbial signatures have been reported across multiple severe anaemia phenotypes (Table 1), including iron deficiency anaemia (IDA) [61,62,63,64,65], anaemia of chronic disease [66,67], aplastic anaemia [68,69], sickle cell disease [70,71,72,73], and severe malarial anaemia [74]. Beyond taxonomic changes, severe anaemia is associated with functional alterations in the gut ecosystem, including increased bacterial virulence potential and intestinal injury [14,75,76]. However, because most studies are observational and conducted in a limited number of populations, it remains unclear whether these intestinal alterations are drivers or consequences of severe anaemia or reflect shared underlying factors. The following sections examine how major causes of severe anaemia, including iron deficiency, malaria, sickle cell disease, and malnutrition may lead to gut dysbiosis.

Iron deficiency is the most common cause of anaemia globally [3,77]. Observational studies have linked IDA with the common dysbiotic microbial signature described above, characterised by reduced microbial diversity, depletion of beneficial commensals, increased intestinal inflammation and expansion of pathobionts [61,62,63,64,65]. However, most of this evidence is derived from cross-sectional studies. Mendelian randomisation studies, predominantly in European ancestry populations, report inconsistent findings. Some studies found associations between genetically predicted iron status and gut taxa (including Ruminococcaceae), while others show little or no evidence for causal effects [54,55]. In contrast, experimental studies consistently support adverse effects of IDA on the gut microbiota. In animal models, IDA remodels gut microbial composition, promotes small intestine bacterial overgrowth, alters SCFA production, and disrupts epithelial barrier integrity [78,79,80,81,82,83]. In vitro studies further demonstrate that iron limitation suppresses microbial pathways involved in SCFA biosynthesis [84]. These alterations appear partially reversible following nutritional interventions, including iron repletion and dietary modification, such as fermented goat’s milk [85,86]. However, iron supplementation itself may disrupt the gut microbiome and promote expansion of siderophilic pathobionts [87,88]. These findings suggest that iron availability is a major ecological determinant of gut microbial composition and function, providing a mechanistic link between IDA, gut dysbiosis, and susceptibility to invasive bacterial infection.

Severe malarial anaemia (SMA) remains a leading cause of hospitalisation and death, particularly among young African children [90]. SMA arises from Plasmodium-driven haemolysis of parasitised and non-parasitised erythrocytes, bone marrow suppression, and inflammation-mediated dyserythropoiesis [91,92]. Evidence linking SMA to the gut microbiome remains limited but suggests disruption of intestinal microbial and barrier homeostasis. In Ugandan children with SMA, stool microbiota demonstrated enrichment of enteric pathobionts, including E. coli and Klebsiella pneumoniae [74]. SMA has also been associated with increased intestinal permeability and endotoxaemia in Kenyan children [93], consistent with enhanced microbial translocation across a compromised epithelial barrier. These alterations contribute to the well-recognised susceptibility of children with SMA to invasive NTS bacteraemia [94,95,96]. However, increased intestinal permeability has also been reported in uncomplicated and severe malaria regardless of severe anaemia [97,98], suggesting that malaria itself might contribute to gut barrier dysfunction. The relative contributions of severe anaemia, malaria parasite pathogenesis, or haemolysis to intestinal dysbiosis remain uncertain.

Sickle cell anaemia (SCA) is a hereditary haemolytic disorder characterised by chronic anaemia, recurrent vaso-occlusion, dysregulated iron metabolism, and persistent inflammation [99]. Although human data remains sparse, SCA is consistently associated with gut dysbiosis characterised by reduced microbial diversity, depletion of SCFA-producing commensals, enrichment of pathobionts including Clostridium XI, Prevotella spp., and Enterobacteriaceae, and impaired intestinal barrier function [70,71,72,73]. Experimental studies support these SCA-mediated gut effects [73,100,101]. These microbial alterations are thought to arise from chronic intestinal hypoxia, repeated ischaemia-reperfusion injury caused by vaso-occlusion, haem exposure, altered iron handling, and sustained inflammatory stress [102]. The resultant gut dysbiosis amplifies systemic inflammation, vaso-occlusion, and pain in SCA patients [102,103,104]. In murine models, iron-restricted dietary interventions improve gut barrier integrity and partially reverse SCA-mediated dysbiosis [105]. Disease-modifying therapies, including hydroxyurea, are also associated with partial restoration of beneficial microbial taxa and improved intestinal homeostasis [106].

Malnutrition is a major determinant of severe anaemia in low-resource settings, with its relative contribution becoming increasingly prominent as malaria transmission declines [6]. Depending on nutritional phenotype, severe anaemia results from deficiencies in key substrates for erythropoiesis (including iron, folate, vitamin B12, and protein), inflammation-mediated iron sequestration, oxidative stress–mediated haemolysis, or impaired bone marrow responsiveness [107,108,109]. Although direct evidence linking malnutrition-associated anaemia to gut microbial disruption is sparse, malnutrition itself is consistently associated with microbial immaturity and gut dysbiosis [110,111,112,113]. These ecological alterations may reflect chronic nutrient deprivation, epithelial atrophy, recurrent enteric infections, and frequent antimicrobial exposure [30]. Given the substantial overlap between malnutrition and severe anaemia burden in endemic settings, malnutrition plausibly functions as an important effect modifier of severe anaemia-gut microbiome pathophysiology. In low-resource settings, anaemia and malnutrition are both linked with EED (also termed environmental enteropathy) [114,115,116,117]. EED is a chronic subclinical disorder of the small intestine characterised by villous blunting, epithelial dysfunction, and reduced barrier capacity [118]. Concomitant EED and disruption of intestinal barrier integrity could further increase gut permeability, facilitate microbial translocation, and predispose children to invasive bacterial infection.

Taken together, current evidence indicates that severe anaemia, irrespective of its underlying aetiology, is associated with similar alterations in the gut ecosystem. Across the discussed severe anaemia aetiologies, common features include reduced microbial diversity, depletion of beneficial SCFA-producing commensals, expansion of pathobionts, impaired intestinal barrier function, and increased gut inflammation. These convergent gut microbial signatures suggest that severe anaemia itself shapes intestinal microbial ecology. However, current evidence is largely associative. Understanding the biological mechanisms underlying this shared intestinal phenotype is, therefore, important to define the contribution of severe anaemia to invasive bacterial infection.

4. Mechanisms Linking Severe Anaemia to Gut Dysbiosis and Invasive Infection

Several interconnected mechanisms likely underpin the development of gut dysbiosis and increased susceptibility of invasive infection in severe anaemia (Figure 1). Central to this framework are intestinal tissue hypoxia, disrupted iron and nutrient homeostasis, compromised epithelial barrier integrity, and impaired mucosal and systemic immune responses (Box 1).

Box 1. Potential consequences of severe anaemia on the gut microbiome, intestinal barrier, and host immunity

Effects on the gut microbiota

• Reduced microbial diversity
• Reduced abundance of commensal and beneficial taxa
• Expansion of facultative anaerobes and enteric pathobionts
• Altered microbial metabolic capacity
• Reduced production of SCFAs, bile acid, indole, and amino acid-derived metabolites
• Impaired colonisation resistance against enteric pathogens
• Altered microbial iron acquisition and siderophore-mediated competition

Effects on mucosa and epithelia

• Reduced oxygen delivery to the intestinal mucosa
• Reduced mucus production and mucus layer integrity
• Increased epithelial cell damage
• Impaired intestinal barrier integrity and increased permeability
• Impaired epithelial cell turnover and repair
• Increased intestinal inflammation
• Reduced mucosal immune function, including secretory IgA and antimicrobial peptide production
• Increased microbial translocation and endotoxaemia

Systemic effects

• Increased susceptibility to invasive bacterial infection
• Impaired innate and adaptive immune cell function
• Increased systemic inflammation
• Dysregulated iron homeostasis and hepcidin signalling
• Increased NTBI and free haem availability for invasive pathogens
• Altered gut–immune signalling

Reduced haemoglobin concentrations impair oxygen delivery throughout the body. Hypoxia in the gut activates hypoxia-inducible factor signalling, which regulates mucus secretion, antimicrobial peptide production, epithelial metabolism, and tight-junction integrity [119,120]. Although these responses are initially adaptive, persistent or severe hypoxia plausibly overwhelms epithelial repair mechanisms. This results in impaired epithelial renewal, reduced goblet- and Paneth-cell function, and diminished expression of tight-junction proteins [15,16]. Hypoxia is likely to remodel the intestinal ecological niche by disrupting epithelial metabolism. Reduced epithelial oxygen consumption, compounded by depletion of butyrate-producing commensals, increases oxygen diffusion into the intestinal lumen [121,122]. This “oxygen leak” favours facultative anaerobes, particularly Enterobacteriaceae, at the expense of obligate anaerobic commensals, further increasing gut dysbiosis [122,123].

Disruption of iron homeostasis amplifies intestinal dysfunction. Iron is a fundamental determinant of microbial competition [39]. Altered iron status, whether arising from iron deficiency, iron sequestration, haemolysis, or iron supplementation, could potentially shift the balance in favour of pathobionts [10]. NTBI and free haem, in haemolytic anaemias, provide a readily accessible nutrient source for invasive pathogens [124,125]. Enterobacteriaceae possess highly efficient iron-acquisition systems, including multiple siderophores and haem uptake pathways [40]. Accelerated erythropoiesis further dysregulates systemic and luminal iron homeostasis, through suppressed production of the iron regulatory hormone hepcidin [94,126,127]. Reduced hepcidin alters intestinal iron flux and modifies iron availability within the distal gut, with downstream consequences for microbial ecology [128].

Progression to bacteraemia requires microbial translocation across the intestinal epithelium. Under physiological conditions, the intestinal barrier restricts intestinal microorganisms from accessing the systemic circulation. Severe anaemia plausible disrupts these protective mechanisms. Severe anaemia-induced NTBI and free haem promote oxidative epithelial injury through generation of reactive oxygen species [129,130]. Experimental models show that severe anaemia reduces expression of epithelial tight-junction proteins such as zonula occludens-1 [15,16]. Reduced production of SCFA and other microbiota-derived metabolites, because of gut dysbiosis, further compromises epithelial integrity and mucosal defence. Expansion of enteric pathobionts, driven by altered oxygen and iron availability, increases bacterial adherence, epithelial invasion, and inflammatory injury. Combined with tissue hypoxia, these alterations weaken intestinal barrier function and promote microbial translocation.

Establishment of invasive bacterial infection ultimately depends on host immune competence. Under physiological conditions, translocation of small numbers of intestinal microorganisms is rapidly contained by coordinated mucosal and systemic immune responses [11,48]. Severe anaemia compromises these immune mechanisms at multiple levels. First, reduced barrier protection, as discussed above, diminishes containment of enteric pathogens at the epithelial surface. Second, severe anaemia is associated with impaired innate immune function, including macrophage activation, cytokine signalling, and neutrophil chemotaxis, phagocytosis, and oxidative burst, which reduces bacterial killing [8,9,131]. Finally, adaptive immunity is compromised through reduced B- and T-cell production and function, although evidence remains limited [8,132]. In disease-specific contexts, such as SCA, functional asplenia further reduces clearance of invasive bacteria [99,133]. As a result, gut bacteria that breach the intestinal barrier are more likely to survive, disseminate, and establish bloodstream infection in individuals with severe anaemia.

5. Therapeutic Interventions in Severe Anaemia

Current management of severe anaemia focuses on rapidly restoring haemoglobin concentrations through iron supplementation or blood transfusion while addressing the underlying cause of anaemia [134]. Although these interventions are often lifesaving, emerging evidence indicates that they also modify the intestinal ecosystem, with potential consequences for gut microbial ecology, intestinal barrier function, and susceptibility to infection. Understanding these microbiome-mediated effects could facilitate the development of therapeutic strategies that optimise haematological recovery while minimising unintended adverse effects on the gut.

5.1. Iron Supplementation

Oral iron supplementation remains the cornerstone of treatment for anaemia [134]. Home-based food fortification with iron alone or as multiple micronutrient powders consistently improves iron status and reduces anaemia in young children across diverse settings [135]. Accordingly, the World Health Organization recommends routine iron supplementation in populations with a high prevalence of anaemia [136]. However, unabsorbed iron reaches the distal gut where it acts as a potent ecological substrate influencing microbial growth and interspecies competition [128].

Luminal iron levels can directly reshape the gut microbiota composition by altering the competitive landscape between commensals and pathobionts [10]. In several studies conducted in low-resource settings, iron supplementation or food fortification promoted expansion of pathogenic Enterobacteriaceae, depletion of Bifidobacterium and other SCFA-producing commensals, increased intestinal inflammation, and a higher incidence of diarrhoeal disease [87,88,137,138,139]. Similar observations have been reported elsewhere. For example, Swedish infants receiving high-iron formula exhibited reduced bifidobacterial abundance [140]. However, most studies have been relatively short in duration and have relied primarily on taxonomic profiling (Table 2), limiting understanding of microbial function, host responses, and long-term clinical significance.

The adverse effects of iron supplementation have not been universally observed. For example, studies in children from Bangladesh, Peru, and South Africa [141,142,143], as well as adults from high-income settings [144,145,146,147], reported little or no effect of iron supplementation on microbial composition, faecal SCFA, or gut inflammation. Similarly, experimental animal iron supplementation studies have produced heterogeneous findings, ranging from pronounced dysbiosis [148,149,150], to minimal or no observable microbiome alterations [83,151]. Such variability likely reflects differences in baseline iron status, iron formulation and dose, age, dietary context, pre-existing microbiome composition, and other potential confounding factors.

Iron-induced microbiome disruption is most relevant in populations already at highest risk of severe anaemia, infection, and EED. This presents a critical therapeutic challenge: how can iron deficiency and anaemia be corrected while preserving a healthy gut microbiome? Several alternative strategies show promise. Co-administration of ferrous sulphate with prebiotic oligosaccharides had minimal effects on gut microbial composition in Kenyan children [139]. Intravenous iron sucrose produced fewer microbiome perturbations than oral iron sulphate in adults with inflammatory bowel disease [152], while ferric maltol caused less dysbiosis than ferrous sulphate in experimental models [153]. Conversely, intermittent iron supplementation did not yield promising haematological recovery in non-pregnant Indian women [146]. Other emerging approaches, including precision iron formulations, lower-dose regimens, and microbiome-directed adjunctive therapies (prebiotics, probiotics, synbiotics, faecal microbiota transfer, or targeted nutritional strategies) warrant further evaluation. Supporting this, washed microbiota transplantation restored butyrate-producing bacteria and improved haemoglobin concentrations in adults with anaemia of chronic disease in China [66].

5.2. Blood Transfusion

Blood transfusion rapidly restores oxygen-carrying capacity and remains the primary treatment for life-threatening severe anaemia. Unlike oral iron, transfusion bypasses the intestinal lumen and, therefore, avoids direct disruptions of the gut microbiota. Nevertheless, indirect effects on gut microbial ecology are biologically plausible.

Although evidence is limited, available studies suggest that transfusion positively influences the gut microbiome. In patients with traumatic haemorrhage, blood transfusion has been associated with increased gut microbial α- and β-diversity [154]. However, interpretation of these findings is complicated by the frequent co-administration of empiric antibiotics and other intensive care interventions in these patients, which independently exert more immediate effects on the gut microbiota [155]. Experimental studies provide stronger mechanistic support. In murine haemorrhage models, whole-blood transfusion partially reversed intestinal dysbiosis, likely by reversing anaemia-associated hypoxia [156].

Transfusion could also, theoretically, have unintended adverse effects on the intestinal environment. Breakdown of transfused RBCs can transiently increase circulating NTBI and free haem. These molecules potentially promote epithelial injury and provide an accessible iron source for enteric pathobionts (Figure 1). Supporting this, blood transfusion has been associated with intestinal injury and necrotising enterocolitis in preterm neonates [157]. However, it remains uncertain whether these complications are caused by blood transfusion itself or the underlying severe anaemia and tissue hypoxia [158,159]. Prospective longitudinal studies are needed to define how blood transfusion interacts with the gut microbiome and whether these effects influence infection risk, recovery, or survival.

6. Conclusion and Recommendations

Despite growing recognition of the gut microbiome as a key regulator of host metabolism and immunity, its role in the pathophysiology of severe anaemia remains incompletely understood (Box 2). Current evidence suggests that severe anaemia and gut dysbiosis are linked through a complex interplay between disrupted iron homeostasis, impaired intestinal barrier function and altered immune responses. However, most available studies are cross-sectional, which limits inference regarding temporality and causality. Addressing these knowledge gaps requires a shift towards longitudinal, integrative, and mechanistically informed studies, particularly in populations with the highest burden of severe anaemia. Such work must move beyond taxonomic profiling to incorporate serial assessments before and after treatment, including iron supplementation, blood transfusion, antimicrobial exposure, and nutritional rehabilitation. Equally important is the systematic measurement of mucosal and systemic immune responses to map the immune circuitry linking anaemia to gut dysbiosis. Integrated multi-omics approaches combining metagenomics, metabolomics, transcriptomics, proteomics, and host phenotyping will be essential to define functional host-microbe interactions that compositional profiling alone cannot capture. A better understanding of the gut-iron-immune axis in severe anaemia may identify new microbiome-informed strategies to improve haematological recovery and reduce invasive bacterial infections, especially in populations where severe anaemia remains a major cause of morbidity and mortality.

Box 2. Key gaps in the severe anaemia-iron-gut microbiome axis

Causality and disease mechanisms

• What are the temporal relationships between severe anaemia, gut dysbiosis, intestinal barrier dysfunction, and invasive infection?
• Are alterations of the gut microbiome reversible following correction of severe anaemia?

Iron homeostasis and microbial ecology

• How do changes in luminal and systemic iron availability influence microbial community structure, function, and pathogen colonisation?
• What are the relative contributions of iron deficiency, hepcidin-mediated iron sequestration, haemolysis, and dietary iron exposure to gut dysbiosis?
• Which microbial functional pathways are most sensitive to disruptions in iron metabolism?

Context-specific determinants in high-burden settings

• How do microbial metabolic functions compare across major severe anaemia aetiologies, including iron deficiency, malaria-associated anaemia, and malnutrition?
• How does EED modify severe anaemia–gut microbiome interactions?
• Are the mechanisms linking severe anaemia and gut dysbiosis consistent across different aetiologies, epidemiological settings, and age groups?

Microbiome informed therapies

• How do iron supplementation, blood transfusion, and emerging iron-modulating therapies influence gut microbial ecology, intestinal barrier function, and infection risk?
• Can microbiome-directed interventions (prebiotics, probiotics, synbiotics, postbiotics, or faecal microbiota transplantation) improve anaemia recovery or reduce invasive bacterial infection?