Manuela M. Santos

Introduction: Ulcerative colitis is a chronic inflammatory disease affecting the colon, and its incidence is rising worldwide. Significant alterations to the composition and function of the gut microbiota that favor the expansion of pathobionts have been shown to be involved in ulcerative colitis. One such pathobiont is Escherichia coli strains carrying the pks island ( pks + E. coli ) that contribute to mucosal injury and exacerbate inflammation. In this study, we investigated whether microbiota-targeting interventions may restrict pks + E. coli expansion and mitigate chemically induced colitis in mice. Results: In mice colonized with the murine pks + E. coli NC101 strain (EcNC101) in which acute colitis was induced by dextran sulfate sodium, oral administration of putrescine significantly reduced disease severity, histological damage, and inflammatory cytokine expression. 16S rRNA gene sequencing revealed marked shifts in gut microbiota composition following putrescine treatment, characterized by an increase in the relative abundance of Actinobacteriota and a decrease of Proteobacteria phyla. Among these, Bifidobacterium pseudolongum was associated with higher colonic acetate levels and reduced colitis severity. In EcNC101-colonized mice with colitis, B. pseudolongum administration significantly alleviated colitis by increasing acetate levels and activating peroxisome proliferator-activated receptor γ (PPAR-γ). Functional assays suggested that acetate production by B. pseudolongum contributes to competitive inhibition of EcNC101 growth. Conclusions: This study highlights the potential of microbiota-modifying interventions, particularly probiotics such as B. pseudolongum , to control pathobionts, reduce inflammation, and improve intestinal health in ulcerative colitis.

The gut microbiota plays a key role in intestinal homeostasis by reinforcing the gut barrier and modulating inflammation. Gut barrier dysfunction or dysregulated inflammatory response in patients with colorectal cancer may lead to an increased risk of surgical complications associated with poor intestinal healing. Microbiota-modifying dietary interventions have the ability to shift microbial community structures and bacterial metabolite production, with profound implications for host health. This review focuses on the potential for short-term, preoperative, dietary fiber interventions in improving colorectal cancer surgical and oncological outcomes. Additionally, this review highlights important considerations for the optimization and personalization of dietary fiber interventions, notably individual- and fiber-specific microbiota responses.

Host–microbiota interactions during the neonatal window of opportunity have gained significant interest as factors influencing long-term health. Factors such as nutrient availability may shape the microbial community, and iron is no exception to this rule. Although the use of iron supplementation is widespread during infancy, this micronutrient is known to have profound effects on gut microbiota. This study aimed to determine how early-life iron supplementation shapes gut microbiota composition and whether it influences recovery from gut dysbiosis later in life. Three-week-old female C57BL/6 mice were fed an iron-excess diet for five weeks during the critical period of microbiota establishment. After a two-week washout period to normalize luminal iron content, dysbiosis was induced using either dextran sulfate sodium-induced acute colitis or antibiotic treatment. Mice were then allowed an 8-week recovery period. Gut microbiota composition was longitudinally analyzed by 16S rRNA gene sequencing of fecal samples. Early-life iron supplementation induced durable alterations in gut microbiota composition, with differences persisting even after luminal iron normalization (β-diversity, PERMANOVA p < 0.01). At the endpoint, mice exposed to an iron-sufficient diet remained significantly more distant from their baseline compared to the excess iron group in both the dextran sulfate sodium (33% greater distance) and antibiotic (41% greater distance) models (both p < 0.05). Notably, this pattern was not observed when supplementation occurred in adulthood. In the dextran sulfate sodium model, mice that received an iron-sufficient diet during early life showed an expansion of the probiotic Ligilactobacillus murinus, which positively correlated with fecal succinate levels. Conversely, in the antibiotic-induced model, early-life exposure to an iron-sufficient diet was associated with a more pronounced dysbiosis characterized by a nearly two-fold-greater loss in α-diversity compared to 500 ppm mice (∆Shannon: 1.98 ± 0.22 vs. 1.02 ± 0.25, p < 0.01). These findings suggest that early-life iron supplementation influences long-term host–microbiota interactions and recovery from gut dysbiosis.

Pks+ Escherichia coli is increasingly implicated in the development of colorectal cancer (CRC), particularly among a rapidly expanding subset of younger patients with early-onset CRC. pks+ E. coli strains produce the genotoxin colibactin, known to cause double-strand DNA breaks and mutations in cell proliferation and differentiation pathways associated with CRC. This article details a method for pks+ E. coli colonization in mice under non-inflammatory conditions, from preparation of bacterial inoculum through to validation of colonization. Following overnight incubation, pks+ E. coli strain E. coli NC101 is administered to antibiotic-conditioned mice via oral gavage. Colonization is assessed in stool by quantifying the number of lactose-fermenting gram-negative colony forming units (CFUs) and by quantitative PCR amplification. Using this protocol, it was shown that, following the successful colonization of C57BL/6 mice with E. coli NC101, supplementation with the dietary fiber inulin promoted the growth of pks+ E. coli, reflected by increased recovery of CFUs, higher abundance of the Enterobacteriaceae family, and increased levels of the clbP gene. In summary, this model allows for the study of preventative and therapeutic treatments targeting a key pathobiont involved in CRC development.

Pks+ Escherichia coli is increasingly implicated in the development of colorectal cancer (CRC), particularly among a rapidly expanding subset of younger patients with early-onset CRC. pks+ E. coli strains produce the genotoxin colibactin, known to cause double-strand DNA breaks and mutations in cell proliferation and differentiation pathways associated with CRC. This article details a method for pks+ E. coli colonization in mice under non-inflammatory conditions, from preparation of bacterial inoculum through to validation of colonization. Following overnight incubation, pks+ E. coli strain E. coli NC101 is administered to antibiotic-conditioned mice via oral gavage. Colonization is assessed in stool by quantifying the number of lactose-fermenting gram-negative colony forming units (CFUs) and by quantitative PCR amplification. Using this protocol, it was shown that, following the successful colonization of C57BL/6 mice with E. coli NC101, supplementation with the dietary fiber inulin promoted the growth of pks+ E. coli, reflected by increased recovery of CFUs, higher abundance of the Enterobacteriaceae family, and increased levels of the clbP gene. In summary, this model allows for the study of preventative and therapeutic treatments targeting a key pathobiont involved in CRC development.

The progression of metabolic dysfunction-associated steatotic liver disease (MASLD) to severe forms, including metabolic dysfunction-associated steatohepatitis (MASH) and liver fibrosis, involves metabolic dysfunction, genetics, and gut dysbiosis. People with HIV (PWH) represent a high-risk group for MASLD, but the role of gut microbiota alterations in disease severity within this population remains poorly understood. We prospectively recruited PWH with MASLD, defined as the controlled attenuation parameter (CAP) ≥ 238 dB/m, and excluded those with viral hepatitis coinfection or alcohol abuse. Severe MASLD was defined as the presence of MASH (cytokeratin-18 ≥ 130.5 U/L) and/or significant liver fibrosis (liver stiffness ≥ 7.1 kPa). Stool samples were collected for 16S rRNA gene sequencing to characterize gut microbiota composition. Functional predictions were generated using PICRUSt. The differential abundance of bacterial taxa and predicted functions were analyzed using a generalized linear model with a negative binomial distribution. Among 34 PWH with MASLD, 18 (53%) met the criteria for severe MASLD. Microbiota profiling revealed significant differences in bacterial genera between the PWH with and without severe MASLD. Enrichment was observed in the Ruminococcus gnavus group, Negativibacillus, Holdemanella, Subdoligranulum, the Eubacterium hallii group, and Butyricicoccus, while depletion was seen in Prevotella, Alloprevotella, Dialister, Catenibacterium, the Christensenellaceae R 7 group, Clostridium sensu stricto, Olsenella, Oscillospiraceae UCG-005, Libanicoccus, and the Eubacterium siraeum group. Predicted functional pathways related to fatty acid degradation, folate biosynthesis, and amino acids metabolism did not differ between groups. MASLD severity in PWH is associated with a distinct gut microbiota signature, though not with functional pathway alterations. Microbial profiling may complement existing non-invasive biomarkers for risk stratification in this high-risk population.

Introduction: Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder of the gastrointestinal tract that frequently requires long-term immunosuppressive therapy, which increases the risk of infections and other complications. During active disease, intestinal bleeding is common and leads to the release of free luminal heme, a pro-inflammatory molecule that can disrupt mucosal integrity, fuel microbial dysbiosis, and amplify inflammation. Interleukin-22 (IL-22) plays a protective role in the gut by promoting epithelial barrier integrity and wound healing. More recently, IL-22 has been shown to induce hemopexin, a heme scavenger protein that limits heme availability and suppresses bacterial growth during systemic infections.Methods: Here we investigate the protective role of IL-22 and hemopexin in the context of colitis using the dextran sodium sulphate (DSS) acute colitis model in mice. Wild-type (Wt) and Il22ra1^-/- mice were used to evaluate the effects of exogenous hemopexin and hemin treatments on colitis severity.Results: IL-22 signaling was crucial for the induction of hemopexin in the colon, as Il22ra1^-/- mice exhibited limited hemopexin induction and more severe colitis, which could be reversed by recombinant hemopexin administration. Additionally, hemin treatment, known to upregulate heme oxygenase-1 (HO-1), failed to show full protective effects in Il22ra1^-/- mice, suggesting that IL-22 signaling contributes to the anti-inflammatory and antioxidant effects of hemin by inducing hemopexin and HO-1.Discussion: These findings reveal a critical protective role for IL-22 by increasing the amount of hemopexin and HO-1 production in the colon, which could be part of a protective mechanism that mitigates DSS-induced colonic inflammation. Given its epithelial-specific and immunomodulatory activity, IL-22 represents a promising therapeutic approach for IBD. Furthermore, hemopexin itself may serve as an adjunct therapy during active disease.

Background: Colorectal cancer (CRC) development is influenced by both iron and gut microbiota composition. While iron supplementation is routinely used to manage anemia in CRC patients, it may also impact gut microbiota and promote tumorigenesis. In this study, we investigated the impact of initial gut microbiota composition on iron-promoted tumorigenesis. We performed fecal microbiota transplantation (FMT) in Apc ^Min/+ mice using samples from healthy controls, CRC patients, and mice, followed by exposure to iron sufficient or iron excess diets. Results: We found that iron supplementation promoted CRC and resulted in distinct gut microbiota changes in Apc ^Min/+ mice receiving FMT from CRC patients (FMT-CRC), but not from healthy controls or mice. Oral treatment with identified bacterial strains, namely Faecalibaculum rodentium, Holdemanella biformis, Bifidobacterium pseudolongum, and Alistipes inops, protected FMT-CRC mice against iron-promoted tumorigenesis. Conclusions: Our findings suggest that microbiota-targeted interventions may mitigate tumorigenic effects of iron supplementation in anemic patients with CRC. Graphical

Figure S5 shows the effect of putrescine on gut microbiota functions

Figure S6 shows growth of pks+ E. coli strains isolated from human samples