Sleep is fundamental to brain, body, mental, and social health. In parallel, the gut microbiome is increasingly recognized as a key regulator of immune, metabolic, endocrine, and neurophysiological processes. This scoping review explored current evidence on gut microbiome alterations in relation to sleep duration and sleep loss, sleep-wake disorders, and circadian rhythm-related phenotypes. Searches of MEDLINE, Embase, and Cochrane were conducted up to February 2024. Of 2059 records identified, 54 studies met the eligibility criteria. Thirty-eight studies were observational, nine interventional, and seven genome-wide association or Mendelian-randomization studies. The most frequently investigated phenotypes were insomnia (15 studies, 28%), obstructive sleep apnea (12 studies, 22%), circadian rhythm or circadian-misalignment phenotypes (10 studies, 19%), and sleep duration or sleep loss/deprivation (9 studies, 17%). Most studies used 16S rRNA gene sequencing to assess gut microbiota composition and diversity, while shotgun metagenomic sequencing and functional analyses were less common. Across disorders, studies reported alterations in microbial diversity, taxonomic composition, short-chain fatty acid-producing taxa, bile acid-related pathways, inflammatory markers, and cardiometabolic or neurophysiological correlates. However, findings were limited by heterogeneous sleep phenotyping, small sample sizes, cross-sectional designs, variable microbiome methods, and inconsistent control of diet, medication use, body mass index, comorbidities, and stool sampling protocols. Current evidence supports an association between sleep-wake and circadian disturbances and gut microbiome alterations, but causality and disorder-specific microbial signatures remain unresolved. Standardized longitudinal and multi-omics studies are needed to clarify mechanisms and therapeutic potential.

Bowel preparation is routinely performed before colonoscopy, yet its immediate effects on the spatial organization of the colonic microbiota at the mucosal interface remain poorly resolved. Here, we introduce a high-resolution endoscopic mucus-harvesting approach, combined with luminal aspirates and mucosal biopsies, to generate a high-resolution, within-subject trajectory of microbiota alterations across distinct colonic niches in healthy adults over the first 24 hours after purging. While luminal bacterial communities remained remarkably stable, with no significant changes in alpha or beta diversity and proportional washout of taxa. In contrast, mucus-associated and mucosal communities underwent a rapid but reversible ecological restructuring, characterized by immediate post-cleansing shifts in composition and transient blooms of Proteobacteria, particularly Enterobacteriaceae. These perturbations were strongest in the 0-12-hour window and varied by individual, consistent with the dominance of personalized baseline microbial signatures. Critically, spatially resolved sampling revealed a key refinement: the Enterobacteriaceae expansion was confined almost exclusively to the superficial mucus layer, a glycan-rich, dynamically oxygenated compartment that is particularly susceptible to mechanical disturbance during lavage, whereas deeper mucus and mucosa-associated communities remained comparatively stable. By 24 hours, both mucosal and mucus-associated microbiota had largely returned to their individualized pre-cleansing configurations, indicating rapid ecosystem resilience and suggesting that the deeper mucus layer functions as a protected microbial reservoir that reseeds the epithelium and lumen once normal physiology is restored. This compartment-specific recovery trajectory contrasts with the prolonged dysbiosis typically observed after antibiotics or infection, underscoring the need for spatially precise sampling to interpret microbiome data collected during clinical endoscopy. Together, these findings establish an endoscopic strategy for probing microbe-mucus interactions in humans and provide a conceptual and methodological framework for interpreting microbiome data obtained during clinical endoscopy.

BACKGROUND:The peptide GPR15L is produced by colonic epithelial cells and has been implicated in T cell recruitment to the large intestine. However, its role in chronic colitis has been unclear so far. OBJECTIVE:To explore the role of GPR15L in the pathogenesis of experimental colitis and IBD. DESIGN:We studied how genetic deletion or overexpression of Gpr15l as well as rectal application of recombinant GPR15L alters the course of acute dextran sodium sulfate colitis and T cell transfer colitis. The impact of GPR15L on microbiota was explored with co-housing, littermate and faecal microbiota transfer studies, by 16S rRNA sequencing as well as anti-microbial assays and shotgun metagenomics. The expression of GPR15L was evaluated across three independent cohorts of patients with IBD and correlated to microbial diversity and flare-free survival. RESULTS:GPR15L clearly mitigated experimental colitis, but this was independent of T cell recruitment and GPR15. Instead, we observed that the effects of GPR15L were mediated by altered microbiomes in the large intestine and, consistently, showed that GPR15L acts as an antimicrobial peptide under anaerobic conditions and shapes microbial communities towards a homeostatic phenotype. Rectal supplementation of GPR15L counteracted experimental colitis. In patients with IBD, GPR15L expression was decreased in active inflammation, correlated with microbial diversity and was associated with flare-free survival. CONCLUSIONS:GPR15L is a host-defence peptide that plays a beneficial role in the pathogenesis of intestinal inflammation. It seems promising to further evaluate its potential as a future therapeutic approach in IBD.

BACKGROUND AND AIMS:Accumulating evidence suggests the microbiota is a key factor in Disorders of Gut-Brain Interaction (DGBI), by affecting host immune and neural systems. However, the underlying mechanisms remain elusive due to their complexity and clinical heterogeneity of patients with DGBIs. We aimed to identify neuroimmune pathways that are critical in microbiota-gut-brain communication during de novo gut colonization. METHODS:We employed a combination of gnotobiotic and state-of-the-art microbial tools, behavioral analysis, immune and pharmacological approaches. Germ-free wild type, TLR signaling-deficient MyD88-/- Ticam1-/- and lymphocyte-deficient SCID mice were studied before and after colonization with specific pathogen-free microbiota, Altered Schaedler Flora, E. coli or S. typhimurium (permanent or transient colonizers). TLR agonists and antagonists, CCR7 antagonist or immunomodulators were used to study immune pathways. We assessed brain c-Fos, brain-derived neurotrophic factor, and dendritic and glial cells by immunofluorescence, expression of neuroimmune genes by NanoString and performed brain proteomics. RESULTS:Bacterial monocolonization, conventionalization or administration of microbial products to germ-free mice altered mouse behavior similarly, acting through Toll-like receptor or nucleotide-binding oligomerization domain signaling. The process required CD11b+CD11c+CD103+ dendritic cell activation and migration into the brain. The change in behavior did not require the continued presence of bacteria and was associated with activation of multiple neuro-immune networks in the gut and the brain. CONCLUSIONS:Changes in neural plasticity occur rapidly upon initial gut microbial colonization and involve innate immune signaling to the brain, mediated by CD11b+CD11c+CD103+ dendritic cell migration. The results identify a new target with therapeutic potential for DGBIs developing in context of increased gut and blood-brain barrier permeability.

Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are characterized by intestinal inflammation and barrier dysfunction. While disruption of the intestinal barrier contributes to the pathogenesis of IBD, yet how colonic inflammation alters small intestinal homeostasis remains poorly defined. Here, we demonstrate that three models of colitis, including 2,4,6-Trinitrobenzenesulfonic acid (TNBS), Dextran Sulfate Sodium (DSS), and oxazolone, induce paracellular barrier dysfunction in the small intestine, with model-specific immune profiles. Th1/Th17-skewed responses (TNBS and DSS) were associated with microbiota-dependent upregulation of myosin light chain kinase (MLCK), RORγt⁺ CD4⁺ T cell expansion, and elevated expression of Nod2, which was not observed under Th2-dominant (oxazolone) conditions. Inhibition of MLCK restored barrier function and suppressed inflammation in a CD4⁺ T cell-dependent manner. Using Nod2-deficient and 2939insC mutant mice, we showed Nod2 as a critical regulator of small intestinal permeability during colitis. Bone marrow chimeras revealed compartment-specific roles of Nod2, with non-hematopoietic Nod2 sufficient to preserve epithelial integrity, while hematopoietic Nod2 expression is required to limit cytokine-mediated inflammation. Moreover, MLCK inhibition ameliorated intestinal lesions only in mice with Nod2 deficiency in the hematopoietic compartment. Finally, microbiota transfer experiments ruled out a causal role for dysbiosis in driving small intestinal permeability defects in Nod2-deficient mice. These findings uncover a Nod2-MLCK-CD4⁺ T cell axis linking colonic inflammation to small intestinal barrier dysfunction and highlight distinct immune-epithelial-microbial mechanisms shaping intestinal homeostasis during colitis.

Microbiome-based therapies are promising new treatment avenues. While global alterations in microbiota composition have been shown in multiple sclerosis, whether and how gut microbiota influence autoimmune responses in an antigen-specific manner is unclear. Here, we genetically engineered gut bacteria to express a brain antigen and dissect their pathogenic potential in a murine model of autoimmune neuroinflammation. Colonization with bacteria expressing myelin - but not ovalbumin-peptide exacerbates an encephalitogenic immune response in the gut by activating antigen-specific T cells as well as B cells leading to accelerated neuroinflammatory disease. These results demonstrate how antigen-specific microbial modulation can influence autoimmunity, providing insight for development of therapeutic strategies targeting specific bacterial taxa for treatment of MS and other autoimmune diseases.

BACKGROUND & AIMS:Formylated peptide receptors 1 and 2 (Fpr1/2 or FPRs) are G-protein-coupled pattern recognition receptors that bind bacterial formylated peptides. The role of FPRs in enteric nervous system (ENS) development and gastrointestinal (GI) motility is unknown. METHODS:We generated mice with germline, epithelial-, and neural crest-specific deletion of the Fpr1/2 locus and assessed ENS structure and GI motility. We also employed a gestational microbiota suppression model using antibiotic-treated wild-type dams, alongside a transient gestational colonization model in pregnant germ-free mice using auxotrophic Escherichia coli, to determine whether temporary restoration of maternal microbiota-Fpr1/2 signaling can regulate embryonic ENS development. Enteric neuronal density at embryonic day 18.5, postnatal day 2 (P2), and in adult mice was assessed by CLARITY immunostaining and confocal imaging of pan neuronal markers (Tuj1, HuD, and Peripherin). Fecal formylated peptide (fMLF) content was measured by mass spectrometry. GI motility was assessed by stool frequency, total GI transit time, and FITC-dextran intestinal transit assay. RESULTS:Germline, epithelial, and neural crest-specific Fpr1/2 deletion resulted in reduced fetal, postnatal, and post weaning ENS density and epithelial innervation with reduced GI motility in post weaned mice. The 3-week-old pups derived from antibiotic-treated pregnant wild-type dams showed significantly reduced ENS density and GI motility, with reduced fecal fMLF. Critically, transient gestational colonization of pregnant germ-free mice with auxotrophic E. coli significantly improved enteric neuronal density and GI motility in 6-week-old offspring. CONCLUSIONS:Collectively our data show that microbiota-Fpr1/2 signaling in the murine gut is critical for normal ENS development and GI motility and identify Fpr1/2 as a potential therapeutic target to correct GI hypomotility. Our data also suggests a cautious approach to antibiotic usage during pregnancy.

A hallmark of the main secreted antibody immunoglobulin A (IgA) is its mutational load that accumulates throughout life. Although this is mainly interpreted in terms of continuing microbial induction, we show that dietary composition during early life can promote IgA induction, its repertoire, and mutational diversification independently of microbial exposure. Using germ-free and colonized mice fed different diets formulated with proprietary grain-based processing or from purified chemicals with different principal macronutrient calorie sources, we found that dietary lipopolysaccharide contamination led to Toll-like receptor (TLR) 4 signaling and promoted germinal center activity in the intestinal immune compartment. The effects of lipopolysaccharide on mucosal immune induction were phenocopied only when presented within colloidal liposomes rather than in dispersed solution. These findings indicate that dietary composition and its formulation can leave a durable impression on the resultant IgA repertoire.

Immunoglobulin (Ig) A is the main antibody isotype found on mucosal surfaces in mammals, where it is predominantly present as a dimer. Here we provide an easy, scalable, efficient, and broadly applicable method to produce and purify monoclonal mouse dimeric IgA from single B cell Ig transcripts to study mucosal antibody responses at single-cell level.

Along a food chain, microbiomes occur in each component and often contribute to the functioning or the health of their host or environment. ‘One Health’ emphasizes the connectivity of each component’s health. Chemical stress typically causes dysbiotic microbiomes, but it remains unclear whether chemical stressors consistently affect the microbiomes of food chain components. Here, we challenged food chain components, including water, sediments, soil, plants, and animals, with three chemical stresses consisting of arsenic (toxic trace element), benzoxazinoids (bioactive plant metabolites), and terbuthylazine (herbicide). We analysed 1064 microbiomes to assess their commonalities and differences in their stress responses. We found that chemical stressors overall decreased microbiome diversity in soil, but not in the other microbiomes. In response to stress, all food chain communities strongly shifted in their composition, generally becoming compositionally more similar to each other. In addition, we observed stochastic effects in host-associated communities (plant, animal). Dysbiotic microbiomes were characterized by different sets of bacteria, which responded specifically to the three chemical stressors. Microbial co-occurrence patterns significantly shifted with either decreased (water, sediment, plant, animal) or increased (soil) network sparsity and numbers of keystone taxa following stress treatments. These results suggest major re-distribution of specific taxa in the overall stress- and component-specific responses of microbiomes with the community stability of plant and animal microbiomes being the most affected by chemical stresses.

INTRODUCTION:Retrospective data suggest association of high-altitude exposure and inflammatory bowel disease flares. Knowledge about underlying pathogenesis remains limited. METHODS:This prospective interventional trial evaluated the effect of 3 hours hypobaric low-pressure chamber exposure on 11 patients with Crohn's disease (CD), 9 with ulcerative colitis (UC), and 10 controls. RESULTS:Proportion of patients with clinical and endoscopic activity did not increase. However, 33.3% of patients with UC experienced a flare. More patients had calprotectin-based activity (>100 μg/g) after the intervention (26.7 vs 63.3%, P = 0.013). Transient changes in certain bacterial strains were seen in controls and patients with UC. DISCUSSION:Low-pressure chamber exposure, although the primary outcome was not met, led to a flare in a third of patients with UC, with changes in calprotectin levels and specific bacterial strains ( Clinicaltrials.gov number, NCT02849821).

The gut microbiota regulates host intestinal serotonin synthesis, thereby promoting the development and maintenance of the enteric nervous system, which controls bowel motility. Functional bowel disorders, including irritable bowel syndrome, are associated with altered serotonin levels and gut microbiota composition. However, it is unclear if the gut microbiota can synthesize bioactive serotonin, which may affect enteric nervous system development. Here, we identify a consortium of the human gut bacteria Limosilactobacillus mucosae and Ligilactobacillus ruminis that synthesizes serotonin in vitro by decarboxylation of 5-hydroxytryptophan and elevates fecal serotonin levels, colonic neuronal density, and serotonin-immunoreactive neurons when introduced into germ-free, serotonin-deficient mice. The consortium normalizes intestinal transit time in germ-free wild-type mice, and we observe decreased fecal abundance of L. mucosae in individuals with irritable bowel syndrome. These findings suggest that specific members of the human gut microbiota synthesize bioactive serotonin that can contribute to gut health.

Background and Aims Accumulating evidence suggests the microbiota is a key factor in disorders of gut-brain interaction (DGBI), by affecting host immune and neural systems. However, the underlying mechanisms remain elusive due to their complexity and clinical heterogeneity of patients with DGBIs. We aimed to identify neuroimmune pathways that are critical in microbiota-gut-brain communication during de novo gut colonization. Methods We employed a combination of gnotobiotic and state-of-the-art microbial tools, behavioral analysis, immune and pharmacological approaches. Germ-free wild type, MyD88−/− Ticam1−/− and SCID mice were studied before and after colonization with specific pathogen-free microbiota, Altered Schaedler Flora, E. coli or S. typhimurium (permanent or transient colonizers). TLR agonists and antagonists, CCR7 antagonist or immunomodulators were used to study immune pathways. We assessed brain c-Fos, brain-derived neurotrophic factor, and dendritic and glial cells by immunofluorescence, expression of neuroimmune genes by NanoString and performed brain proteomics. Results Bacterial monocolonization, conventionalization or administration of microbial products to germ-free mice altered mouse behavior similarly, acting through Toll-like receptor or nucleotide-binding oligomerization domain signaling. The process required CD11b+CD11c+CD103+ cell activation and migration into the brain. The change in behavior did not require the continued presence of bacteria and was associated with activation of multiple neuro-immune networks in the gut and the brain. Conclusions Changes in neural plasticity occur rapidly upon initial gut microbial colonization and involve innate immune signaling to the brain, mediated by CD11b+CD11c+CD103+ cell migration. The results identify a new target with therapeutic potential for DGBIs developing in context of increased gut and blood-brain barrier permeability. Highlights ### Competing Interest Statement The authors have declared no competing interest. * DGBI : Disorders of Gut-Brain Interaction IBS : Irritable Bowel Syndrome GF : Germ-free ASF : Altered Schaedler Flora SPF : Specific Pathogen Free DC : Dendritic cell TLR : Toll-Like Receptor NOD : Nucleotide-binding Oligomerization Domain CCR7 : Chemokine Receptor 7 BDNF : Brain-Derived Neurotrophic Factor LPS : Lipopolysaccharide SCID : Severe Combined ImmunoDeficiency PBS : Phosphate-Buffered Saline TBS : Tris-Buffered Saline BSA : Bovine Serum Albumin

Leukemia stem cells (LSCs) are resistant to therapy and immune control. The reason for their resistance to elimination by cytotoxic T cells (CTLs) remains unclear. This study shows that specific low abundant Gram-negative intestinal commensals of the genus Sutterella suppress the anti-leukemia immune response in chronic myeloid leukemia (CML). We found that germ-free and specific opportunistic pathogen-free (SOPF) mice are protected from CML development and that colonization of SOPF mice with Sutterella wadsworthensis , but not other related and unrelated bacterial strains, rescues CML development. A higher prevalence of this microbe resulted in Myd88/TRIF-mediated CTL exhaustion in SPF compared to SOPF CML mice as evidenced by higher surface expression of exhaustion markers on CTLs, a reduced capacity to produce interferon-gamma and granzyme B and to kill LSCs in vitro . These findings provide new insights into the immune control of LSCs and identify Sutterella species as regulators of anti-leukemic immunity in CML. ### Competing Interest Statement The authors have declared no competing interest.

After failed biliary cannulation via standard endoscopic retrograde cholangiography approach, endoscopic-ultrasound-based rendezvous-endoscopic retrograde cholangiography (EUS-RV-ERC) is a valid alternative. One of the challenging factors in this setting is the management of the guidewire. Here, we propose a method, where a slim endoscope is used to stabilize the guidewire and optimize wire manipulation in a patient who underwent EUS-RV-ERC via a transgastric approach. This was executed in a patient suffering from severe alcoholic pancreatitis presented with a severely narrowed duodenum due to extrinsic compression and inflammation in the setting of cholangitis Tokyo Grade III. Keywords case report , cholangitis , jaundice , pancreatitis , rendezvous ERCP

Transcriptional recording by CRISPR spacer acquisition from RNA endows engineered Escherichia coli with synthetic memory, which through Record-seq reveals transcriptome-scale records. Microbial sentinels that traverse the gastrointestinal tract capture a wide range of genes and pathways that describe interactions with the host, including quantitative shifts in the molecular environment that result from alterations in the host diet, induced inflammation, and microbiome complexity. We demonstrate multiplexed recording using barcoded CRISPR arrays, enabling the reconstruction of transcriptional histories of isogenic bacterial strains in vivo. Record-seq therefore provides a scalable, noninvasive platform for interrogating intestinal and microbial physiology throughout the length of the intestine without manipulations to host physiology and can determine how single microbial genetic differences alter the way in which the microbe adapts to the host intestinal environment.

After failed biliary cannulation via standard endoscopic retrograde cholangiography approach, endoscopic-ultrasound-based rendezvous-endoscopic retrograde cholangiography (EUS-RV-ERC) is a valid alternative. One of the challenging factors in this setting is the management of the guidewire. Here, we propose a method, where a slim endoscope is used to stabilize the guidewire and optimize wire manipulation in a patient who underwent EUS-RV-ERC via a transgastric approach. This was executed in a patient suffering from severe alcoholic pancreatitis presented with a severely narrowed duodenum due to extrinsic compression and inflammation in the setting of cholangitis Tokyo Grade III.

The small intestinal microbiota has a crucial role in gastrointestinal health, affecting digestion, immune function, bile acid homeostasis and nutrient metabolism. The challenges of accessibility at this site mean that our knowledge of the small intestinal microbiota is less developed than of the colonic or faecal microbiota. Here, we summarize the features and fluctuations of the microbiota along the small intestinal tract, focusing on humans, and discuss physicochemical factors and assessment methods, including the technical challenges of investigating the low microbial biomass of the proximal small bowel. We highlight the essential protective mechanisms of the small intestine, including motility, the paracellular barrier and mucus, and secretory immunity, to show their roles in limiting excessive exposure of host tissues to microbial metabolites. We address current knowledge gaps, particularly the variability among individuals, the effects of dysbiosis of the small intestinal microbiota on health and how different taxa in small intestinal microbiota could compensate for each other functionally. The small intestinal microbiota has a key influence on digestion, immunity and nutrient metabolism but is poorly understood in comparison with the faecal and colonic microbiota. This Perspective discusses the features of the small intestinal microbiota, highlighting technical challenges, knowledge gaps and implications for health.