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The circadian clock orchestrates ∼24-hour oscillations of gastrointestinal epithelial structure and function that drive diurnal rhythms in gut microbiota. Here, we use experimental and computational approaches in intestinal organoids to reveal reciprocal effects of gut microbial metabolites on epithelial timekeeping by an epigenetic mechanism.We cultured enteroids in media supplemented with sterile supernatants from the altered Schaedler Flora (ASF), a defined murine microbiota. Circadian oscillations of bioluminescent PER2 and Bmal1 were measured in the presence or absence of individual ASF supernatants. Separately, we applied machine learning to ASF metabolomics to identify phase-shifting metabolites.Sterile filtrates from 3 of 7 ASF species (ASF360 Lactobacillus intestinalis, ASF361 Ligilactobacillus murinus, and ASF502 Clostridium species) induced minimal alterations in circadian rhythms, whereas filtrates from 4 ASF species (ASF356 Clostridium species, ASF492 Eubacterium plexicaudatum, ASF500 Pseudoflavonifactor species, and ASF519 Parabacteroides goldsteinii) induced profound, concentration-dependent phase shifts. Random forest classification identified short-chain fatty acid (SCFA) (butyrate, propionate, acetate, and isovalerate) production as a discriminating feature of ASF "shifters." Experiments with SCFAs confirmed machine learning predictions, with a median phase shift of 6.2 hours in murine enteroids. Pharmacologic or botanical histone deacetylase (HDAC) inhibitors yielded similar findings. Further, mithramycin A, an inhibitor of HDAC inhibition, reduced SCFA-induced phase shifts by 20% (P.05) and conditional knockout of HDAC3 in enteroids abrogated butyrate effects on Per2 expression. Key findings were reproducible in human Bmal1-luciferase enteroids, colonoids, and Per2-luciferase Caco-2 cells.Gut microbe-generated SCFAs entrain intestinal epithelial circadian rhythms by an HDACi-dependent mechanism, with critical implications for understanding microbial and circadian network regulation of intestinal epithelial homeostasis.

Background & Aims Environmental enteric dysfunction (EED) limits the Sustainable Development Goals of improved childhood growth and survival. We applied mucosal genomics to advance our understanding of EED. Methods The Study of Environmental Enteropathy and Malnutrition (SEEM) followed 416 children from birth to 24 months in a rural district in Pakistan. Biomarkers were measured at 9 months and tested for association with growth at 24 months. The duodenal methylome and transcriptome were determined in 52 undernourished SEEM participants and 42 North American controls and patients with celiac disease. Results After accounting for growth at study entry, circulating insulin-like growth factor-1 (IGF-1) and ferritin predicted linear growth, whereas leptin correlated with future weight gain. The EED transcriptome exhibited suppression of antioxidant, detoxification, and lipid metabolism genes, and induction of anti-microbial response, interferon, and lymphocyte activation genes. Relative to celiac disease, suppression of antioxidant and detoxification genes and induction of antimicrobial response genes were EED-specific. At the epigenetic level, EED showed hyper-methylation of epithelial metabolism and barrier function genes, and hypo-methylation of immune response and cell proliferation genes. Duodenal coexpression modules showed association between lymphocyte proliferation and epithelial metabolic genes and histologic severity, fecal energy loss, and wasting (weight-for-length/height Z < -2.0). Leptin was associated with expression of epithelial carbohydrate metabolism and stem cell renewal genes. Immune response genes were attenuated by giardia colonization. Conclusions Children with reduced circulating IGF-1 are more likely to experience stunting. Leptin and a gene signature for lymphocyte activation and dysregulated lipid metabolism are implicated in wasting, suggesting new approaches for EED refractory to nutritional intervention. ClinicalTrials.gov, Number: NCT03588013. (https://clinicaltrials.gov/ct2/show/NCT03588013), Graphical abstract

Prolonged episodes of acute diarrhea (ProD; duration 7-13 days) or persistent diarrhea (PD; duration ≥14 days) are important causes of undernutrition, yet the epidemiology and nutritional impact of ProD are poorly understood.We conducted a 10-year cohort study of 414 children from a Brazilian shantytown who were followed from birth; data were collected on diarrhea, enteric pathogens, and anthropometry.During 1276 child-years of observation, we recorded 3257 diarrheal episodes. ProD was twice as common as PD (12% and 5% of episodes, respectively); ProD and PD together accounted for 50% of all days with diarrhea. ProD was more common in infants whose mothers had not completed primary school (relative risk [RR], 2.1; 95% confidence interval: 1.02-2.78). Early weaning was associated with earlier onset of ProD (Spearman ρ = 0.309; P = .005). Infants with ProD were twice as likely to develop PD in later childhood (log rank, P = .002) compared with infants with only acute diarrhea (AD; duration7 days), even after controlling for confounders. Children's growth was more severely stunted before their first episode of ProD, compared with AD (mean height-for-age Z score (HAZ) -0.81 vs -0.51, respectively, P.05, unpaired t test). Following ProD, HAZ (ΔHAZ = -0.232) and weight-for-age (ΔWAZ = -0.26) significantly decreased (P.005 in paired t tests). ProD was associated with Cryptosporidium and Shigella infections.ProD accounts for significant morbidity and identifies children at risk of a vicious cycle of diarrhea and malnutrition. Further studies are needed to address the recognition and control of ProD and its consequences in resource-limited settings and assess its role in PD pathogenesis.

Background & Aims Enterococcus faecalis is a human intestinal commensal that produces extracellular superoxide and promotes chromosome instability via macrophage-induced bystander effects. We investigated the ability of 4-hydroxy-2-nonenal (4-HNE), a diffusible breakdown product of ω-6 polyunsaturated fatty acids, to mediate these effects. Methods 4-HNE was purified from E faecalis –infected macrophages; its genotoxicity was assessed in human colon cancer (HCT116) and primary murine colon epithelial (YAMC) cell lines. Results 4-HNE induced G 2 –M cell cycle arrest, led to formation γH2AX foci, and disrupted the mitotic spindle in both cell lines. Binucleate tetraploid cells that formed after incubation with 4-HNE were associated with the activation of stathmin and microtubule catastrophe. Silencing glutathione S -transferase α4, a scavenger of 4-HNE, increased the susceptibility of epithelial cells to 4-HNE–induced genotoxicity. Interleukin-10 knockout mice colonized with superoxide-producing E faecalis developed inflammation and colorectal cancer, whereas colonization with a superoxide-deficient strain resulted in inflammation but not cancer. 4-HNE–protein adducts were found in the lamina propria and macrophages in areas of colorectal inflammation. Conclusions 4-HNE can act as an autochthonous mitotic spindle poison in normal colonic epithelial and colon cancer cells. This finding links the macrophage-induced bystander effects to colorectal carcinogenesis.

Background&Aims:Circadian rhythms govern a wide array of intestinal epithelial functions in mammals, including nutrient absorption, microbial sensing, migration, and self-renewal. In the absence of coordinating signals generated by the central pacemaker activity of the suprachiasmatic nucleus, mammalian cells derived from peripheral tissues typically require an external cue such as a serum shock or steroid pulse to synchronize circadian rhythms in culture. Building on our recent finding of robust circadian rhythms in mouse small intestinal organoids (enteroids) derived from PERIOD2:LUCIFERASE (PER2:LUC) mice, we tested the capacity of PER2::LUC enteroids to synchronize circadian rhythms in the absence of these external cues.Methods:We generated PER2::LUC jejunal enteroids and maintained them in an incubating luminometer to measure real time oscillations of PER2 abundance. Enteroid experiments were performed under typical culture conditions in the presence or absence of MatrigelTM. Prior to bioluminescent recordings, populations of enteroids were subjected to a 2-hour 50% serum shock vs. a dexamethasone pulse to synchronize clock vs. no external synchronization. Separately, unsynchronized enteroids were incubated in the presence or absence of steroid receptor antagonist RU-486. Results: Serum-shocked and dexamethasone-treated enteroids displayed synchronized circadian rhythms of PER2 abundance immediately upon recording. The amplitude and persistence of these rhythms were increased in enteroids embedded in MatrigelTM vs. those suspended in media. In the absence of a serum shock or dexamethasone pulse, enteroids spontaneously developed synchronized circadian rhythms within 12 hours of recording. RU486 treatment prior to bioluminescent recording significantly delayed the onset of this spontaneous synchronization and dampened the amplitude of PER2 oscillations by 2to 6-fold. Conclusions: PERIOD2::LUCIFERASE enteroids autonomously synchronize circadian rhythms, providing further evidence of a tightly regulated peripheral clock intrinsic to the intestinal epithelium. Additional studies addressing the role of glucocorticoids in coordinating circadian rhythms in enteroids and in vivo should yield novel insights regarding circadian regulation of gut homeostasis and stem cell dynamics and pharmacologic effects of glucocorticoids on the intestinal epithelium.

Background: In acute porphyria, repletion of intrahepatic heme, with exogenously administered heme, suppresses the overproduction of δ-aminolaevulinic acid (ALA) and porphobilinogen (PBG). The effect of reducing heme breakdown has been assessed by administering tin protoporphyrin, a competitive inhibitor of heme oxygenase. Methods: The effect of tin protoporphyrin, 1 μmol/kg, and heme arginate, 3 mg/kg, individually and combined was compared with placebo in patients with an acute porphyric crisis. The treatments were given by intravenous infusion on three successive mornings. Thirty-four attacks were studied in 8 patients (9 placebo, 10 heme arginate alone, 4 tin protoporphyrin alone, and 11 combination treatments). Results: Placebo and tin protoporphyrin alone had little effect on ALA and PBG excretion. Following heme arginate alone or combined with tin protoporphyrin, there was a marked and similar suppression of both ALA and PBG excretion (P < 0.005 for each, compared with pretreatment values). However, on the 5th day after discontinuing treatment, the excretion of ALA and PBG were both lower following combination therapy than following heme arginate alone (P < 0.005 and P < 0.01, respectively). Conclusions: These findings suggest that inhibition of heme oxygenase by tin protoporphyrin prolongs the biochemical remission induced by heme arginate in the porphyric crisis.

Heterogeneity of colonic mucin glycoprotein was examined in rectal mucosal biopsy specimens from a variety of primate species (Saguinus oedipus, n = 18; Macaca mulatta, n = 2; Macaca fascicularis, n = 2; Aotus trivirgatus, n = 2; Saimiri sciureus, n = 2; and Callithrix jacchus, n = 2). After initial separation of radiolabeled mucin and nonmucin glycoproteins solubilized from mucosal biopsy specimens, at least five labeled mucin components were found in monkey rectal mucosa in contrast to the six mucin fractions observed in the human colon. Although primates consistently lacked the earliest eluting component present in human colonic mucin, other mucin components cochromatographed with comparable fractions previously identified in human colonic biopsy specimens. The relative proportions of each fraction were consistent throughout all species except the cotton-top tamarin (S. oedipus), an animal that develops a chronic colitis. The cotton-top tamarin was found to have a markedly reduced amount of one mucin component (IV) in a manner analogous to the reduction in a human mucin fraction previously noted in patients with ulcerative colitis. Sequential evaluation of mucin profiles in cotton-top tamarins (n = 12) treated with sulfasalazine (50 mg/kg X day) or placebo in a 10-wk double-blind crossover study demonstrated the persistence of the selective reduction in tamarin species IV unrelated to disease activity. In contrast, the relative amount of tamarin mucin III was greater in association with increased disease activity than that observed in association with reduced disease activity (46% +/- 11% total mucin vs. 19% +/- 7% total mucin posttreatment).