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Hall B, Levy S, Dufault-Thompson K, Arp G, Zhong A, Ndjite GM, Weiss A, Braccia D, Jenkins C, Grant MR, Abeysinghe S, Yang Y, Jermain MD, Wu CH, Ma B, Jiang X. BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. Nat Microbiol 2024; 9:173-184. [PMID: 38172624 PMCID: PMC10769871 DOI: 10.1038/s41564-023-01549-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Metabolism of haem by-products such as bilirubin by humans and their gut microbiota is essential to human health, as excess serum bilirubin can cause jaundice and even neurological damage. The bacterial enzymes that reduce bilirubin to urobilinogen, a key step in this pathway, have remained unidentified. Here we used biochemical analyses and comparative genomics to identify BilR as a gut-microbiota-derived bilirubin reductase that reduces bilirubin to urobilinogen. We delineated the BilR sequences from similar reductases through the identification of key residues critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes species. Analysis of human gut metagenomes revealed that BilR is nearly ubiquitous in healthy adults, but prevalence is decreased in neonates and individuals with inflammatory bowel disease. This discovery sheds light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.
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Affiliation(s)
- Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
| | - Sophia Levy
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | | | - Gabriela Arp
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Aoshu Zhong
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Glory Minabou Ndjite
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Ashley Weiss
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Domenick Braccia
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Conor Jenkins
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Maggie R Grant
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Stephenie Abeysinghe
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Madison D Jermain
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Chih Hao Wu
- Program of Computational Biology, Bioinformatics, and Genomics, University of Maryland, College Park, MD, USA
| | - Bing Ma
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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Hall B, Levy S, Dufault-Thompson K, Ndjite GM, Weiss A, Braccia D, Jenkins C, Yang Y, Arp G, Abeysinghe S, Jermain M, Wu CH, Jiang X. Discovery of the gut microbial enzyme responsible for bilirubin reduction to urobilinogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527579. [PMID: 36798240 PMCID: PMC9934709 DOI: 10.1101/2023.02.07.527579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The degradation of heme and the interplay of its catabolic derivative, bilirubin, between humans and their gut microbiota is an essential facet of human health. However, the hypothesized bacterial enzyme that reduces bilirubin to urobilinogen, a key step that produces the excretable waste products of this pathway, has remained unidentified. In this study, we used a combination of biochemical analyses and comparative genomics to identify a novel enzyme, BilR, that can reduce bilirubin to urobilinogen. We delineated the BilR sequences from other members of the Old Yellow Enzyme family through the identification of key residues in the active site that are critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes in the gut microbiome. Our analysis of human gut metagenomes showed that BilR is a common feature of a healthy adult human microbiome but has a decreased prevalence in neonates and IBD patients. This discovery sheds new light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.
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Affiliation(s)
- Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD 20742, United States
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD 20742, United States
| | - Sophia Levy
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD 20742, United States
| | - Keith Dufault-Thompson
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Glory Minabou Ndjite
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD 20742, United States
| | - Ashley Weiss
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD 20742, United States
| | - Domenick Braccia
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD 20742, United States
| | - Conor Jenkins
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Gabi Arp
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD 20742, United States
| | - Stephenie Abeysinghe
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD 20742, United States
| | - Madison Jermain
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD 20742, United States
| | - Chih Hao Wu
- Program of Computational Biology, Bioinformatics, and Genomics, University of Maryland, College Park, MD 20742, United States
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
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Hamoud AR, Weaver L, Stec DE, Hinds TD. Bilirubin in the Liver-Gut Signaling Axis. Trends Endocrinol Metab 2018; 29:140-150. [PMID: 29409713 PMCID: PMC5831340 DOI: 10.1016/j.tem.2018.01.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/02/2018] [Accepted: 01/05/2018] [Indexed: 02/08/2023]
Abstract
Bilirubin is a component of the heme catabolic pathway that is essential for liver function and has been shown to reduce hepatic fat accumulation. High plasma bilirubin levels are reflective of liver disease due to an injurious effect on hepatocytes. In healthy liver, bilirubin is conjugated and excreted to the intestine and converted by microbes to urobilinoids, which are reduced to the predominant pigment in feces, stercobilin, or reabsorbed. The function of urobilinoids in the gut or their physiological relevance of reabsorption is not well understood. In this review, we discuss the relationship of hepatic bilirubin signaling to the intestinal microbiota and its regulation of the liver-gut axis, as well as its capacity to mediate these processes.
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Affiliation(s)
- Abdul-Rizaq Hamoud
- Center for Hypertension and Personalized Medicine, Department of Physiology & Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Lauren Weaver
- Center for Hypertension and Personalized Medicine, Department of Physiology & Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - David E Stec
- Department of Physiology & Biophysics, Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Terry D Hinds
- Center for Hypertension and Personalized Medicine, Department of Physiology & Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA.
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Hewitt MA, Girgis GN, Brash M, Smith TK. Effects of feed-borne Fusarium mycotoxins on performance, serum chemistry, and intestinal histology of New Zealand White fryer rabbits1. J Anim Sci 2012; 90:4833-8. [DOI: 10.2527/jas.2012-5264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- M. A. Hewitt
- Department of Animal and Poultry Science, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - G. N. Girgis
- Department of Animal and Poultry Science, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - M. Brash
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - T. K. Smith
- Department of Animal and Poultry Science, University of Guelph, Guelph, ON, Canada, N1G 2W1
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Asymptotics and bioavailability in a 17-compartment pharmacokinetic model with enterohepatic circulation and remetabolization. Math Biosci 2006; 203:19-36. [PMID: 16616213 DOI: 10.1016/j.mbs.2006.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 12/23/2005] [Accepted: 02/21/2006] [Indexed: 11/26/2022]
Abstract
A 17-compartment linear pharmacokinetic model is designed, describing the complex process of enterohepatic circulation as a superposition of the net (remetabolizationfree) enterohepatic circulation, and remetabolization with subsequent intestinal absorption of the parent drug. Basically, the model is built by doubling the model describing the circulation of the parent drug in the body, so that the remetabolizable metabolite circulates in a model of the same structure as does the parent compound. The two submodels are cross-connected with arrows denoting the transition of the particular substance into the complementary part of the complex model. Asymptotic properties of the model are investigated, in particular, explicit formulas for its pharmacokinetic endpoints are given using the elements of its transition probability matrix. Conversely, taking account of the effect of bile cannulation, intravenous, intraportal and oral administration of the drug, as well as of the intravenous and intraportal administration of the remetabolizable metabolite, the transition probabilities of the system are determined in terms of certain measurable pharmacokinetic endpoints and the flow rates through the kidneys, liver and the cardiac output. Finally, the influence of the enterohepatic circulation and remetabolization process on bioavailability is examined. In particular, the inclusion-exclusion formula is derived, expressing its joint efficiency (defined as the relative increase of bioavailability) by means of the efficiencies of the net enterohepatic circulation and of the remetabolization process.
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Méndez-Sánchez N, Roldán-Valadez E, Flores MA, Cárdenas-Vázquez R, Uribe M. Zinc salts precipitate unconjugated bilirubin in vitro and inhibit enterohepatic cycling of bilirubin in hamsters. Eur J Clin Invest 2001; 31:773-80. [PMID: 11589719 DOI: 10.1046/j.1365-2362.2001.00879.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND We have evidence for enterohepatic cycling of bilirubin experimentally and in vivo in humans. This study was designed to investigate whether Zn salts might inhibit such cycling of bilirubin. MATERIALS AND METHODS Micellar bile salt solutions with unconjugated bilirubin were prepared, appropriate concentrations of Zn salts were added, and unconjugated bilirubin precipitation was measured. Hamsters and Wistar rats were fed a chow diet or a chow diet enriched with 1% ZnSO4, and bilirubin secretion rates were monitored. RESULTS Unconjugated bilirubin was precipitated maximally (90%) after a 10-min incubation with 5 mM Zn salts in the pH range of 6.8-9.0. In control hamsters, total bilirubin secretion rates into bile were 36.0 +/- 2.8 nmol h(-1) 100g(-1) body weight, whereas they were 25.0 +/- 3.3 nmol h-1 100(-1) g in the ZnSO4 group (P < 0.05). CONCLUSIONS Zn salts that flocculate at physiological pH adsorb unconjugated bilirubin almost completely from unsaturated micellar BS solutions. In addition, Zn salts administered orally suppress biliary bilirubin secretion rates in hamsters. These findings suggest that the administration of Zn salts may inhibit the enterohepatic cycling of unconjugated bilirubin in humans who are predisposed to pigment gallstone formation due to diet, disease or drugs.
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Affiliation(s)
- N Méndez-Sánchez
- Medica Sur Clinic Foundation and National Autonomous University of Mexico (UNAM), Mexico City, Mexico.
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Kotal P, Fevery J. Quantitation of urobilinogen in feces, urine, bile and serum by direct spectrophotometry of zinc complex. Clin Chim Acta 1991; 202:1-9. [PMID: 1807863 DOI: 10.1016/0009-8981(91)90250-g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Previous methods to quantitate urobilinogen lack precision due to either incomplete reduction of urobilin or to losses of pigment before the use of Ehrlich's aldehyde reaction or due to pigment precipitation, as occurs in Schlesinger's fluorescent assay. The present procedure modifies the latter assay to obviate described problems as it is based on direct spectrophotometry (or spectrofluorometry) of a zinc complex of urobilin in dimethylsulfoxide. The sample is extracted with dimethylsulfoxide to increase recovery of urobilinogen from samples of various origin (feces, urine, bile, serum etc.) and to prevent the precipitation of proteins. After oxidation of urobilinogen with iodine, the concentration of the resulting urobilin is directly determined from the absorption (or fluorescent) spectrum. High sensitivity and high specificity for the procedure result from the high value of absorption coefficient and by the characteristic absorption spectrum of zinc complex of urobilin, respectively. Within-day and day-to-day coefficients of variation of stool and bile samples range from 1.6 to 9.2%. The smallest concentration of urobilinogen measurable by spectrophotometry is approximately 0.5 mumol/l, by fluorometry it is 0.25 mumol/l. The recovery varies from 82.2 to 93.8% depending on re-extraction of the sample. The method is linear in the range of 1 to 35 mumol/l and of 0.5 to 17.5 mumol/l for spectrophotometric and fluorescent determinations, respectively. The results obtained with the present method correlated well with Ehrlich's determination (r2 = 0.912), but are approximately two-fold higher. Storage of the samples at -20 degrees C or extraction with dimethylsulfoxide prior to storage are good ways for sample preservation. Twenty stool samples from healthy adults were determined.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- P Kotal
- 1st Medical Department, Charles University, Prague, Czechoslovakia
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Kotal P, Fevery J. Urobilinogen-i is a major derivative of bilirubin in bile of homozygous Gunn rats. Biochem J 1990; 268:181-5. [PMID: 2140507 PMCID: PMC1131409 DOI: 10.1042/bj2680181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gunn rats lack bilirubin UDP-glycosyltransferases, but diazo-negative derivatives of bilirubin have been described in their bile. In order to investigate this alternative disposal of bilirubin, crude bile samples from Gunn and Wistar rats were directly analysed by h.p.l.c. Besides bilirubin (in Gunn rats) or its glycosides (in Wistar rats), two major compounds were detected. A yellow one corresponded to the previously documented vitamin B-2 and was equally prominent in Gunn rats or Wistar-rat bile. The other compound was colourless, but on standing in contact with air it was spontaneously oxidized to a pinkish-yellow pigment. It was far more prominent in Gunn-rat bile. Analysis of bile obtained after intravenous injection of [14C]bilirubin to Gunn rats demonstrated that this compound was highly labelled. Freezing and thawing of the bile resulted in the formation of a series of diazo-negative derivatives, demonstrating that the original compound was quite labile. Spectral (adsorption and fluorescent) and chromatographic (h.p.l.c., t.l.c. and paper chromatography) analysis of the oxidized form of the labelled compound allowed its identification as urobilin-i. The colourless compound secreted in bile was urobilinogen-i. Administration of neomycin and bacitracin to Gunn rats or gut resection suppressed the biliary excretion of urobilinogen and thus confirmed its intestinal origin. Urobilinogen seems thus to represent the major bilirubin derivative present in Gunn-rat bile. Its breakdown products might represent the so-far-unidentified diazo-negative polar bilirubin derivatives. Since only a small amount of bilirubin is present in Gunn-rat bile, the urobilinogen formed in the intestinal lumen seems to be derived from bilirubin reaching the gut via routes other than the biliary one.
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Affiliation(s)
- P Kotal
- Department of Medical Research, Catholic University of Leuven Campus Gasthuisberg, Belgium
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10
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Fort AT. Prenatal intrusion into the amnion. A review of the diagnostic, therapeutic, and research results. Am J Obstet Gynecol 1971; 110:432-55. [PMID: 4932527 DOI: 10.1016/0002-9378(71)90749-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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11
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Mazzuchin A, Walton RJ, Thibert RJ. Determination of total and conjugated glucuronic acid in serum and urine employing a modified naphthoresorcinol reagent. BIOCHEMICAL MEDICINE 1971; 5:135-57. [PMID: 5131449 DOI: 10.1016/0006-2944(71)90082-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Bernstein RB, Novy MJ, Piasecki GJ, Lester R, Jackson BT. Bilirubin metabolism in the fetus. J Clin Invest 1969; 48:1678-88. [PMID: 4980771 PMCID: PMC535739 DOI: 10.1172/jci106133] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bilirubin metabolism was studied in dog and monkey fetuses. Bilirubin-(3)H was administered to fetal animals in utero by prolonged intravenous infusion. Fetal plasma disappearance, hepatic uptake, biliary excretion, and placental transfer of bilirubin-(3)H were measured.Bilirubin metabolism and excretion in the fetus was much less efficient than in the adult. Fetal plasma levels of tritium were elevated for prolonged periods, and the combined rate of placental and fetal hepatic excretion was lower than normal values for adult hepatic excretion. Species differences were noted. Hepatic conjugation and excretion appeared to be the primary mechanism of fetal metabolism in the dog. In contrast, the amounts of conjugated bilirubin-(3)H excreted in fetal monkey bile were negligible. Small amounts of (3)H-labeled bilirubin derivatives were excreted in fetal bile, but 10 times as much of the administered material was transferred intact across the placenta and excreted by the maternal liver. The relationship of this functional difference to known anatomic and biochemical species differences is discussed. Preliminary observations on alternate routes of fetal bilirubin metabolism were obtained.
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13
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Harris RC. The newer hyperbilirubinemias. Dis Mon 1968:1-32. [PMID: 4968708 DOI: 10.1016/s0011-5029(68)80008-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Abstract
A technique is described for preparation in the guinea pig of an in situ, isolated, vascularized gall bladder that exhibits normal absorptive functions. Absorption of labeled bile pigments from the gall bladder was determined by the subsequent excretion of radioactivity in hepatic bile. Over a wide range of concentrations, unconjugated bilirubin-(14)C was well absorbed, whereas transfer of conjugated bilirubin proceeded slowly. Mesobilirubinogen-(3)H was absorbed poorly from whole bile, but was absorbed as rapidly as unconjugated bilirubin from a solution of pure conjugated bile salt. Bilirubin absorption was not impaired by iodoacetamide, 1.5 mM, or dinitrophenol, 1.0 mM, even though water transport was affected. This indicated that absorption of bilirubin was not dependent upon water transport, nor upon energy-dependent processes. The linear relationship between absorption and concentration of pigment at low concentrations in bile salt solutions suggested that pigment was transferred by passive diffusion. At higher pigment concentrations or in whole bile, this simple relationship was modified by interactions of pigment with bile salts and other constituents of bile. These interactions did not necessarily involve binding of bilirubin in micelles. The slow absorption of the more polar conjugates and photo-oxidative derivatives of bilirubin suggested that bilirubin was absorbed principally by nonionic, and partially, by ionic diffusion. Concentrations of pure conjugated bile salts above 3.5 mM were found to be injurious to the gall bladder mucosa. This mucosal injury did not affect the kinetics of bilirubin absorption. During in vitro incubation of bile at 37 degrees C, decay of bilirubin and hydrolysis of the conjugate proceeded as first-order reactions. The effects of these processes on the kinetics of bilirubin absorption, and their possible role in the formation of "white bile" and in the demonstrated appearance of unconjugated bilirubin in hepatic bile, are discussed.
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Lester R, Klein PD. Bile pigment excretion: a comparison of the biliary excretion of bilirubin and bilirubin derivatives. J Clin Invest 1966; 45:1839-46. [PMID: 5927213 PMCID: PMC292868 DOI: 10.1172/jci105487] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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