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Lee JW, Cowley ES, Wolf PG, Doden HL, Murai T, Caicedo KYO, Ly LK, Sun F, Takei H, Nittono H, Daniel SL, Cann I, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM. Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes. Gut Microbes 2022; 14:2132903. [PMID: 36343662 PMCID: PMC9645264 DOI: 10.1080/19490976.2022.2132903] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The gut microbiome of vertebrates is capable of numerous biotransformations of bile acids, which are responsible for intestinal lipid digestion and function as key nutrient-signaling molecules. The human liver produces bile acids from cholesterol predominantly in the A/B-cis orientation in which the sterol rings are "kinked", as well as small quantities of A/B-trans oriented "flat" stereoisomers known as "primary allo-bile acids". While the complex multi-step bile acid 7α-dehydroxylation pathway has been well-studied for conversion of "kinked" primary bile acids such as cholic acid (CA) and chenodeoxycholic acid (CDCA) to deoxycholic acid (DCA) and lithocholic acid (LCA), respectively, the enzymatic basis for the formation of "flat" stereoisomers allo-deoxycholic acid (allo-DCA) and allo-lithocholic acid (allo-LCA) by Firmicutes has remained unsolved for three decades. Here, we present a novel mechanism by which Firmicutes generate the "flat" bile acids allo-DCA and allo-LCA. The BaiA1 was shown to catalyze the final reduction from 3-oxo-allo-DCA to allo-DCA and 3-oxo-allo-LCA to allo-LCA. Phylogenetic and metagenomic analyses of human stool samples indicate that BaiP and BaiJ are encoded only in Firmicutes and differ from membrane-associated bile acid 5α-reductases recently reported in Bacteroidetes that indirectly generate allo-LCA from 3-oxo-Δ4-LCA. We further map the distribution of baiP and baiJ among Firmicutes in human metagenomes, demonstrating an increased abundance of the two genes in colorectal cancer (CRC) patients relative to healthy individuals.
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Affiliation(s)
- Jae Won Lee
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Elise S. Cowley
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia G. Wolf
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Institute for Health Research and Policy, University of Illinois Chicago, Chicago, IL, USA,University of Illinois Cancer Center, University of Illinois Chicago, Chicago, IL, USA
| | - Heidi L. Doden
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Tsuyoshi Murai
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | | | - Lindsey K. Ly
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Furong Sun
- Mass Spectrometry Laboratory, School of Chemical Sciences, University of Illinois Urbana-Champaign, IL, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Tokyo, Japan
| | | | - Steven L. Daniel
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL, USA
| | - Isaac Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - H. Rex Gaskins
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, Urbana, IL, USA
| | | | - João M. P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jason M. Ridlon
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, Urbana, IL, USA,Center for Advanced Study, University of Illinois Urbana-Champaign, Urbana, IL, USA,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,CONTACT Jason M. Ridlon Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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Cerqueira FM, Photenhauer AL, Doden HL, Brown AN, Abdel-Hamid AM, Moraïs S, Bayer EA, Wawrzak Z, Cann I, Ridlon JM, Hopkins JB, Koropatkin NM. Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome. J Biol Chem 2022; 298:101896. [PMID: 35378131 PMCID: PMC9112005 DOI: 10.1016/j.jbc.2022.101896] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/08/2023] Open
Abstract
Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure-function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (Kd ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.
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Affiliation(s)
- Filipe M Cerqueira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Amanda L Photenhauer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Heidi L Doden
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Aric N Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ahmed M Abdel-Hamid
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Sarah Moraïs
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Edward A Bayer
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Zdzislaw Wawrzak
- Northwestern University, Synchrotron Research Center, Life Science Collaborative Access Team, Lemont, Illinois, USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Illinois, USA; Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme), University of Illinois at Urbana-Champaign, Illinois, USA
| | - Jesse B Hopkins
- Biophysics Collaborative Access Team, Illinois Institute of Technology, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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Abstract
Bile acids are detergent molecules that solubilize dietary lipids and lipid-soluble vitamins. Humans synthesize bile acids with α-orientation hydroxyl groups which can be biotransformed by gut microbiota to toxic, hydrophobic bile acids, such as deoxycholic acid (DCA). Gut microbiota can also convert hydroxyl groups from the α-orientation through an oxo-intermediate to the β-orientation, resulting in more hydrophilic, less toxic bile acids. This interconversion is catalyzed by regio- (C-3 vs. C-7) and stereospecific (α vs. β) hydroxysteroid dehydrogenases (HSDHs). So far, genes encoding the urso- (7α-HSDH & 7β-HSDH) and iso- (3α-HSDH & 3β-HSDH) bile acid pathways have been described. Recently, multiple human gut clostridia were reported to encode 12α-HSDH, which interconverts DCA and 12-oxolithocholic acid (12-oxoLCA). 12β-HSDH completes the epi-bile acid pathway by converting 12-oxoLCA to the 12β-bile acid denoted epiDCA; however, a gene(s) encoding this enzyme has yet to be identified. We confirmed 12β-HSDH activity in cultures of Clostridium paraputrificum ATCC 25780. From six candidate C. paraputrificum ATCC 25780 oxidoreductase genes, we discovered the first gene (DR024_RS09610) encoding bile acid 12β-HSDH. Phylogenetic analysis revealed unforeseen diversity for 12β-HSDH, leading to validation of two additional bile acid 12β-HSDHs through a synthetic biology approach. By comparison to a previous phylogenetic analysis of 12α-HSDH, we identified the first potential C-12 epimerizing strains: Collinsella tanakaei YIT 12063 and Collinsella stercoris DSM 13279. A Hidden Markov Model search against human gut metagenomes located putative 12β-HSDH genes in about 30% of subjects within the cohorts analyzed, indicating this gene is relevant in the human gut microbiome.
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Affiliation(s)
- Heidi L. Doden
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Patricia G. Wolf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA,Institute for Health Research and Policy, University of Illinois, Chicago, IL, USA,Cancer Education and Career Development Program, University of Illinois, Chicago, IL, USA
| | - H. Rex Gaskins
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA,Cancer Center at Illinois, Urbana, IL, USA
| | | | - João M. P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jason M. Ridlon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA,Cancer Center at Illinois, Urbana, IL, USA,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,CONTACT Jason M. Ridlon Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
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Wen J, Mercado GP, Volland A, Doden HL, Lickwar CR, Crooks T, Kakiyama G, Kelly C, Cocchiaro JL, Ridlon JM, Rawls JF. Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine. Sci Adv 2021; 7:eabg1371. [PMID: 34301599 PMCID: PMC8302129 DOI: 10.1126/sciadv.abg1371] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
Bile salt synthesis, secretion into the intestinal lumen, and resorption in the ileum occur in all vertebrate classes. In mammals, bile salt composition is determined by host and microbial enzymes, affecting signaling through the bile salt-binding transcription factor farnesoid X receptor (Fxr). However, these processes in other vertebrate classes remain poorly understood. We show that key components of hepatic bile salt synthesis and ileal transport pathways are conserved and under control of Fxr in zebrafish. Zebrafish bile salts consist primarily of a C27 bile alcohol and a C24 bile acid that undergo multiple microbial modifications including bile acid deconjugation that augments Fxr activity. Using single-cell RNA sequencing, we provide a cellular atlas of the zebrafish intestinal epithelium and uncover roles for Fxr in transcriptional and differentiation programs in ileal and other cell types. These results establish zebrafish as a nonmammalian vertebrate model for studying bile salt metabolism and Fxr signaling.
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Affiliation(s)
- Jia Wen
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Gilberto Padilla Mercado
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Alyssa Volland
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Heidi L Doden
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Colin R Lickwar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Taylor Crooks
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Cecelia Kelly
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Jordan L Cocchiaro
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA
| | - Jason M Ridlon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA.
- Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
- Cancer Center of Illinois, Urbana, IL, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, NC, USA.
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Abstract
Advances in technology are only beginning to reveal the complex interactions between hosts and their resident microbiota that have co-evolved over centuries. In this review, we present compelling evidence that implicates the host-associated microbiome in the generation of 11β-hydroxyandrostenedione, leading to the formation of potent 11-oxy-androgens. Microbial steroid-17,20-desmolase cleaves the side-chain of glucocorticoids (GC), including cortisol (and its derivatives of cortisone, 5α-dihydrocortisol, and also (allo)- 3α, 5α-tetrahydrocortisol, but not 3α-5β-tetrahydrocortisol) and drugs (prednisone and dexamethasone). In addition to side-chain cleavage, we discuss the gut microbiome's robust potential to transform a myriad of steroids, mirroring much of the host's metabolism. We also explore the overlooked role of intestinal steroidogenesis and efflux pumps as a potential route for GC transport into the gut. Lastly, we propose several health implications from microbial steroid-17,20-desmolase function, including aberrant mineralocorticoid, GC, and androgen receptor signaling in colonocytes, immune cells, and prostate cells, which may exacerbate disease states.
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Affiliation(s)
- Lindsey K Ly
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Heidi L Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jason M Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Cancer Center of Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA.
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6
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Wolf PG, Devendran S, Doden HL, Ly LK, Moore T, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Kakiyama G, Kashyap P, McCracken VJ, Gaskins HR, Gillevet PM, Ridlon JM. Berberine alters gut microbial function through modulation of bile acids. BMC Microbiol 2021; 21:24. [PMID: 33430766 PMCID: PMC7798349 DOI: 10.1186/s12866-020-02020-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid profiles. Reduction in lipids, particularly cholesterol, is achieved partly through up-regulation of bile acid synthesis and excretion into the gastrointestinal tract (GI). The efficacy of BBR is also thought to be dependent on structural and functional alterations of the gut microbiome. However, knowledge of the effects of BBR on gut microbiome communities is currently lacking. Distinguishing indirect effects of BBR on bacteria through altered bile acid profiles is particularly important in understanding how dietary nutraceuticals alter the microbiome. RESULTS Germfree mice were colonized with a defined minimal gut bacterial consortium capable of functional bile acid metabolism (Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Bilophila wadsworthia, Clostridium hylemonae, Clostridium hiranonis, Blautia producta; B4PC2). Multi-omics (bile acid metabolomics, 16S rDNA sequencing, cecal metatranscriptomics) were performed in order to provide a simple in vivo model from which to identify network-based correlations between bile acids and bacterial transcripts in the presence and absence of dietary BBR. Significant alterations in network topology and connectivity in function were observed, despite similarity in gut microbial alpha diversity (P = 0.30) and beta-diversity (P = 0.123) between control and BBR treatment. BBR increased cecal bile acid concentrations, (P < 0.05), most notably deoxycholic acid (DCA) (P < 0.001). Overall, analysis of transcriptomes and correlation networks indicates both bacterial species-specific responses to BBR, as well as functional commonalities among species, such as up-regulation of Na+/H+ antiporter, cell wall synthesis/repair, carbohydrate metabolism and amino acid metabolism. Bile acid concentrations in the GI tract increased significantly during BBR treatment and developed extensive correlation networks with expressed genes in the B4PC2 community. CONCLUSIONS This work has important implications for interpreting the effects of BBR on structure and function of the complex gut microbiome, which may lead to targeted pharmaceutical interventions aimed to achieve the positive physiological effects previously observed with BBR supplementation.
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Affiliation(s)
- Patricia G Wolf
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, IL, USA
- Cancer Education and Career Development Program, University of Illinois, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Saravanan Devendran
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelburg, Germany
| | - Heidi L Doden
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lindsey K Ly
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Tyler Moore
- Center for Microbiome Analysis, George Mason University, Manassas, VA, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, 152-0011, Japan
| | - Hiroshi Nittono
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, 152-0011, Japan
| | - Tsuyoshi Murai
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Takao Kurosawa
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - George E Chlipala
- University of Illinois Chicago Research Resources Center, University of Illinois Chicago, Chicago, IL, USA
| | - Stefan J Green
- University of Illinois Chicago Research Resources Center, University of Illinois Chicago, Chicago, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Purna Kashyap
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Vance J McCracken
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center of Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Patrick M Gillevet
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelburg, Germany
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center of Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.
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7
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Streidl T, Karkossa I, Segura Muñoz RR, Eberl C, Zaufel A, Plagge J, Schmaltz R, Schubert K, Basic M, Schneider KM, Afify M, Trautwein C, Tolba R, Stecher B, Doden HL, Ridlon JM, Ecker J, Moustafa T, von Bergen M, Ramer-Tait AE, Clavel T. The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice. Gut Microbes 2021; 13:1-21. [PMID: 33382950 PMCID: PMC7781625 DOI: 10.1080/19490976.2020.1854008] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/09/2020] [Accepted: 11/11/2020] [Indexed: 02/04/2023] Open
Abstract
Extibacter muris is a newly described mouse gut bacterium which metabolizes cholic acid (CA) to deoxycholic acid (DCA) via 7α-dehydroxylation. Although bile acids influence metabolic and inflammatory responses, few in vivo models exist for studying their metabolism and impact on the host. Mice were colonized from birth with the simplified community Oligo-MM12 with or without E. muris. As the metabolism of bile acids is known to affect lipid homeostasis, mice were fed either a low- or high-fat diet for eight weeks before sampling and analyses targeting the gut and liver. Multiple Oligo-MM12 strains were capable of deconjugating primary bile acids in vitro. E. muris produced DCA from CA either as pure compound or in mouse bile. This production was inducible by CA in vitro. Ursodeoxycholic, chenodeoxycholic, and β-muricholic acid were not metabolized under the conditions tested. All gnotobiotic mice were stably colonized with E. muris, which showed higher relative abundances after HF diet feeding. The presence of E. muris had minor, diet-dependent effects on Oligo-MM12 communities. The secondary bile acids DCA and surprisingly LCA and their taurine conjugates were detected exclusively in E. muris-colonized mice. E. muris colonization did not influence body weight, white adipose tissue mass, liver histopathology, hepatic aspartate aminotransferase, or blood levels of cholesterol, insulin, and paralytic peptide (PP). However, proteomics revealed shifts in hepatic pathways involved in amino acid, glucose, lipid, energy, and drug metabolism in E. muris-colonized mice. Liver fatty acid composition was substantially altered by dietary fat but not by E. muris.In summary, E. muris stably colonized the gut of mice harboring a simplified community and produced secondary bile acids, which affected proteomes in the liver. This new gnotobiotic mouse model can now be used to study the pathophysiological role of secondary bile acids in vivo.
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Affiliation(s)
- Theresa Streidl
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | | | - Claudia Eberl
- Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Alex Zaufel
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University, Graz, Austria
| | - Johannes Plagge
- Research Group Lipid Metabolism, ZIEL Institute for Food & Health, Technical University, Munich, Germany
| | - Robert Schmaltz
- Department of Food Science & Technology, University of Nebraska-Lincoln, NE, USA
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Marijana Basic
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Kai Markus Schneider
- Department of Internal Medicine III, University Hospital of RWTH, Aachen, Germany
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mamdouh Afify
- Institute for Laboratory Animal Science, Faculty of Medicine, University Hospital of RWTH, Aachen, Germany
- Clinic for Cardiology (Internal Medicine I), University Hospital of RWTH, Aachen, Germany
| | - Christian Trautwein
- Department of Internal Medicine III, University Hospital of RWTH, Aachen, Germany
| | - René Tolba
- Institute for Laboratory Animal Science, Faculty of Medicine, University Hospital of RWTH, Aachen, Germany
| | - Bärbel Stecher
- Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, Munich, Germany
- German Center for Infection Research (DZIF); Partner Site Munich, Munich, Germany
| | - Heidi L. Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jason M. Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Josef Ecker
- Research Group Lipid Metabolism, ZIEL Institute for Food & Health, Technical University, Munich, Germany
| | - Tarek Moustafa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University, Graz, Austria
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
- Institute of Biochemistry, Leipzig University, Leipzig, Germany
| | - Amanda E. Ramer-Tait
- Department of Food Science & Technology, University of Nebraska-Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Hannover, NE, USA
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
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8
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Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hernández SB, Heine V, Buhl EM, M D'Agostino P, Cumbo F, Fischöder T, Wyschkon M, Looft T, Parreira VR, Abt B, Doden HL, Ly L, Alves JMP, Reichlin M, Flisikowski K, Suarez LN, Neumann AP, Suen G, de Wouters T, Rohn S, Lagkouvardos I, Allen-Vercoe E, Spröer C, Bunk B, Taverne-Thiele AJ, Giesbers M, Wells JM, Neuhaus K, Schnieke A, Cava F, Segata N, Elling L, Strowig T, Ridlon JM, Gulder TAM, Overmann J, Clavel T. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nat Commun 2020; 11:6389. [PMID: 33319778 PMCID: PMC7738495 DOI: 10.1038/s41467-020-19929-w] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/02/2020] [Indexed: 02/08/2023] Open
Abstract
Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota. The authors present a public collection of 117 bacterial isolates from the pig gut, including the description of 38 novel taxa. Interesting functions discovered in these organisms include a new fucosyltransferease and sactipeptide-like molecules encoded by biosynthetic gene clusters.
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Affiliation(s)
- David Wylensek
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Afrizal Afrizal
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany
| | - Neeraj Kumar
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany.,ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Esther Wortmann
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany
| | - Tianzhe Liu
- Chair of Technical Biochemistry, Technical University of Dresden, Dresden, Germany
| | - Saravanan Devendran
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sara B Hernández
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Viktoria Heine
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Eva M Buhl
- Electron Microscopy Facility, Institute of Pathology, RWTH University Hospital, Aachen, Germany
| | - Paul M D'Agostino
- Chair of Technical Biochemistry, Technical University of Dresden, Dresden, Germany
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Thomas Fischöder
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Marzena Wyschkon
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Torey Looft
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Valeria R Parreira
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Birte Abt
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Heidi L Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lindsey Ly
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - João M P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Krzysztof Flisikowski
- Chair of Livestock Biotechnology, Weihenstephan School of Life Science, Technical University of Munich, Freising, Germany
| | - Laura Navarro Suarez
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Hamburg, Germany
| | - Anthony P Neumann
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Sascha Rohn
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Hamburg, Germany.,Institute of Food Technolgy and Food Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Ilias Lagkouvardos
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.,Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center of Marine Research, Heraklion, Greece
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anja J Taverne-Thiele
- Host-Microbe Interactomics Group, Department of Animal Science, Wageningen University, Wageningen, The Netherlands
| | - Marcel Giesbers
- Electron Microscopy Center, Wageningen University, Wageningen, The Netherlands
| | - Jerry M Wells
- Host-Microbe Interactomics Group, Department of Animal Science, Wageningen University, Wageningen, The Netherlands
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Angelika Schnieke
- ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.,Chair of Livestock Biotechnology, Weihenstephan School of Life Science, Technical University of Munich, Freising, Germany
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Lothar Elling
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Hannover Medical School, Hannover, Germany
| | - Jason M Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA.,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technical University of Dresden, Dresden, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany.
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9
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Doden HL, Pollet RM, Mythen SM, Wawrzak Z, Devendran S, Cann I, Koropatkin NM, Ridlon JM. Structural and biochemical characterization of 20β-hydroxysteroid dehydrogenase from Bifidobacterium adolescentis strain L2-32. J Biol Chem 2019; 294:12040-12053. [PMID: 31209107 DOI: 10.1074/jbc.ra119.009390] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/11/2019] [Indexed: 01/20/2023] Open
Abstract
Anaerobic bacteria inhabiting the human gastrointestinal tract have evolved various enzymes that modify host-derived steroids. The bacterial steroid-17,20-desmolase pathway cleaves the cortisol side chain, forming pro-androgens predicted to impact host physiology. Bacterial 20β-hydroxysteroid dehydrogenase (20β-HSDH) regulates cortisol side-chain cleavage by reducing the C-20 carboxyl group on cortisol, yielding 20β-dihydrocortisol. Recently, the gene encoding 20β-HSDH in Butyricicoccus desmolans ATCC 43058 was reported, and a nonredundant protein search yielded a candidate 20β-HSDH gene in Bifidobacterium adolescentis strain L2-32. B. adolescentis 20β-HSDH could regulate cortisol side-chain cleavage by limiting pro-androgen formation in bacteria such as Clostridium scindens and 21-dehydroxylation by Eggerthella lenta Here, the putative B. adolescentis 20β-HSDH was cloned, overexpressed, and purified. 20β-HSDH activity was confirmed through whole-cell and pure enzymatic assays, and it is specific for cortisol. Next, we solved the structures of recombinant 20β-HSDH in both the apo- and holo-forms at 2.0-2.2 Å resolutions, revealing close overlap except for rearrangements near the active site. Interestingly, the structures contain a large, flexible N-terminal region that was investigated by gel-filtration chromatography and CD spectroscopy. This extended N terminus is important for protein stability because deletions of varying lengths caused structural changes and reduced enzymatic activity. A nonconserved extended N terminus was also observed in several short-chain dehydrogenase/reductase family members. B. adolescentis strains capable of 20β-HSDH activity could alter glucocorticoid metabolism in the gut and thereby serve as potential probiotics for the management of androgen-dependent diseases.
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Affiliation(s)
- Heidi L Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Rebecca M Pollet
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Sean M Mythen
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, Illinois 60439
| | - Saravanan Devendran
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Isaac Cann
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Jason M Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Cancer Center of Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
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