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Vestergaard MV, Allin KH, Eriksen C, Zakerska-Banaszak O, Arasaradnam RP, Alam MT, Kristiansen K, Brix S, Jess T. Gut microbiota signatures in inflammatory bowel disease. United European Gastroenterol J 2024; 12:22-33. [PMID: 38041519 PMCID: PMC10859715 DOI: 10.1002/ueg2.12485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/10/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence. OBJECTIVES Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients. METHODS We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms. RESULTS Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found. CONCLUSIONS Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.
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Affiliation(s)
- Marie Vibeke Vestergaard
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Kristine H Allin
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
| | - Carsten Eriksen
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Ramesh P Arasaradnam
- Warwick Medical School & Cancer Research Centre, University of Leicester, Leicester, UK
| | - Mohammad T Alam
- Warwick Medical School & Cancer Research Centre, University of Leicester, Leicester, UK
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Karsten Kristiansen
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Brix
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
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Hishiya N, Uno K, Nakano A, Konishi M, Higashi S, Eguchi S, Ariyoshi T, Matsumoto A, Oka K, Takahashi M, Suzuki Y, Horiuchi S, Hirai N, Ogawa Y, Ogawa T, Nakano R, Mikasa K, Kasahara K, Yano H. Association between the gut microbiome and organic acid profiles in a Japanese population with HIV infection. J Infect Chemother 2024; 30:58-66. [PMID: 37708940 DOI: 10.1016/j.jiac.2023.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
INTRODUCTION An increased incidence of metabolic syndrome has been observed in human immunodeficiency virus (HIV)-infected individuals. In contrast, gut dysbiosis is involved in various pathogeneses, including vascular endothelial disorders. Organic acids, including short-chain fatty acids (SCFAs), are essential for maintaining gut homeostasis. Therefore, this study aimed to explore the gut microbiome profile and organic acids in a Japanese population infected with HIV. METHODS Forty-nine patients with HIV infection on combination antiretroviral therapy (cART) were enrolled and divided into the high and low CD4 groups based on a CD4 cutoff of 350 cells/μL. Stool samples were analyzed by 16S ribosomal RNA next-generation sequencing and high-performance liquid chromatography. The association between the gut microbiome, including bacterial taxa and organic acids, was statistically analyzed. RESULTS The fecal microbial community composition was significantly different between HIV patients with CD4 counts above and below 350 cells/μL. The relative abundance of Roseburia, Prevotella, Prevotella_9, and [Clostridium]_methylpentosum_group were significantly enriched in the high CD4 group. Fecal succinic acid tended to be more abundant in the low CD4 group, and acetic, propionic, and butyric acids tended to be more abundant in the high CD4 group. Roseburia was positively correlated with butyric acid levels. Prevotella_9 and Prevotella were negatively correlated with succinic acid levels and positively correlated with acetic and propionic acid levels. CONCLUSIONS This study showed intestinal dysbiosis bordering on a CD4 count of 350 in patients with HIV infection undergoing cART. These findings might help in understanding intestinal damage and systemic inflammation in HIV infection.
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Affiliation(s)
- Naokuni Hishiya
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Infectious Diseases, Nara City Hospital, 1-50-1 Higashikidera-cho, Nara-Shi, Nara, 630-8305, Japan
| | - Kenji Uno
- Department of Infectious Diseases, Minami-Nara General Medical Center, 8-1 Fukugami, Oyodo-Cho, Yoshino-Gun, Nara, 638-8551, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan.
| | - Mitsuru Konishi
- Center for Health Control, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Seiya Higashi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Shuhei Eguchi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Tadashi Ariyoshi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Asami Matsumoto
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Kentaro Oka
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Motomichi Takahashi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9 Toro-Cho, Kita-Ku, Saitama-Shi, Saitama, 331-0804, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Saori Horiuchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Nobuyasu Hirai
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Gastroenterology, Seichokai Fuchu Hospital, 1-10-17 Hiko-Cho, Izumi, Osaka, 594-0076, Japan
| | - Yoshihiko Ogawa
- Department of Infectious Diseases, Sakai City Medical Center, 1-1-1 Ebaraji-Cho, Nishi-Ku, Sakai, Osaka, 593-8304, Japan
| | - Taku Ogawa
- Department of Microbiology and Infection Control, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Keiichi Mikasa
- Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan; Department of Internal Medicine, Nara Koseikai Hospital, 769-3 Shigi-cho, Yamatokoriyama, Nara, 639-1039, Japan
| | - Kei Kasahara
- Center for Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
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Edmunds CE, Welch CB, Lourenco JM, Callaway TR, Pringle TD, Dove CR. The Effects of Dietary Manganese and Selenium on Growth and the Fecal Microbiota of Nursery Piglets. Vet Sci 2023; 10:650. [PMID: 37999473 PMCID: PMC10675067 DOI: 10.3390/vetsci10110650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
The objective of this study was to determine the impact of varying dietary manganese and selenium concentrations, antioxidant cofactors, on the growth performance and fecal microbial populations of nursery pigs. The piglets (N = 120) were blocked by weight (5.22 ± 0.7 kg) and sex. The pens (n = 5/treatment) within a block were randomly assigned to diets in a 2 × 3 factorial design to examine the effects of Se (0.1 and 0.3 mg/kg added Se) and Mn (0, 12, and 24 mg/kg added Mn) and were fed in three phases (P1 = d 1-7, P2 = d 8-21, P3 = d 22-35). The pigs and orts were weighed weekly. Fecal samples were collected d 0 and 35 for 16S rRNA bacterial gene sequencing and VFA analysis. The data were analyzed as factorial via GLM in SAS. There was a linear response (p < 0.05) in overall ADG across dietary Mn. Supplementing 24 mg/kg Mn tended to decrease (p < 0.10) the relative abundance of many bacteria possessing pathogenic traits relative to Mn controls. Meanwhile, increasing Mn concentration tended to foster the growth of bacteria correlated with gut health and improved growth (p < 0.10). The data from this study provide preliminary evidence on the positive effects of manganese on growth and gut health of nursery pigs.
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Affiliation(s)
- Clint E. Edmunds
- School of Sciences, Clayton State University, Morrow, GA 30260, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
| | - Christina B. Welch
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
| | - Jeferson M. Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
| | - Todd R. Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
| | - T. Dean Pringle
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Quincy, FL 32351, USA;
| | - C. Robert Dove
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA; (C.B.W.); (J.M.L.); (T.R.C.); (C.R.D.)
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Elizalde-Torrent A, Borgognone A, Casadellà M, Romero-Martin L, Escribà T, Parera M, Rosales-Salgado Y, Díaz-Pedroza J, Català-Moll F, Noguera-Julian M, Brander C, Paredes R, Olvera A. Vaccination with an HIV T-Cell Immunogen (HTI) Using DNA Primes Followed by a ChAdOx1-MVA Boost Is Immunogenic in Gut Microbiota-Depleted Mice despite Low IL-22 Serum Levels. Vaccines (Basel) 2023; 11:1663. [PMID: 38005995 PMCID: PMC10675013 DOI: 10.3390/vaccines11111663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the important role of gut microbiota in the maturation of the immune system, little is known about its impact on the development of T-cell responses to vaccination. Here, we immunized C57BL/6 mice with a prime-boost regimen using DNA plasmid, the Chimpanzee Adenovirus, and the modified Vaccinia Ankara virus expressing a candidate HIV T-cell immunogen and compared the T-cell responses between individuals with an intact or antibiotic-depleted microbiota. Overall, the depletion of the gut microbiota did not result in significant differences in the magnitude or breadth of the immunogen-specific IFNγ T-cell response after vaccination. However, we observed marked changes in the serum levels of four cytokines after vaccinating microbiota-depleted animals, particularly a significant reduction in IL-22 levels. Interestingly, the level of IL-22 in serum correlated with the abundance of Roseburia in the large intestine of mice in the mock and vaccinated groups with intact microbiota. This short-chain fatty acid (SCFA)-producing bacterium was significantly reduced in the vaccinated, microbiota-depleted group. Therefore, our results indicate that, although microbiota depletion reduces serum levels of IL-22, the powerful vaccine regime used could have overcome the impact of microbiota depletion on IFNγ-producing T-cell responses.
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Affiliation(s)
- Aleix Elizalde-Torrent
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Alessandra Borgognone
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Maria Casadellà
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Luis Romero-Martin
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autonoma de Barcelona (UAB), 08193 Cerdanyola del Valles, Spain
| | - Tuixent Escribà
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Mariona Parera
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Yaiza Rosales-Salgado
- Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (Y.R.-S.); (J.D.-P.)
| | - Jorge Díaz-Pedroza
- Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (Y.R.-S.); (J.D.-P.)
| | - Francesc Català-Moll
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Marc Noguera-Julian
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- Facultat de Medicina, Universitat de Vic—Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- CIBERINFEC—ISCIII, 28029 Madrid, Spain
| | - Christian Brander
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- Facultat de Medicina, Universitat de Vic—Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- CIBERINFEC—ISCIII, 28029 Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Aelix Therapeutics, 08028 Barcelona, Spain
| | - Roger Paredes
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- Facultat de Medicina, Universitat de Vic—Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- CIBERINFEC—ISCIII, 28029 Madrid, Spain
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, 08916 Badalona, Spain
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, 08916 Badalona, Spain
| | - Alex Olvera
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- CIBERINFEC—ISCIII, 28029 Madrid, Spain
- Facultat de Ciències, Tecnologia i Enginyeries, Universitat de Vic—Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
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Satoh T. New prebiotics by ketone donation. Trends Endocrinol Metab 2023:S1043-2760(23)00091-7. [PMID: 37271711 DOI: 10.1016/j.tem.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/29/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023]
Abstract
Integrity of the microbiome is an essential element for human gut health. 3-Hydroxybutyrate (3HB) secreted into the gut lumen has gained attention as a regulator of gut physiology, including stem cell expansion. In this opinion, I propose new prebiotics leading to gut health by use of a ketone (3HB) donor. When exogenous 3HB is supplied through ketone donation, it has the potential to markedly improve gut health by altering the gut microbiome and systemic metabolic status. Poly-hydroxybutyrate (PHB) donates 3HB and primarily influences microbiota, making it an effective prebiotic for improving the gut environment. Thus, exogenous 3HB donation to the lumen of the gut may aid gut health by maintaining the integrity of microbiome.
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Affiliation(s)
- Takumi Satoh
- Department of Antiaging Food Research, School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji 192-0982, Japan.
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Yang Q, Van Haute M, Korth N, Sattler S, Rose D, Juritsch A, Shao J, Beede K, Schmaltz R, Price J, Toy J, Ramer-Tait AE, Benson AK. The waxy mutation in sorghum and other cereal grains reshapes the gut microbiome by reducing levels of multiple beneficial species. Gut Microbes 2023; 15:2178799. [PMID: 37610979 PMCID: PMC9980621 DOI: 10.1080/19490976.2023.2178799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/16/2022] [Accepted: 02/02/2023] [Indexed: 08/25/2023] Open
Abstract
Waxy starches from cereal grains contain >90% amylopectin due to naturally occurring mutations that block amylose biosynthesis. Waxy starches have unique organoleptic characteristics (e.g. sticky rice) as well as desirable physicochemical properties for food processing. Using isogenic pairs of wild type sorghum lines and their waxy derivatives, we studied the effects of waxy starches in the whole grain context on the human gut microbiome. In vitro fermentations with human stool microbiomes show that beneficial taxonomic and metabolic signatures driven by grain from wild type parental lines are lost in fermentations of grain from the waxy derivatives and the beneficial signatures can be restored by addition of resistant starch. These undesirable effects are conserved in fermentations of waxy maize, wheat, rice and millet. We also demonstrate that humanized gnotobiotic mice fed low fiber diets supplemented with 20% grain from isogenic pairs of waxy vs. wild type parental sorghum have significant differences in microbiome composition and show increased weight gain. We conclude that the benefits of waxy starches on food functionality can have unintended tradeoff effects on the gut microbiome and host physiology that could be particularly relevant in human populations consuming large amounts of waxy grains.
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Affiliation(s)
- Qinnan Yang
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
| | - Mallory Van Haute
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
| | - Nate Korth
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
- Complex Biosystems Graduate Program, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Scott Sattler
- Wheat, Sorghum and Forage Research Unit, USDA-Agricultural Research Service, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Devin Rose
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Anthony Juritsch
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
| | - Jing Shao
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
| | - Kristin Beede
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
| | - Robert Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
| | - Jeff Price
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
| | - John Toy
- Wheat, Sorghum and Forage Research Unit, USDA-Agricultural Research Service, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
| | - Andrew K. Benson
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center at the University of Nebraska, Lincoln, NE, USA
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Abstract
Faecalibacterium and Roseburia are major producers of butyrate in the intestine. A reduced abundance of the organisms and a concurrent reduction in butyrate levels are associated with inflammatory bowel disease.
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Affiliation(s)
- Howard Faden
- Department of Pediatrics Division of Infectious Diseases, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
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Li N, Bai C, Zhao L, Sun Z, Ge Y, Li X. The Relationship Between Gut Microbiome Features and Chemotherapy Response in Gastrointestinal Cancer. Front Oncol 2022; 11:781697. [PMID: 35004303 PMCID: PMC8733568 DOI: 10.3389/fonc.2021.781697] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Objective The prognosis of advanced gastrointestinal cancer is poor. There are studies indicating that gut microbes might have the predictive ability to evaluate the outcome of cancer therapy, especially immunotherapy. There is limited evidence to date on the influence of microbes on chemotherapeutic response. Design In total, 130 patients with advanced or metastatic esophageal (n=40), gastric (n=46), and colorectal cancer (n=44) were enrolled. We included 147 healthy people as controls and used 16S rRNA sequencing to analyze the fecal microbiota. Results Significant differences in the abundance of fecal microbiota between patients with gastrointestinal cancer and controls were identified. The abundance of Bacteroides fragilis, Escherichia coli, Akkermansia muciniphila, Clostridium hathewayi, and Alistipes finegoldii were significantly increased in the patient group. Faecalibacterium prausnitzii, Roseburia faecis, Clostridium clostridioforme, Blautia producta, Bifidobacterium adolescent, and Butyricicoccus pullicaecorum taxa were significantly more abundant in the controls. The amount of R. faecis in non-responders (NR) was more likely to decrease significantly after chemotherapy, while the amount mostly increased in responders (R) (P=0.040). The optimal abundance variation of R. faecis may be a predictor for distinguishing patients with PD from those with non-PD in all patients with gastrointestinal cancer, with a sensitivity of 75.0% and a specificity of 93.9%. Conclusion The gut microbiome of patients with esophageal cancer, gastric cancer, and colorectal cancer differs from those of healthy people. The abundance alteration of R. faecis in patients with GI cancer might be a predictor of chemotherapy efficacy.
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Affiliation(s)
- Ningning Li
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunmei Bai
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Zhao
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhao Sun
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuping Ge
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyuan Li
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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9
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Nie K, Ma K, Luo W, Shen Z, Yang Z, Xiao M, Tong T, Yang Y, Wang X. Roseburia intestinalis: A Beneficial Gut Organism From the Discoveries in Genus and Species. Front Cell Infect Microbiol 2021; 11:757718. [PMID: 34881193 PMCID: PMC8647967 DOI: 10.3389/fcimb.2021.757718] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
Roseburia intestinalis is an anaerobic, Gram-positive, slightly curved rod-shaped flagellated bacterium that produces butyrate in the colon. R. intestinalis has been shown to prevent intestinal inflammation and maintain energy homeostasis by producing metabolites. Evidence shows that this bacterium contributes to various diseases, such as inflammatory bowel disease, type 2 diabetes mellitus, antiphospholipid syndrome, and atherosclerosis. This review reveals the potential therapeutic role of R. intestinalis in human diseases. Patients with inflammatory bowel disease exhibit significant changes in R. intestinalis abundance, and they may benefit a lot from modulations targeting R. intestinalis. The data reviewed here demonstrate that R. intestinalis plays its role in regulating barrier homeostasis, immune cells, and cytokine release through its metabolite butyrate, flagellin and other. Recent advancements in the application of primary culture technology, culture omics, single-cell sequencing, and metabonomics technology have improved research on Roseburia and revealed the benefits of this bacterium in human health and disease treatment.
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Affiliation(s)
- Kai Nie
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Kejia Ma
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Weiwei Luo
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Zhaohua Shen
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Zhenyu Yang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Mengwei Xiao
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Ting Tong
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Yuanyuan Yang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
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10
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Gu M, Chen N, Sun H, Li Z, Chen X, Zhou J, Zhang Y. Roseburia Abundance Associates With Severity, Evolution and Outcome of Acute Ischemic Stroke. Front Cell Infect Microbiol 2021; 11:669322. [PMID: 34737970 PMCID: PMC8562073 DOI: 10.3389/fcimb.2021.669322] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022] Open
Abstract
Stroke induces disorder of gut microbiota, however, whether this disorder differs according to stroke severity and its role in the evolution and outcome of stroke is currently unknown. Here we explored the composition and structure of fecal microbiome based on 68 acute ischemic stroke patients presenting with minor symptoms (admission National Institute of Health Stroke Scale (NIHSS) ≤ 3) and 67 patients with non-minor stroke (admission NIHSS 4-34) using high-throughput Illumina sequencing of the 16S rRNA. There was no significant difference in α-diversity indices, but the principal coordinate analysis of the microbiota indicated clear separation of the two groups. The significantly enriched butyrate-producing genus Roseburia in the minor stroke group was negatively correlated with fasting glucose, while the Erysipelotrichaceae incertae sedis abundant in non-minor stroke patients was positively correlated with stress hyperglycemia (i.e. fasting glucose/glycated hemoglobin ratio). Moreover, the relative abundance of genus Roseburia was also significantly associated with the dynamic changes of NIHSS score, as well as short-term and long-term functional outcomes. Our results suggested that stroke affects microbiota composition in a manner differentiated by stroke severity, and the enrichment of genus Roseburia may play a protective role in stroke evolution and outcome. Our findings strengthen the relevance of specific taxa for stroke severity that might allow targeted therapy in acute ischemic stroke.
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Affiliation(s)
- Mengmeng Gu
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Nihong Chen
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Department of Neurology, Nanjing Yuhua Hospital, Yuhua Branch of Nanjing First Hospital, Nanjing, China
| | - Huanhuan Sun
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhongyuan Li
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiangliang Chen
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Junshan Zhou
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yingdong Zhang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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11
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Sost MM, Ahles S, Verhoeven J, Verbruggen S, Stevens Y, Venema K. A Citrus Fruit Extract High in Polyphenols Beneficially Modulates the Gut Microbiota of Healthy Human Volunteers in a Validated In Vitro Model of the Colon. Nutrients 2021; 13:nu13113915. [PMID: 34836169 PMCID: PMC8619629 DOI: 10.3390/nu13113915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
The effect of a Citrus Fruit Extract high in the polyphenols hesperidin and naringin (CFE) on modulation of the composition and activity of the gut microbiota was tested in a validated, dynamic in vitro model of the colon (TIM-2). CFE was provided at two doses (250 and 350 mg/day) for 3 days. CFE led to a dose-dependent increase in Roseburia, Eubacterium ramulus, and Bacteroides eggerthii. There was a shift in production of short-chain fatty acids, where acetate production increased on CFE, while butyrate decreased. In overweight and obesity, acetate has been shown to increase fat oxidation when produced in the distal gut, and stimulate secretion of appetite-suppressive neuropeptides. Thus, the data in the in vitro model point towards mechanisms underlying the effects of the polyphenols in CFE with respect to modulation of the gut microbiota, both in composition and activity. These results should be confirmed in a clinical trial.
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Affiliation(s)
- Mônica Maurer Sost
- Centre for Healthy Eating & Food Innovation (HEFI), Campus Venlo, Maastricht University, Villafloraweg 1, 5928 SZ Venlo, The Netherlands; (M.M.S.); (J.V.); (S.V.)
| | - Sanne Ahles
- BioActor B.V., 6229 GS Maastricht, The Netherlands; (S.A.); (Y.S.)
- Department of Nutrition and Movement Sciences, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jessica Verhoeven
- Centre for Healthy Eating & Food Innovation (HEFI), Campus Venlo, Maastricht University, Villafloraweg 1, 5928 SZ Venlo, The Netherlands; (M.M.S.); (J.V.); (S.V.)
| | - Sanne Verbruggen
- Centre for Healthy Eating & Food Innovation (HEFI), Campus Venlo, Maastricht University, Villafloraweg 1, 5928 SZ Venlo, The Netherlands; (M.M.S.); (J.V.); (S.V.)
| | - Yala Stevens
- BioActor B.V., 6229 GS Maastricht, The Netherlands; (S.A.); (Y.S.)
- Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Campus Venlo, Maastricht University, Villafloraweg 1, 5928 SZ Venlo, The Netherlands; (M.M.S.); (J.V.); (S.V.)
- Correspondence: ; Tel.: +31-622-435-111
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12
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Stražar M, Mourits VP, Koeken VACM, de Bree LCJ, Moorlag SJCFM, Joosten LAB, van Crevel R, Vlamakis H, Netea MG, Xavier RJ. The influence of the gut microbiome on BCG-induced trained immunity. Genome Biol 2021; 22:275. [PMID: 34551799 PMCID: PMC8456614 DOI: 10.1186/s13059-021-02482-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 12/23/2020] [Accepted: 08/30/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high inter-individual variation in specific and nonspecific, or trained, immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown. RESULTS Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling after 2 weeks and 3 months. Metagenomics based on de novo genome assembly reveals 43 immunomodulatory taxa. The nonspecific, trained immune response is detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlates with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, is associated positively with Ruminococcus and Eggerthella lenta. The identified immunomodulatory taxa also have the strongest effects on circulating metabolites, with Roseburia affecting phenylalanine metabolism. This is corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner. CONCLUSIONS Variability in cytokine production after BCG vaccination is associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia is found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination.
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Affiliation(s)
| | - Vera P Mourits
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valerie A C M Koeken
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine (CiiM) & TWINCORE, Joint Ventures Between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - L Charlotte J de Bree
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Research Center for Vitamins and Vaccines, Bandim Health Project, Statens Serum Institut, Copenhagen, Denmark
- Odense Patient Data Explorative Network, University of Southern Denmark/Odense University Hospital, Odense, Denmark
| | - Simone J C F M Moorlag
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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13
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Denoth L, Juillerat P, Kremer AE, Rogler G, Scharl M, Yilmaz B, Bluemel S, On Behalf Of The Swiss Ibd Cohort Study. Modulation of the Mucosa-Associated Microbiome Linked to the PTPN2 Risk Gene in Patients with Primary Sclerosing Cholangitis and Ulcerative Colitis. Microorganisms 2021; 9:1752. [PMID: 34442830 DOI: 10.3390/microorganisms9081752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/31/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022] Open
Abstract
Gut microbiota appears to be involved in the pathogenesis of primary sclerosing cholangitis (PSC). The protein tyrosine phosphatase nonreceptor 2 (PTPN2) gene risk variant rs1893217 is associated with gut dysbiosis in inflammatory bowel disease (IBD), and PTPN2 was mentioned as a possible risk gene for PSC. This study assessed the microbial profile of ulcerative colitis (UC) patients with PSC and without PSC (non-PSC). Additionally, effects of the PTPN2 risk variant were assessed. In total, 216 mucosal samples from ileum, colon, and rectum were collected from 7 PSC and 42 non-PSC patients, as well as 28 control subjects (non-IBD). The microbial composition was derived from 16S rRNA sequencing data. Overall, bacterial richness was highest in PSC patients, who also had a higher relative abundance of the genus Roseburia compared to non-PSC, as well as Haemophilus, Fusobacterium, Bifidobacterium, and Actinobacillus compared to non-IBD, as well as a lower relative abundance of Bacteroides compared to non-PSC and non-IBD, respectively. After exclusion of patients with the PTPN2 risk variant, Brachyspira was higher in PSC compared to non-PSC, while, solely in colon samples, Eubacterium and Tepidimonas were higher in PSC vs. non-IBD. In conclusion, this study underlines the presence of gut mucosa-associated microbiome changes in PSC patients and rather weakens the role of PTPN2 as a PSC risk gene.
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14
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Bredeck G, Kämpfer AAM, Sofranko A, Wahle T, Lison D, Ambroise J, Stahlmecke B, Albrecht C, Schins RPF. Effects of dietary exposure to the engineered nanomaterials CeO 2, SiO 2, Ag, and TiO 2 on the murine gut microbiome. Nanotoxicology 2021; 15:934-950. [PMID: 34380002 DOI: 10.1080/17435390.2021.1940339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rodent studies on the effects of engineered nanomaterials (ENM) on the gut microbiome have revealed contradictory results. Our aim was to assess the effects of four well-investigated model ENM using a realistic exposure scenario. Two independent ad libitum feeding studies were performed. In study 1, female mice from the local breeding facility received feed pellets containing 1% CeO2 or 1% SiO2 for three weeks. In study 2, both female and male mice were purchased and exposed to 0.2% Ag-PVP or 1% TiO2 for four weeks. A next generation 16S rDNA sequencing-based approach was applied to assess impacts on the gut microbiome. None of the ENM had an effect on the α- or β-diversity. A decreased relative abundance of the phylum Actinobacteria was observed in SiO2 exposed mice. In female mice, the relative abundance of the genus Roseburia was increased with Ag exposure. Furthermore, in study 2, a sex-related difference in the β-diversity was observed. A difference in the β-diversity was also shown between the female control mice of the two studies. We did not find major effects on the gut microbiome. This contrast to other studies may be due to variations in the study design. Our investigation underlined the important role of the sex of test animals and their microbiome composition prior to ENM exposure initiation. Hence, standardization of microbiome studies is strongly required to increase comparability. The ENM-specific effects on Actinobacteria and Roseburia, two taxa pivotal for the human gut homeostasis, warrant further research on their relevance for health.
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Affiliation(s)
- Gerrit Bredeck
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Angela A M Kämpfer
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Adriana Sofranko
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Tina Wahle
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Dominique Lison
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain, Brussels, Belgium
| | - Jérôme Ambroise
- Centre de Technologies Moléculaires Appliquées, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - Burkhard Stahlmecke
- Institute for Energy and Environmental Technology e.V. (IUTA), Duisburg, Germany
| | - Catrin Albrecht
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Roel P F Schins
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
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15
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Liu C, Shao W, Gao M, Liu J, Guo Q, Jin J, Meng F. Changes in intestinal flora in patients with type 2 diabetes on a low-fat diet during 6 months of follow-up. Exp Ther Med 2020; 20:40. [PMID: 32952631 PMCID: PMC7480128 DOI: 10.3892/etm.2020.9167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is closely associated with changes in the composition of the gut microbiota. To date, studies on the gut microbiota have focused on the genus-level composition and microbial gene sets, whereas changes in the microbiota after clinical treatment have remained largely elusive. In the present study, 16 subjects with T2DM were enrolled and treated long-term with a low-fat diet. Stool samples were collected at the initial diagnosis and after 1, 3 and 6 months of treatment, and named as group T0, T1, T2 and T3, respectively. Simultaneously, stool samples from 16 healthy individuals were collected as a control (group C). In addition, 16S ribosomal RNA sequencing was performed to detect differences in the microbiota between the groups. Following the low-fat diet treatment, the patients' fasting plasma glucose, plasma glucose 2 h after challenge, glycosylated haemoglobin A1c and body mass index (BMI) decreased significantly. The composition of the phylum in patients with type 2 diabetes mellitus was similar to that in healthy individuals. A total of 23 genera from four phyla, namely Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria, were determined to be different between group T0 and group C, while only 8 genera were different between group T3 and group C. Repeated analysis of variance suggested a complex change during the low-fat diet treatment. The butyrate-producing bacteria Anaerotruncus exhibited a slight increase, while Roseburia was significantly increased at the T1 stage but then gradually decreased at the later stage. In summary, a low-fat diet was effective for patients with T2DM in reducing blood glucose and the BMI, and, to a certain extent, improving the intestinal flora to reach a normal composition. The study was registered in the Chinese Clinical Trial Registry (ChiCTR; registration no. ChiCTR1900028663).
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Affiliation(s)
- Chengguo Liu
- Department of Endocrinology, Zhoushan Putuo District People's Hospital, Zhoushan, Zhejiang 316199, P.R. China
| | - Wei Shao
- Department of Gastroenterology, Zhoushan Putuo District People's Hospital, Zhoushan, Zhejiang 316199, P.R. China
| | - Ming Gao
- Department of General Surgery, Zhoushan Putuo District People's Hospital, Zhoushan, Zhejiang 316199, P.R. China
| | - Jinyao Liu
- Department of Endocrinology, Zhoushan Putuo District People's Hospital, Zhoushan, Zhejiang 316199, P.R. China
| | - Qiongyao Guo
- Department of Endocrinology, Zhoushan Putuo District People's Hospital, Zhoushan, Zhejiang 316199, P.R. China
| | - Jie Jin
- Department of Research Service, Zhiyuan Medical Inspection Institute Co., Ltd, Hangzhou, Zhejiang 310006, P.R. China
| | - Fei Meng
- Department of Research Service, Zhiyuan Medical Inspection Institute Co., Ltd, Hangzhou, Zhejiang 310006, P.R. China
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16
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Hillman ET, Kozik AJ, Hooker CA, Burnett JL, Heo Y, Kiesel VA, Nevins CJ, Oshiro JM, Robins MM, Thakkar RD, Wu ST, Lindemann SR. Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species. Microb Genom 2020; 6:mgen000399. [PMID: 32589566 PMCID: PMC7478625 DOI: 10.1099/mgen.0.000399] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Roseburia species are important denizens of the human gut microbiome that ferment complex polysaccharides to butyrate as a terminal fermentation product, which influences human physiology and serves as an energy source for colonocytes. Previous comparative genomics analyses of the genus Roseburia have examined polysaccharide degradation genes. Here, we characterize the core and pangenomes of the genus Roseburia with respect to central carbon and energy metabolism, as well as biosynthesis of amino acids and B vitamins using orthology-based methods, uncovering significant differences among species in their biosynthetic capacities. Variation in gene content among Roseburia species and strains was most significant for cofactor biosynthesis. Unlike all other species of Roseburia that we analysed, Roseburia inulinivorans strains lacked biosynthetic genes for riboflavin or pantothenate but possessed folate biosynthesis genes. Differences in gene content for B vitamin synthesis were matched with differences in putative salvage and synthesis strategies among species. For example, we observed extended biotin salvage capabilities in R. intestinalis strains, which further suggest that B vitamin acquisition strategies may impact fitness in the gut ecosystem. As differences in the functional potential to synthesize components of biomass (e.g. amino acids, vitamins) can drive interspecies interactions, variation in auxotrophies of the Roseburia spp. genomes may influence in vivo gut ecology. This study serves to advance our understanding of the potential metabolic interactions that influence the ecology of Roseburia spp. and, ultimately, may provide a basis for rational strategies to manipulate the abundances of these species.
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Affiliation(s)
- Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN 47907, USA
| | - Ariangela J. Kozik
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN 47907, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
- Present address: Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Casey A. Hooker
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - John L. Burnett
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - Yoojung Heo
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Violet A. Kiesel
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Clayton J. Nevins
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
- Present address: Department of Soil and Water Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Jordan M.K.I. Oshiro
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Melissa M. Robins
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Riya D. Thakkar
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA
| | - Sophie Tongyu Wu
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
| | - Stephen R. Lindemann
- Purdue University Interdisciplinary Life Science Program (PULSe), Purdue University, West Lafayette, IN 47907, USA
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
- Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA
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17
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Castellanos N, Diez GG, Antúnez-Almagro C, Bressa C, Bailén M, González-Soltero R, Pérez M, Larrosa M. Key Bacteria in the Gut Microbiota Network for the Transition between Sedentary and Active Lifestyle. Microorganisms 2020; 8:E785. [PMID: 32456263 PMCID: PMC7285274 DOI: 10.3390/microorganisms8050785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Physical activity modifies the gut microbiota, exerting health benefits on the host; however, the specific bacteria associated with exercise are not yet known. In this work, we propose a novel method, based on hierarchical topology, to study the differences between the microbiota of active and sedentary lifestyles, and to identify relevant bacterial taxa. Our results show that the microbiota network found in active people has a significantly higher overall efficiency and higher transmissibility rate. We also identified key bacteria in active and sedentary networks that could be involved in the conversion of an active microbial network to a sedentary microbial network and vice versa.
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Affiliation(s)
- Nazareth Castellanos
- Nirakara Lab, Mindfulness and cognitive Science extraordinary Chair, Universidad Complutense de Madrid, 28223 Madrid, Spain; (N.C.); (G.G.D.)
| | - Gustavo G. Diez
- Nirakara Lab, Mindfulness and cognitive Science extraordinary Chair, Universidad Complutense de Madrid, 28223 Madrid, Spain; (N.C.); (G.G.D.)
| | | | - Carlo Bressa
- Masmicrobiota group, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain; (C.B.); (M.B.); (R.G.-S.)
| | - María Bailén
- Masmicrobiota group, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain; (C.B.); (M.B.); (R.G.-S.)
| | - Rocío González-Soltero
- Masmicrobiota group, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain; (C.B.); (M.B.); (R.G.-S.)
| | - Margarita Pérez
- Faculty of Sport and Health Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain;
| | - Mar Larrosa
- Masmicrobiota group, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain; (C.B.); (M.B.); (R.G.-S.)
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18
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Robinson H, Barrett H, Gomez-Arango L, McIntyre HD, Callaway L, Dekker Nitert M. Ketonuria Is Associated with Changes to the Abundance of Roseburia in the Gut Microbiota of Overweight and Obese Women at 16 Weeks Gestation: A Cross-Sectional Observational Study. Nutrients 2019; 11:E1836. [PMID: 31398880 DOI: 10.3390/nu11081836] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome in pregnancy has been associated with various maternal metabolic and hormonal markers involved in glucose metabolism. Maternal ketones are of particular interest due to the rise in popularity of low-carbohydrate diets. We assessed for differences in the composition of the gut microbiota in pregnant women with and without ketonuria at 16 weeks gestation. Fecal samples were obtained from 11 women with fasting ketonuria and 11 matched controls. The samples were analyzed to assess for differences in gut microbiota composition by 16S rRNA sequencing. Supervised hierarchical clustering analysis showed significantly different beta-diversity between women with and without ketonuria, but no difference in the alpha-diversity. Group comparisons and network analysis showed that ketonuria was associated with an increased abundance of the butyrate-producing genus Roseburia. The bacteria that contributed the most to the differences in the composition of the gut microbiota included Roseburia, Methanobrevibacter, Uncl. RF39, and Dialister in women with ketonuria and Eggerthella, Phascolarctobacterium, Butyricimonas, and Uncl. Coriobacteriaceae in women without ketonuria. This study found that the genus Roseburia is more abundant in the gut microbiota of pregnant women with ketonuria. Roseburia is a butyrate producing bacterium and may increase serum ketone levels.
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19
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Patterson AM, Mulder IE, Travis AJ, Lan A, Cerf-Bensussan N, Gaboriau-Routhiau V, Garden K, Logan E, Delday MI, Coutts AGP, Monnais E, Ferraria VC, Inoue R, Grant G, Aminov RI. Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity. Front Immunol 2017; 8:1166. [PMID: 29018440 PMCID: PMC5622956 DOI: 10.3389/fimmu.2017.01166] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/04/2017] [Indexed: 12/19/2022] Open
Abstract
Objective Roseburia hominis is a flagellated gut anaerobic bacterium belonging to the Lachnospiraceae family within the Firmicutes phylum. A significant decrease of R. hominis colonization in the gut of ulcerative colitis patients has recently been demonstrated. In this work, we have investigated the mechanisms of R. hominis–host cross talk using both murine and in vitro models. Design The complete genome sequence of R. hominis A2-183 was determined. C3H/HeN germ-free mice were mono-colonized with R. hominis, and the host–microbe interaction was studied using histology, transcriptome analyses and FACS. Further investigations were performed in vitro and using the TLR5KO and DSS-colitis murine models. Results In the bacterium, R. hominis, host gut colonization upregulated genes involved in conjugation/mobilization, metabolism, motility, and chemotaxis. In the host cells, bacterial colonization upregulated genes related to antimicrobial peptides, gut barrier function, toll-like receptors (TLR) signaling, and T cell biology. CD4+CD25+FoxP3+ T cell numbers increased in the lamina propria of both mono-associated and conventional mice treated with R. hominis. Treatment with the R. hominis bacterium provided protection against DSS-induced colitis. The role of flagellin in host–bacterium interaction was also investigated. Conclusion Mono-association of mice with R. hominis bacteria results in specific bidirectional gene expression patterns. A set of genes thought to be important for host colonization are induced in R. hominis, while the host cells respond by strengthening gut barrier function and enhancing Treg population expansion, possibly via TLR5-flagellin signaling. Our data reveal the immunomodulatory properties of R. hominis that could be useful for the control and treatment of gut inflammation.
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Affiliation(s)
- Angela M Patterson
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Imke E Mulder
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Anthony J Travis
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Annaig Lan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Nadine Cerf-Bensussan
- INSERM, UMR1163, Lab Intestinal Immunity, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité and Institut Imagine, Paris, France
| | - Valerie Gaboriau-Routhiau
- INSERM, UMR1163, Lab Intestinal Immunity, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité and Institut Imagine, Paris, France.,Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Karen Garden
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Elizabeth Logan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Margaret I Delday
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Alistair G P Coutts
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Edouard Monnais
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Vanessa C Ferraria
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Ryo Inoue
- Kyoto Prefectural University, Kyoto, Japan
| | - George Grant
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.,School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Rustam I Aminov
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
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20
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Vermeire S, Joossens M, Verbeke K, Wang J, Machiels K, Sabino J, Ferrante M, Van Assche G, Rutgeerts P, Raes J. Donor Species Richness Determines Faecal Microbiota Transplantation Success in Inflammatory Bowel Disease. J Crohns Colitis 2016; 10:387-94. [PMID: 26519463 PMCID: PMC4946755 DOI: 10.1093/ecco-jcc/jjv203] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/25/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Faecal microbiota transplantation is a successful therapy for patients with refractory Clostridium difficile infections. It has also been suggested as a treatment option for inflammatory bowel disease, given the role of the intestinal microbiota in this disease. We assessed the impact of faecal microbiota transplantation in patients with inflammatory bowel disease and studied predictors of clinical (non-)response in microbial profiles of donors and patients. METHODS Fourteen refractory patients (8 with ulcerative colitis and 6 with Crohn's disease) underwent ileocolonoscopy with faecal microbiota transplantation through a nasojejunal (n = 9) or rectal (n = 5) tube. Efficacy was assessed by endoscopic healing at week 8, clinical activity scores and C-reactive protein measurement. Faecal microbiota was analysed by 16S rDNA pyrosequencing. RESULTS There was no significant improvement among the 6 patients with Crohn's disease at week 8 following faecal microbiota transplantation. One patient experienced temporary clinical remission for 6 weeks. In contrast, 2/8 patients with ulcerative colitis had endoscopic remission at week 8, and of the 6 remaining patients with ulcerative colitis, 1 reported temporary remission for 6 weeks. The donor microbiota richness and the number of transferred phylotypes were associated with treatment success. Persistent increased C-reactive protein 2 weeks after transplantation was predictive of failure of response. CONCLUSION Faecal microbiota transplantation led to endoscopic and long-term (>2 years) remission in 2 out of 8 ulcerative colitis patients. Higher donor richness was associated with successful transplant. Therefore, faecal microbiota transplantation with donor prescreening could be a treatment option for selected refractory ulcerative colitis patients.
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Affiliation(s)
- Severine Vermeire
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | | | - Kristin Verbeke
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Jun Wang
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium,VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Kathleen Machiels
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - João Sabino
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Marc Ferrante
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Gert Van Assche
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Paul Rutgeerts
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium,VIB, Center for the Biology of Disease, Leuven, Belgium
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21
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O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K, J Flint H. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom 2016; 2:e000043. [PMID: 28348841 PMCID: PMC5320581 DOI: 10.1099/mgen.0.000043] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/11/2015] [Indexed: 12/25/2022] Open
Abstract
Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
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Affiliation(s)
- Paul O Sheridan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Jennifer C Martin
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | | | | | - Hugh M B Harris
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Annick Bernalier-Donadille
- 4 Unité de Microbiologie INRA, Centre de Recherche de Clermont-Ferrand/Theix, 63122 Saint Genès Champanelle, France
| | - Sylvia H Duncan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Paul W O'Toole
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Karen P Scott
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Harry J Flint
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
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