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Gilliland A, Chan JJ, De Wolfe TJ, Yang H, Vallance BA. Pathobionts in Inflammatory Bowel Disease: Origins, Underlying Mechanisms, and Implications for Clinical Care. Gastroenterology 2024; 166:44-58. [PMID: 37734419 DOI: 10.1053/j.gastro.2023.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
The gut microbiota plays a significant role in the pathogenesis of both forms of inflammatory bowel disease (IBD), namely, Crohn's disease (CD) and ulcerative colitis (UC). Although evidence suggests dysbiosis and loss of beneficial microbial species can exacerbate IBD, many new studies have identified microbes with pathogenic qualities, termed "pathobionts," within the intestines of patients with IBD. The concept of pathobionts initiating or driving the chronicity of IBD has largely focused on the putative aggravating role that adherent invasive Escherichia coli may play in CD. However, recent studies have identified additional bacterial and fungal pathobionts in patients with CD and UC. This review will highlight the characteristics of these pathobionts and their implications for IBD treatment. Beyond exploring the origins of pathobionts, we discuss those associated with specific clinical features and the potential mechanisms involved, such as creeping fat (Clostridium innocuum) and impaired wound healing (Debaryomyces hansenii) in patients with CD as well as the increased fecal proteolytic activity (Bacteroides vulgatus) seen as a biomarker for UC severity. Finally, we examine the potential impact of pathobionts on current IBD therapies, and several new approaches to target pathobionts currently in the early stages of development. Despite recognizing that pathobionts likely contribute to the pathogenesis of IBD, more work is needed to define their modes of action. Determining whether causal relationships exist between pathobionts and specific disease characteristics could pave the way for improved care for patients, particularly for those not responding to current IBD therapies.
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Affiliation(s)
- Ashley Gilliland
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Jocelyn J Chan
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Travis J De Wolfe
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Hyungjun Yang
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce A Vallance
- Division of Gastroenterology, Department of Pediatrics, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada.
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2
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Kelly C, Jawahar J, Davey L, Everitt JI, Galanko JA, Anderson C, Avendano JE, McCann JR, Sartor RB, Valdivia RH, Rawls JF. Spontaneous episodic inflammation in the intestines of mice lacking HNF4A is driven by microbiota and associated with early life microbiota alterations. mBio 2023; 14:e0150423. [PMID: 37526424 PMCID: PMC10470520 DOI: 10.1128/mbio.01504-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 08/02/2023] Open
Abstract
The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals who mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. Whereas IBD clinical presentation is well described, how interactions between microbiota and host genotype impact early subclinical stages of the disease remains unclear. The transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has been associated with human IBD, and deletion of Hnf4a in intestinal epithelial cells (IECs) in mice (Hnf4aΔIEC) leads to spontaneous colonic inflammation by 6-12 mo of age. Here, we tested if pathology in Hnf4aΔIEC mice begins earlier in life and if microbiota contribute to that process. Longitudinal analysis revealed that Hnf4aΔIEC mice reared in specific pathogen-free (SPF) conditions develop episodic elevated fecal lipocalin 2 (Lcn2) and loose stools beginning by 4-5 wk of age. Lifetime cumulative Lcn2 levels correlated with histopathological features of colitis at 12 mo. Antibiotic and gnotobiotic tests showed that these phenotypes in Hnf4aΔIEC mice were dependent on microbiota. Fecal 16S rRNA gene sequencing in SPF Hnf4aΔIEC and control mice disclosed that genotype significantly contributed to differences in microbiota composition by 12 mo, and longitudinal analysis of the Hnf4aΔIEC mice with the highest lifetime cumulative Lcn2 revealed that microbial community differences emerged early in life when elevated fecal Lcn2 was first detected. These microbiota differences included enrichment of a novel phylogroup of Akkermansia muciniphila in Hnf4aΔIEC mice. We conclude that HNF4A functions in IEC to shape composition of the gut microbiota and protect against episodic inflammation induced by microbiota throughout the lifespan. IMPORTANCE The inflammatory bowel diseases (IBD), characterized by chronic inflammation of the intestine, affect millions of people around the world. Although significant advances have been made in the clinical management of IBD, the early subclinical stages of IBD are not well defined and are difficult to study in humans. This work explores the subclinical stages of disease in mice lacking the IBD-associated transcription factor HNF4A in the intestinal epithelium. Whereas these mice do not develop overt disease until late in adulthood, we find that they display episodic intestinal inflammation, loose stools, and microbiota changes beginning in very early life stages. Using germ-free and antibiotic-treatment experiments, we reveal that intestinal inflammation in these mice was dependent on the presence of microbiota. These results suggest that interactions between host genotype and microbiota can drive early subclinical pathologies that precede the overt onset of IBD and describe a mouse model to explore those important processes.
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Affiliation(s)
- Cecelia Kelly
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jayanth Jawahar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jeffrey I. Everitt
- Department of Pathology, Research Animal Pathology Core, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph A. Galanko
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chelsea Anderson
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan E. Avendano
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - R. Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
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3
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Manghi P, Blanco-Míguez A, Manara S, NabiNejad A, Cumbo F, Beghini F, Armanini F, Golzato D, Huang KD, Thomas AM, Piccinno G, Punčochář M, Zolfo M, Lesker TR, Bredon M, Planchais J, Glodt J, Valles-Colomer M, Koren O, Pasolli E, Asnicar F, Strowig T, Sokol H, Segata N. MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice. Cell Rep 2023; 42:112464. [PMID: 37141097 PMCID: PMC10242440 DOI: 10.1016/j.celrep.2023.112464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/10/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.
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Affiliation(s)
- Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | - Amir NabiNejad
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marius Bredon
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Julien Planchais
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | - Jeremy Glodt
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | | | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | | | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy.
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4
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Hu Q, Yu L, Zhai Q, Zhao J, Tian F. Anti-Inflammatory, Barrier Maintenance, and Gut Microbiome Modulation Effects of Saccharomyces cerevisiae QHNLD8L1 on DSS-Induced Ulcerative Colitis in Mice. Int J Mol Sci 2023; 24:ijms24076721. [PMID: 37047694 PMCID: PMC10094816 DOI: 10.3390/ijms24076721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
The use of probiotics has been considered as a new therapy option for ulcerative colitis (UC), and yeast has recently received widespread recommendation for human health. In this study, the probiotic characteristics of four yeast strains, Saccharomyces boulardii CNCMI-745, Kluyveromyces marxianus QHBYC4L2, Saccharomyces cerevisiae QHNLD8L1, and Debaryomyces hansenii QSCLS6L3, were evaluated in vitro; their ability to ameliorate dextran sulfate sodium (DSS)-induced colitis was investigated. Among these, S. cerevisiae QHNLD8L1 protected against colitis, which was reflected by increased body weight, colon length, histological injury relief, decreased gut inflammation markers, and intestinal barrier restoration. The abundance of the pathogenic bacteria Escherichia–Shigella and Enterococcaceae in mice with colitis decreased after S. cerevisiae QHNLD8L1 treatment. Moreover, S. cerevisiae QHNLD8L1 enriched beneficial bacteria Lactobacillus, Faecalibaculum, and Butyricimonas, enhanced carbon metabolism and fatty acid biosynthesis function, and increased short chain fatty acid (SCFAs) production. Taken together, our results indicate the great potential of S. cerevisiae QHNLD8L1 supplementation for the prevention and alleviation of UC.
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Affiliation(s)
- Qianjue Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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5
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Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L, Golzato D, Armanini F, Cumbo F, Huang KD, Manara S, Masetti G, Pinto F, Piperni E, Punčochář M, Ricci L, Zolfo M, Farrant O, Goncalves A, Selma-Royo M, Binetti AG, Becerra JE, Han B, Lusingu J, Amuasi J, Amoroso L, Visconti A, Steves CM, Falchi M, Filosi M, Tett A, Last A, Xu Q, Qin N, Qin H, May J, Eibach D, Corrias MV, Ponzoni M, Pasolli E, Spector TD, Domenici E, Collado MC, Segata N. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 2023; 614:125-135. [PMID: 36653448 PMCID: PMC9892008 DOI: 10.1038/s41586-022-05620-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/02/2022] [Indexed: 01/19/2023]
Abstract
The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.
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Affiliation(s)
| | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Elisa Piperni
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | | | - Liviana Ricci
- Department CIBIO, University of Trento, Trento, Italy
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Olivia Farrant
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Goncalves
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Marta Selma-Royo
- Department CIBIO, University of Trento, Trento, Italy
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Ana G Binetti
- Instituto de Lactología Industrial (CONICET-UNL), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jimmy E Becerra
- Grupo de Investigación Alimentación y Comportamiento Humano, Universidad Metropolitana, Barranquilla, Colombia
| | - Bei Han
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - John Lusingu
- National Institute for Medical Research, Tanga Medical Research Centre, Tanga, Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire M Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna Last
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Qian Xu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Realbio Genomics Institute, Shanghai, China
| | - Nan Qin
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Realbio Genomics Institute, Shanghai, China
| | - Huanlong Qin
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples 'Federico II', Portici, Italy
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Enrico Domenici
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Computational and Systems Biology (COSBI), Microsoft Research Foundation, Rovereto, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
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Dietary Supplementation with Black Raspberries Altered the Gut Microbiome Composition in a Mouse Model of Colitis-Associated Colorectal Cancer, although with Differing Effects for a Healthy versus a Western Basal Diet. Nutrients 2022; 14:nu14245270. [PMID: 36558431 PMCID: PMC9786988 DOI: 10.3390/nu14245270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
Black raspberries (BRB) are rich in anthocyanins with purported anti-inflammatory properties. However, it is not known whether dietary supplementation would ameliorate Western-diet enhanced gut inflammation and colon tumorigenesis. We employed a mouse model of colitis-associated colorectal cancer (CAC) to determine the effects of dietary supplementation with 5 to 10% (w/w) whole, freeze-dried BRB in male C57BL/6J mice fed either a standard healthy diet (AIN93G) or the total Western diet (TWD). In a pilot study, BRB suppressed colitis and colon tumorigenesis while also shifting the composition of the fecal microbiome in favor of taxa with purported health benefits, including Bifidobacterium pseudolongum. In a follow-up experiment using a 2 × 2 factorial design with AIN and TWD basal diets with and without 10% (w/w) BRB, supplementation with BRB reduced tumor multiplicity and increased colon length, irrespective of the basal diet, but it did not apparently affect colitis symptoms, colon inflammation or mucosal injury based on histopathological findings. However, BRB intake increased alpha diversity, altered beta diversity and changed the relative abundance of Erysipelotrichaceae, Bifidobacteriaceae, Streptococcaceae, Rikenellaceae, Ruminococcaceae and Akkermansiaceae, among others, of the fecal microbiome. Notably, changes in microbiome profiles were inconsistent with respect to the basal diet consumed. Overall, these studies provide equivocal evidence for in vivo anti-inflammatory effects of BRB on colitis and colon tumorigenesis; yet, BRB supplementation led to dynamic changes in the fecal microbiome composition over the course of disease development.
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Dark-purple rice extract modulates gut microbiota composition in acetic acid– and indomethacin-induced inflammatory bowel disease in rats. Int Microbiol 2022; 26:423-434. [PMID: 36484910 DOI: 10.1007/s10123-022-00309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Ulcerative colitis (UC) and Crohn's disease (CD) are two major forms of inflammatory bowel disease (IBD). The disease has been linked with gut microbiota dysbiosis in which the balance of commensal communities is disrupted. Accumulating evidence demonstrates that treatment with biologically active compounds can modulate gut microbiota composition in animal models. Our previous work has also shown the beneficial effect of Luem Pua (LP) rice extract, which is rich in anthocyanins, on inflammation. However, its effect on gut microbiota is yet to be explored. In this study, we profiled fecal microbiota of acetic acid (AA)-induced UC and indomethacin (ID)-induced CD rat models with and without pretreatment with LP rice extract by 16S rRNA gene sequencing. The results showed that gut microbiota communities of rats were altered by both AA-induced UC and ID-induced CD. The relative abundances of beneficial bacteria, especially the Lachnospiraceae NK4A136 group and Lactobacillus, were decreased in the AA-induced UC model, while some opportunistic pathogens (Bacteroides, Escherichia/Shigella, Fusobacterium, and Veillonella) were raised by ID-induced CD. Interestingly, pretreatment with LP rice extract before AA-inducing UC in rats increased the proportion of the butyrate-producing bacteria (Lachnospiraceae NK4A136 group). The abundances of these beneficial bacteria and other SCFA-producing bacteria were unaffected by the indomethacin treatment with LP. Overall, our study revealed different impacts of AA-induced UC and ID-induced CD on changes in community composition and hinted at how LP may protect against UC by modifying the gut microbiota.
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Boix-Amorós A, Monaco H, Sambataro E, Clemente JC. Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease. Gut Microbes 2022; 14:2107866. [PMID: 36104776 PMCID: PMC9481095 DOI: 10.1080/19490976.2022.2107866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.
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Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Hilary Monaco
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Elisa Sambataro
- Department of Biological Sciences, CUNY Hunter College, New York, NY, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA,CONTACT Jose C. Clemente Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY10029USA
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9
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Lyalina S, Stepanauskas R, Wu F, Sanjabi S, Pollard KS. Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community. PLoS One 2022; 17:e0261795. [PMID: 35417481 PMCID: PMC9007364 DOI: 10.1371/journal.pone.0261795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/01/2022] [Indexed: 12/16/2022] Open
Abstract
Laboratory mice are widely studied as models of mammalian biology, including the microbiota. However, much of the taxonomic and functional diversity of the mouse gut microbiome is missed in current metagenomic studies, because genome databases have not achieved a balanced representation of the diverse members of this ecosystem. Towards solving this problem, we used flow cytometry and low-coverage sequencing to capture the genomes of 764 single cells from the stool of three laboratory mice. From these, we generated 298 high-coverage microbial genome assemblies, which we annotated for open reading frames and phylogenetic placement. These genomes increase the gene catalog and phylogenetic breadth of the mouse microbiota, adding 135 novel species with the greatest increase in diversity to the Muribaculaceae and Bacteroidaceae families. This new diversity also improves the read mapping rate, taxonomic classifier performance, and gene detection rate of mouse stool metagenomes. The novel microbial functions revealed through our single-cell genomes highlight previously invisible pathways that may be important for life in the murine gastrointestinal tract.
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Affiliation(s)
- Svetlana Lyalina
- Gladstone Institutes, San Francisco, CA, United States of America
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States of America
| | - Frank Wu
- Gladstone Institutes, San Francisco, CA, United States of America
| | - Shomyseh Sanjabi
- Gladstone Institutes, San Francisco, CA, United States of America
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, United States of America
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA, United States of America
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, United States of America
- Chan-Zuckerberg Biohub, San Francisco, CA, United States of America
- * E-mail:
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10
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Kundu P, Stagaman K, Kasschau K, Holden S, Shulzhenko N, Sharpton TJ, Raber J. Fecal Implants From App NL-G-F and App NL-G-F/E4 Donor Mice Sufficient to Induce Behavioral Phenotypes in Germ-Free Mice. Front Behav Neurosci 2022; 16:791128. [PMID: 35210996 PMCID: PMC8860839 DOI: 10.3389/fnbeh.2022.791128] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome and the gut brain axis are potential determinants of Alzheimer's disease (AD) etiology or severity and gut microbiota might coordinate with the gut-brain axis to regulate behavioral phenotypes in AD mouse models. Using 6-month-old human amyloid precursor protein (hAPP) knock-in (KI) mice, which contain the Swedish and Iberian mutations [APP NL-F (App NL-F)] or the Arctic mutation as third mutation [APP NL-G-F (App NL-G-F)], behavioral and cognitive performance is associated with the gut microbiome and APP genotype modulates this association. In this study, we determined the feasibility of behavioral testing of mice in a biosafety cabinet and whether stool from 6-month-old App NL-G-F mice or App NL-G-F crossed with human apoE4 targeted replacement mice is sufficient to induce behavioral phenotypes in 4-5 month-old germ-free C57BL/6J mice 4 weeks following inoculation. We also compared the behavioral phenotypes of the recipient mice with that of the donor mice. Finally, we assessed cortical Aβ levels and analyzed the gut microbiome in the recipient mice. These results show that it is feasible to behaviorally test germ-free mice inside a biosafety cabinet. However, the host genotype was critical in modulating the pattern of induced behavioral phenotypes as compared to those seen in the genotype- and sex-match donor mice. Male mice that received stool from App NL-G-F and App NL-G-F/E4 donor genotypes tended to have lower body weight as compared to wild type, an effect not observed among donor mice. Additionally, App NL-G-F/E4 recipient males, but not females, showed impaired object recognition. Insoluble Aβ40 levels were detected in App NL-G-F and App NL-G-F/E4 recipient mice. Recipients of App NL-G-F, but not App NL-G-F/E4, donor mice carried cortical insoluble Aβ40 levels that positively correlated with activity levels on the first and second day of open field testing. For recipient mice, the interaction between donor genotype and several behavioral scores predicted gut microbiome alpha-diversity. Similarly, two behavioral performance scores predicted microbiome composition in recipient mice, but this association was dependent on the donor genotype. These data suggest that genotypes of the donor and recipient might need to be considered for developing novel therapeutic strategies targeting the gut microbiome in AD and other neurodegenerative disorders.
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Affiliation(s)
- Payel Kundu
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristin Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Sarah Holden
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
| | - Natalia Shulzhenko
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
- Division of Neuroscience ONPRC, Department of Neurology, Psychiatry, and Radiation Medicine, Oregon Health & Science University, Portland, OR, United States
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
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11
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Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol 2021; 17:e1009442. [PMID: 34784344 PMCID: PMC8714082 DOI: 10.1371/journal.pcbi.1009442] [Citation(s) in RCA: 656] [Impact Index Per Article: 218.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/28/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata to microbial community measurements, due in part to their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and often in the form of count or compositional measurements. Here we introduce an optimized combination of novel and established methodology to assess multivariable association of microbial community features with complex metadata in population-scale observational studies. Our approach, MaAsLin 2 (Microbiome Multivariable Associations with Linear Models), uses generalized linear and mixed models to accommodate a wide variety of modern epidemiological studies, including cross-sectional and longitudinal designs, as well as a variety of data types (e.g., counts and relative abundances) with or without covariates and repeated measurements. To construct this method, we conducted a large-scale evaluation of a broad range of scenarios under which straightforward identification of meta-omics associations can be challenging. These simulation studies reveal that MaAsLin 2's linear model preserves statistical power in the presence of repeated measures and multiple covariates, while accounting for the nuances of meta-omics features and controlling false discovery. We also applied MaAsLin 2 to a microbial multi-omics dataset from the Integrative Human Microbiome (HMP2) project which, in addition to reproducing established results, revealed a unique, integrated landscape of inflammatory bowel diseases (IBD) across multiple time points and omics profiles.
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Affiliation(s)
- Himel Mallick
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington DC, United States of America
| | - Lauren J. McIver
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Siyuan Ma
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Yancong Zhang
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Long H. Nguyen
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Timothy L. Tickle
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - George Weingart
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Boyu Ren
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Emma H. Schwager
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Suvo Chatterjee
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kelsey N. Thompson
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jeremy E. Wilkinson
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Ayshwarya Subramanian
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Yiren Lu
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Levi Waldron
- Department of Epidemiology and Biostatistics, CUNY School of Public Health, New York City, New York, United States of America
| | - Joseph N. Paulson
- Department of Biostatistics, Product Development, Genentech, Inc., South San Francisco, California, United States of America
| | - Eric A. Franzosa
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Hector Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Curtis Huttenhower
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
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12
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Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol 2021. [PMID: 34784344 DOI: 10.1101/2021.01.20.427420v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
It is challenging to associate features such as human health outcomes, diet, environmental conditions, or other metadata to microbial community measurements, due in part to their quantitative properties. Microbiome multi-omics are typically noisy, sparse (zero-inflated), high-dimensional, extremely non-normal, and often in the form of count or compositional measurements. Here we introduce an optimized combination of novel and established methodology to assess multivariable association of microbial community features with complex metadata in population-scale observational studies. Our approach, MaAsLin 2 (Microbiome Multivariable Associations with Linear Models), uses generalized linear and mixed models to accommodate a wide variety of modern epidemiological studies, including cross-sectional and longitudinal designs, as well as a variety of data types (e.g., counts and relative abundances) with or without covariates and repeated measurements. To construct this method, we conducted a large-scale evaluation of a broad range of scenarios under which straightforward identification of meta-omics associations can be challenging. These simulation studies reveal that MaAsLin 2's linear model preserves statistical power in the presence of repeated measures and multiple covariates, while accounting for the nuances of meta-omics features and controlling false discovery. We also applied MaAsLin 2 to a microbial multi-omics dataset from the Integrative Human Microbiome (HMP2) project which, in addition to reproducing established results, revealed a unique, integrated landscape of inflammatory bowel diseases (IBD) across multiple time points and omics profiles.
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Affiliation(s)
- Himel Mallick
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington DC, United States of America
| | - Lauren J McIver
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Siyuan Ma
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Yancong Zhang
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Long H Nguyen
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Timothy L Tickle
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - George Weingart
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Boyu Ren
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Emma H Schwager
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Suvo Chatterjee
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kelsey N Thompson
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jeremy E Wilkinson
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Ayshwarya Subramanian
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Yiren Lu
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Levi Waldron
- Department of Epidemiology and Biostatistics, CUNY School of Public Health, New York City, New York, United States of America
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech, Inc., South San Francisco, California, United States of America
| | - Eric A Franzosa
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Hector Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Curtis Huttenhower
- Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
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13
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Sun Z, Li J, Wang W, Liu Y, Liu J, Jiang H, Lu Q, Ding P, Shi R, Zhao X, Yuan W, Tan X, Shi X, Xing Y, Mao T. Qingchang Wenzhong Decoction Accelerates Intestinal Mucosal Healing Through Modulation of Dysregulated Gut Microbiome, Intestinal Barrier and Immune Responses in Mice. Front Pharmacol 2021; 12:738152. [PMID: 34557102 PMCID: PMC8452913 DOI: 10.3389/fphar.2021.738152] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/24/2021] [Indexed: 12/20/2022] Open
Abstract
Inflammatory bowel disease (IBD), a group of multifactorial and inflammatory infirmities, is closely associated with dysregulation of gut microbiota and host metabolome, but effective treatments are currently limited. Qingchang Wenzhong Decoction (QCWZD) is an effective and classical traditional herbal prescription for the treatment of IBD and has been proved to attenuate intestinal inflammation in a model of acute colitis. However, the role of QCWZD in recovery phase of colitis is unclear. Here, we demonstrated that mice treated with QCWZD showed a faster recovery from dextran sulfate sodium (DSS)-induced epithelial injury, accompanied by reduced mucosal inflammation and attenuated intestinal dysbiosis using bacterial 16S rRNA amplicon sequencing compared to those receiving sterile water. The protective effects of QCWZD are gut microbiota dependent, as demonstrated by fecal microbiome transplantation and antibiotics treatment. Gut microbes transferred from QCWZD-treated mice displayed a similar role in mucosal protection and epithelial regeneration as QCWZD on colitis in mice, and depletion of the gut microbiota through antibiotics treatments diminished the beneficial effects of QCWZD on colitis mice. Moreover, metabolomic analysis revealed metabolic profiles alternations in response to the gut microbiota reprogrammed by QCWZD intervention, especially enhanced tryptophan metabolism, which may further accelerate intestinal stem cells-mediated epithelial regeneration to protect the integrity of intestinal mucosa through activation of Wnt/β-catenin signals. Collectively, our results suggested that orally administrated QCWZD accelerates intestinal mucosal healing through the modulation of dysregulated gut microbiota and metabolism, thus regulating intestinal stem cells-mediated epithelial proliferation, and hold promise for novel microbial-based therapies in the treatment of IBD.
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Affiliation(s)
- Zhongmei Sun
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China.,Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Junxiang Li
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wenting Wang
- Department of Traditional Chinese Medicine, Beijing Yangfangdian Hospital, Beijing, China
| | - Yuyue Liu
- Department of Pathology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jia Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Hui Jiang
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qiongqiong Lu
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Panghua Ding
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Rui Shi
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xingjie Zhao
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wenjing Yuan
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xiang Tan
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaojun Shi
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yunqi Xing
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Tangyou Mao
- Department of Gastroenterology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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14
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Pham T, Sokol H, Halioua B, Pourcel G, Brun M, Pain E, Testa D. Immune-mediated inflammatory diseases and nutrition: results from an online survey on patients' practices and perceptions. BMC Nutr 2021; 7:38. [PMID: 34266484 PMCID: PMC8283994 DOI: 10.1186/s40795-021-00446-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Background The central role of microbiota and the contribution of diet in immune-mediated inflammatory diseases (IMID) are increasingly examined. However, patients’ perspectives on nutrition and its impact on their disease has not received a lot of attention. We aimed to directly collect information from patients with IMID about their dietary behaviors and their perceptions of the influence of nutrition on their disease. Methods Adult patients with rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, Crohn’s disease, ulcerative colitis or psoriasis registered in an online patient community were invited to participate in the study and complete an online self-administered questionnaire. We assessed patients’ dietary knowledge and choices by collecting information on the diet regimens they were following or recommended and their perceptions of the diet and its consequences on their disease. Results Fifty patients per target disease were included with a mean age of 48.1 years (95%CI 46.7–49.6). Other sociodemographic and clinical characteristics varied across the diseases. Since diagnosis, 44% of the patients changed their eating habits, mainly patients with inflammatory bowel disease with 69% of these making the change on their own initiative. Patients who did not change their diet habits reported not having received nutritional advice from their healthcare professionals (HCP) in 69% of the cases. The perceived impact of nutrition on their symptoms was mixed (overall 74% of the patients reported positive consequences and 60% negative ones) and varied across the diseases. Patients with psoriasis only experienced positive consequences from changing their diet, such as reduction of stress and improved mental health, while patients with Crohn’s disease reported more negative effects such as increased fatigue and disturbed sleep. Patients with rheumatic diseases and ulcerative colitis reported weight loss and better physical fitness, but also increased fatigue. Conclusions Even if differences exist across diseases, the importance of nutrition and its potential positive role in symptom management is acknowledged by the majority of the patients. However, there is a need and a demand from patients to receive more dietary advice. Developing therapeutic education tools on nutrition for people with IMID and involving patients’ organizations would provide useful information and encourage communication between HCP and patients.
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Affiliation(s)
- Thao Pham
- Service de rhumatologie, Hôpital Sainte-Marguerite, Aix Marseille Univ, Assistance publique - Hôpitaux de Marseille, Marseille, France
| | - Harry Sokol
- Gastroenterology department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012, Paris, France.,INRAE, UMR1319 Micalis & AgroParisTech, 78350, Jouy en Josas, France
| | | | | | | | - Emilie Pain
- Carenity, Communauté de patients en ligne, Paris, France.
| | - Damien Testa
- Carenity, Communauté de patients en ligne, Paris, France
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15
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Welch CB, Lourenco JM, Krause TR, Seidel DS, Fluharty FL, Pringle TD, Callaway TR. Evaluation of the Fecal Bacterial Communities of Angus Steers With Divergent Feed Efficiencies Across the Lifespan From Weaning to Slaughter. Front Vet Sci 2021; 8:597405. [PMID: 34268344 PMCID: PMC8275654 DOI: 10.3389/fvets.2021.597405] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 05/27/2021] [Indexed: 11/30/2022] Open
Abstract
Numerous studies have examined the link between the presence of specific gastrointestinal bacteria and the feed efficiency of cattle. However, cattle undergo dietary changes during their productive life which can cause fluctuations in their microbial consortium. The objective of the present study was to assess changes in the fecal microbiome of beef steers genetically selected to be divergent in feedlot feed efficiency, to determine whether differences in their fecal microbiomes could be detected as early as weaning, and continued throughout the rearing process regardless of dietary changes. Fecal samples were collected at weaning, yearling age, and slaughter for a group of 63 steers. Based on their feedlot-finishing performance, the steers were selected and divided into two groups according to their residual feed intake (RFI): efficient steers (low-RFI; n = 7) and inefficient steers (high-RFI; n = 8). To ascertain the fecal microbial consortium and volatile fatty acid (VFA) content, 16S rRNA gene sequencing and VFA analysis were performed. Overall, bacterial evenness and diversity were greater at weaning compared to yearling and slaughter for both efficiency groups (P < 0.001). Feedlot RFI linearly decreased as both Shannon diversity and Ruminococcaceae abundance increased (R2 = 65.6 and 60.7%, respectively). Abundances of Ruminococcaceae, Rikenellaceae, and Christensenellaceae were higher at weaning vs. yearling age and slaughter (P < 0.001); moreover, these families were consistently more abundant in the feces of the low-RFI steers (for most of the timepoints evaluated; P ≤ 0.05), compared to the high-RFI steers. Conversely, abundances of Bifidobacteriaceae were numerically higher in the feces of the high-RFI steers throughout their lifespan. Total VFA concentrations increased at slaughter compared to weaning and yearling for both efficiency groups (P < 0.001). The acetate:propionate ratio decreased linearly (P < 0.001) throughout the life of the steers regardless of their efficiency, reflective of dietary changes. Our results indicate that despite fluctuations due to animal age and dietary changes, specific bacterial families may be correlated with feed efficiency of steers. Furthermore, such differences may be identifiable at earlier stages of the production cycle, potentially as early as weaning.
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Affiliation(s)
- Christina B Welch
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Jeferson M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Taylor R Krause
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Darren S Seidel
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Francis L Fluharty
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - T Dean Pringle
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Todd R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
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16
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Diet and gut microbiome enterotype are associated at the population level in African buffalo. Nat Commun 2021; 12:2267. [PMID: 33859184 PMCID: PMC8050287 DOI: 10.1038/s41467-021-22510-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/02/2021] [Indexed: 12/19/2022] Open
Abstract
Studies in humans and laboratory animals link stable gut microbiome “enterotypes” with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease. There are stable relationships between diet and microbiome in humans and lab animals. A study on African buffalo finds that diet influences microbiome variation and enterotype formation. Three pathogens may associate with microbiome depending on host diet, suggesting nutrition impacts relationships between gut microbiome and host health.
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17
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Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ. Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation. Cell Host Microbe 2021; 29:362-377.e11. [PMID: 33440172 PMCID: PMC7954989 DOI: 10.1016/j.chom.2020.12.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/24/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023]
Abstract
Immunomodulatory drugs can inhibit bacterial growth, yet their mechanism of action, spectrum, and clinical relevance remain unknown. Methotrexate (MTX), a first-line rheumatoid arthritis (RA) treatment, inhibits mammalian dihydrofolate reductase (DHFR), but whether it directly impacts gut bacteria is unclear. We show that MTX broadly alters the human gut microbiota. Drug sensitivity varied across strains, but the mechanism of action against DHFR appears conserved between mammalian and bacterial cells. RA patient microbiotas were sensitive to MTX, and changes in gut bacterial taxa and gene family abundance were distinct between responders and non-responders. Transplantation of post-treatment samples into germ-free mice given an inflammatory trigger led to reduced immune activation relative to pre-treatment controls, enabling identification of MTX-modulated bacterial taxa associated with intestinal and splenic immune cells. Thus, conservation in cellular pathways across domains of life can result in broad off-target drug effects on the human gut microbiota with consequences for immune function.
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Affiliation(s)
- Renuka R Nayak
- Rheumatology Division, Department of Medicine, University of California, San Francisco, CA 94143, USA; Department of Microbiology & Immunology, University of California, San Francisco, CA 94143, USA
| | - Margaret Alexander
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143, USA
| | - Ishani Deshpande
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143, USA
| | - Kye Stapleton-Gray
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143, USA
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Carles Ubeda
- Centro Superior de Investigación en Salud Pública - FISABIO, Valencia, Spain; CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Jose U Scher
- Department of Medicine, New York University, New York, NY 10003, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Kundu P, Torres ERS, Stagaman K, Kasschau K, Okhovat M, Holden S, Ward S, Nevonen KA, Davis BA, Saito T, Saido TC, Carbone L, Sharpton TJ, Raber J. Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in App NL-G-F, App NL-F, and wild type mice. Sci Rep 2021; 11:4678. [PMID: 33633159 PMCID: PMC7907263 DOI: 10.1038/s41598-021-83851-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetic mechanisms occurring in the brain as well as alterations in the gut microbiome composition might contribute to Alzheimer’s disease (AD). Human amyloid precursor protein knock-in (KI) mice contain the Swedish and Iberian mutations (AppNL-F) or those two and also the Arctic mutation (AppNL-G-F). In this study, we assessed whether behavioral and cognitive performance in 6-month-old AppNL-F, AppNL-G-F, and C57BL/6J wild-type (WT) mice was associated with the gut microbiome, and whether the genotype modulates this association. The genotype effects observed in behavioral tests were test-dependent. The biodiversity and composition of the gut microbiome linked to various aspects of mouse behavioral and cognitive performance but differences in genotype modulated these relationships. These genotype-dependent associations include members of the Lachnospiraceae and Ruminococcaceae families. In a subset of female mice, we assessed DNA methylation in the hippocampus and investigated whether alterations in hippocampal DNA methylation were associated with the gut microbiome. Among other differentially methylated regions, we identified a 1 Kb region that overlapped ing 3′UTR of the Tomm40 gene and the promoter region of the Apoe gene that and was significantly more methylated in the hippocampus of AppNL-G-F than WT mice. The integrated gut microbiome hippocampal DNA methylation analysis revealed a positive relationship between amplicon sequence variants (ASVs) within the Lachnospiraceae family and methylation at the Apoe gene. Hence, these microbes may elicit an impact on AD-relevant behavioral and cognitive performance via epigenetic changes in AD-susceptibility genes in neural tissue or that such changes in the epigenome can elicit alterations in intestinal physiology that affect the growth of these taxa in the gut microbiome.
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Affiliation(s)
- Payel Kundu
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eileen Ruth S Torres
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Kristin Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Sarah Holden
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Samantha Ward
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Brett A Davis
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA.,Departments of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA.,Departments of Medical Informatics and Clinical Epidemiology, Portland, OR, 97239, USA.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA.,Department of Statistics, Oregon State University, Corvallis, OR, 97331, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA. .,Departments of Neurology, Psychiatry, and Radiation Medicine, Division of Neuroscience ONPRC, Oregon Health & Science University, Portland, OR, 97239, USA. .,College of Pharmacy, Oregon State University, Corvallis, OR, 97331, USA. .,Department of Behavioral Neuroscience, L470, Oregon Health & Science University, 3181SW Sam Jackson Park Road, Portland, OR, 97239, USA.
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Park H, Yeo S, Kang S, Huh CS. Longitudinal Microbiome Analysis in a Dextran Sulfate Sodium-Induced Colitis Mouse Model. Microorganisms 2021; 9:370. [PMID: 33673349 PMCID: PMC7917662 DOI: 10.3390/microorganisms9020370] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
The role of the gut microbiota in the pathogenesis of inflammatory bowel disease (IBD) has been in focus for decades. Although metagenomic observations in patients/animal colitis models have been attempted, the microbiome results were still indefinite and broad taxonomic presumptions were made due to the cross-sectional studies. Herein, we conducted a longitudinal microbiome analysis in a dextran sulfate sodium (DSS)-induced colitis mouse model with a two-factor design based on serial DSS dose (0, 1, 2, and 3%) and duration for 12 days, and four mice from each group were sacrificed at two-day intervals. During the colitis development, a transition of the cecal microbial diversity from the normal state to dysbiosis and dynamic changes of the populations were observed. We identified genera that significantly induced or depleted depending on DSS exposure, and confirmed the correlations of the individual taxa to the colitis severity indicated by inflammatory biomarkers (intestinal bleeding and neutrophil-derived indicators). Of note, each taxonomic population showed its own susceptibility to the changing colitis status. Our findings suggest that an understanding of the individual susceptibility to colitis conditions may contribute to identifying the role of the gut microbes in the pathogenesis of IBD.
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Affiliation(s)
- Hyunjoon Park
- Research Institute of Eco-Friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea;
- Advanced Green Energy and Environment Institute, Handong Global University, Pohang 37554, Korea
| | - Soyoung Yeo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | - Seokwon Kang
- Department of Life Sciences, Handong Global University, Pohang 37554, Korea;
| | - Chul Sung Huh
- Research Institute of Eco-Friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea;
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea
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20
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Recovery and Community Succession of the Zostera marina Rhizobiome after Transplantation. Appl Environ Microbiol 2021; 87:AEM.02326-20. [PMID: 33187993 DOI: 10.1128/aem.02326-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/04/2020] [Indexed: 12/26/2022] Open
Abstract
Seagrasses can form mutualisms with their microbiomes that facilitate the exchange of energy sources, nutrients, and hormones and ultimately impact plant stress resistance. Little is known about community succession within the belowground seagrass microbiome after disturbance and its potential role in the plant's recovery after transplantation. We transplanted Zostera marina shoots with and without an intact rhizosphere and cultivated plants for 4 weeks while characterizing microbiome recovery and effects on plant traits. Rhizosphere and root microbiomes were compositionally distinct, likely representing discrete microbial niches. Furthermore, microbiomes of washed transplants were initially different from those of sod transplants and recovered to resemble an undisturbed state within 14 days. Conspicuously, changes in the microbial communities of washed transplants corresponded with changes in the rhizosphere sediment mass and root biomass, highlighting the strength and responsive nature of the relationship between plants, their microbiome, and the environment. Potential mutualistic microbes that were enriched over time include those that function in the cycling and turnover of sulfur, nitrogen, and plant-derived carbon in the rhizosphere environment. These findings highlight the importance and resilience of the seagrass microbiome after disturbance. Consideration of the microbiome will have meaningful implications for habitat restoration practices.IMPORTANCE Seagrasses are important coastal species that are declining globally, and transplantation can be used to combat these declines. However, the bacterial communities associated with seagrass rhizospheres and roots (the microbiome) are often disturbed or removed completely prior to transplantation. The seagrass microbiome benefits seagrasses through metabolite, nutrient, and phytohormone exchange and contributes to the ecosystem services of seagrass meadows by cycling sulfur, nitrogen, and carbon. This experiment aimed to characterize the importance and resilience of the seagrass belowground microbiome by transplanting Zostera marina with and without intact rhizospheres and tracking microbiome and plant morphological recovery over 4 weeks. We found the seagrass microbiome to be resilient to transplantation disturbance, recovering after 14 days. Additionally, microbiome recovery was linked with seagrass morphology, coinciding with increases in the rhizosphere sediment mass and root biomass. The results of this study can be used to include microbiome responses in informing future restoration work.
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21
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Zhang X, Yi N. Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data. Bioinformatics 2020; 36:2345-2351. [PMID: 31904815 DOI: 10.1093/bioinformatics/btz973] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/24/2019] [Accepted: 01/01/2020] [Indexed: 01/03/2023] Open
Abstract
MOTIVATION Longitudinal metagenomics data, including both 16S rRNA and whole-metagenome shotgun sequencing data, enhanced our abilities to understand the dynamic associations between the human microbiome and various diseases. However, analytic tools have not been fully developed to simultaneously address the main challenges of longitudinal metagenomics data, i.e. high-dimensionality, dependence among samples and zero-inflation of observed counts. RESULTS We propose a fast zero-inflated negative binomial mixed modeling (FZINBMM) approach to analyze high-dimensional longitudinal metagenomic count data. The FZINBMM approach is based on zero-inflated negative binomial mixed models (ZINBMMs) for modeling longitudinal metagenomic count data and a fast EM-IWLS algorithm for fitting ZINBMMs. FZINBMM takes advantage of a commonly used procedure for fitting linear mixed models, which allows us to include various types of fixed and random effects and within-subject correlation structures and quickly analyze many taxa. We found that FZINBMM remarkably outperformed in computational efficiency and was statistically comparable with two R packages, GLMMadaptive and glmmTMB, that use numerical integration to fit ZINBMMs. Extensive simulations and real data applications showed that FZINBMM outperformed other previous methods, including linear mixed models, negative binomial mixed models and zero-inflated Gaussian mixed models. AVAILABILITY AND IMPLEMENTATION FZINBMM has been implemented in the R package NBZIMM, available in the public GitHub repository http://github.com//nyiuab//NBZIMM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xinyan Zhang
- Department of Biostatistics, Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA 30458, USA
| | - Nengjun Yi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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22
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Bradley R, Langley BO, Ryan JJ, Phipps J, Hanes DA, Stack E, Jansson JK, Metz TO, Stevens JF. Xanthohumol microbiome and signature in healthy adults (the XMaS trial): a phase I triple-masked, placebo-controlled clinical trial. Trials 2020; 21:835. [PMID: 33028396 PMCID: PMC7542976 DOI: 10.1186/s13063-020-04769-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Natural products may provide a source for the discovery and development of adjunctive pharmacological interventions to modulate the inflammatory pathways contributing to chronic disease. Xanthohumol, a flavonoid from the hops plant (Humulus lupulus), has antioxidant and anti-inflammatory properties and may act as a prebiotic to the intestinal microbiota. Xanthohumol is not currently approved as a drug by the US Food and Drug Administration (FDA), but is available as a dietary supplement and ingredient in medical foods. To formally test the safety of xanthohumol, a phase I clinical trial ("XMaS") was designed and approved under an Investigational New Drug application to the US FDA. The main objective is to examine the clinical safety and subjective tolerability of xanthohumol in healthy adults compared to placebo. Additional aims are to monitor biomarkers related to inflammation, gut permeability, bile acid metabolism, routes, and in vivo products of xanthohumol metabolism, and to evaluate xanthohumol's impact on gut microbial composition. METHODS The safety and tolerability of xanthohumol in healthy adults will be evaluated in a triple-masked, randomized, placebo-controlled trial. Participants will be randomized to either 24 mg/day of xanthohumol or placebo for 8 weeks. Blood cell counts, hepatic and renal function tests, electrolytes, and self-reported health-related quality of life measures will be collected every 2 weeks. Participants will be queried for adverse events throughout the trial. Xanthohumol metabolites in blood, urine, and stool will be measured. Biomarkers to be evaluated include plasma tumor necrosis factor-alpha, various interleukins, soluble CD14, lipopolysaccharide-binding protein, fecal calprotectin, and bile acids to assess impact on inflammatory and gut permeability-related mechanisms in vivo. Stool samples will be analyzed to determine effects on the gut microbiome. DISCUSSION This phase I clinical trial of xanthohumol will assess safety and tolerability in healthy adults, collect extensive biomarker data for assessment of potential mechanism(s), and provide comparison data necessary for future phase II trials in chronic disease(s). The design and robustness of the planned safety and mechanistic evaluations planned provide a model for drug discovery pursuits from natural products. TRIAL REGISTRATION ClinicalTrials.gov NCT03735420 . Registered on November 8, 2018.
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Affiliation(s)
- Ryan Bradley
- National University of Natural Medicine, Portland, USA.
| | | | | | - John Phipps
- National University of Natural Medicine, Portland, USA
| | | | - Emily Stack
- National University of Natural Medicine, Portland, USA
| | | | - Thomas O Metz
- Pacific Northwest National Laboratory, Richland, USA
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23
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Miyoshi J, Lee STM, Kennedy M, Puertolas M, Frith M, Koval JC, Miyoshi S, Antonopoulos DA, Leone V, Chang EB. Metagenomic Alterations in Gut Microbiota Precede and Predict Onset of Colitis in the IL10 Gene-Deficient Murine Model. Cell Mol Gastroenterol Hepatol 2020; 11:491-502. [PMID: 32835897 PMCID: PMC7797374 DOI: 10.1016/j.jcmgh.2020.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Inflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive biomarkers for the disease development and clinical course are sorely needed for development of prevention and early intervention strategies that can be implemented to improve clinical outcomes. Since gut microbiome alterations can reflect and/or contribute to impending host health changes, we examined whether gut microbiota metagenomic profiles would provide more robust measures for predicting disease outcomes in colitis-prone hosts. METHODS Using the interleukin (IL) 10 gene-deficient (IL10 KO) murine model where early life dysbiosis from antibiotic (cefoperozone [CPZ]) treated dams vertically transferred to pups increases risk for colitis later in life, we investigated temporal metagenomic profiles in the gut microbiota of post-weaning offspring and determined their relationship to eventual clinical outcomes. RESULTS Compared to controls, offspring acquiring maternal CPZ-induced dysbiosis exhibited a restructuring of intestinal microbial membership in both bacteriome and mycobiome that was associated with alterations in specific functional subsystems. Furthermore, among IL10 KO offspring from CPZ-treated dams, several functional subsystems, particularly nitrogen metabolism, diverged between mice that developed spontaneous colitis (CPZ-colitis) versus those that did not (CPZ-no-colitis) at a time point prior to eventual clinical outcome. CONCLUSIONS Our findings provide support that functional metagenomic profiling of gut microbes has potential and promise meriting further study for development of tools to assess risk and manage human IBD.
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Affiliation(s)
- Jun Miyoshi
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois; Department of Gastroenterology and Hepatology, Kyorin University School of Medicine, Tokyo, Japan
| | - Sonny T M Lee
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois; Division of Biology, Kansas State University, Manhattan, Kansas
| | - Megan Kennedy
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois; Medical Scientist Training Program, Pritzker School of Medicine, University of Chicago, Chicago, Illinois
| | - Mora Puertolas
- Department of Pediatrics, University of Chicago Knapp Center for Biomedical Discovery, Chicago, Illinois
| | - Mary Frith
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois; Medical Scientist Training Program, Pritzker School of Medicine, University of Chicago, Chicago, Illinois
| | - Jason C Koval
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois
| | - Sawako Miyoshi
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois; Department of General Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Dionysios A Antonopoulos
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois; Biosciences Division, Argonne National Laboratory, Lemont, Illinois
| | - Vanessa Leone
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois
| | - Eugene B Chang
- Department of Medicine, Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois.
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24
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Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice. PLoS One 2020; 15:e0228358. [PMID: 32208434 PMCID: PMC7093000 DOI: 10.1371/journal.pone.0228358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Abstract
Inflammatory bowel disease results from alterations in the immune system and intestinal microbiota. The role of intestinal epithelial cells (IECs) in maintaining gut homeostasis is well known and its perturbation often causes gastrointestinal disorders including IBD. The epithelial specific adaptor protein (AP)-1B is involved in the establishment of the polarity of IECs. Deficiency of the AP-1B μ subunit (Ap1m2-/-) leads to the development of chronic colitis in mice. However, how this deficiency affects the gut microbes and its potential functions remains elusive. To gain insights into the gut microbiome of Ap1m2-/- mice having the colitis phenotype, we undertook shotgun metagenomic sequencing analysis of knockout mice. We found important links to the microbial features involved in altering various physiological pathways, including carbohydrate metabolism, nutrient transportation, oxidative stress, and bacterial pathogenesis (cell motility). In addition, an increased abundance of sulfur-reducing and lactate-producing bacteria has been observed which may aggravate the colitis condition.
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25
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Abstract
Understanding how health-promoting microbiota are established and their beneficial interactions with the host is of critical biomedical importance. The current high throughput data acquisition technologies allow for integrating components of the gut ecosystem. The richness of data types and large number of measured variables involved underscores the critical importance of the appropriate choice of analytical and computational methods that can be used to model this complex ecosystem. This review outlines currently used approaches to perform analyses of data obtained as a result of interrogation of the gut-microbiota ecosystem and the challenges associated with these methodological and computational efforts. The problem of large dimensionality versus small numbers of samples is explained with discussions of clustering, dimensionality reduction, and statistical testing. Predictive modeling and data integration specific to the gut ecosystem are also discussed.
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Affiliation(s)
- Ivan Ivanov
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, USA.
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26
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Sharpton TJ, Combrink L, Arnold HK, Gaulke CA, Kent M. Harnessing the gut microbiome in the fight against anthelminthic drug resistance. Curr Opin Microbiol 2020; 53:26-34. [PMID: 32114334 DOI: 10.1016/j.mib.2020.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 01/08/2023]
Abstract
Intestinal helminth parasites present major challenges to the welfare of humans and threaten the global food supply. While the discovery of anthelminthic drugs empowered our ability to offset these harms to society, the alarming rise of anthelminthic drug resistance mitigates contemporary efforts to treat and control intestinal helminthic infections. Fortunately, emerging research points to potential opportunities to combat anthelminthic drug resistance by harnessing the gut microbiome as a resource for discovering novel therapeutics and informing responsible drug administration. In this review, we highlight research that demonstrates this potential and provide rationale to support increased investment in efforts to uncover and translationally utilize knowledge about how the gut microbiome mediates intestinal helminthic infection and its outcomes.
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Affiliation(s)
- Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA; Department of Statistics, Oregon State University, Corvallis, OR, 97331, USA.
| | - Leigh Combrink
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA; Department of Biomedical Sciences, Oregon State University, Corvallis, OR, 97331, USA
| | - Holly K Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA; Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, 97331, USA
| | | | - Michael Kent
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA; Department of Biomedical Sciences, Oregon State University, Corvallis, OR, 97331, USA
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27
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Flannery JE, Stagaman K, Burns AR, Hickey RJ, Roos LE, Giuliano RJ, Fisher PA, Sharpton TJ. Gut Feelings Begin in Childhood: the Gut Metagenome Correlates with Early Environment, Caregiving, and Behavior. mBio 2020; 11:e02780-19. [PMID: 31964729 PMCID: PMC6974564 DOI: 10.1128/mbio.02780-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
Psychosocial environments impact normative behavioral development in children, increasing the risk of problem behaviors and psychiatric disorders across the life span. Converging evidence demonstrates that early normative development is affected by the gut microbiome, which itself can be altered by early psychosocial environments. However, much of our understanding of the gut microbiome's role in early development stems from nonhuman animal models and predominately focuses on the first years of life, during peri- and postnatal microbial colonization. As a first step to identify if these findings translate to humans and the extent to which these relationships are maintained after initial microbial colonization, we conducted a metagenomic investigation among a cross-sectional sample of early school-aged children with a range of adverse experiences and caregiver stressors and relationships. Our results indicate that the taxonomic and functional composition of the gut microbiome correlates with behavior during a critical period of child development. Furthermore, our analysis reveals that both socioeconomic risk exposure and child behaviors associate with the relative abundances of specific taxa (e.g., Bacteroides and Bifidobacterium species) as well as functional modules encoded in their genomes (e.g., monoamine metabolism) that have been linked to cognition and health. While we cannot infer causality within this study, these findings suggest that caregivers may moderate the gut microbiome's link to environment and behaviors beyond the first few years of life.IMPORTANCE Childhood is a formative period of behavioral and biological development that can be modified, for better or worse, by the psychosocial environment that is in part determined by caregivers. Not only do our own genes and the external environment influence such developmental trajectories, but the community of microbes living in, on, and around our bodies-the microbiome-plays an important role as well. By surveying the gut microbiomes of a cross-sectional cohort of early school-aged children with a range of psychosocial environments and subclinical mental health symptoms, we demonstrated that caregiving behaviors modified the child gut microbiome's association to socioeconomic risk and behavioral dysregulation.
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Affiliation(s)
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Adam R Burns
- Department of Medicine Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Roxana J Hickey
- Biology of the Built Environment Center, University of Oregon, Eugene, Oregon, USA
- Phylagen, San Francisco, California, USA
| | - Leslie E Roos
- Department of Psychology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ryan J Giuliano
- Department of Psychology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Philip A Fisher
- Department of Psychology, University of Oregon, Eugene, Oregon, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
- Department of Statistics, Oregon State University, Corvallis, Oregon, USA
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28
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Jiang D, Armour CR, Hu C, Mei M, Tian C, Sharpton TJ, Jiang Y. Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Front Genet 2019; 10:995. [PMID: 31781153 PMCID: PMC6857202 DOI: 10.3389/fgene.2019.00995] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022] Open
Abstract
The advent of large-scale microbiome studies affords newfound analytical opportunities to understand how these communities of microbes operate and relate to their environment. However, the analytical methodology needed to model microbiome data and integrate them with other data constructs remains nascent. This emergent analytical toolset frequently ports over techniques developed in other multi-omics investigations, especially the growing array of statistical and computational techniques for integrating and representing data through networks. While network analysis has emerged as a powerful approach to modeling microbiome data, oftentimes by integrating these data with other types of omics data to discern their functional linkages, it is not always evident if the statistical details of the approach being applied are consistent with the assumptions of microbiome data or how they impact data interpretation. In this review, we overview some of the most important network methods for integrative analysis, with an emphasis on methods that have been applied or have great potential to be applied to the analysis of multi-omics integration of microbiome data. We compare advantages and disadvantages of various statistical tools, assess their applicability to microbiome data, and discuss their biological interpretability. We also highlight on-going statistical challenges and opportunities for integrative network analysis of microbiome data.
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Affiliation(s)
- Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Courtney R Armour
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Chenxiao Hu
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Meng Mei
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Chuan Tian
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Statistics, Oregon State University, Corvallis, OR, United States
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, OR, United States
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Bian X, Wu W, Yang L, Lv L, Wang Q, Li Y, Ye J, Fang D, Wu J, Jiang X, Shi D, Li L. Administration of Akkermansia muciniphila Ameliorates Dextran Sulfate Sodium-Induced Ulcerative Colitis in Mice. Front Microbiol 2019; 10:2259. [PMID: 31632373 PMCID: PMC6779789 DOI: 10.3389/fmicb.2019.02259] [Citation(s) in RCA: 311] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/17/2019] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) develop as a result of complex interactions among genes, innate immunity and environmental factors, which are related to the gut microbiota. Multiple clinical and animal data have shown that Akkermansia muciniphila is associated with a healthy mucosa. However, its precise role in colitis is currently unknown. Our study aimed to determine its protective effects and underlying mechanisms in a dextran sulfate sodium (DSS)-induced colitis mouse model. Twenty-four C57BL/6 male mice were administered A. muciniphila MucT or phosphate-buffered saline (PBS) once daily by oral gavage for 14 days. Colitis was induced by drinking 2% DSS from days 0 to 6, followed by 2 days of drinking normal water. Mice were weighed daily and then sacrificed on day 8. We found that A. muciniphila improved DSS-induced colitis, which was evidenced by reduced weight loss, colon length shortening and histopathology scores and enhanced barrier function. Serum and tissue levels of inflammatory cytokines and chemokines (TNF-α, IL1α, IL6, IL12A, MIP-1A, G-CSF, and KC) decreased as a result of A. muciniphila administration. Analysis of 16S rDNA sequences showed that A. muciniphila induced significant gut microbiota alterations. Furthermore, correlation analysis indicated that pro-inflammatory cytokines and other injury factors were negatively associated with Verrucomicrobia, Akkermansia, Ruminococcaceae, and Rikenellaceae, which were prominently abundant in A. muciniphila-treated mice. We confirmed that A. muciniphila treatment could ameliorate mucosal inflammation either via microbe-host interactions, which protect the gut barrier function and reduce the levels of inflammatory cytokines, or by improving the microbial community. Our findings suggest that A. muciniphila may be a potential probiotic agent for ameliorating colitis.
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Affiliation(s)
- Xiaoyuan Bian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Wenrui Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Liya Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Qing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Yating Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Jianzhong Ye
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Daiqiong Fang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Jingjing Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Xianwan Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Ding Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
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30
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Burge KY, Hannah L, Eckert JV, Gunasekaran A, Chaaban H. The Protective Influence of Chondroitin Sulfate, a Component of Human Milk, on Intestinal Bacterial Invasion and Translocation. J Hum Lact 2019; 35:538-549. [PMID: 31051086 PMCID: PMC6615959 DOI: 10.1177/0890334419845338] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Human milk is known to be protective against necrotizing enterocolitis, a devastating intestinal inflammatory disease affecting the preterm population. Although the pathogenesis of necrotizing enterocolitis is yet to be solidified, intestinal integrity dysfunction, bacterial invasion and/or translocation, and inflammation may play important roles. Glycosaminoglycans, compounds naturally prevalent in both human milk and the intestine, are thought to be anti-inflammatory and capable of altering bacterial interactions within the gut. RESEARCH AIM In this study, we aimed to evaluate the potential of chondroitin sulfate, the most prominent class of glycosaminoglycans in human milk, to protect against bacterial infection in an intestinal in vitro model. METHODS T84 cell monolayers were treated with chondroitin sulfate and cell viability was assessed across a number of doses. Monolayers were then pretreated with chondroitin sulfate and subsequently challenged with E. coli invasion and translocation to evaluate any protective role of the compound against infection. Tight junction barrier function was assessed by transepithelial electrical resistance, and cytokine levels were evaluated. RESULTS Chondroitin sulfate at any dose up to 750 μg/ml was not associated with any statistically significant decrease in cell viability. Additionally, chondroitin sulfate at 750 μg/ml was associated with a 75% decrease in both bacterial invasion and translocation compared to control. CONCLUSIONS These data suggest chondroitin sulfate may protect against bacterial infection through a reduction in both invasion and translocation, importantly without attendant reduction in cell viability.
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Affiliation(s)
- Kathryn Y Burge
- 1 Neonatal Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Lindsey Hannah
- 1 Neonatal Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jeffrey V Eckert
- 1 Neonatal Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Aarthi Gunasekaran
- 1 Neonatal Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hala Chaaban
- 1 Neonatal Perinatal Medicine, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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Abstract
PURPOSE OF REVIEW Immune dysregulation disorders are among the most rapidly growing set of inborn errors of immunity. One particular subset is the category where early-onset inflammatory bowel disease (IBD) is the most common manifestation. These disorders are being increasingly appreciated although there has been minimal effort to articulate a unified approach to their diagnosis and management. This review will cover current thinking and strategies related to diagnosis and management of very early-onset IBD. RECENT FINDINGS There is an expanding set of monogenic causes of early-onset IBD. In many cases, the precise genetic cause dictates management. Lessons learned from the management of these monogenic conditions can sometimes be extrapolated to other refractory cases of IBD. SUMMARY An integrated approach to diagnosis, risk analysis, and management can include diagnostic approaches not often utilized for traditional IBD such as whole exome sequencing. Management can also include nontraditional approaches such as targeted biologics or hematopoietic cell transplantation.
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32
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Armour CR, Nayfach S, Pollard KS, Sharpton TJ. A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. mSystems 2019; 4:e00332-18. [PMID: 31098399 PMCID: PMC6517693 DOI: 10.1128/msystems.00332-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/23/2019] [Indexed: 01/07/2023] Open
Abstract
While recent research indicates that human health is affected by the gut microbiome, the functional mechanisms that underlie host-microbiome interactions remain poorly resolved. Metagenomic clinical studies can address this problem by revealing specific microbial functions that stratify healthy and diseased individuals. To improve our understanding of the relationship between the gut microbiome and health, we conducted the first integrative functional analysis of nearly 2,000 publicly available fecal metagenomic samples obtained from eight clinical studies. We identified characteristics of the gut microbiome that associate generally with disease, including functional alpha-diversity, beta-diversity, and beta-dispersion. Using regression modeling, we identified specific microbial functions that robustly stratify diseased individuals from healthy controls. Many of these functions overlapped multiple diseases, suggesting a general role in host health, while others were specific to a single disease and may indicate disease-specific etiologies. Our results clarify potential microbiome-mediated mechanisms of disease and reveal features of the microbiome that may be useful for the development of microbiome-based diagnostics. IMPORTANCE The composition of the gut microbiome associates with a wide range of human diseases, but the mechanisms underpinning these associations are not well understood. To shift toward a mechanistic understanding, we integrated distinct metagenomic data sets to identify functions encoded in the gut microbiome that associate with multiple diseases, which may be important to human health. Additionally, we identified functions that associate with specific diseases, which may elucidate disease-specific etiologies. We demonstrated that the functions encoded in the microbiome can be used to classify disease status, but the inclusion of additional patient covariates may be necessary to obtain sufficient accuracy. Ultimately, this analysis advances our understanding of the gut microbiome functions that constitute a healthy microbiome and identifies potential targets for microbiome-based diagnostics and therapeutics.
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Affiliation(s)
- Courtney R. Armour
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, USA
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Stephen Nayfach
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Gladstone Institutes, San Francisco, California, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, California, USA
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, California, USA
- Chan-Zuckerberg Biohub, San Francisco, California, USA
| | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
- Department of Statistics, Oregon State University, Corvallis, Oregon, USA
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33
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Kelly CJ, Alexeev EE, Farb L, Vickery TW, Zheng L, Eric L C, Kitzenberg DA, Battista KD, Kominsky DJ, Robertson CE, Frank DN, Stabler SP, Colgan SP. Oral vitamin B 12 supplement is delivered to the distal gut, altering the corrinoid profile and selectively depleting Bacteroides in C57BL/6 mice. Gut Microbes 2019; 10:654-662. [PMID: 31062653 PMCID: PMC6866687 DOI: 10.1080/19490976.2019.1597667] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Vitamin B12 is a critical nutrient for humans as well as microbes. Due to saturable uptake, high dose oral B12 supplements are largely unabsorbed and reach the distal gut where they are available to interact with the microbiota. The aim of this study was to determine if oral B12 supplementation in mice alters 1) the concentration of B12 and related corrinoids in the distal gut, 2) the fecal microbiome, 3) short chain fatty acids (SCFA), and 4) susceptibility to experimental colitis. C57BL/6 mice (up to 24 animals/group) were supplemented with oral 3.94 µg/ml cyanocobalamin (B12), a dose selected to approximate a single 5 mg supplement for a human. Active vitamin B12 (cobalamin), and four B12-analogues ([ADE]CN-Cba, [2Me-ADE]CN-Cba, [2MeS-ADE]CN-Cba, CN-Cbi) were analyzed in cecal and fecal contents using liquid chromatography/mass spectrometry (LC/MS), in parallel with evaluation of fecal microbiota, cecal SCFA, and susceptibility to dextran sodium sulfate (DSS) colitis. At baseline, active B12 was a minor constituent of overall cecal (0.86%) and fecal (0.44%) corrinoid. Oral B12 supplementation increased active B12 at distal sites by >130-fold (cecal B12 increased from 0.08 to 10.60 ng/mg, fecal B12 increased from 0.06 to 7.81 ng/ml) and reduced microbe-derived fecal corrinoid analogues ([ADE]CN-Cba, [2Me-ADE]CN-Cba, [2MeS-ADE]CN-Cba). Oral B12 had no effect on cecal SCFA. Microbial diversity was unaffected by this intervention, however a selective decrease in Bacteroides was observed with B12 treatment. Lastly, no difference in markers of DSS-induced colitis were detected with B12 treatment.
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Affiliation(s)
- Caleb J Kelly
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA,CONTACT Sean P. Colgan Mucosal Inflammation Program, University of Colorado, 12700 East 19th Ave. MS B-146, Aurora, CO 80045, USA
| | - Erica E Alexeev
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Linda Farb
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Thad W Vickery
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Leon Zheng
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Campbell Eric L
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA,Centre for Experimental Medicine, Queens University, Belfast, UK
| | - David A Kitzenberg
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Kayla D Battista
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Douglas J Kominsky
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Centre for Experimental Medicine, Queens University, Belfast, UK,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Sally P Stabler
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Sean P Colgan
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
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Dobranowski PA, Tang C, Sauvé JP, Menzies SC, Sly LM. Compositional changes to the ileal microbiome precede the onset of spontaneous ileitis in SHIP deficient mice. Gut Microbes 2019; 10:578-598. [PMID: 30760087 PMCID: PMC6748580 DOI: 10.1080/19490976.2018.1560767] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Inflammatory bowel disease, encompassing both ulcerative colitis and Crohn's disease, is characterized by chronic, relapsing-remitting gastrointestinal inflammation of unknown etiology. SHIP deficient mice develop fully penetrant, spontaneous ileitis at 6 weeks of age, and thus offer a tractable model of Crohn's disease-like inflammation. Since disruptions to the microbiome are implicated in the pathogenesis of Crohn's disease, we conducted a 16S rRNA gene survey of the ileum, cecum, colon, and stool contents of SHIP+/+ and SHIP-/- mice. We predicted that diversity and compositional changes would occur after, and possibly prior to, the onset of overt disease. No differences were found in alpha diversity, but significant changes in beta diversity and specific commensal populations were observed in the ileal compartment of SHIP deficient mice after the onset of overt disease. Specifically, reductions in the Bacteroidales taxa, Muribaculum intestinale, and an expansion in Lactobacillus were most notable. In contrast, expansions to bacterial taxa previously associated with inflammation, including Bacteroides, Parabacteroides, and Prevotella were observed in the ilea of SHIP deficient mice prior to the onset of overt disease. Finally, antibiotic treatment reduced the development of intestinal inflammation in SHIP-/- mice. Thus, our findings indicate that SHIP is involved in maintaining ileal microbial homeostasis. These results have broader implications for humans, since reduced SHIP protein levels have been reported in people with Crohn's disease.
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Affiliation(s)
| | | | | | | | - Laura May Sly
- University of British Columbia,BC Children’s Hospital research institute,CONTACT Laura May Sly BC Children’s Hospital research institute, 950 West 28th Avenue, A5-142TRB, Vancouver, British Columbia V5Z 4H4, Canada
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35
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Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN, Van Domselaar G. A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist? MICROBIOME 2018; 6:221. [PMID: 30545401 PMCID: PMC6292067 DOI: 10.1186/s40168-018-0603-4] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 11/25/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N = 20), ulcerative colitis (UC; N = 19), multiple sclerosis (MS; N = 19), and rheumatoid arthritis (RA; N = 21) versus healthy controls (HC; N = 23). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach. RESULTS Significant microbial community differences between cohorts were observed (pseudo F = 4.56; p = 0.01). Richness and diversity were significantly different between cohorts (pFDR < 0.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR < 0.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR < 0.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC = 0.93 and AUC = 0.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance. CONCLUSIONS This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.
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Affiliation(s)
- Jessica D. Forbes
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB Canada
- University of Manitoba IBD Clinical and Research Centre, Winnipeg, MB Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Chih-yu Chen
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Ruth-Ann Marrie
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB Canada
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB Canada
| | - Hani El-Gabalawy
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB Canada
- Arthritis Centre, University of Manitoba, Winnipeg, MB Canada
| | - Teresa de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, MB Canada
| | - Michelle Alfa
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB Canada
| | - Charles N. Bernstein
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB Canada
- University of Manitoba IBD Clinical and Research Centre, Winnipeg, MB Canada
| | - Gary Van Domselaar
- University of Manitoba IBD Clinical and Research Centre, Winnipeg, MB Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB Canada
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36
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Gaulke CA, Rolshoven J, Wong CP, Hudson LG, Ho E, Sharpton TJ. Marginal Zinc Deficiency and Environmentally Relevant Concentrations of Arsenic Elicit Combined Effects on the Gut Microbiome. mSphere 2018; 3:e00521-18. [PMID: 30518676 PMCID: PMC6282007 DOI: 10.1128/msphere.00521-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/30/2018] [Indexed: 01/16/2023] Open
Abstract
Extensive research shows that dietary variation and toxicant exposure impact the gut microbiome, yielding effects on host physiology. However, prior work has mostly considered such exposure-microbiome interactions through the lens of single-factor exposures. In practice, humans exposed to toxicants vary in their dietary nutritional status, and this variation may impact subsequent exposure of the gut microbiome. For example, chronic arsenic exposure affects 200 million people globally and is often comorbid with zinc deficiency. Zinc deficiency can enhance arsenic toxicity, but it remains unknown how zinc status impacts the gut microbiome's response to arsenic exposure and whether this response links to host toxicity. Using 16S amplicon sequencing, we examined the combinatorial effects of exposure to environmentally relevant concentrations of arsenic on the composition of the microbiome in C57BL/6 mice fed diets varying in zinc concentration. Arsenic exposure and marginal zinc deficiency independently altered microbiome diversity. When combined, their effects on microbiome community structure were amplified. Generalized linear models identified microbial taxa whose relative abundance in the gut was perturbed by zinc deficiency, arsenic, or their interaction. Further, we correlated taxonomic abundances with host DNA damage, adiponectin expression, and plasma zinc concentration to identify taxa that may mediate host physiological responses to arsenic exposure or zinc deficiency. Arsenic exposure and zinc restriction also result in increased DNA damage and decreased plasma zinc. These physiological changes are associated with the relative abundance of several gut taxa. These data indicate that marginal zinc deficiency sensitizes the microbiome to arsenic exposure and that the microbiome associates with some toxicological effects of arsenic.IMPORTANCE Xenobiotic compounds, such as arsenic, have the potential to alter the composition and functioning of the gut microbiome. The gut microbiome may also interact with these compounds to mediate their impact on the host. However, little is known about how dietary variation may reshape how the microbiome responds to xenobiotic exposures or how these modified responses may in turn impact host physiology. Here, we investigated the combinatorial effects of marginal zinc deficiency and physiologically relevant concentrations of arsenic on the microbiome. Both zinc deficiency and arsenic exposure were individually associated with altered microbial diversity and when combined elicited synergistic effects. Microbial abundance also covaried with host physiological changes, indicating that the microbiome may contribute to or be influenced by these pathologies. Collectively, this work demonstrates that dietary zinc intake influences the sensitivity of the microbiome to subsequent arsenic exposure.
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Affiliation(s)
| | - John Rolshoven
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Carmen P Wong
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico, USA
| | - Emily Ho
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, Oregon, USA
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, USA
- Moore Family Center for Whole Grain Foods, Nutrition and Preventive Health, Oregon State University, Corvallis, Oregon, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
- Department of Statistics, Oregon State University, Corvallis, Oregon, USA
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37
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Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L. Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Front Microbiol 2018; 9:2559. [PMID: 30425690 PMCID: PMC6218438 DOI: 10.3389/fmicb.2018.02559] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022] Open
Abstract
Dysbiosis of the gut microbiome, including elevated abundance of putative leading bacterial triggers such as E. coli in inflammatory bowel disease (IBD) patients, is of great interest. To date, most E. coli studies in IBD patients are focused on clinical isolates, overlooking their relative abundances and turnover over time. Metagenomics-based studies, on the other hand, are less focused on strain-level investigations. Here, using recently developed bioinformatic tools, we analyzed the abundance and properties of specific E. coli strains in a Crohns disease (CD) patient longitudinally, while also considering the composition of the entire community over time. In this report, we conducted a pilot study on metagenomic-based, strain-level analysis of a time-series of E. coli strains in a left-sided CD patient, who exhibited sustained levels of E. coli greater than 100X healthy controls. We: (1) mapped out the composition of the gut microbiome over time, particularly the presence of E. coli strains, and found that the abundance and dominance of specific E. coli strains in the community varied over time; (2) performed strain-level de novo assemblies of seven dominant E. coli strains, and illustrated disparity between these strains in both phylogenetic origin and genomic content; (3) observed that strain ST1 (recovered during peak inflammation) is highly similar to known pathogenic AIEC strains NC101 and LF82 in both virulence factors and metabolic functions, while other strains (ST2-ST7) that were collected during more stable states displayed diverse characteristics; (4) isolated, sequenced, experimentally characterized ST1, and confirmed the accuracy of the de novo assembly; and (5) assessed growth capability of ST1 with a newly reconstructed genome-scale metabolic model of the strain, and showed its potential to use substrates found abundantly in the human gut to outcompete other microbes. In conclusion, inflammation status (assessed by the blood C-reactive protein and stool calprotectin) is likely correlated with the abundance of a subgroup of E. coli strains with specific traits. Therefore, strain-level time-series analysis of dominant E. coli strains in a CD patient is highly informative, and motivates a study of a larger cohort of IBD patients.
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Affiliation(s)
- Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Sergey Nurk
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Margarita Akseshina
- St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia
| | - Qiyun Zhu
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Christopher Gemmell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Connor Gianetto-Hill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Nelly Leung
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Jon Sanders
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Paul L Beck
- Division of Gastroenterology, University of Calgary, Calgary, AB, Canada
| | - Weizhong Li
- Human Longevity Inc., San Diego, CA, United States.,J. Craig Venter Institute, La Jolla, CA, United States
| | - William J Sandborn
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States.,Inflammatory Bowel Disease Center, University of California, San Diego, La Jolla, CA, United States
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Larry Smarr
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States.,California Institute for Telecommunications and Information Technology, University of California, San Diego, La Jolla, CA, United States
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38
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Zhang WQ, Zhao SK, Luo JW, Dong XP, Hao YT, Li H, Shan L, Zhou Y, Shi HB, Zhang ZY, Peng CL, Zhao XG. Alterations of fecal bacterial communities in patients with lung cancer. Am J Transl Res 2018; 10:3171-3185. [PMID: 30416659 PMCID: PMC6220220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/07/2018] [Indexed: 06/09/2023]
Abstract
Emerging evidence suggests the microbiome may affect a number of diseases, including lung cancer. However, the direct relationship between gut bacteria and lung cancer remains uncharacterized. In this study, we directly sequenced the hypervariable V1-V2 regions of the 16S rRNA gene in fecal samples from patients with lung cancer and healthy volunteers. Unweighted principal coordinate analysis (PCoA) revealed a clear difference in the bacterial community membership between the lung cancer group and the healthy control group. The lung cancer group had remarkably higher levels of Bacteroidetes, Fusobacteria, Cyanobacteria, Spirochaetes, and Lentisphaerae but dramatically lower levels of Firmicutes and Verrucomicrobia than the healthy control group (P < 0.05). Despite significant interindividual variation, eight predominant genera were significantly different between the two groups. The lung cancer group had higher levels of Bacteroides, Veillonella, and Fusobacterium but lower levels of Escherichia-Shigella, Kluyvera, Fecalibacterium, Enterobacter, and Dialister than the healthy control group (P < 0.05). Most notably, correlations between certain specific bacteria and serum inflammatory biomarkers were identified. Our findings demonstrated an altered bacterial community in patients with lung cancer, providing a significant step in understanding the relationship between gut bacteria and lung cancer. To our knowledge, this is the first study to evaluate the correlations between certain specific bacteria and inflammatory indicators. To better understand this relationship, further studies should investigate the underlying mechanisms of gut bacteria in lung cancer animal models.
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Affiliation(s)
- Wei-Quan Zhang
- Department of Thoracic Surgery, The Second Hospital of Shandong UniversityShandong, P. R. China
- School of Medicine, Shandong UniversityJinan 250000, Shandong, P. R. China
| | - Shu-Kang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong UniversityShandong, P. R. China
- School of Medicine, Shandong UniversityJinan 250000, Shandong, P. R. China
| | - Jun-Wen Luo
- Department of Thoracic Surgery, The Second Hospital of Shandong UniversityShandong, P. R. China
- School of Medicine, Shandong UniversityJinan 250000, Shandong, P. R. China
| | - Xiao-Peng Dong
- Department of Thoracic Surgery, The Second Hospital of Shandong UniversityShandong, P. R. China
| | - Ying-Tao Hao
- Department of Thoracic Surgery, The Second Hospital of Shandong UniversityShandong, P. R. China
| | - Hui Li
- Department of Pathology, The Second Hospital of Shandong UniversityShandong, P. R. China
| | - Lei Shan
- Department of Thoracic Surgery, The Second Hospital of Shandong UniversityShandong, P. R. China
| | - Yong Zhou
- Cancer Center, The Second Hospital of Shandong UniversityShandong, P. R. China
| | - Hu-Bo Shi
- Department of Thoracic Surgery, Shandong Provincial Chest HospitalJinan 250000, Shandong, P. R. China
| | - Zai-Yun Zhang
- Cancer Center, The Second Hospital of Shandong UniversityShandong, P. R. China
| | - Chuan-Liang Peng
- Department of Thoracic Surgery, The Second Hospital of Shandong UniversityShandong, P. R. China
| | - Xiao-Gang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong UniversityShandong, P. R. China
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39
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Abstract
Darwin referred to life as a struggle. Organisms compete for limited resources in nature, and their traits influence the outcome. Darwin referred to life as a struggle. Organisms compete for limited resources in nature, and their traits influence the outcome. Victory carries great weight as winners survive, reproduce, and progenate subsequent generations. Consequently, organismal traits that influence fitness drive adaptation and their discovery clarifies evolution. Recent research implicates the vertebrate gut microbiome as an agent of fitness, selection, and evolution. Going forward, we must define the functional effects of the gut microbiome to determine how it impacts evolution. Specifically, we must quantify how gut microbiome function diversifies in concert with vertebrate radiation and resolve specific functions that influence natural selection. In so doing, we can discover and potentially capitalize upon the mechanisms by which our gut microbiomes impact our physiology and fitness. Ultimately, we may come to find that while life involves struggle, it also depends upon cooperation.
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