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Hertel J, Heinken A, Fässler D, Thiele I. Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses. CELL REPORTS METHODS 2023; 3:100615. [PMID: 37848031 PMCID: PMC10626217 DOI: 10.1016/j.crmeth.2023.100615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 05/23/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Understanding the effects of the microbiome on the host's metabolism is core to enlightening the role of the microbiome in health and disease. Herein, we develop the paradigm of in silico in vivo association pattern analyses, combining microbiome metabolome association studies with in silico constraint-based community modeling. Via theoretical dissection of confounding and causal paths, we show that in silico in vivo association pattern analyses allow for causal inference on microbiome-metabolome relations in observational data. We justify the corresponding theoretical criterion by structural equation modeling of host-microbiome systems, integrating deterministic microbiome community modeling into population statistics approaches. We show the feasibility of our approach on a published multi-omics dataset (n = 347), demonstrating causal microbiome-metabolite relations for 26 out of 54 fecal metabolites. In summary, we generate a promising approach for causal inference in metabolic host-microbiome interactions by integrating hypothesis-free screening association studies with knowledge-based in silico modeling.
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Affiliation(s)
- Johannes Hertel
- School of Medicine, University of Galway, Galway, Ireland; Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland; UMRS Inserm 1256 NGERE (Nutrition-Genetics-Environmental Risks), Institute of Medical Research (Pôle BMS) - University of Lorraine, Vandoeuvre-les-Nancy, France
| | - Daniel Fässler
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland; Discipline of Microbiology, University of Galway, Galway, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; Ryan Institute, University of Galway, Galway, Ireland.
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2
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Gut Microbiota, Intestinal Morphometric Characteristics, and Gene Expression in Relation to the Growth Performance of Chickens. Animals (Basel) 2022; 12:ani12243474. [PMID: 36552394 PMCID: PMC9774407 DOI: 10.3390/ani12243474] [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: 10/12/2022] [Revised: 11/04/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
this study aimed to investigate the growth mechanism in a local breed of chickens by comparing the highest weight (HW) and the lowest weight in their microbiota, histological characteristics, and gene expression. Golden Montazah chickens, an Egyptian breed, were reared until they were 49 days old. All of the birds were fed ad libitum by a starter diet from day 1 until day 21, followed by a grower diet from day 21 to the end of the study. At 49 days old, the forty-eight birds with the heaviest body weight (HW) and the lightest body weight (LW) were chosen. Blood biochemical and histological morphometric parameters, electron microscopy, and intestinal nutrient transporter gene expression were studied in the sampled jejunum. The microbial composition and functions of the content and mucosa in HW and LW chickens were studied using 16S rRNA gene sequencing. The histological morphometric parameters were all more significantly (p < 0.05) increased in the HW chickens than in the LW chickens. Total protein, albumin, and triglycerides in serum were significantly higher (p < 0.05) in the HW chickens than in the LW chickens. The microbiome profile in the gut showed that Microbacterium and Sphingomonas were positively correlated with the body weights. In the local breed, there were significant differences in the intestinal microstructure which could enhance the growth mechanism and body weight. Our findings showed that some microbial components were significantly associated with body weight and their interactions with the host could be inferred to explain why these interactions might alter the host’s metabolic responses. Further investigation into combining bioinformatics with lab experiments in chickens will help us to understand how gut bacteria can change the host’s metabolism by special metabolic features in the gastrointestinal system.
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3
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Krueger QA, Shore MH, Reitzel AM. Comparative transmission of bacteria from Artemia salina and Brachionus plicatilis to the cnidarian Nematostella vectensis. FEMS Microbiol Ecol 2022; 98:fiac096. [PMID: 36036952 PMCID: PMC9521339 DOI: 10.1093/femsec/fiac096] [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: 03/04/2022] [Revised: 08/08/2022] [Accepted: 08/19/2022] [Indexed: 12/14/2022] Open
Abstract
The microbial community associated with animals (microbiome) is essential for development, physiology, and health of host organisms. A critical step to understand the assembly of microbiomes is to determine how effectively bacteria colonize and establish within the host. Bacteria commonly colonize hosts through vertical transmission, passively from the environment, or through food consumption. Using the prey feeding method (PFM), we test transmittance of Bacillus velezensis, Pseudoalteromonas spiralis, and Vibrio alginolyticus to Nematostella vectensis using two prey, Artemia salina and Brachionus plicatilis. We compare PFM to a solution uptake method (SUM) to quantify the concentration of bacteria in these host organisms, with plate counts. Larvae had a similar uptake with SUM at 6 h but had greater concentrations at 48 h versus PFM. Juveniles acquired similar concentrations at 6 h for SUM and PFM using B. plicatilis and A. salina. At 2 days, the quantity of bacteria vectored from PFM increased. After 7 days the CFUs decreased 2-fold with B. plicatilis and A. salina relative to the 2-day concentrations, and further decreased after 14 days. Therefore, prey-mediated methods provide greater microbe transplantation than SUM after 24 h, supporting this approach as a more successful inoculation method of individual bacterial species.
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Affiliation(s)
- Quinton A Krueger
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Woodward Hall, Charlotte, NC 28223, United States
| | - Madisun H Shore
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Woodward Hall, Charlotte, NC 28223, United States
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Woodward Hall, Charlotte, NC 28223, United States
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Chaudhuri S, Srivastava A. Network approach to understand biological systems: From single to multilayer networks. J Biosci 2022. [DOI: 10.1007/s12038-022-00285-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xiang X, Poli D, Degnan BM, Degnan SM. Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:722-732. [PMID: 35895230 PMCID: PMC9385839 DOI: 10.1007/s10126-022-10138-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Investigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. Here, we address this gap in knowledge with the aim of helping others to choose an appropriate RNA-Seq approach for analysis of animal host-bacterial symbiont transcriptomes. Specifically, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont. Annotated genomes of the sponge host and the three most abundant bacterial symbionts, which can comprise up to 95% of the adult microbiome, are available. Importantly, this allows for transcriptomes to be accurately mapped to these genomes, and thus quantitatively assessed and compared. The two strategies that we compare here are (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq) and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to simultaneously capture gene expression in host and symbionts and thus to analyse holobiont transcriptomes.
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Affiliation(s)
- Xueyan Xiang
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Present Address: BGI-Shenzhen, Shenzhen, 518083 China
| | - Davide Poli
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Present Address: School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Bernard M. Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Sandie M. Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
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Liu B, Chen B, Yi J, Long H, Wen H, Tian F, Liu Y, Xiao L, Li L. Liuwei Dihuang Decoction Alleviates Cognitive Dysfunction in Mice With D-Galactose-Induced Aging by Regulating Lipid Metabolism and Oxidative Stress via the Microbiota-Gut-Brain Axis. Front Neurosci 2022; 16:949298. [PMID: 35844229 PMCID: PMC9283918 DOI: 10.3389/fnins.2022.949298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Background Aging is an important cause of cognitive dysfunction. Liuwei Dihuang decoction (LW), a commonly applied Chinese medicine formula, is widely used for the treatment of aging-related diseases in China. Previously, LW was confirmed to be effective in prolonging life span and reducing oxidative stress in aged mice. Unfortunately, the underlying mechanism of LW remains unclear. The aim of this study was to interpret the mechanism by which LW alleviates cognitive dysfunction related to aging from the perspective of the microbiota-gut-brain axis. Method All C57BL/6 mice (n = 60) were randomly divided into five groups: the control, model, vitamin E (positive control group), low-dose LW and high-dose LW groups (n = 12 in each group). Except for those in the control group, D-galactose was subcutaneously injected into mice in the other groups to induce the aging model. The antiaging effect of LW was evaluated by the water maze test, electron microscopy, 16S rRNA sequencing, combined LC–MS and GC–MS metabolomics, and ELISA. Results Liuwei Dihuang decoction ameliorated cognitive dysfunction and hippocampal synaptic ultrastructure damage in aging mice. Moreover, LW decreased Proteobacteria abundance and increased gut microbiota diversity in aging mice. Metabolomic analysis showed that LW treatment was associated with the significantly differential abundance of 14 metabolites, which were mainly enriched in apelin signaling, sphingolipid metabolism, glycerophospholipid and other metabolic pathways. Additionally, LW affected lipid metabolism and oxidative stress in aging mice. Finally, we also found that LW-regulated microbial species such as Proteobacteria and Fibrobacterota had potential relationships with lipid metabolism, oxidative stress and hippocampal metabolites. Conclusion In brief, LW improved cognitive function in aging mice by regulating lipid metabolism and oxidative stress through restoration of the homeostasis of the microbiota-gut-brain axis.
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Affiliation(s)
- Baiyan Liu
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
- Hunan Academy of Chinese Medicine, Changsha, China
- *Correspondence: Baiyan Liu,
| | - Bowei Chen
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Jian Yi
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
- Hunan Academy of Chinese Medicine, Changsha, China
| | - Hongping Long
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Huiqiao Wen
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Fengming Tian
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Yingfei Liu
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Lan Xiao
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Lisong Li
- College of Information Science and Engineering, Hunan University of Chinese Medicine, Changsha, China
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Milenkovic D, Capel F, Combaret L, Comte B, Dardevet D, Evrard B, Guillet C, Monfoulet LE, Pinel A, Polakof S, Pujos-Guillot E, Rémond D, Wittrant Y, Savary-Auzeloux I. Targeting the gut to prevent and counteract metabolic disorders and pathologies during aging. Crit Rev Food Sci Nutr 2022; 63:11185-11210. [PMID: 35730212 DOI: 10.1080/10408398.2022.2089870] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Impairment of gut function is one of the explanatory mechanisms of health status decline in elderly population. These impairments involve a decline in gut digestive physiology, metabolism and immune status, and associated to that, changes in composition and function of the microbiota it harbors. Continuous deteriorations are generally associated with the development of systemic dysregulations and ultimately pathologies that can worsen the initial health status of individuals. All these alterations observed at the gut level can then constitute a wide range of potential targets for development of nutritional strategies that can impact gut tissue or associated microbiota pattern. This can be key, in a preventive manner, to limit gut functionality decline, or in a curative way to help maintaining optimum nutrients bioavailability in a context on increased requirements, as frequently observed in pathological situations. The aim of this review is to give an overview on the alterations that can occur in the gut during aging and lead to the development of altered function in other tissues and organs, ultimately leading to the development of pathologies. Subsequently is discussed how nutritional strategies that target gut tissue and gut microbiota can help to avoid or delay the occurrence of aging-related pathologies.
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Affiliation(s)
- Dragan Milenkovic
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Frédéric Capel
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Lydie Combaret
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Blandine Comte
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Dominique Dardevet
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Bertrand Evrard
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Christelle Guillet
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | | | - Alexandre Pinel
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Sergio Polakof
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Estelle Pujos-Guillot
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Didier Rémond
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Yohann Wittrant
- Human Nutrition Unit, UMR1019, University Clermont Auvergne, INRAE, Clermont-Ferrand, France
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Tang R, Yi J, Lu S, Chen B, Liu B. Therapeutic Effect of Buyang Huanwu Decoction on the Gut Microbiota and Hippocampal Metabolism in a Rat Model of Cerebral Ischemia. Front Cell Infect Microbiol 2022; 12:873096. [PMID: 35774407 PMCID: PMC9237419 DOI: 10.3389/fcimb.2022.873096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/11/2022] [Indexed: 12/04/2022] Open
Abstract
Buyang Huanwu decoction (BHD) is a well-known Chinese herbal prescription. It has been widely used in the clinical treatment of cerebral ischemia (CI) in China. However, the mechanism underlying the treatment of CI with BHD remains to be elucidated. In this study, we combined microbiomic and metabolomic strategies to explore the therapeutic effects of BHD on middle cerebral artery occlusion (MCAO) in rats. Our results showed that BHD could effectively improve neurological severity scores and alleviate neuronal damage in rats with MCAO. BHD could also reduce the level of peripheral proinflammatory cytokines and inhibit neuroinflammation. 16S rRNA sequencing showed that BHD could increase the relative abundances of the genera Lactobacillus, Faecalibacterium, Ruminococcaceae_UCG-002, etc., while decreasing the relative abundances of the genera Escherichia-Shigella, Klebsiella, Streptococcus, Coprococcus_2, Enterococcus, etc. Untargeted metabolomic analysis of hippocampal samples showed that 17 significantly differentially abundant metabolites and 9 enriched metabolic pathways were linked with BHD treatment. We also found that the regulatory effects of BHD on metabolites were correlated with the differentially abundant microbial taxa. The predicted function of the gut microbiota and the metabolic pathway enrichment results showed that purine metabolism, glutamatergic synapses, arginine and proline metabolism, and alanine, aspartic acid and glutamate metabolism were involved in the effects of BHD. These pathways may be related to pathological processes such as excitotoxicity, neuroinflammation, and energy metabolism disorder in CI. In summary, these findings suggest that regulation of hippocampal metabolism and of the composition and function of the gut microbiota may be important mechanisms underlying the effect of BHD in the treatment of CI.
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Affiliation(s)
- Rongmei Tang
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Jian Yi
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Shuangying Lu
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Bowei Chen
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Baiyan Liu
- College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, China
- *Correspondence: Baiyan Liu,
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Zou H, Zhang M, Zhu X, Zhu L, Chen S, Luo M, Xie Q, Chen Y, Zhang K, Bu Q, Wei Y, Ye T, Li Q, Yan X, Zhou Z, Yang C, Li Y, Zhou H, Zhang C, You X, Zheng G, Zhao G. Ginsenoside Rb1 Improves Metabolic Disorder in High-Fat Diet-Induced Obese Mice Associated With Modulation of Gut Microbiota. Front Microbiol 2022; 13:826487. [PMID: 35516426 PMCID: PMC9062662 DOI: 10.3389/fmicb.2022.826487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota plays an important role in metabolic homeostasis. Previous studies demonstrated that ginsenoside Rb1 might improve obesity-induced metabolic disorders through regulating glucose and lipid metabolism in the liver and adipose tissues. Due to low bioavailability and enrichment in the intestinal tract of Rb1, we hypothesized that modulation of the gut microbiota might account for its pharmacological effects as well. Here, we show that oral administration of Rb1 significantly decreased serum LDL-c, TG, insulin, and insulin resistance index (HOMA-IR) in mice with a high-fat diet (HFD). Dynamic profiling of the gut microbiota showed that this metabolic improvement was accompanied by restoring of relative abundance of some key bacterial genera. In addition, the free fatty acids profiles in feces were significantly different between the HFD-fed mice with or without Rb1. The content of eight long-chain fatty acids (LCFAs) was significantly increased in mice with Rb1, which was positively correlated with the increase of Akkermansia and Parasuttereller, and negatively correlated with the decrease of Oscillibacter and Intestinimonas. Among these eight increased LCFAs, eicosapentaenoic acid (EPA), octadecenoic acids, and myristic acid were positively correlated with metabolic improvement. Furthermore, the colonic expression of the free fatty acid receptors 4 (Ffar4) gene was significantly upregulated after Rb1 treatment, in response to a notable increase of LCFA in feces. These findings suggested that Rb1 likely modulated the gut microbiota and intestinal free fatty acids profiles, which should be beneficial for the improvement of metabolic disorders in HFD-fed mice. This study provides a novel mechanism of Rb1 for the treatment of metabolic disorders induced by obesity, which may provide a therapeutic avenue for the development of new nutraceutical-based remedies for treating metabolic diseases, such as hyperlipidemia, insulin resistance, and type 2 diabetes.
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Affiliation(s)
- Hong Zou
- State Key Laboratory of Genetic Engineering, Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
- Engineering Laboratory for Nutrition, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Man Zhang
- Master Lab for Innovative Application of Nature Products, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaoting Zhu
- Zhejiang Hongguan Bio-Pharma Co., Ltd., Jiaxing, China
| | - Liyan Zhu
- Zhejiang Hongguan Bio-Pharma Co., Ltd., Jiaxing, China
| | - Shuo Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Mingjing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qinglian Xie
- Engineering Laboratory for Nutrition, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yue Chen
- Master Lab for Innovative Application of Nature Products, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Kangxi Zhang
- Master Lab for Innovative Application of Nature Products, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qingyun Bu
- Master Lab for Innovative Application of Nature Products, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yuchen Wei
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tao Ye
- Zhejiang Hongguan Bio-Pharma Co., Ltd., Jiaxing, China
| | - Qiang Li
- Suzhou BiomeMatch Therapeutics Co., Ltd., Shanghai, China
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yu Li
- Engineering Laboratory for Nutrition, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Haokui Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- *Correspondence: Haokui Zhou,
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Chenhong Zhang,
| | - Xiaoyan You
- Master Lab for Innovative Application of Nature Products, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
- Xiaoyan You,
| | - Guangyong Zheng
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- Guangyong Zheng,
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, Department of Microbiology and Immunology, School of Life Sciences, Fudan University, Shanghai, China
- Master Lab for Innovative Application of Nature Products, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
- Suzhou BiomeMatch Therapeutics Co., Ltd., Shanghai, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- Guoping Zhao,
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Mohammad FK, Palukuri MV, Shivakumar S, Rengaswamy R, Sahoo S. A Computational Framework for Studying Gut-Brain Axis in Autism Spectrum Disorder. Front Physiol 2022; 13:760753. [PMID: 35330929 PMCID: PMC8940246 DOI: 10.3389/fphys.2022.760753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 12/28/2022] Open
Abstract
Introduction The integrity of the intestinal epithelium is crucial for human health and is harmed in autism spectrum disorder (ASD). An aberrant gut microbial composition resulting in gut-derived metabolic toxins was found to damage the intestinal epithelium, jeopardizing tissue integrity. These toxins further reach the brain via the gut-brain axis, disrupting the normal function of the brain. A mechanistic understanding of metabolic disturbances in the brain and gut is essential to design effective therapeutics and early intervention to block disease progression. Herein, we present a novel computational framework integrating constraint based tissue specific metabolic (CBM) model and whole-body physiological pharmacokinetics (PBPK) modeling for ASD. Furthermore, the role of gut microbiota, diet, and oxidative stress is analyzed in ASD. Methods A representative gut model capturing host-bacteria and bacteria-bacteria interaction was developed using CBM techniques and patient data. Simultaneously, a PBPK model of toxin metabolism was assembled, incorporating multi-scale metabolic information. Furthermore, dynamic flux balance analysis was performed to integrate CBM and PBPK. The effectiveness of a probiotic and dietary intervention to improve autism symptoms was tested on the integrated model. Results The model accurately highlighted critical metabolic pathways of the gut and brain that are associated with ASD. These include central carbon, nucleotide, and vitamin metabolism in the host gut, and mitochondrial energy and amino acid metabolisms in the brain. The proposed dietary intervention revealed that a high-fiber diet is more effective than a western diet in reducing toxins produced inside the gut. The addition of probiotic bacteria Lactobacillus acidophilus, Bifidobacterium longum longum, Akkermansia muciniphila, and Prevotella ruminicola to the diet restores gut microbiota balance, thereby lowering oxidative stress in the gut and brain. Conclusion The proposed computational framework is novel in its applicability, as demonstrated by the determination of the whole-body distribution of ROS toxins and metabolic association in ASD. In addition, it emphasized the potential for developing novel therapeutic strategies to alleviate autism symptoms. Notably, the presented integrated model validates the importance of combining PBPK modeling with COBRA -specific tissue details for understanding disease pathogenesis.
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Affiliation(s)
- Faiz Khan Mohammad
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Meghana Venkata Palukuri
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Shruti Shivakumar
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Raghunathan Rengaswamy
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Swagatika Sahoo
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India
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Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care. Pathogens 2022; 11:pathogens11020121. [PMID: 35215065 PMCID: PMC8879973 DOI: 10.3390/pathogens11020121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.
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Bukharin OV, Andryushchenko SV, Perunova NB, Ivanova EV. Environmental Determination of Indigenous Bifidobacteria of the Human Intestine. HERALD OF THE RUSSIAN ACADEMY OF SCIENCES 2022; 92:629-635. [PMID: 36340323 PMCID: PMC9628474 DOI: 10.1134/s1019331622050033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/09/2022]
Abstract
The environmental determination of indigenous (constantly present) bifidobacteria of the human large intestine is considered in this review. Environmental determination (from the Latin determinere, "I determine") is understood as a set of natural phenomena of a habitat (biotope) that determine the role of indigenous microorganisms in the microbiocenosis. Using the symbiotic approach, an attempt is made to identify the environmental conditions for the habitat of bifidobacteria and their physiological effects in the microsymbiocenosis. The features of indigenous bifidobacteria in terms of their nature have been established: evolutionary-genetic (phylogenetic remoteness, genome conservation, metabolic specialization), biochemical (lysozyme resistance, constitutive acetate production), and physiological (microbial "friend-foe" identification, immunoregulation), which are important in adaptation (persistence) and the provision of mutualistic effects and stability of the bifidoflora in the population.
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Affiliation(s)
- O. V. Bukharin
- Institute for Cellular and Intracellular Symbiosis (ICIS), Ural Branch, Russian Academy of Sciences, Orenburg, Russia
| | - S. V. Andryushchenko
- Institute for Cellular and Intracellular Symbiosis (ICIS), Ural Branch, Russian Academy of Sciences, Orenburg, Russia
| | - N. B. Perunova
- Institute for Cellular and Intracellular Symbiosis (ICIS), Ural Branch, Russian Academy of Sciences, Orenburg, Russia
| | - E. V. Ivanova
- Institute for Cellular and Intracellular Symbiosis (ICIS), Ural Branch, Russian Academy of Sciences, Orenburg, Russia
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Seif Y, Palsson BØ. Path to improving the life cycle and quality of genome-scale models of metabolism. Cell Syst 2021; 12:842-859. [PMID: 34555324 PMCID: PMC8480436 DOI: 10.1016/j.cels.2021.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 02/17/2021] [Accepted: 06/23/2021] [Indexed: 11/28/2022]
Abstract
Genome-scale models of metabolism (GEMs) are key computational tools for the systems-level study of metabolic networks. Here, we describe the "GEM life cycle," which we subdivide into four stages: inception, maturation, specialization, and amalgamation. We show how different types of GEM reconstruction workflows fit in each stage and proceed to highlight two fundamental bottlenecks for GEM quality improvement: GEM maturation and content removal. We identify common characteristics contributing to increasing quality of maturing GEMs drawing from past independent GEM maturation efforts. We then shed some much-needed light on the latent and unrecognized but pervasive issue of content removal, demonstrating the substantial effects of model pruning on its solution space. Finally, we propose a novel framework for content removal and associated confidence-level assignment which will help guide future GEM development efforts, reduce duplication of effort across groups, potentially aid automated reconstruction platforms, and boost the reproducibility of model development.
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Affiliation(s)
- Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Bernhard Ørn Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
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14
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Nguyen QP, Karagas MR, Madan JC, Dade E, Palys TJ, Morrison HG, Pathmasiri WW, McRitche S, Sumner SJ, Frost HR, Hoen AG. Associations between the gut microbiome and metabolome in early life. BMC Microbiol 2021; 21:238. [PMID: 34454437 PMCID: PMC8400760 DOI: 10.1186/s12866-021-02282-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationship within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function in order to characterize the taxa-function relationship in early life. RESULTS Stool samples collected from infants enrolled in the New Hampshire Birth Cohort Study (NHBCS) at approximately 6-weeks (n = 158) and 12-months (n = 282) of age were profiled using targeted and untargeted nuclear magnetic resonance (NMR) spectroscopy as well as DNA sequencing of the V4-V5 hypervariable region from the bacterial 16S rRNA gene. There was significant inter-omic concordance based on Procrustes analysis (6 weeks: p = 0.056; 12 months: p = 0.001), however this association was no longer significant when accounting for phylogenetic relationships using generalized UniFrac distance metric (6 weeks: p = 0.376; 12 months: p = 0.069). Sparse canonical correlation analysis showed significant correlation, as well as identifying sets of microbe/metabolites driving microbiome-metabolome relatedness. Performance of machine learning models varied across different metabolites, with support vector machines (radial basis function kernel) being the consistently top ranked model. However, predictive R2 values demonstrated poor predictive performance across all models assessed (avg: - 5.06% -- 6 weeks; - 3.7% -- 12 months). Conversely, the Spearman correlation metric was higher (avg: 0.344-6 weeks; 0.265-12 months). This demonstrated that taxonomic relative abundance was not predictive of metabolite concentrations. CONCLUSIONS Our results suggest a degree of overall association between taxonomic profiles and metabolite concentrations. However, lack of predictive capacity for stool metabolic signatures reflects, in part, the possible role of functional redundancy in defining the taxa-function relationship in early life as well as the bidirectional nature of the microbiome-metabolome association. Our results provide evidence in favor of a multi-omic approach for microbiome studies, especially those focused on health outcomes.
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Affiliation(s)
- Quang P. Nguyen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
- Department of Pediatrics, Children’s Hospital at Dartmouth, Hanover, NH USA
| | - Erika Dade
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
| | - Thomas J. Palys
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
| | - Hilary G. Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA USA
| | - Wimal W. Pathmasiri
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Susan McRitche
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Susan J. Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - H. Robert Frost
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
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15
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Xie XQ, Geng Y, Guan Q, Ren Y, Guo L, Lv Q, Lu ZM, Shi JS, Xu ZH. Influence of Short-Term Consumption of Hericium erinaceus on Serum Biochemical Markers and the Changes of the Gut Microbiota: A Pilot Study. Nutrients 2021; 13:1008. [PMID: 33800983 PMCID: PMC8004025 DOI: 10.3390/nu13031008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/15/2022] Open
Abstract
Hericium erinaceus (H. erinaceus) is widely studied as a medicinal and edible fungus. Recent studies have shown that H. erinaceus has protective effects for diseases, such as inflammatory bowel disease and cancer, which are related to gut microbiota. To investigate the benefits of H. erinaceus intake on gut microbiota and blood indices in adulthood, we recruited 13 healthy adults to consume H. erinaceus powder as a dietary supplement. Blood changes due to H. erinaceus consumption were determined by routine hematological examination and characterized by serum biochemical markers. Microbiota composition was profiled by 16S ribosomal RNA gene sequencing. Results showed that daily H. erinaceus supplementation increased the alpha diversity within the gut microbiota community, upregulated the relative abundance of some short-chain fatty acid (SCFA) producing bacteria (Kineothrix alysoides, Gemmiger formicilis, Fusicatenibacter saccharivorans, Eubacterium rectale, Faecalibacterium prausnitzii), and downregulated some pathobionts (Streptococcus thermophilus, Bacteroides caccae, Romboutsia timonensis). Changes within the gut microbiota were correlated with blood chemical indices including alkaline phosphatase (ALP), low-density lipoprotein (LDL), uric acid (UA), and creatinine (CREA). Thus, we found that the gut microbiota alterations may be part of physiological adaptations to a seven-day H. erinaceus supplementation, potentially influencing beneficial health effects.
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Affiliation(s)
- Xiao-Qian Xie
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China; (X.-Q.X.); (Y.R.); (Q.L.); (J.-S.S.)
| | - Yan Geng
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China; (X.-Q.X.); (Y.R.); (Q.L.); (J.-S.S.)
| | - Qijie Guan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; (Q.G.); (L.G.); (Z.-M.L.); (Z.-H.X.)
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Yilin Ren
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China; (X.-Q.X.); (Y.R.); (Q.L.); (J.-S.S.)
| | - Lin Guo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; (Q.G.); (L.G.); (Z.-M.L.); (Z.-H.X.)
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Qiqi Lv
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China; (X.-Q.X.); (Y.R.); (Q.L.); (J.-S.S.)
| | - Zhen-Ming Lu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; (Q.G.); (L.G.); (Z.-M.L.); (Z.-H.X.)
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Jin-Song Shi
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, China; (X.-Q.X.); (Y.R.); (Q.L.); (J.-S.S.)
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; (Q.G.); (L.G.); (Z.-M.L.); (Z.-H.X.)
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Karta J, Bossicard Y, Kotzamanis K, Dolznig H, Letellier E. Mapping the Metabolic Networks of Tumor Cells and Cancer-Associated Fibroblasts. Cells 2021; 10:304. [PMID: 33540679 PMCID: PMC7912987 DOI: 10.3390/cells10020304] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Metabolism is considered to be the core of all cellular activity. Thus, extensive studies of metabolic processes are ongoing in various fields of biology, including cancer research. Cancer cells are known to adapt their metabolism to sustain high proliferation rates and survive in unfavorable environments with low oxygen and nutrient concentrations. Hence, targeting cancer cell metabolism is a promising therapeutic strategy in cancer research. However, cancers consist not only of genetically altered tumor cells but are interwoven with endothelial cells, immune cells and fibroblasts, which together with the extracellular matrix (ECM) constitute the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs), which are linked to poor prognosis in different cancer types, are one important component of the TME. CAFs play a significant role in reprogramming the metabolic landscape of tumor cells, but how, and in what manner, this interaction takes place remains rather unclear. This review aims to highlight the metabolic landscape of tumor cells and CAFs, including their recently identified subtypes, in different tumor types. In addition, we discuss various in vitro and in vivo metabolic techniques as well as different in silico computational tools that can be used to identify and characterize CAF-tumor cell interactions. Finally, we provide our view on how mapping the complex metabolic networks of stromal-tumor metabolism will help in finding novel metabolic targets for cancer treatment.
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Affiliation(s)
- Jessica Karta
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belval, Luxembourg; (J.K.); (Y.B.); (K.K.)
| | - Ysaline Bossicard
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belval, Luxembourg; (J.K.); (Y.B.); (K.K.)
| | - Konstantinos Kotzamanis
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belval, Luxembourg; (J.K.); (Y.B.); (K.K.)
| | - Helmut Dolznig
- Tumor Stroma Interaction Group, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090 Vienna, Austria;
| | - Elisabeth Letellier
- Molecular Disease Mechanisms Group, Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belval, Luxembourg; (J.K.); (Y.B.); (K.K.)
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Maiti S, Grivas G, Choi K, Dai W, Ding Y, Acosta DP, Hahn J, Jayaraman A. MODELING INTER-KINGDOM REGULATION OF INFLAMMATORY SIGNALING IN HUMAN INTESTINAL EPITHELIAL CELLS. Comput Chem Eng 2020; 140. [PMID: 32669746 DOI: 10.1016/j.compchemeng.2020.106954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human gastrointestinal (GI) tract is colonized by a highly diverse and complex microbial community (i.e., microbiota). The microbiota plays an important role in the development of the immune system, specifically mediating inflammatory responses, however the exact mechanisms are poorly understood. We have developed a mathematical model describing the effect of indole on host inflammatory signaling in HCT-8 human intestinal epithelial cells. In this model, indole modulates transcription factor nuclear factor κ B (NF-κB) and produces the chemokine interleukin-8 (IL-8) through the activation of the aryl hydrocarbon receptor (AhR). Phosphorylated NF-κB exhibits dose and time-dependent responses to indole concentrations and IL-8 production shows a significant down-regulation for 0.1 ng/mL TNF-α stimulation. The model shows agreeable simulation results with the experimental data for IL-8 secretion and normalized NF-κB values. Our results suggest that microbial metabolites such as indole can modulate inflammatory signaling in HTC-8 cells through receptor-mediated processes.
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Affiliation(s)
- Shreya Maiti
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX
| | - Genevieve Grivas
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY
| | - Kyungoh Choi
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX
| | - Wei Dai
- Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY
| | - Yufang Ding
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX
| | | | - Juergen Hahn
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY.,Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX
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18
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Tran H, McConville M, Loukopoulos P. Metabolomics in the study of spontaneous animal diseases. J Vet Diagn Invest 2020; 32:635-647. [PMID: 32807042 PMCID: PMC7488963 DOI: 10.1177/1040638720948505] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Using analytical chemistry techniques such as nuclear magnetic resonance (NMR) spectroscopy and liquid or gas chromatography-mass spectrometry (LC/GC-MS), metabolomics allows detection of most endogenous and exogenous metabolites in a biological sample. Metabolomics has a wide range of applications, and has been employed in nutrition science, toxicology, environmental studies, and systems biology. Metabolomics is particularly useful in biomedical science, and has been used for diagnostic laboratory testing, identifying targets for drug development, and monitoring drug metabolism, mode of action, and toxicity. Despite its immense potential, metabolomics remains underutilized in the study of spontaneous animal diseases. Our aim was to comprehensively review the existing literature on the use of metabolomics in spontaneous veterinary diseases. Three databases were used to find journal articles that applied metabolomics in veterinary medicine. A screening process was then conducted to eliminate references that did not meet the eligibility criteria; only primary research studies investigating spontaneous animal disease were included; 38 studies met the inclusion criteria. The main techniques used were NMR and MS. All studies detected metabolite alterations in diseased animals compared with non-diseased animals. Metabolomics was mainly used to study diseases of the digestive, reproductive, and musculoskeletal systems. Inflammatory conditions made up the largest proportion of studies when articles were categorized by disease process. Following a comprehensive analysis of the literature on metabolomics in spontaneous veterinary diseases, we concluded that metabolomics, although in its early stages in veterinary research, is a promising tool regarding diagnosis, biomarker discovery, and in uncovering new insights into disease pathophysiology.
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Affiliation(s)
- Helena Tran
- Melbourne Veterinary School, Faculty of
Veterinary and Agricultural Sciences, University of Melbourne, Melbourne,
Victoria, Australia
| | - Malcolm McConville
- Bio21 Institute, Metabolomics Australia,
University of Melbourne, Melbourne, Victoria, Australia
| | - Panayiotis Loukopoulos
- Melbourne Veterinary School, Faculty of
Veterinary and Agricultural Sciences, University of Melbourne, Melbourne,
Victoria, Australia
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19
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Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R, Thiele I. Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions. BMC Biol 2020; 18:62. [PMID: 32517799 PMCID: PMC7285525 DOI: 10.1186/s12915-020-00775-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/27/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a systemic disease clinically defined by the degeneration of dopaminergic neurons in the brain. While alterations in the gut microbiome composition have been reported in PD, their functional consequences remain unclear. Herein, we addressed this question by an analysis of stool samples from the Luxembourg Parkinson's Study (n = 147 typical PD cases, n = 162 controls). RESULTS All individuals underwent detailed clinical assessment, including neurological examinations and neuropsychological tests followed by self-reporting questionnaires. Stool samples from these individuals were first analysed by 16S rRNA gene sequencing. Second, we predicted the potential secretion for 129 microbial metabolites through personalised metabolic modelling using the microbiome data and genome-scale metabolic reconstructions of human gut microbes. Our key results include the following. Eight genera and seven species changed significantly in their relative abundances between PD patients and healthy controls. PD-associated microbial patterns statistically depended on sex, age, BMI, and constipation. Particularly, the relative abundances of Bilophila and Paraprevotella were significantly associated with the Hoehn and Yahr staging after controlling for the disease duration. Furthermore, personalised metabolic modelling of the gut microbiomes revealed PD-associated metabolic patterns in the predicted secretion potential of nine microbial metabolites in PD, including increased methionine and cysteinylglycine. The predicted microbial pantothenic acid production potential was linked to the presence of specific non-motor symptoms. CONCLUSION Our results suggest that PD-associated alterations of the gut microbiome can translate into substantial functional differences affecting host metabolism and disease phenotype.
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Affiliation(s)
- Federico Baldini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, Ireland
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Estelle Sandt
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Lukas Pavelka
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg City, Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg City, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg.
- School of Medicine, National University of Ireland, Galway, Ireland.
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
- APC Microbiome, Cork, Ireland.
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Tal O, Selvaraj G, Medina S, Ofaim S, Freilich S. NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. Microorganisms 2020; 8:microorganisms8060840. [PMID: 32503277 PMCID: PMC7356744 DOI: 10.3390/microorganisms8060840] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
Metabolic conversions allow organisms to produce a set of essential metabolites from the available nutrients in an environment, frequently requiring metabolic exchanges among co-inhabiting organisms. Genomic-based metabolic simulations are being increasingly applied for exploring metabolic capacities, considering different environments and different combinations of microorganisms. NetMet is a web-based tool and a software package for predicting the metabolic performances of microorganisms and their corresponding combinations in user-defined environments. The algorithm takes, as input, lists of (i) species-specific enzymatic reactions (EC numbers), and (ii) relevant metabolic environments. The algorithm generates, as output, lists of (i) compounds that individual species can produce in each given environment, and (ii) compounds that are predicted to be produced through complementary interactions. The tool is demonstrated in two case studies. First, we compared the metabolic capacities of different haplotypes of the obligatory fruit and vegetable pathogen Candidatus Liberibacter solanacearum to those of their culturable taxonomic relative Liberibacter crescens. Second, we demonstrated the potential production of complementary metabolites by pairwise combinations of co-occurring endosymbionts of the plant phloem-feeding whitefly Bemisia tabaci.
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21
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Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. Brief Bioinform 2020; 20:1032-1056. [PMID: 29186315 DOI: 10.1093/bib/bbx156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.
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Affiliation(s)
| | | | | | - Anália Lourenço
- Dpto. de Informática - Universidade de Vigo, ESEI - Escuela Superior de Ingeniería Informática, Edificio politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
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22
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Crestani E, Harb H, Charbonnier LM, Leirer J, Motsinger-Reif A, Rachid R, Phipatanakul W, Kaddurah-Daouk R, Chatila TA. Untargeted metabolomic profiling identifies disease-specific signatures in food allergy and asthma. J Allergy Clin Immunol 2020; 145:897-906. [PMID: 31669435 PMCID: PMC7062570 DOI: 10.1016/j.jaci.2019.10.014] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/10/2019] [Accepted: 10/01/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Food allergy (FA) affects an increasing proportion of children for reasons that remain obscure. Novel disease biomarkers and curative treatment options are strongly needed. OBJECTIVE We sought to apply untargeted metabolomic profiling to identify pathogenic mechanisms and candidate disease biomarkers in patients with FA. METHODS Mass spectrometry-based untargeted metabolomic profiling was performed on serum samples of children with either FA alone, asthma alone, or both FA and asthma, as well as healthy pediatric control subjects. RESULTS In this pilot study patients with FA exhibited a disease-specific metabolomic signature compared with both control subjects and asthmatic patients. In particular, FA was uniquely associated with a marked decrease in sphingolipid levels, as well as levels of a number of other lipid metabolites, in the face of normal frequencies of circulating natural killer T cells. Specific comparison of patients with FA and asthmatic patients revealed differences in the microbiota-sensitive aromatic amino acid and secondary bile acid metabolism. Children with both FA and asthma exhibited a metabolomic profile that aligned with that of FA alone but not asthma. Among children with FA, the history of severe systemic reactions and the presence of multiple FAs were associated with changes in levels of tryptophan metabolites, eicosanoids, plasmalogens, and fatty acids. CONCLUSIONS Children with FA have a disease-specific metabolomic profile that is informative of disease mechanisms and severity and that dominates in the presence of asthma. Lower levels of sphingolipids and ceramides and other metabolomic alterations observed in children with FA might reflect the interplay between an altered microbiota and immune cell subsets in the gut.
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Affiliation(s)
- Elena Crestani
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Hani Harb
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Louis-Marie Charbonnier
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Jonathan Leirer
- Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC
| | - Rima Rachid
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Wanda Phipatanakul
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences and the Duke Institute for Brain Sciences, Duke University, Durham, NC
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Mass.
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23
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Chowdhury S, Fong SS. Computational Modeling of the Human Microbiome. Microorganisms 2020; 8:microorganisms8020197. [PMID: 32023941 PMCID: PMC7074762 DOI: 10.3390/microorganisms8020197] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/20/2022] Open
Abstract
The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.
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Affiliation(s)
- Shomeek Chowdhury
- Integrative Life Sciences, Virginia Commonwealth University, 1000 West Cary Street, Richmond, VA 23284 USA;
| | - Stephen S. Fong
- Chemical and Life Science Engineering, Virginia Commonwealth University, 601 West Main Street, Richmond, VA 23284, USA
- Correspondence:
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24
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Liu HH, Lin YC, Chung CS, Liu K, Chang YH, Yang CH, Chen Y, Ni YH, Chang PF. Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes. Sci Rep 2019; 9:16836. [PMID: 31727954 PMCID: PMC6856387 DOI: 10.1038/s41598-019-53173-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
Bowel microbiota is a "metaorgan" of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the "other glycan degradation" pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = -0.97, p < 0.002) between the scores and the abundance of "glycogen degradation" in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10-4). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10-5) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.
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Affiliation(s)
- Hong-Hsing Liu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, 350, Taiwan. .,Pediatrics, En Chu Kong Hospital, Sanxia District, New Taipei City, 237, Taiwan.
| | - Yu-Chen Lin
- Pediatrics, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan.,Electronic Engineering, Oriental Institute of Technology, Pan-Chiao District, New Taipei City, 220, Taiwan
| | - Chen-Shuan Chung
- Internal Medicine, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan
| | - Kevin Liu
- Pediatrics, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan
| | - Ya-Hui Chang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, 350, Taiwan
| | - Chung-Hsiang Yang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, 350, Taiwan
| | - Yun Chen
- Pediatric Surgery, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan
| | - Yen-Hsuan Ni
- Pediatrics, National Taiwan University Hospital, Zhongzheng District, Taipei, 100, Taiwan
| | - Pi-Feng Chang
- Pediatrics, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan. .,Electronic Engineering, Oriental Institute of Technology, Pan-Chiao District, New Taipei City, 220, Taiwan.
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25
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Frioux C, Fremy E, Trottier C, Siegel A. Scalable and exhaustive screening of metabolic functions carried out by microbial consortia. Bioinformatics 2019; 34:i934-i943. [PMID: 30423063 PMCID: PMC6129287 DOI: 10.1093/bioinformatics/bty588] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Motivation The selection of species exhibiting metabolic behaviors of interest is a challenging step when switching from the investigation of a large microbiota to the study of functions effectiveness. Approaches based on a compartmentalized framework are not scalable. The output of scalable approaches based on a non-compartmentalized modeling may be so large that it has neither been explored nor handled so far. Results We present the Miscoto tool to facilitate the selection of a community optimizing a desired function in a microbiome by reporting several possibilities which can be then sorted according to biological criteria. Communities are exhaustively identified using logical programming and by combining the non-compartmentalized and the compartmentalized frameworks. The benchmarking of 4.9 million metabolic functions associated with the Human Microbiome Project, shows that Miscoto is suited to screen and classify metabolic producibility in terms of feasibility, functional redundancy and cooperation processes involved. As an illustration of a host-microbial system, screening the Recon 2.2 human metabolism highlights the role of different consortia within a family of 773 intestinal bacteria. Availability and implementation Miscoto source code, instructions for use and examples are available at: https://github.com/cfrioux/miscoto.
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Affiliation(s)
| | - Enora Fremy
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | | | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
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26
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Badal VD, Wright D, Katsis Y, Kim HC, Swafford AD, Knight R, Hsu CN. Challenges in the construction of knowledge bases for human microbiome-disease associations. MICROBIOME 2019; 7:129. [PMID: 31488215 PMCID: PMC6728997 DOI: 10.1186/s40168-019-0742-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 08/20/2019] [Indexed: 05/05/2023]
Abstract
The last few years have seen tremendous growth in human microbiome research, with a particular focus on the links to both mental and physical health and disease. Medical and experimental settings provide initial sources of information about these links, but individual studies produce disconnected pieces of knowledge bounded in context by the perspective of expert researchers reading full-text publications. Building a knowledge base (KB) consolidating these disconnected pieces is an essential first step to democratize and accelerate the process of accessing the collective discoveries of human disease connections to the human microbiome. In this article, we survey the existing tools and development efforts that have been produced to capture portions of the information needed to construct a KB of all known human microbiome-disease associations and highlight the need for additional innovations in natural language processing (NLP), text mining, taxonomic representations, and field-wide vocabulary standardization in human microbiome research. Addressing these challenges will enable the construction of KBs that help identify new insights amenable to experimental validation and potentially clinical decision support.
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Affiliation(s)
- Varsha Dave Badal
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Dustin Wright
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Yannis Katsis
- Scalable Knowledge Intelligence, IBM Research-Almaden, 650 Harry Road, San Jose, CA 95120 USA
| | - Ho-Cheol Kim
- Scalable Knowledge Intelligence, IBM Research-Almaden, 650 Harry Road, San Jose, CA 95120 USA
| | - Austin D. Swafford
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
- UCSD Health Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Chun-Nan Hsu
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
- Department of Neurosciences and Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
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27
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Anani H, Abou Abdallah R, Chelkha N, Fontanini A, Ricaboni D, Mailhe M, Raoult D, Fournier PE. Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum. Sci Rep 2019; 9:7931. [PMID: 31138831 PMCID: PMC6538751 DOI: 10.1038/s41598-019-44343-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/09/2019] [Indexed: 12/22/2022] Open
Abstract
We used phenotypic, genomic and phylogenetic information following the taxono-genomics approach to demonstrate that strain Marseille–P3254, isolated from an ileal sample of a 76-year old woman who underwent upper and lower digestive tract endoscopy for esophagitis and colonic polyp, is representative of a novel bacterial genus within the family Erysipelotrichaceae in the phylum Firmicutes. It is an anaerobic Gram-negative bacterium without catalase and oxidase activities. The genome of strain Marseille–P3254 is 2,468,496-bp long with a 40.1% G + C content. This new bacterium is most closely related to Eubacterium dolichum, with which it shares 90.7% 16S rRNA sequence similarity. In addition, genomic comparison using the digital DNA–DNA hybridization and OrthoANI analyses between the novel organism and the E. dolichum type strain revealed identities of 25.2 and 68.91%, respectively. The major fatty acids were C16: 0, C18: 1n9 and C18: 0. Based on these data, we propose the creation of the new genus Merdibacter gen. nov., with strain Marseille-P3254T (=CSUR P3254 = DSM 103534) being the type strain of the new species Merdibacter massiliensis gen. nov., sp. nov.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Abou Abdallah
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nisrine Chelkha
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Anthony Fontanini
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Davide Ricaboni
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Morgane Mailhe
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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28
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Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. MICROBIOME 2019; 7:75. [PMID: 31092280 PMCID: PMC6521386 DOI: 10.1186/s40168-019-0689-3] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/26/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe interactions, a mechanistic, multi-scale computational systems biology approach that integrates the different types of omic data is needed. Here, we use a systematic workflow to computationally model bile acid metabolism in gut microbes and microbial communities. RESULTS Therefore, we first performed a comparative genomic analysis of bile acid deconjugation and biotransformation pathways in 693 human gut microbial genomes and expanded 232 curated genome-scale microbial metabolic reconstructions with the corresponding reactions (available at https://vmh.life ). We then predicted the bile acid biotransformation potential of each microbe and in combination with other microbes. We found that each microbe could produce maximally six of the 13 secondary bile acids in silico, while microbial pairs could produce up to 12 bile acids, suggesting bile acid biotransformation being a microbial community task. To investigate the metabolic potential of a given microbiome, publicly available metagenomics data from healthy Western individuals, as well as inflammatory bowel disease patients and healthy controls, were mapped onto the genomes of the reconstructed strains. We constructed for each individual a large-scale personalized microbial community model that takes into account strain-level abundances. Using flux balance analysis, we found considerable variation in the potential to deconjugate and transform primary bile acids between the gut microbiomes of healthy individuals. Moreover, the microbiomes of pediatric inflammatory bowel disease patients were significantly depleted in their bile acid production potential compared with that of controls. The contributions of each strain to overall bile acid production potential across individuals were found to be distinct between inflammatory bowel disease patients and controls. Finally, bottlenecks limiting secondary bile acid production potential were identified in each microbiome model. CONCLUSIONS This large-scale modeling approach provides a novel way of analyzing metagenomics data to accelerate our understanding of the metabolic interactions between the host and gut microbiomes in health and diseases states. Our models and tools are freely available to the scientific community.
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Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Dmitry A Ravcheev
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Federico Baldini
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Laurent Heirendt
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ronan M T Fleming
- Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Faculty of Science, University of Leiden, Leiden, The Netherlands
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, University Road, Galway, Ireland.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, University Road, Galway, Ireland.
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29
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AYDIN MA, AGIRBAS EP, AYDIN S. Can disruption of microbiota composition be the chemical basis of Parkinson's disease and schizophrenia? BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2019; 38:1-2. [PMID: 30705796 PMCID: PMC6343051 DOI: 10.12938/bmfh.2018-019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/10/2018] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Suleyman AYDIN
- Department of Medical Biochemistry and Clinical Biochemistry, School of Medicine, Firat University, Elazig 23119, Turkey,*Corresponding author. Suleyman Aydin (E-mail: )
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30
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Synthetic gutomics: Deciphering the microbial code for futuristic diagnosis and personalized medicine. METHODS IN MICROBIOLOGY 2019. [DOI: 10.1016/bs.mim.2019.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Behr C, Sperber S, Jiang X, Strauss V, Kamp H, Walk T, Herold M, Beekmann K, Rietjens I, van Ravenzwaay B. Microbiome-related metabolite changes in gut tissue, cecum content and feces of rats treated with antibiotics. Toxicol Appl Pharmacol 2018; 355:198-210. [DOI: 10.1016/j.taap.2018.06.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/09/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022]
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32
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Parker A, Lawson MAE, Vaux L, Pin C. Host-microbe interaction in the gastrointestinal tract. Environ Microbiol 2018; 20:2337-2353. [PMID: 28892253 PMCID: PMC6175405 DOI: 10.1111/1462-2920.13926] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/25/2017] [Accepted: 08/31/2017] [Indexed: 12/13/2022]
Abstract
The gastrointestinal tract is a highly complex organ in which multiple dynamic physiological processes are tightly coordinated while interacting with a dense and extremely diverse microbial population. From establishment in early life, through to host-microbe symbiosis in adulthood, the gut microbiota plays a vital role in our development and health. The effect of the microbiota on gut development and physiology is highlighted by anatomical and functional changes in germ-free mice, affecting the gut epithelium, immune system and enteric nervous system. Microbial colonisation promotes competent innate and acquired mucosal immune systems, epithelial renewal, barrier integrity, and mucosal vascularisation and innervation. Interacting or shared signalling pathways across different physiological systems of the gut could explain how all these changes are coordinated during postnatal colonisation, or after the introduction of microbiota into germ-free models. The application of cell-based in-vitro experimental systems and mathematical modelling can shed light on the molecular and signalling pathways which regulate the development and maintenance of homeostasis in the gut and beyond.
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Affiliation(s)
- Aimée Parker
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| | | | - Laura Vaux
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
| | - Carmen Pin
- Quadram Institute BioscienceNorwich Research ParkNR4 7UAUK
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33
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Sertbas M, Ulgen KO. Unlocking Human Brain Metabolism by Genome-Scale and Multiomics Metabolic Models: Relevance for Neurology Research, Health, and Disease. ACTA ACUST UNITED AC 2018; 22:455-467. [DOI: 10.1089/omi.2018.0088] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mustafa Sertbas
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | - Kutlu O. Ulgen
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
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34
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Abstract
An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities. Common approaches to investigate the human microbiota include high-throughput sequencing with subsequent correlative analyses. However, to understand the ecology of the human gut microbiota and consequently design novel treatments for diseases, it is important to represent the different interactions between microbes with their associated metabolites. Computational systems biology approaches can give further mechanistic insights by constructing data- or knowledge-driven networks that represent microbe interactions. In this minireview, we will discuss current approaches in systems biology to analyze the human gut microbiota, with a particular focus on constraint-based modeling. We will discuss various community modeling techniques with their advantages and differences, as well as their application to predict the metabolic mechanisms of intestinal microbial communities. Finally, we will discuss future perspectives and current challenges of simulating realistic and comprehensive models of the human gut microbiota.
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Affiliation(s)
- Eugen Bauer
- Luxembourg Centre for Systems Biomedicine, Universite du Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, Universite du Luxembourg, Esch-sur-Alzette, Luxembourg
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35
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Constraint-based modeling in microbial food biotechnology. Biochem Soc Trans 2018; 46:249-260. [PMID: 29588387 PMCID: PMC5906707 DOI: 10.1042/bst20170268] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 12/19/2022]
Abstract
Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype–phenotype relationships. This is essential for the rational improvement of industrial strains, which can further be facilitated through various model-guided strain design approaches. CBM of microbial communities offers a valuable tool for the rational design of defined food cultures, where it can catalyze hypothesis generation and provide unintuitive rationales for the development of enhanced community phenotypes and, consequently, novel or improved food products. In the industrial-scale production of microorganisms for food cultures, CBM may enable a knowledge-driven bioprocess optimization by rationally identifying strategies for growth and stability improvement. Through these applications, we believe that CBM can become a powerful tool for guiding the areas of strain development, culture development and process optimization in the production of food cultures. Nevertheless, in order to make the correct choice of the modeling framework for a particular application and to interpret model predictions in a biologically meaningful manner, one should be aware of the current limitations of CBM.
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36
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Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Gonzalez GAP, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RM, Nielsen J, Thiele I, Palsson BO. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol 2018; 36:272-281. [PMID: 29457794 PMCID: PMC5840010 DOI: 10.1038/nbt.4072] [Citation(s) in RCA: 390] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 01/10/2018] [Indexed: 12/14/2022]
Abstract
Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.
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Affiliation(s)
- Elizabeth Brunk
- Department of Bioengineering, University of California San Diego CA 92093
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Swagatika Sahoo
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | | | - Ali Altunkaya
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andreas Dräger
- Applied Bioinformatics Group, Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, 72076 Tübingen, Germany
| | - Nathan Mih
- Department of Bioengineering, University of California San Diego CA 92093
| | - Francesco Gatto
- Department of Bioengineering, University of California San Diego CA 92093
- Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden
| | - Avlant Nilsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden
| | | | - Maike Kathrin Aurich
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | - Andreas Prlić
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anand Sastry
- Department of Bioengineering, University of California San Diego CA 92093
| | - Anna D. Danielsdottir
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | - Almut Heinken
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | - Alberto Noronha
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | - Peter W. Rose
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, and Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ronan M.T. Fleming
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | - Jens Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-Sur-Alzette, Luxembourg
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego CA 92093
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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Mhlongo MI, Piater LA, Madala NE, Labuschagne N, Dubery IA. The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:112. [PMID: 29479360 PMCID: PMC5811519 DOI: 10.3389/fpls.2018.00112] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/22/2018] [Indexed: 05/21/2023]
Abstract
Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes/-bacteria (PGPR), resulting in priming of defense, or induced resistance in the plant host. The knowledge of plant-plant and plant-microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze 100s of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground 'signalomics', and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial - and priming events.
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Affiliation(s)
- Msizi I. Mhlongo
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni E. Madala
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Nico Labuschagne
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
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Magnúsdóttir S, Thiele I. Modeling metabolism of the human gut microbiome. Curr Opin Biotechnol 2017; 51:90-96. [PMID: 29258014 DOI: 10.1016/j.copbio.2017.12.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/15/2022]
Abstract
The human gut microbiome plays an important part in human health. The complexity of the microbiome makes it difficult to determine the detailed metabolic functions and cross-talk occurs between the individual species. In silico systems biology studies of the microbiome can help to identify metabolite exchanges among gut microbes. Constraint-based reconstruction and analysis methods use biochemically accurate genome-scale metabolic networks of microorganisms to simulate metabolism between species in a given microbiome and help generate novel hypotheses on microbial interactions. Here, we review metabolic modeling studies that have investigated metabolic functions of the gut microbiome.
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Affiliation(s)
- Stefanía Magnúsdóttir
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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39
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Zuñiga C, Zaramela L, Zengler K. Elucidation of complexity and prediction of interactions in microbial communities. Microb Biotechnol 2017; 10:1500-1522. [PMID: 28925555 PMCID: PMC5658597 DOI: 10.1111/1751-7915.12855] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ. Interpretation of these multi-omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. Here, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.
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Affiliation(s)
- Cristal Zuñiga
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Livia Zaramela
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Karsten Zengler
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
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40
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Abstract
Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. For the gastroenterologist, this technology opens up a rapidly evolving set of challenges and opportunities for generating novel insights into the health of patients on the basis of microbiota characterizations from intestinal, hepatic or extraintestinal samples. Alterations in gut microbiota composition correlate with intestinal and extraintestinal disease and, although only a few mechanisms are known, the microbiota are still an attractive target for developing biomarkers for disease detection and management as well as potential therapeutic applications. In this Review, we summarize the major decision points confronting new entrants to the field or for those designing new projects in microbiome research. We provide recommendations based on current technology options and our experience of sequencing platform choices. We also offer perspectives on future applications of microbiome research, which we hope convey the promise of this technology for clinical applications.
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41
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Chronic Rhinosinusitis and the Evolving Understanding of Microbial Ecology in Chronic Inflammatory Mucosal Disease. Clin Microbiol Rev 2017; 30:321-348. [PMID: 27903594 DOI: 10.1128/cmr.00060-16] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation. This review presents a comprehensive discussion of the current understanding of bacterial, fungal, and viral associations with CRS, with a specific focus on the transition to the new perspective offered in recent years by modern technology in microbiological research. Clinical implications of this new perspective, including the role of antimicrobials, are discussed in depth. While principally framed within the context of CRS, this discussion also provides an analogue for reframing our understanding of many similarly complex and poorly understood chronic inflammatory diseases for which roles of microbes have been suggested but specific mechanisms of disease remain unclear. Finally, further technological advancements on the horizon, and current pressing questions for CRS microbiological research, are considered.
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42
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Muhrez K, Largeau B, Emond P, Montigny F, Halimi JM, Trouillas P, Barin-Le Guellec C. Single nucleotide polymorphisms of ABCC2 modulate renal secretion of endogenous organic anions. Biochem Pharmacol 2017; 140:124-138. [DOI: 10.1016/j.bcp.2017.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/17/2017] [Indexed: 01/11/2023]
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43
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Ofaim S, Ofek-Lalzar M, Sela N, Jinag J, Kashi Y, Minz D, Freilich S. Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation. Front Microbiol 2017; 8:1606. [PMID: 28878756 PMCID: PMC5572346 DOI: 10.3389/fmicb.2017.01606] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/07/2017] [Indexed: 12/25/2022] Open
Abstract
Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups. Once a function-taxonomy link is established, prediction of the impact of dominant taxa on the overall community performances is assessed by simulating removal or addition of edges (taxa associated functions). This approach is demonstrated on metagenomic data describing the microbial communities from the root environment of two crop plants – wheat and cucumber. Predictions for environment-dependent effects revealed differences between treatments (root vs. soil), corresponding to documented observations. Metabolism of specific plant exudates (e.g., organic acids, flavonoids) was linked with distinct taxonomic groups in simulated root, but not soil, environments. These dependencies point to the impact of these metabolite families as determinants of community structure. Simulations of the activity of pairwise combinations of taxonomic groups (order level) predicted the possible production of complementary metabolites. Complementation profiles allow formulating a possible metabolic role for observed co-occurrence patterns. For example, production of tryptophan-associated metabolites through complementary interactions is unique to the tryptophan-deficient cucumber root environment. Our approach enables formulation of testable predictions for species contribution to community activity and exploration of the functional outcome of structural shifts in complex bacterial communities. Understanding community-level metabolism is an essential step toward the manipulation and optimization of microbial function. Here, we introduce an analysis framework addressing three key challenges of such data: producing quantified links between taxonomy and function; contextualizing discrete functions into communal networks; and simulating environmental impact on community performances. New technologies will soon provide a high-coverage description of biotic and a-biotic aspects of complex microbial communities such as these found in gut and soil. This framework was designed to allow the integration of high-throughput metabolomic and metagenomic data toward tackling the intricate associations between community structure, community function, and metabolic inputs.
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Affiliation(s)
- Shany Ofaim
- Newe Ya'ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel.,Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Maya Ofek-Lalzar
- Institute of Soil, Water and Environmental Sciences, Agricultural Research OrganizationBeit Dagan, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani CenterBeit Dagan, Israel
| | - Jiandong Jinag
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Yechezkel Kashi
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research OrganizationBeit Dagan, Israel
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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45
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Bosi E, Bacci G, Mengoni A, Fondi M. Perspectives and Challenges in Microbial Communities Metabolic Modeling. Front Genet 2017; 8:88. [PMID: 28680442 PMCID: PMC5478693 DOI: 10.3389/fgene.2017.00088] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/09/2017] [Indexed: 01/31/2023] Open
Abstract
Bacteria have evolved to efficiently interact each other, forming complex entities known as microbial communities. These "super-organisms" play a central role in maintaining the health of their eukaryotic hosts and in the cycling of elements like carbon and nitrogen. However, despite their crucial importance, the mechanisms that influence the functioning of microbial communities and their relationship with environmental perturbations are obscure. The study of microbial communities was boosted by tremendous advances in sequencing technologies, and in particular by the possibility to determine genomic sequences of bacteria directly from environmental samples. Indeed, with the advent of metagenomics, it has become possible to investigate, on a previously unparalleled scale, the taxonomical composition and the functional genetic elements present in a specific community. Notwithstanding, the metagenomic approach per se suffers some limitations, among which the impossibility of modeling molecular-level (e.g., metabolic) interactions occurring between community members, as well as their effects on the overall stability of the entire system. The family of constraint-based methods, such as flux balance analysis, has been fruitfully used to translate genome sequences in predictive, genome-scale modeling platforms. Although these techniques have been initially developed for analyzing single, well-known model organisms, their recent improvements allowed engaging in multi-organism in silico analyses characterized by a considerable predictive capability. In the face of these advances, here we focus on providing an overview of the possibilities and challenges related to the modeling of metabolic interactions within a bacterial community, discussing the feasibility and the perspectives of this kind of analysis in the (near) future.
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Affiliation(s)
| | | | - Alessio Mengoni
- Department of Biology, University of FlorenceFlorence, Italy
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46
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Riella LV, Bagley J, Iacomini J, Alegre ML. Impact of environmental factors on alloimmunity and transplant fate. J Clin Invest 2017; 127:2482-2491. [PMID: 28481225 DOI: 10.1172/jci90596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although gene-environment interactions have been investigated for many years to understand people's susceptibility to autoimmune diseases or cancer, a role for environmental factors in modulating alloimmune responses and transplant outcomes is only now beginning to emerge. New data suggest that diet, hyperlipidemia, pollutants, commensal microbes, and pathogenic infections can all affect T cell activation, differentiation, and the kinetics of graft rejection. These observations reveal opportunities for novel therapeutic interventions to improve graft outcomes as well as for noninvasive biomarker discovery to predict or diagnose graft deterioration before it becomes irreversible. In this Review, we will focus on the impact of these environmental factors on immune function and, when known, on alloimmune function, as well as on transplant fate.
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Affiliation(s)
- Leonardo V Riella
- Schuster Family Transplantation Research Center, Renal Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jessamyn Bagley
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Sackler School of Biomedical Sciences Programs in Immunology and Genetics, Boston, Massachusetts, USA
| | - John Iacomini
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Sackler School of Biomedical Sciences Programs in Immunology and Genetics, Boston, Massachusetts, USA
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47
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Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr 2017; 57:1-24. [PMID: 28393285 PMCID: PMC5847071 DOI: 10.1007/s00394-017-1445-8] [Citation(s) in RCA: 1374] [Impact Index Per Article: 196.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays.
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48
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Behr C, Kamp H, Fabian E, Krennrich G, Mellert W, Peter E, Strauss V, Walk T, Rietjens IMCM, van Ravenzwaay B. Gut microbiome-related metabolic changes in plasma of antibiotic-treated rats. Arch Toxicol 2017; 91:3439-3454. [PMID: 28337503 DOI: 10.1007/s00204-017-1949-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/23/2017] [Indexed: 12/13/2022]
Abstract
The intestinal microbiota contributes to the metabolism of its host. Adequate identification of the microbiota's impact on the host plasma metabolites is lacking. As antibiotics have a profound effect on the microbial composition and hence on the mammalian-microbiota co-metabolism, we studied the effects of antibiotics on the "functionality of the microbiome"-defined as the production of metabolites absorbed by the host. This metabolomics study presents insights into the mammalian-microbiome co-metabolism of endogenous metabolites. To identify plasma metabolites related to microbiome changes due to antibiotic treatment, we have applied broad-spectrum antibiotics belonging to the class of aminoglycosides (neomycin, gentamicin), fluoroquinolones (moxifloxacin, levofloxacin) and tetracyclines (doxycycline, tetracycline). These were administered orally for 28 days to male rats including blood sampling for metabolic profiling after 7, 14 and 28 days. Fluoroquinolones and tetracyclines can be absorbed from the gut; whereas, aminoglycosides are poorly absorbed. Hippuric acid, indole-3-acetic acid and glycerol were identified as key metabolites affected by antibiotic treatment, beside changes mainly concerning amino acids and carbohydrates. Inter alia, effects on indole-3-propionic acid were found to be unique for aminoglycosides, and on 3-indoxylsulfate for tetracyclines. For each class of antibiotics, specific metabolome patterns could be established in the MetaMap®Tox data base, which contains metabolome data for more than 550 reference compounds. The results suggest that plasma-based metabolic profiling (metabolomics) could be a suitable tool to investigate the effect of antibiotics on the functionality of the microbiome and to obtain insight into the mammalian-microbiome co-metabolism.
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Affiliation(s)
- C Behr
- BASF SE, 67056, Ludwigshafen, Germany
| | - H Kamp
- BASF SE, 67056, Ludwigshafen, Germany
| | - E Fabian
- BASF SE, 67056, Ludwigshafen, Germany
| | | | - W Mellert
- BASF SE, 67056, Ludwigshafen, Germany
| | - E Peter
- Metanomics GmbH, 10589, Berlin, Germany
| | - V Strauss
- BASF SE, 67056, Ludwigshafen, Germany
| | - T Walk
- Metanomics GmbH, 10589, Berlin, Germany
| | - I M C M Rietjens
- Division of Toxicology, Wageningen University, 6700 EA, Wageningen, The Netherlands
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49
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Yilmaz LS, Walhout AJ. Metabolic network modeling with model organisms. Curr Opin Chem Biol 2017; 36:32-39. [PMID: 28088694 PMCID: PMC5458607 DOI: 10.1016/j.cbpa.2016.12.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/21/2016] [Indexed: 12/25/2022]
Abstract
Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases. Here, we discuss GSMNMs of most highly used model organisms with the emphasis on recent reconstructions.
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Affiliation(s)
- L Safak Yilmaz
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States.
| | - Albertha Jm Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States.
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50
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Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RMT, Thiele I. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol 2016; 35:81-89. [DOI: 10.1038/nbt.3703] [Citation(s) in RCA: 434] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023]
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