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Ziaka M, Exadaktylos A. Pathophysiology of acute lung injury in patients with acute brain injury: the triple-hit hypothesis. Crit Care 2024; 28:71. [PMID: 38454447 PMCID: PMC10918982 DOI: 10.1186/s13054-024-04855-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
It has been convincingly demonstrated in recent years that isolated acute brain injury (ABI) may cause severe dysfunction of peripheral extracranial organs and systems. Of all potential target organs and systems, the lung appears to be the most vulnerable to damage after ABI. The pathophysiology of the bidirectional brain-lung interactions is multifactorial and involves inflammatory cascades, immune suppression, and dysfunction of the autonomic system. Indeed, the systemic effects of inflammatory mediators in patients with ABI create a systemic inflammatory environment ("first hit") that makes extracranial organs vulnerable to secondary procedures that enhance inflammation, such as mechanical ventilation (MV), surgery, and infections ("second hit"). Moreover, accumulating evidence supports the knowledge that gut microbiota constitutes a critical superorganism and an organ on its own, potentially modifying various physiological functions of the host. Furthermore, experimental and clinical data suggest the existence of a communication network among the brain, gastrointestinal tract, and its microbiome, which appears to regulate immune responses, gastrointestinal function, brain function, behavior, and stress responses, also named the "gut-microbiome-brain axis." Additionally, recent research evidence has highlighted a crucial interplay between the intestinal microbiota and the lungs, referred to as the "gut-lung axis," in which alterations during critical illness could result in bacterial translocation, sustained inflammation, lung injury, and pulmonary fibrosis. In the present work, we aimed to further elucidate the pathophysiology of acute lung injury (ALI) in patients with ABI by attempting to develop the "double-hit" theory, proposing the "triple-hit" hypothesis, focused on the influence of the gut-lung axis on the lung. Particularly, we propose, in addition to sympathetic hyperactivity, blast theory, and double-hit theory, that dysbiosis and intestinal dysfunction in the context of ABI alter the gut-lung axis, resulting in the development or further aggravation of existing ALI, which constitutes the "third hit."
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Affiliation(s)
- Mairi Ziaka
- Clinic for Geriatric Medicine, Center for Geriatric Medicine and Rehabilitation, Kantonsspital Baselland, Bruderholz, Switzerland.
- Department of Emergency Medicine, Inselspital, University Hospital, University of Bern, Bern, Switzerland.
| | - Aristomenis Exadaktylos
- Department of Emergency Medicine, Inselspital, University Hospital, University of Bern, Bern, Switzerland
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2
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Ben Cheikh Y, Massol F, Giusti-Petrucciani N, Travers MA. Impact of epizootics on mussel farms: Insights into microbiota composition of Mytilus species. Microbiol Res 2024; 280:127593. [PMID: 38184970 DOI: 10.1016/j.micres.2023.127593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/05/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Outbreaks of marine mussel mortality on French farms could have different aetiologies. One of them implies Vibrio splendidus strains. Beyond the involvement of this pathogen, there is considerable evidence that diseases often result from interactions between several microbes and the host. In this study, we explored the bacterial communities associated with mussel species and the surrounding water collected from a mussel farm affected by mortalities. The microbiota of Mytilus edulis, Mytilus galloprovincialis and their hybrids displayed an abnormal abundance of Proteobacteria, in particular the genera Vibrio, Cobetia and Arcobacter. Despite the dysbiosis, the Mediterranean mussel showed a different microbiota profile with a higher richness and presence of the phylum Bacteroidetes. Bipartite network analyses at the level of bacteria families confirmed this finding and showed that the microbiomes of M. edulis and the hybrids tended to cluster together. In addition, injection of mussels with the virulent V. splendidus induced less mortality rate in M. galloprovincialis compared to the other Mytilus sp. suggesting a better resistance of the Mediterranean mussel to infection. Our findings point to a probable aetiology of pathobiome-mediated disease in mussels. To fully understand this phenomenon, more knowledge is needed on the roles of pathobiotic systems and their development during disease establishment.
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Affiliation(s)
- Yosra Ben Cheikh
- UMR-I 02 Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO), Université Le Havre Normandie, Cedex 76063 Le Havre, France.
| | - François Massol
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nathalie Giusti-Petrucciani
- UMR-I 02 Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO), Université Le Havre Normandie, Cedex 76063 Le Havre, France
| | - Marie-Agnès Travers
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, F-34090 Montpellier, France
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3
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McCoy R, Oldroyd S, Yang W, Wang K, Hoven D, Bulmer D, Zilbauer M, Owens RM. In Vitro Models for Investigating Intestinal Host-Pathogen Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306727. [PMID: 38155358 PMCID: PMC10885678 DOI: 10.1002/advs.202306727] [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: 09/15/2023] [Revised: 12/01/2023] [Indexed: 12/30/2023]
Abstract
Infectious diseases are increasingly recognized as a major threat worldwide due to the rise of antimicrobial resistance and the emergence of novel pathogens. In vitro models that can adequately mimic in vivo gastrointestinal physiology are in high demand to elucidate mechanisms behind pathogen infectivity, and to aid the design of effective preventive and therapeutic interventions. There exists a trade-off between simple and high throughput models and those that are more complex and physiologically relevant. The complexity of the model used shall be guided by the biological question to be addressed. This review provides an overview of the structure and function of the intestine and the models that are developed to emulate this. Conventional models are discussed in addition to emerging models which employ engineering principles to equip them with necessary advanced monitoring capabilities for intestinal host-pathogen interrogation. Limitations of current models and future perspectives on the field are presented.
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Affiliation(s)
- Reece McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Sophie Oldroyd
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Woojin Yang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Kaixin Wang
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Darius Hoven
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - David Bulmer
- Department of PharmacologyUniversity of CambridgeCambridgeCB2 1PDUK
| | - Matthias Zilbauer
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Róisín M. Owens
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
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Belyaeva IA, Bombardirova EP, Turti TV. New Strategies for Enhancement of Infant Milk Formulas Composition. CURRENT PEDIATRICS 2022. [DOI: 10.15690/vsp.v21i6.2468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This article covers the issues of remodeling breast milk’s protective properties during creating infant milk formulas. First of all, this concerns the conditions for normal intestinal microbiota development in growing organism. Its quantitative and qualitative features are the trigger of either sanogenetic, or pathological immune and metabolic reactions, and also determine gut-brain axis functioning. The protective significance of prebiotic composition diversity of mammalian milk and the inductive role of breast milk oligosaccharides are shown. The modern concept of synbiotics role in gastrointestinal tract and other systems functioning, as well as the use of modern synbiotics in the creation of infant formulas (available Russian formula included) are presented.
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Affiliation(s)
- I. A. Belyaeva
- Research Institute of Pediatrics and Children’s Health in Petrovsky National Research Centre of Surgery; Pirogov Russian National Research Medical University; Morozovskaya Children’s City Hospital
| | - E. P. Bombardirova
- Research Institute of Pediatrics and Children’s Health in Petrovsky National Research Centre of Surgery
| | - T. V. Turti
- Research Institute of Pediatrics and Children’s Health in Petrovsky National Research Centre of Surgery; Pirogov Russian National Research Medical University; Research Institute for Healthcare Organization and Medical Management
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Peretti S, Torracchi S, Russo E, Bonomi F, Fiorentini E, Aoufy KE, Bruni C, Lepri G, Orlandi M, Chimenti MS, Guiducci S, Amedei A, Matucci-Cerinic M, Bellando Randone S. The Yin-Yang Pharmacomicrobiomics on Treatment Response in Inflammatory Arthritides: A Narrative Review. Genes (Basel) 2022; 14:89. [PMID: 36672830 PMCID: PMC9859330 DOI: 10.3390/genes14010089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
(1) Background: Gut microbiota (GM) is the set of microorganisms inhabiting the gastroenteric tract that seems to have a role in the pathogenesis of rheumatic diseases. Recently, many authors proved that GM may influence pharmacodynamics and pharmacokinetics of several drugs with complex interactions that are studied by the growing field of pharmacomicrobiomics. The aim of this review is to highlight current evidence on pharmacomicrobiomics applied to the main treatments of Rheumatoid Arthritis and Spondyloarthritis in order to maximize therapeutic success, in the framework of Personalized Medicine. (2) Methods: We performed a narrative review concerning pharmacomicrobiomics in inflammatory arthritides. We evaluated the influence of gut microbiota on treatment response of conventional Disease Modifying Anti-Rheumatic drugs (cDMARDs) (Methotrexate and Leflunomide) and biological Disease Modifying Anti-Rheumatic drugs (bDMARDs) (Tumor necrosis factor inhibitors, Interleukin-17 inhibitors, Interleukin 12/23 inhibitors, Abatacept, Janus Kinase inhibitors and Rituximab). (3) Results: We found a great amount of studies concerning Methotrexate and Tumor Necrosis Inhibitors (TNFi). Conversely, fewer data were available about Interleukin-17 inhibitors (IL-17i) and Interleukin 12/23 inhibitors (IL-12/23i), while none was identified for Janus Kinase Inhibitors (JAKi), Tocilizumab, Abatacept and Rituximab. We observed that microbiota and drugs are influenced in a mutual and reciprocal way. Indeed, microbiota seems to influence therapeutic response and efficacy, whereas in the other hand, drugs may restore healthy microbiota. (4) Conclusions: Future improvement in pharmacomicrobiomics could help to detect an effective biomarker able to guide treatment choice and optimize management of inflammatory arthritides.
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Affiliation(s)
- Silvia Peretti
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Sara Torracchi
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Edda Russo
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Francesco Bonomi
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Elisa Fiorentini
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Khadija El Aoufy
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Cosimo Bruni
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
- Department of Rheumatology, University Hospital of Zurich, University of Zurich, 8006 Zurich, Switzerland
| | - Gemma Lepri
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Martina Orlandi
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Maria Sole Chimenti
- Rheumatology, Allergology and Clinical Immunology, Department of Medicina dei Sistemi, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Serena Guiducci
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Marco Matucci-Cerinic
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases (UnIRAR), IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Silvia Bellando Randone
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
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6
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Ma PJ, Wang MM, Wang Y. Gut microbiota: A new insight into lung diseases. Biomed Pharmacother 2022; 155:113810. [DOI: 10.1016/j.biopha.2022.113810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/24/2022] [Accepted: 10/03/2022] [Indexed: 11/02/2022] Open
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7
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Pinho RM, Garas LC, Huang BC, Weimer BC, Maga EA. Malnourishment affects gene expression along the length of the small intestine. Front Nutr 2022; 9:894640. [PMID: 36118759 PMCID: PMC9478944 DOI: 10.3389/fnut.2022.894640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Malnourishment is a risk factor for childhood mortality, jeopardizing the health of children by aggravating pneumonia/acute respiratory infections and diarrheal diseases. Malnourishment causes morphophysiological changes resulting in stunting and wasting that have long-lasting consequences such as cognitive deficit and metabolic dysfunction. Using a pig model of malnutrition, the interplay between the phenotypic data displayed by the malnourished animals, the gene expression pattern along the intestinal tract, microbiota composition of the intestinal contents, and hepatic metabolite concentrations from the same animals were correlated using a multi-omics approach. Samples from the duodenum, jejunum, and ileum of malnourished (protein and calorie-restricted diet) and full-fed (no dietary restrictions) piglets were subjected to RNA-seq. Gene co-expression analysis and phenotypic correlations were made with WGCNA, while the integration of transcriptome with microbiota composition and the hepatic metabolite profile was done using mixOmics. Malnourishment caused changes in tissue gene expression that influenced energetic balance, cell proliferation, nutrient absorption, and response to stress. Repression of antioxidant genes, including glutathione peroxidase, in coordination with induction of metal ion transporters corresponded to the hepatic metabolite changes. These data indicate oxidative stress in the intestine of malnourished animals. Furthermore, several of the phenotypes displayed by these animals could be explained by changes in gene expression.
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Affiliation(s)
- Raquel M. Pinho
- Department of Animal Science, University of California, Davis, Davis, CA, United States
- *Correspondence: Raquel M. Pinho
| | - Lydia C. Garas
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - B. Carol Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Elizabeth A. Maga
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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8
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Toni T, Alverdy J, Gershuni V. Re-examining chemically defined liquid diets through the lens of the microbiome. Nat Rev Gastroenterol Hepatol 2021; 18:903-911. [PMID: 34594028 PMCID: PMC8815794 DOI: 10.1038/s41575-021-00519-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Trends in nutritional science are rapidly shifting as information regarding the value of eating unprocessed foods and its salutary effect on the human microbiome emerge. Unravelling the evolution and ecology by which humans have harboured a microbiome that participates in every facet of health and disease is daunting. Most strikingly, the host habitat has sought out naturally occurring foodstuff that can fulfil its own metabolic needs and also the needs of its microbiota, each of which remain inexorably connected to one another. With the introduction of modern medicine and complexities of critical care, came the assumption that the best way to feed a critically ill patient is by delivering fibre-free chemically defined sterile liquid foods (that is, total enteral nutrition). In this Perspective, we uncover the potential flaws in this assumption and discuss how emerging technology in microbiome sciences might inform the best method of feeding malnourished and critically ill patients.
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Affiliation(s)
- Tiffany Toni
- University of Chicago, Pritzker School of Medicine, Chicago, IL, USA
| | - John Alverdy
- University of Chicago, Pritzker School of Medicine, Chicago, IL, USA
| | - Victoria Gershuni
- University of Pennsylvania, Department of Surgery, Philadelphia, PA, USA and Washington University in St Louis, Department of Surgery, St Louis, MO, USA,Corresponding author
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9
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Ma H, Zhao Y, Li L, Liu Y. Effects of Combinations of Goat Milk and Oligosaccharides on Altering the Microbiota, Immune Responses, and Short Chain Fatty Acid Levels in the Small Intestines of Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8828-8837. [PMID: 34314156 DOI: 10.1021/acs.jafc.1c03408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Goat milk and oligosaccharides play important roles in gastrointestinal health. A combination of goat milk with three oligosaccharides, stachyose (STS), fructo-oligosaccharide (FOS), and a prebiotics mixture (FGS), was fed to mice. Changes and functions of the microbiota, short chain fatty acid (SCFA) concentrations, and immune gene expression in the small intestines were determined. The FOS treatment increased the beneficial bacteria Lactobacillus and Bifidobacterium, the FGS treatment helped stabilize the microbial community, and the STS treatment significantly enhanced microbial diversity and the growth of Bacteroidetes. The oligosaccharide treatments regulated the gene expression levels of the immune factors tumor necrosis factor alpha (Tnfα), granzyme B (Gzmb), perforin (Prf), and aryl hydrocarbon receptor (Ahr). Stachyose significantly increased the concentrations of acetate and propionate compared with other treatments. These findings demonstrate that STS is the preferred carbon source for microbiota, slightly modulates SCFA production, and results in low immunogenicity in the small intestines of mice.
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Affiliation(s)
- Haorui Ma
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Yu Zhao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Linqiang Li
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Yongfeng Liu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
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10
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Insights into health-promoting effects of Jew's ear (Auricularia auricula-judae). Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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11
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Vander Wyst KB, Ortega-Santos CP, Toffoli SN, Lahti CE, Whisner CM. Diet, adiposity, and the gut microbiota from infancy to adolescence: A systematic review. Obes Rev 2021; 22:e13175. [PMID: 33590719 PMCID: PMC10762698 DOI: 10.1111/obr.13175] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 12/14/2022]
Abstract
Early life gut microbiota are affected by several factors that make identification of microbial-adiposity relationships challenging. This review evaluates studies that have investigated the gut microbiota composition associated with adiposity in infants, children, and adolescents and provides evidence-based nutrition recommendations that address microbiota-adiposity links. Electronic databases were systematically searched through January 2020. Eligible studies were published in English and analyzed gut microbiota and adiposity among individuals aged birth to 18 years. Abstracts and full-text articles were reviewed by three independent reviewers. Of 45 full-text articles reviewed, 33 were included. No difference in abundance was found for Bacteroidetes (n = 7/15 articles), Firmicutes (n = 10/17), Actinobacteria (n = 8/12), Proteobacteria (n = 8/12), Tenericutes (n = 4/5), and Verrucomicrobia (n = 4/6) with adiposity. Lower abundance of Christensenellaceae (n = 3/5) and Rikenellaceae (n = 6/8) but higher abundance of F. prausnitzii (n = 3/5) and Prevotella (n = 5/7) were associated with adiposity. A lack of consensus exists for gut microbial composition associations with adiposity. A healthy gut microbiota is associated with a diet rich in fruits and vegetables with moderate consumption of animal fat and protein. Future research should use more robust sequencing technologies to identify all bacterial taxa associated with adiposity and evaluate how diet effects these adiposity-associated microbes.
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Affiliation(s)
- Kiley B Vander Wyst
- College of Health Solutions, Arizona State University, Phoenix, Arizona, USA
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, Arizona, USA
| | | | - Samantha N Toffoli
- College of Health Solutions, Arizona State University, Phoenix, Arizona, USA
| | - Caroline E Lahti
- College of Liberal Arts and Sciences, Arizona State University, Phoenix, Arizona, USA
| | - Corrie M Whisner
- College of Health Solutions, Arizona State University, Phoenix, Arizona, USA
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Abstract
AbstractThis article aims to provide a thorough overview of the use of Artificial Intelligence (AI) techniques in studying the gut microbiota and its role in the diagnosis and treatment of some important diseases. The association between microbiota and diseases, together with its clinical relevance, is still difficult to interpret. The advances in AI techniques, such as Machine Learning (ML) and Deep Learning (DL), can help clinicians in processing and interpreting these massive data sets. Two research groups have been involved in this Scoping Review, working in two different areas of Europe: Florence and Sarajevo. The papers included in the review describe the use of ML or DL methods applied to the study of human gut microbiota. In total, 1109 papers were considered in this study. After elimination, a final set of 16 articles was considered in the scoping review. Different AI techniques were applied in the reviewed papers. Some papers applied ML, while others applied DL techniques. 11 papers evaluated just different ML algorithms (ranging from one to eight algorithms applied to one dataset). The remaining five papers examined both ML and DL algorithms. The most applied ML algorithm was Random Forest and it also exhibited the best performances.
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13
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Gut microbial metabolites as multi-kingdom intermediates. Nat Rev Microbiol 2020; 19:77-94. [PMID: 32968241 DOI: 10.1038/s41579-020-0438-4] [Citation(s) in RCA: 531] [Impact Index Per Article: 132.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
The gut microbiota contributes to host physiology through the production of a myriad of metabolites. These metabolites exert their effects within the host as signalling molecules and substrates for metabolic reactions. Although the study of host-microbiota interactions remains challenging due to the high degree of crosstalk both within and between kingdoms, metabolite-focused research has identified multiple actionable microbial targets that are relevant for host health. Metabolites, as the functional output of combined host and microorganism interactions, provide a snapshot in time of an extraordinarily complex multi-organism system. Although substantial work remains towards understanding host-microbiota interactions and the underlying mechanisms, we review the current state of knowledge for each of the major classes of microbial metabolites with emphasis on clinical and translational research implications. We provide an overview of methodologies available for measurement of microbial metabolites, and in addition to discussion of key challenges, we provide a potential framework for integration of discovery-based metabolite studies with mechanistic work. Finally, we highlight examples in the literature where this approach has led to substantial progress in understanding host-microbiota interactions.
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14
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The link “Cancer and autoimmune diseases” in the light of microbiota: Evidence of a potential culprit. Immunol Lett 2020; 222:12-28. [DOI: 10.1016/j.imlet.2020.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 12/15/2022]
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15
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Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome-Commensalism and Postbiotic Effects. Metabolites 2020; 10:metabo10040167. [PMID: 32344519 PMCID: PMC7240951 DOI: 10.3390/metabo10040167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022] Open
Abstract
Oligosaccharides from human or bovine milk selectively stimulate growth or metabolism of bacteria associated with the lower gastrointestinal tract of infants. Results from complex infant-type co-cultures point toward a possible synergistic effect of combining bovine milk oligosaccharides (BMO) and lactose (LAC) on enhancing the metabolism of Bifidobacterium longum subsp. longum and inhibition of Clostridium perfringens. We examine the interaction between B. longum subsp. longum and the commensal Parabacteroides distasonis, by culturing them in mono- and co-culture with different carbohydrates available. To understand the interaction between BMO and lactose on B. longum subsp. longum and test the potential postbiotic effect on C. perfringens growth and/or metabolic activity, we inoculated C. perfringens into fresh media and compared the metabolic changes to C. perfringens in cell-free supernatant from B. longum subsp. longum fermented media. In co-culture, B. longum subsp. longum benefits from P. distasonis (commensalism), especially in a lactose-rich environment. Furthermore, B. longum subsp. longum fermentation of BMO + LAC impaired C. perfringens’ ability to utilize BMO as a carbon source (potential postbiotic effect).
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16
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Lim MY, Hong S, Kim BM, Ahn Y, Kim HJ, Nam YD. Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study. Sci Rep 2020; 10:1789. [PMID: 32019987 PMCID: PMC7000387 DOI: 10.1038/s41598-020-58719-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 01/21/2020] [Indexed: 11/09/2022] Open
Abstract
The gut microbiome is related to various host health conditions through metabolites produced by microbiota. Investigating their relationships involves association analysis of the population-level microbiome and metabolome data, which requires the appropriate collection, handling, and storage of specimens. Simplification of the specimen handling processes will facilitate such investigations. As a pilot study for population-level studies, we collected the fecal samples from three volunteers and tested whether a single sample collection procedure, particularly using OMNIgene-GUT, can be used to reliably obtain both microbiome and metabolome data. We collected fecal samples from three young and healthy Korean adults, stored them at room temperature with and without OMNIgene-GUT solution up to three weeks, and analyzed their microbiome and metabolite profiles. We found that the microbiome profiles were stably maintained in OMNIgene-GUT solution for 21 days, and the abundance relationships among metabolites were well preserved, although their absolute abundances slightly varied over time. Our results show that a single sampling procedure suffices to obtain a fecal sample for collecting gut microbiome and gut metabolome data of an individual. We expect that the health effects of gut microbiome via fecal metabolites can be further understood by increasing the sampling size to the population level.
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Affiliation(s)
- Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea
| | - Seungpyo Hong
- Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea
| | - Bo-Min Kim
- EZmass Co., Ltd., Gyeongsangnam-do, 52828, Republic of Korea
| | - Yongju Ahn
- Theragen Etex Bio Institute, Gyeonggi-do, 16229, Republic of Korea
| | - Hyun-Jin Kim
- EZmass Co., Ltd., Gyeongsangnam-do, 52828, Republic of Korea.,Department of Food Science and Technology, Division of Applied Life Sciences (BK21 Plus), Institute of Agriculture and Life Science, Gyeongsang National University, Gyeongsangnam-do, 52828, Republic of Korea
| | - Young-Do Nam
- Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea. .,Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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17
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Lin Y, Ma C, Bezabeh T, Wang Z, Liang J, Huang Y, Zhao J, Liu X, Ye W, Tang W, Ouyang T, Wu R. 1 H NMR-based metabolomics reveal overlapping discriminatory metabolites and metabolic pathway disturbances between colorectal tumor tissues and fecal samples. Int J Cancer 2019; 145:1679-1689. [PMID: 30720869 DOI: 10.1002/ijc.32190] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 01/29/2019] [Indexed: 02/05/2023]
Abstract
Previous studies have compared fecal metabolites from healthy and colorectal cancer (CRC) patients to predict the pro-CRC signatures. However, the systemic mechanistic link between feces and colonic tissues of CRC patients is still limited. The current study was a paralleled investigation of colonic tumor tissues and their normal adjacent tissues alongside patient-matched feces by using 1 H nuclear magnetic resonance spectroscopy combined with pattern recognition to investigate how fecal metabolic phenotypes are linked to the changes in colorectal tumor profiles. A set of overlapping discriminatory metabolites across feces and tumor tissues of CRC were identified, including elevated levels of lactate, glutamate, alanine, succinate and reduced amounts of butyrate. These changes could indicate the networks for metabolic pathway perturbations in CRC potentially involved in the disruptions of glucose and glycolytic metabolism, TCA cycle, glutaminolysis, and short chain fatty acids metabolism. Furthermore, changes in fecal acetate were positively correlated with alterations of glucose and myo-inositol in colorectal tumor tissues, implying enhanced energy production for rapid cell proliferation. Compared to other fecal metabolites, acetate demonstrated the highest diagnostic performance for diagnosing CRC, with an AUC of 0.843 in the training set, and a good predictive ability in the validation set. Overall, these associations provide evidence of distinct metabolic signatures and metabolic pathway disturbances between the colonic tissues and feces within the same individual, and changes of fecal metabolic signature could reflect the CRC tissue microenvironment, highlighting the significance of the distinct fecal metabolic profiles as potential novel and noninvasive relevant indicators for CRC detection.
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Affiliation(s)
- Yan Lin
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Changchun Ma
- Radiation Oncology, Cancer Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Tedros Bezabeh
- College of Natural & Applied Sciences, University of Guam, UOG Station, Mangilao, Guam
| | - Zhening Wang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Jiahao Liang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Yao Huang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Jiayun Zhao
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Xinmu Liu
- Department of Surgery, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Wei Ye
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Wan Tang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Ting Ouyang
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Renhua Wu
- Department of Radiology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
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18
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Jakobsen LMA, Sundekilde UK, Andersen HJ, Nielsen DS, Bertram HC. Lactose and Bovine Milk Oligosaccharides Synergistically Stimulate B. longum subsp. longum Growth in a Simplified Model of the Infant Gut Microbiome. J Proteome Res 2019; 18:3086-3098. [PMID: 31264424 DOI: 10.1021/acs.jproteome.9b00211] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Increasing awareness of the importance of a healthy Bifidobacterium-rich microbiome has led to a need for more knowledge on how different prebiotic carbohydrates specifically impact the infant microbiome, especially as a community instead of single bacterial targets. In this study, we combined proton nuclear magnetic resonance (1H NMR) metabolomics and molecular biology methods for quantification of bacteria to compare the prebiotic effect of bovine milk oligosaccharides (BMO) and synthetic galacto oligosaccharides (GOS) using mono- and cocultures of eight major bacteria related to a healthy infant microbiome. The results revealed that BMO treatments supported growth of Bifidobacterium longum subsp. longum and Parabacteroides distasonis, while at the same time growth of Clostridium perfringens and Escherichia coli was inhibited. In addition, there was a synergistic effect of combining lactose and BMO in regards to reducing C. perfringens, maintaining stable numbers of P. distasonis and simultaneously increasing numbers of the beneficial B. longum subsp. longum. These results indicate that the oligosaccharide composition plays a vital role in shaping the developing microbiota.
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Affiliation(s)
- Louise M A Jakobsen
- Department of Food Science , Aarhus University , Kirstinebjergvej 10 , Årslev 5792 , Denmark
| | - Ulrik K Sundekilde
- Department of Food Science , Aarhus University , Kirstinebjergvej 10 , Årslev 5792 , Denmark
| | - Henrik J Andersen
- Arla Food Ingredients Group P/S , Sønderhøj 10 , Viby J 8260 , Denmark
| | - Dennis S Nielsen
- Department of Food Science , University of Copenhagen , Rolighedsvej 30 , Frederiksberg C 1958 , Denmark
| | - Hanne C Bertram
- Department of Food Science , Aarhus University , Kirstinebjergvej 10 , Årslev 5792 , Denmark
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19
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Wang Z, Qi Q. Gut microbial metabolites associated with HIV infection. Future Virol 2019; 14:335-347. [PMID: 31263508 PMCID: PMC6595475 DOI: 10.2217/fvl-2019-0002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023]
Abstract
HIV infection has been associated with alterations in gut microbiota and related microbial metabolite production. However, the mechanisms of how these functional microbial metabolites may affect HIV immunopathogenesis and comorbidities, such as cardiovascular disease and other metabolic diseases, remain largely unknown. Here we review the current understanding of gut microbiota and related metabolites in the context of HIV infection. We focus on several bacteria-produced metabolites, including tryptophan catabolites, short-chain fatty acids and trimethylamine-N-oxide (TMAO), and discuss their implications in HIV infection and comorbidities. We also prospect future studies using integrative multiomics approaches to better understand host-microbiota-metabolites interactions in HIV infection, and facilitate integrative medicine utilizing the microbiota in HIV infection.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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20
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The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut. Microbiol Mol Biol Rev 2019; 83:83/2/e00054-18. [PMID: 30867232 DOI: 10.1128/mmbr.00054-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human intestinal ecosystem is characterized by a complex interplay between different microorganisms and the host. The high variation within the human population further complicates the quest toward an adequate understanding of this complex system that is so relevant to human health and well-being. To study host-microbe interactions, defined synthetic bacterial communities have been introduced in gnotobiotic animals or in sophisticated in vitro cell models. This review reinforces that our limited understanding has often hampered the appropriate design of defined communities that represent the human gut microbiota. On top of this, some communities have been applied to in vivo models that differ appreciably from the human host. In this review, the advantages and disadvantages of using defined microbial communities are outlined, and suggestions for future improvement of host-microbe interaction models are provided. With respect to the host, technological advances, such as the development of a gut-on-a-chip system and intestinal organoids, may contribute to more-accurate in vitro models of the human host. With respect to the microbiota, due to the increasing availability of representative cultured isolates and their genomic sequences, our understanding and controllability of the human gut "core microbiota" are likely to increase. Taken together, these advancements could further unravel the molecular mechanisms underlying the human gut microbiota superorganism. Such a gain of insight would provide a solid basis for the improvement of pre-, pro-, and synbiotics as well as the development of new therapeutic microbes.
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21
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Low YM, Chong CW, Yap IKS, Chai LC, Clarke SC, Ponnampalavanar S, Abdul Jabar K, Md Yusof MY, Teh CSJ. Elucidating the survival and response of carbapenem resistant Klebsiella pneumoniae after exposure to imipenem at sub-lethal concentrations. Pathog Glob Health 2018; 112:378-386. [PMID: 30380366 DOI: 10.1080/20477724.2018.1538281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The increasing prevalence of antibiotic resistant pathogens poses a serious threat to global health. However, less emphasis has been placed to co-relate the gene expression and metabolism of antibiotic resistant pathogens. This study aims to elucidate gene expression and variations in metabolism of multidrug resistant Klebsiella pneumoniae after exposure to antibiotics. Phenotypic responses of three genotypically distinct carbapenem resistant Klebsiella pneumoniae (CRKP) strains untreated and treated with sub-lethal concentrations of imipenem were investigated via phenotype microarrays (PM). The gene expression and metabolism of the strain harboring blaNDM-1 before and after exposure to sub-lethal concentration of imipenem were further investigated by RNA-sequencing (RNA-Seq) and 1H NMR spectroscopy respectively. Most genes related to cell division, central carbon metabolism and nucleotide metabolism were downregulated after imipenem treatment. Similarly, 1H NMR spectra obtained from treated CRKP showed decrease in levels of bacterial end products (acetate, pyruvate, succinate, formate) and metabolites involved in nucleotide metabolism (uracil, xanthine, hypoxanthine) but elevated levels of glycerophosphocholine. The presence of anserine was also observed for the treated CRKP while FAPγ-adenine and methyladenine were only present in untreated bacterial cells. As a conclusion, the studied CRKP strain exhibited decrease in central carbon metabolism, cell division and nucleotide metabolism after exposure to sub-lethal concentrations of imipenem. The understanding of the complex biological system of this multidrug resistant bacterium may help in the development of novel strategies and potential targets for the management of the infections.
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Affiliation(s)
- Ye Mun Low
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Chun Wie Chong
- b Department of Life Sciences, School of Pharmacy , International Medical University , Bukit Jalil , Kuala Lumpur , Malaysia.,c Centre for Translational Research, Institute for Research, Development and Innovation , International Medical University , Kuala Lumpur , Malaysia
| | - Ivan Kok Seng Yap
- d Clinical Research Centre, Sarawak General Hospital , Jalan Hospital , Kuching , Malaysia
| | - Lay Ching Chai
- e Institute of Biological Sciences , University of Malaya , Kuala Lumpur , Malaysia
| | - Stuart C Clarke
- f Faculty of Medicine and Institute for Life Sciences and Global Health Research Institute , University of Southampton , Southampton , UK.,g NIHR Southampton Biomedical Research Centre , Southampton , UK.,h School of Postgraduate Studies , International Medical University , Kuala Lumpur , Malaysia
| | | | - Kartini Abdul Jabar
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Mohd Yasim Md Yusof
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Cindy Shuan Ju Teh
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
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22
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Wang Z, Zolnik CP, Qiu Y, Usyk M, Wang T, Strickler HD, Isasi CR, Kaplan RC, Kurland IJ, Qi Q, Burk RD. Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies. Front Cell Infect Microbiol 2018; 8:301. [PMID: 30234027 PMCID: PMC6127643 DOI: 10.3389/fcimb.2018.00301] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/07/2018] [Indexed: 12/24/2022] Open
Abstract
Background: Integrated microbiome and metabolomics analyses hold the potential to reveal interactions between host and microbiota in relation to disease risks. However, there are few studies evaluating how field methods influence fecal microbiome characterization and metabolomics profiling. Methods: Five fecal collection methods [immediate freezing at -20°C without preservative, OMNIgene GUT, 95% ethanol, RNAlater, and Flinders Technology Associates (FTA) cards] were used to collect 40 fecal samples from eight healthy volunteers. We performed gut microbiota 16S rRNA sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chained fatty acids (SCFAs). Metrics included α-diversity and β-diversity as well as distributions of predominant phyla. To evaluate the concordance with the "gold standard" immediate freezing, the intraclass correlation coefficients (ICCs) for alternate fecal collection systems were calculated. Correlations between SCFAs and gut microbiota were also examined. Results: The FTA cards had the highest ICCs compared to the immediate freezing method for α-diversity indices (ICCs = 0.96, 0.96, 0.76 for Shannon index, Simpson's Index, Chao-1 Index, respectively), followed by OMNIgene GUT, RNAlater, and 95% ethanol. High ICCs (all >0.88) were observed for all methods for the β-diversity metric. For untargeted metabolomics, in comparison to immediate freezing which detected 621 metabolites at ≥75% detectability level, 95% ethanol showed the largest overlapping set of metabolites (n = 430; 69.2%), followed by FTA cards (n = 330; 53.1%) and OMNIgene GUT (n = 213; 34.3%). Both OMNIgene GUT (ICCs = 0.82, 0.93, 0.64) and FTA cards (ICCs = 0.87, 0.85, 0.54) had acceptable ICCs for the top three predominant SCFAs (butyric acid, propionic acid and acetic acid). Nominally significant correlations between bacterial genera and SCFAs (P < 0.05) were observed in fecal samples collected by different methods. Of note, a high correlation between the genus Blautia (known butyrate producer) and butyric acid was observed for both immediate freezing (r = 0.83) and FTA cards (r = 0.74). Conclusions: Four alternative fecal collection methods are generally comparable with immediate freezing, but there are differences in certain measures of the gut microbiome and fecal metabolome across methods. Choice of method depends on the research interests, simplicity of fecal collection procedures and ease of transportation to the lab, especially for large epidemiological studies.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Christine P. Zolnik
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Biology, Long Island University, Brooklyn, NY, United States
| | - Yunping Qiu
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Diabetes Center, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Howard D. Strickler
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Irwin J. Kurland
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Diabetes Center, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, United States
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23
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Hedblom GA, Reiland HA, Sylte MJ, Johnson TJ, Baumler DJ. Segmented Filamentous Bacteria - Metabolism Meets Immunity. Front Microbiol 2018; 9:1991. [PMID: 30197636 PMCID: PMC6117376 DOI: 10.3389/fmicb.2018.01991] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 08/07/2018] [Indexed: 12/28/2022] Open
Abstract
Segmented filamentous bacteria (SFB) are a group of host-adapted, commensal organisms that attach to the ileal epithelium of vertebrate and invertebrate hosts. A genetic relative of the genus Clostridium, these morphologically unique bacteria display a replication and differentiation lifecycle initiated by epithelial tissue binding and filamentation. SFB intimately bind to the surface of absorptive intestinal epithelium without inducing an inflammatory response. Rather, their presence impacts the generation of innate and differentiation of acquired immunity, which impact the clearance of extracellular bacterial or fungal pathogens in the gastrointestinal and respiratory tracts. SFB have recently garnered attention due to their role in promoting adaptive and innate immunity in mice and rats through the differentiation and maturation of Th17 cells in the intestinal tract and production of immunoglobulin A (IgA). SFB are the first commensal bacteria identified that impact the maturation and development of Th17 cells in mice. Recently, microbiome studies have revealed the presence of Candidatus Arthromitus (occasionally designated as Candidatus Savagella), a proposed candidate species of SFB, in higher proportions in higher-performing flocks as compared to matched lower-performing flocks, suggesting that SFB may serve to establish a healthy gut and protect commercial turkeys from pathogens resulting in morbidity and decreased performance. In this review we seek to describe the life cycle, host specificity, and genetic capabilities of SFB, such as bacterial metabolism, and how these factors influence the host immunity and microbiome. Although the role of SFB to induce antigen-specific Th17 cells in poultry is unknown, they may play an important role in modulating the immune response in the intestinal tract to promote resistance against some infectious diseases and promote food-safety. This review demonstrates the importance of studying and further characterizing commensal, host-specific bacteria in food-producing animals and their importance to animal health.
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Affiliation(s)
- Grant A Hedblom
- Department of Food Science and Nutrition, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Holly A Reiland
- Department of Food Science and Nutrition, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Matthew J Sylte
- Food Safety and Enteric Pathogens Research Unit, USDA-ARS National Animal Disease Center, Ames, IA, United States
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota Twin Cities, Saint Paul, MN, United States.,The Microbial and Plant Genomics Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - David J Baumler
- Department of Food Science and Nutrition, University of Minnesota Twin Cities, Saint Paul, MN, United States.,The Microbial and Plant Genomics Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States.,The Biotechnology Institute, University of Minnesota Twin Cities, Saint Paul, MN, United States
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24
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Fecal Microbiota Transplantation in Experimental Ulcerative Colitis Reveals Associated Gut Microbial and Host Metabolic Reprogramming. Appl Environ Microbiol 2018; 84:AEM.00434-18. [PMID: 29728388 DOI: 10.1128/aem.00434-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/20/2018] [Indexed: 12/26/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is gaining attention for the treatment of ulcerative colitis (UC). Data from individual case studies have suggested that FMT may be beneficial for UC, but the detailed microbial and molecular basis remains unknown. Here, we employ 16S rRNA gene sequencing and metabolomics to investigate the influence of FMT on gut microbial community composition and host metabolism in the dextran sulfate sodium-induced UC rat model. The findings from this pilot study suggest that FMT from normal donors to UC recipients could alleviate UC symptoms without close resemblance of donor's gut microbial and metabolic pattern. Meanwhile, FMT from UC donors to normal recipient rats triggered UC symptoms, UC-prone microbial shift, and host metabolic adaption. Gut microbiota under normal conditions could maintain stable species richness and diversity upon FMT intervention, but the disturbed gut microbiota under UC conditions could not maintain such homeostasis. Significant correlations between altered bacterial composition and host metabolism could be assigned to the pathological effects of UC (accounting for 8.0 to 16.2% of total variance) and/or the FMT intervention effects (3.9 to 7.0% of total variance). Overall, our study reveals diverse gut microbial shifts in UC related FMT and their association with host metabolic reprogramming.IMPORTANCE This study combined clinical symptoms measurement, 16S rRNA gene microbial profiling and metabolomics to comprehensively investigate the gut bacterial and host metabolic association and reprogramming in FMT-treated experimental UC. These data can advance our understanding of the effect of FMT on UC and the involvement of gut microbial dysbiosis in the development of UC.
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25
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Serum metabolomics study in a group of Parkinson's disease patients from northern India. Clin Chim Acta 2018; 480:214-219. [DOI: 10.1016/j.cca.2018.02.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 12/14/2022]
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26
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Dou J, Bennett MR. Synthetic Biology and the Gut Microbiome. Biotechnol J 2018; 13:e1700159. [PMID: 28976641 PMCID: PMC5882594 DOI: 10.1002/biot.201700159] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/23/2017] [Indexed: 12/19/2022]
Abstract
The gut microbiome plays a crucial role in maintaining human health. Functions performed by gastrointestinal microbes range from regulating metabolism to modulating immune and nervous system development. Scientists have attempted to exploit this importance through the development of engineered probiotics that are capable of producing and delivering small molecule therapeutics within the gut. However, existing synthetic probiotics are simplistic and fail to replicate the complexity and adaptability of native homeostatic mechanisms. In this review, the ways in which the tools and approaches of synthetic biology have been applied to improve the efficacy of therapeutic probiotics, and the ways in which they might be applied in the future is discussed. Simple devices, such as a bistable switches and integrase memory arrays, have been successfully implemented in the mammalian gut, and models for targeted delivery in this environment have also been developed. In the future, it will be necessary to introduce concepts such as logic-gating and biocontainment mechanisms into synthetic probiotics, as well as to expand the collection of relevant biosensors. Ideally, this will bring us closer to a reality in which engineered therapeutic microbes will be able to accurately diagnose and effectively respond to a variety of disease states.
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Affiliation(s)
- Jennifer Dou
- Department of Biosciences, Rice University, Houston, TX 77005
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, Houston, TX 77005
- Department of Bioengineering, Rice University, Houston, TX 77005
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27
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Yu LM, Zhao KJ, Wang SS, Wang X, Lu B. Gas chromatography/mass spectrometry based metabolomic study in a murine model of irritable bowel syndrome. World J Gastroenterol 2018; 24:894-904. [PMID: 29491683 PMCID: PMC5829153 DOI: 10.3748/wjg.v24.i8.894] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/12/2018] [Accepted: 01/20/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To study the role of microbial metabolites in the modulation of biochemical and physiological processes in irritable bowel syndrome (IBS). METHODS In the current study, using a metabolomic approach, we analyzed the key metabolites differentially excreted in the feces of control mice and mice with IBS, with or without Clostridium butyricum (C. butyricum) treatment. C57BL/6 mice were divided into control, IBS, and IBS + C. butyricum groups. In the IBS and IBS + C. butyricum groups, the mice were subjected to water avoidance stress (WAS) for 1 h/d for ten days. Gas chromatography/mass spectrometry (GC-MS) together with multivariate analysis was employed to compare the fecal samples between groups. RESULTS WAS exposure established an appropriate model of IBS in mice, with symptoms of visceral hyperalgesia and diarrhea. The differences in the metabolite profiles between the control group and IBS group significantly changed with the progression of IBS (days 0, 5, 10, and 17). A total of 14 differentially excreted metabolites were identified between the control and IBS groups, and phenylethylamine was a major metabolite induced by stress. In addition, phenylalanine metabolism was found to be the most relevant metabolic pathway. Between the IBS group and IBS + C. butyricum group, 10 differentially excreted metabolites were identified. Among these, pantothenate and coenzyme A (CoA) biosynthesis metabolites, as well as steroid hormone biosynthesis metabolites were identified as significantly relevant metabolic pathways. CONCLUSION The metabolic profile of IBS mice is significantly altered compared to control mice. Supplementation with C. butyricum to IBS mice may provide a considerable benefit by modulating host metabolism.
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Affiliation(s)
- Lei-Min Yu
- Department of Gastroenterology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, Zhejiang Province, China
- First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China
| | - Ke-Jia Zhao
- Department of Gastroenterology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, Zhejiang Province, China
- First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China
| | - Shuang-Shuang Wang
- Department of Gastroenterology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, Zhejiang Province, China
- First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China
| | - Xi Wang
- Key Laboratory of Digestive Pathophysiology of Zhejiang Province, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China
| | - Bin Lu
- Department of Gastroenterology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, Zhejiang Province, China
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28
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Chong J, Xia J. Computational Approaches for Integrative Analysis of the Metabolome and Microbiome. Metabolites 2017; 7:E62. [PMID: 29156542 PMCID: PMC5746742 DOI: 10.3390/metabo7040062] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics) to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies. In this review, we provide an overview of different computational approaches that have been used in recent years for integrative analysis of metabolome and microbiome data, ranging from statistical correlation analysis to metabolic network-based modeling approaches. Throughout the process, we strive to present a unified conceptual framework for multi-omics integration and interpretation, as well as point out potential future directions.
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Affiliation(s)
- Jasmine Chong
- Institute of Parasitology, McGill University, Montreal, QC H3A 0G4, Canada.
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, QC H3A 0G4, Canada.
- Department of Animal Science, McGill University, Montreal, QC H3A 0G4, Canada.
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Shibata N, Kunisawa J, Kiyono H. Dietary and Microbial Metabolites in the Regulation of Host Immunity. Front Microbiol 2017; 8:2171. [PMID: 29163449 PMCID: PMC5681998 DOI: 10.3389/fmicb.2017.02171] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
Mucosal surfaces in the body, especially the intestine, are constantly exposed to trillions of microbiomes. Accumulating evidence has revealed that changes in the composition of the gut microbiome, especially that of the commensal bacteria population, are frequently associated with immunologic disorders. These changes coincide with changes in the production of certain dietary metabolites. Recent studies have uncovered the molecular and cellular mechanisms underlying the relationships among diet, commensal bacteria, and the host immune system. In this review, we describe how dietary and microbial metabolites modulate host immunity.
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Affiliation(s)
- Naoko Shibata
- Division of Mucosal Immunology, Department of Microbiology and Immunology and International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Mucosal Immunology, School of Medicine, Chiba University, Chiba, Japan.,Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Jun Kunisawa
- Division of Mucosal Immunology, Department of Microbiology and Immunology and International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.,Graduate School of Medicine, Graduate School of Pharmaceutical Sciences, Graduate School of Dentistry, Osaka University, Osaka, Japan.,Department of Microbiology and Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroshi Kiyono
- Division of Mucosal Immunology, Department of Microbiology and Immunology and International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Hirata SI, Kunisawa J. Gut microbiome, metabolome, and allergic diseases. Allergol Int 2017; 66:523-528. [PMID: 28693971 DOI: 10.1016/j.alit.2017.06.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 05/30/2017] [Accepted: 06/02/2017] [Indexed: 02/06/2023] Open
Abstract
The number of patients with allergic and inflammatory disorders has been increasing during the past several decades. Accumulating evidence has refined our understanding of the relationship between allergic diseases and the gut microbiome. In addition, the gut microbiome is now known to produce both useful and harmful metabolites from dietary materials. These metabolites and bacterial components help to regulate host immune responses and potentially affect the development of allergic diseases. Here, we describe recent findings regarding the immunologic crosstalk between commensal bacteria and dietary components in the regulation of host immunity and the influence of this relationship on the development of allergic diseases.
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Martin FPJ, Montoliu I, Kussmann M. Metabonomics of ageing – Towards understanding metabolism of a long and healthy life. Mech Ageing Dev 2017; 165:171-179. [DOI: 10.1016/j.mad.2016.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/21/2016] [Indexed: 12/18/2022]
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Chatterji T, Singh S, Sen M, Singh AK, Agarwal GR, Singh DK, Srivastava JK, Singh A, Srivastava RN, Roy R. Proton NMR metabolic profiling of CSF reveals distinct differentiation of meningitis from negative controls. Clin Chim Acta 2017; 469:42-52. [PMID: 28315295 DOI: 10.1016/j.cca.2017.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND Cerebrospinal fluid (CSF) is an essential bio-fluid of the central nervous system (CNS), playing a vital role in the protection of CNS and performing neuronal function regulation. The chemical composition of CSF varies during onset of meningitis, neurodegenerative disorders (positive controls) and in traumatic cases (negative controls). METHODS The study design was broadly categorized into meningitis cases, negative controls and positive controls. Further differentiation among the three groups was carried out using Principal Component Analysis (PCA) followed by supervised Partial Least Square Discriminant Analysis (PLS-DA). RESULTS The statistical analysis of meningitis vs. negative controls using PLS-DA model resulted in R2 of 0.97 and Q2 of 0.85. There was elevation in the levels of ketone bodies, total free amino acids, glutamine, creatine, citrate and choline containing compounds (choline and GPC) in meningitis cases. Similarly, meningitis vs. positive controls resulted in R2 of 0.80 and Q2 of 0.60 and showed elevation in the levels of total free amino acids, glutamine, creatine/creatinine and citrate in the meningitis group. Four cases of HIV were identified by PLS-DA model as well as by clinical investigations. CONCLUSION On the basis of metabolic profile it was found that negative control CSF samples are more appropriate for differentiation of meningitis than positive control CSF samples.
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Affiliation(s)
- Tanushri Chatterji
- Department of Microbiology, Dr. Ram Manohar Lohia Institute of Medical Sciences (RMLIMS), Vibhuti Khand, Gomti Nagar, Lucknow 226010, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Malhaur. Lucknow 226028, India
| | - Suruchi Singh
- Centre of Biomedical Research, formerly Centre of Biomedical Magnetic Resonance (CBMR), Sanjay Gandhi Postgraduate Institute of Medical Sciences Campus, Rae Bareli Road, Lucknow 226014, India
| | - Manodeep Sen
- Department of Microbiology, Dr. Ram Manohar Lohia Institute of Medical Sciences (RMLIMS), Vibhuti Khand, Gomti Nagar, Lucknow 226010, India.
| | - Ajai Kumar Singh
- Department of Neurology, Dr. Ram Manohar Lohia Institute of Medical Sciences (RMLIMS), Vibhuti Khand, Gomti Nagar, Lucknow 226010, India
| | - Gaurav Raj Agarwal
- Department of Radiodiagnosis, Dr. Ram Manohar Lohia Institute of Medical Sciences (RMLIMS), Vibhuti Khand, Gomti Nagar, Lucknow 226010, India
| | - Deepak Kumar Singh
- Department of Neurosurgery, Dr. Ram Manohar Lohia Institute of Medical Sciences (RMLIMS), Vibhuti Khand, Gomti Nagar, Lucknow 226010, India
| | | | - Alka Singh
- Department of Orthopaedics, King George's Medical University, Shahmina Road, Chowk, Lucknow 226003, India
| | - Rajeshwar Nath Srivastava
- Department of Orthopaedics, King George's Medical University, Shahmina Road, Chowk, Lucknow 226003, India
| | - Raja Roy
- Centre of Biomedical Research, formerly Centre of Biomedical Magnetic Resonance (CBMR), Sanjay Gandhi Postgraduate Institute of Medical Sciences Campus, Rae Bareli Road, Lucknow 226014, India.
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Shankar V, Gouda M, Moncivaiz J, Gordon A, Reo NV, Hussein L, Paliy O. Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets. mSystems 2017; 2:e00169-16. [PMID: 28191503 PMCID: PMC5296411 DOI: 10.1128/msystems.00169-16] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/12/2017] [Indexed: 02/08/2023] Open
Abstract
Previous studies indicated that populations consuming a Mediterranean diet rich in fiber, vegetables, and fruits have a significantly lower risk of cardiovascular and metabolic diseases than populations of industrialized societies consuming diets enriched in processed carbohydrates, animal proteins, and fats. To explore the potential contributions of gut microbiota to the observed diet-related metabolic effects, we conducted an integrative analysis of distal gut microbiota composition and functions and intestinal metabolites in Egyptian and U.S. teenagers. All Egyptian gut microbial communities belonged to the Prevotella enterotype, whereas all but one of the U.S. samples were of the Bacteroides enterotype. The intestinal environment of Egyptians was characterized by higher levels of short-chain fatty acids, a higher prevalence of microbial polysaccharide degradation-encoding genes, and a higher proportion of several polysaccharide-degrading genera. Egyptian gut microbiota also appeared to be under heavier bacteriophage pressure. In contrast, the gut environment of U.S. children was rich in amino acids and lipid metabolism-associated compounds; contained more microbial genes encoding protein degradation, vitamin biosynthesis, and iron acquisition pathways; and was enriched in several protein- and starch-degrading genera. Levels of 1-methylhistamine, a biomarker of allergic response, were elevated in U.S. guts, as were the abundances of members of Faecalibacterium and Akkermansia, two genera with recognized anti-inflammatory effects. The revealed corroborating differences in fecal microbiota structure and functions and metabolite profiles between Egyptian and U.S. teenagers are consistent with the nutrient variation between Mediterranean and Western diets. IMPORTANCE The human gastrointestinal microbiota functions as an important mediator of diet for host metabolism. To evaluate how consumed diets influence the gut environment, we carried out simultaneous interrogations of distal gut microbiota and metabolites in samples from healthy children in Egypt and the United States. While Egyptian children consumed a Mediterranean diet rich in plant foods, U.S. children consumed a Western diet high in animal protein, fats, and highly processed carbohydrates. Consistent with the consumed diets, Egyptian gut samples were enriched in polysaccharide-degrading microbes and end products of polysaccharide fermentation and U.S. gut samples were enriched in proteolytic microbes and end products of protein and fat metabolism. Thus, the intestinal microbiota might be selected on the basis of the diets that we consume, which can open opportunities to affect gut health through modulation of gut microbiota with dietary supplementations.
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Affiliation(s)
- V. Shankar
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - M. Gouda
- Department of Human Nutrition, National Research Centre, Giza, Egypt
| | - J. Moncivaiz
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - A. Gordon
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - N. V. Reo
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - L. Hussein
- Department of Human Nutrition, National Research Centre, Giza, Egypt
| | - O. Paliy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
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Integrated Role of Bifidobacterium animalis subsp. lactis Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus Monkeys. mSystems 2016; 1:mSystems00128-16. [PMID: 27921083 PMCID: PMC5128019 DOI: 10.1128/msystems.00128-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/01/2016] [Indexed: 02/03/2023] Open
Abstract
To investigate the impact of probiotic supplementation of infant formula on immune parameters, intestinal microbiota, and metabolism, five individually housed infant rhesus monkeys exclusively fed standard infant formula supplemented with probiotics (Bifidobacterium animalis subsp. lactis HN019) from birth until 3 months of age were compared with five standard formula-fed and five breast-fed monkeys. Anthropometric measurements, serum insulin, immune parameters, fecal microbiota, and metabolic profiles of serum, urine, and feces were evaluated. Consumption of B. lactis-supplemented formula reduced microbial diversity, restructured the fecal microbial community, and altered the fecal metabolome at the last two time points, in addition to increasing short-chain fatty acids in serum and urine. Circulating CCL22 was lower and threonine, branched-chain amino acids, urea, and allantoin, as well as dimethylglycine in serum and urine, were increased in the group supplemented with B. lactis compared with the standard formula-fed group. These results support a role of probiotics as effectors of gut microbial activity regulating amino acid utilization and nitrogen cycling. Future risk-benefit analyses are still needed to consolidate the existing knowledge on the long-term consequences of probiotic administration during infancy. IMPORTANCE Probiotics are becoming increasingly popular due to their perceived effects on health, despite a lack of mechanistic information on how they impart these benefits. Infant formula and complementary foods are common targets for supplementation with probiotics. However, different probiotic strains have different properties, and there is a lack of data on long-term health effects on the consumer. Given the increasing interest in supplementation with probiotics and the fact that the gastrointestinal tracts of infants are still immature, we sought to determine whether consumption of infant formula containing the probiotic Bifidobacterium animalis subsp. lactis HN019 for 3 months starting at birth would impact gut microbial colonization, as well as infant immunity and metabolism, when compared with consumption of formula alone.
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Le Roy CI, Mappley LJ, La Ragione RM, Woodward MJ, Claus SP. NMR-based metabolic characterization of chicken tissues and biofluids: a model for avian research. Metabolomics 2016; 12:157. [PMID: 27729831 PMCID: PMC5025519 DOI: 10.1007/s11306-016-1105-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/17/2016] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Poultry is one of the most consumed meat in the world and its related industry is always looking for ways to improve animal welfare and productivity. It is therefore essential to understand the metabolic response of the chicken to new feed formulas, various supplements, infections and treatments. OBJECTIVES As a basis for future research investigating the impact of diet and infections on chicken's metabolism, we established a high-resolution proton nuclear magnetic resonance (NMR)-based metabolic atlas of the healthy chicken (Gallus gallus). METHODS Metabolic extractions were performed prior to 1H-NMR and 2D NMR spectra acquisition on twelve biological matrices: liver, kidney, spleen, plasma, egg yolk and white, colon, caecum, faecal water, ileum, pectoral muscle and brain of 6 chickens. Metabolic profiles were then exhaustively characterized. RESULTS Nearly 80 metabolites were identified. A cross-comparison of these matrices was performed to determine metabolic variations between and within each section and highlighted that only eight core metabolites were systematically found in every matrice. CONCLUSION This work constitutes a database for future NMR-based metabolomic investigations in relation to avian production and health.
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Affiliation(s)
- Caroline Ivanne Le Roy
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, Reading, RG6 6AP UK
| | - Luke John Mappley
- Department of cancer research, University College London, London, UK
| | - Roberto Marcello La Ragione
- Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guilford, Surrey, GU2 7AL UK
| | - Martin John Woodward
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, Reading, RG6 6AP UK
| | - Sandrine Paule Claus
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, Reading, RG6 6AP UK
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Montoliu I, Cominetti O, Boulangé CL, Berger B, Siddharth J, Nicholson J, Martin FPJ. Modeling Longitudinal Metabonomics and Microbiota Interactions in C57BL/6 Mice Fed a High Fat Diet. Anal Chem 2016; 88:7617-26. [PMID: 27396289 DOI: 10.1021/acs.analchem.6b01343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Longitudinal studies aim typically at following populations of subjects over time and are important to understand the global evolution of biological processes. When it comes to longitudinal omics data, it will often depend on the overall objective of the study, and constraints imposed by the data, to define the appropriate modeling tools. Here, we report the use of multilevel simultaneous component analysis (MSCA), orthogonal projection on latent structures (OPLS), and regularized canonical correlation analysis (rCCA) to study associations between specific longitudinal urine metabonomics data and microbiome data in a diet-induced obesity model using C57BL/6 mice. (1)H NMR urine metabolic profiling was performed on samples collected weekly over a period of 13 weeks, and stool microbial composition was assessed using 16S rRNA gene sequencing at three specific time periods (baseline, first week response, end of study). MSCA and OPLS allowed us to explore longitudinal urine metabonomics data in relation to the dietary groups, as well as dietary effects on body weight. In addition, we report a data integration strategy based on regularized CCA and correlation analyses of urine metabonomics data and 16S rRNA gene sequencing data to investigate the functional relationships between metabolites and gut microbial composition. Thanks to this workflow enabling the breakdown of this data set complexity, the most relevant patterns could be extracted to further explore physiological processes at an anthropometric, cellular, and molecular level.
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Affiliation(s)
- Ivan Montoliu
- Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Building H, 1015 Lausanne, Switzerland.,Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Ornella Cominetti
- Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Building H, 1015 Lausanne, Switzerland
| | - Claire L Boulangé
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Bernard Berger
- Nestlé Research Center , Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland
| | - Jay Siddharth
- Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Building H, 1015 Lausanne, Switzerland
| | - Jeremy Nicholson
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London , Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - François-Pierre J Martin
- Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Building H, 1015 Lausanne, Switzerland
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Lin Y, Ma C, Liu C, Wang Z, Yang J, Liu X, Shen Z, Wu R. NMR-based fecal metabolomics fingerprinting as predictors of earlier diagnosis in patients with colorectal cancer. Oncotarget 2016; 7:29454-64. [PMID: 27107423 PMCID: PMC5045409 DOI: 10.18632/oncotarget.8762] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/14/2016] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its earlier detection for optimal disease management. A metabolomics based approach provides potential for noninvasive identification of biomarkers of colorectal carcinogenesis, as well as dissection of molecular pathways of pathophysiological conditions. Here, proton nuclear magnetic resonance spectroscopy (1HNMR) -based metabolomic approach was used to profile fecal metabolites of 68 CRC patients (stage I/II=20; stage III=25 and stage IV=23) and 32 healthy controls (HC). Pattern recognition through principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) was applied on 1H-NMR processed data for dimension reduction. OPLS-DA revealed that each stage of CRC could be clearly distinguished from HC based on their metabolomic profiles. Successive analyses identified distinct disturbances to fecal metabolites of CRC patients at various stages, compared with those in cancer free controls, including reduced levels of acetate, butyrate, propionate, glucose, glutamine, and elevated quantities of succinate, proline, alanine, dimethylglycine, valine, glutamate, leucine, isoleucine and lactate. These altered fecal metabolites potentially involved in the disruption of normal bacterial ecology, malabsorption of nutrients, increased glycolysis and glutaminolysis. Our findings revealed that the fecal metabolic profiles of healthy controls can be distinguished from CRC patients, even in the early stage (stage I/II), highlighting the potential utility of NMR-based fecal metabolomics fingerprinting as predictors of earlier diagnosis in CRC patients.
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Affiliation(s)
- Yan Lin
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Changchun Ma
- Radiation Oncology, Affiliated Tumor Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Chengkang Liu
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Zhening Wang
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Jurong Yang
- Shantou University, Central Laboratory and NMR Unit, Shantou 515041, Guangdong, China
| | - Xinmu Liu
- Surgery Deparment, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Zhiwei Shen
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Renhua Wu
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou 515041, Guangdong, China
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Stefanis C, Mantzourani I, Plessas S, Alexopoulos A, Galanis A, Bezirtzoglou E, Kandylis P, Varzakas T. Reviewing Classical and Molecular Techniques Regarding Profiling of Probiotic Character of Microorganisms. CURRENT RESEARCH IN NUTRITION AND FOOD SCIENCE 2016. [DOI: 10.12944/crnfsj.4.1.05] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In recent years the roles of probiotics as functional ingredients in food has been highly adopted by the consumers and are under constant investigation by the scientific community. As a result, several probiotic-containing foods have been introduced in the market with an annual share of several billion dollars. Of particular interest in the probiotics research is the profiling of probiotic character of the microbes involving both in vitro and in vivo approaches. Initially traditional microbiological techniques were used; however they suffer by many limitations and therefore the development of new techniques, which are primarily based on the analysis of nucleic acids have been introduced. The scope of this review is to present current knowledge about the methodological approaches that are used to quantify and characterize the potential probiotic character of microorganisms. Moreover, it will focus on molecular and non-molecular tools and finally will report some new perspectives in the study of probiotics using omics techniques.
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Affiliation(s)
- Christos Stefanis
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Ioanna Mantzourani
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Stavros Plessas
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Athanasios Alexopoulos
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Alexis Galanis
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Dragana University Campus, GR68100, Alexandroupolis, Greece
| | - Eugenia Bezirtzoglou
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Panagiotis Kandylis
- Department of Food Technology, Technological and Educational Institution of Peloponnese, Antikalamos, Kalamata, Greece
| | - Theodoros Varzakas
- Department of Food Technology, Technological and Educational Institution of Peloponnese, Antikalamos, Kalamata, Greece
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Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis. Sci Rep 2016; 6:23214. [PMID: 26983596 PMCID: PMC4794715 DOI: 10.1038/srep23214] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/29/2016] [Indexed: 01/14/2023] Open
Abstract
In this study, we investigated the risk associated with suspension of probiotics administration in tilapia, an animal model that may mimic immune-compromised conditions in humans. Tilapias were fed for 14 days using a probiotics-supplemented diet, followed by a three-day suspension of probiotics treatment and a subsequent challenge by Aeromonas hydrophila. Unexpectedly, the suspension of a probiotic strain Lactobacillus plantarum JCM1149 significantly triggered susceptibility of the host to A. hydrophila. We further observed that suspension of JCM1149 resulted in host gut microbiota dysbiosis and the subsequent disorder in the intestinal metabolites (bile acids, amino acids, and glucose) and damage in the intestinal epithelium, giving rise to a condition similar to antibiotics-induced gut dysbiosis, which collectively impaired tilapia’s gut health and resistance to pathogenic challenges. Additionally, we determined that JCM1149 adhered relatively poorly to tilapia intestinal mucosa and was rapidly released from the gastrointestinal tract (GIT) after suspension, with the rapid loss of probiotic strain probably being the direct cause of gut dysbiosis. Finally, three other probiotic Lactobacillus strains with low intestinal mucosa binding activity showed similar rapid loss phenotype following administration suspension, and induced higher host susceptibility to infection, indicating that the risk is a generic phenomenon in Lactobacillus.
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Vasylyeva TL, Singh R. Gut Microbiome and Kidney Disease in Pediatrics: Does Connection Exist? Front Microbiol 2016; 7:235. [PMID: 26973613 PMCID: PMC4776082 DOI: 10.3389/fmicb.2016.00235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/15/2016] [Indexed: 01/01/2023] Open
Abstract
Child development is a unique and continuous process that is impacted by genetics and environmental factors. Gut microbiome changes with development and depends on the stage of gut maturation, nutrition, and overall health. In spite of emerging data and active study in adults, the gut-renal axis in pediatrics has not been well considered and investigated. This review will focus on the current knowledge of gut microbiota impacts on kidney disease with extrapolation to the pediatric population.
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Affiliation(s)
- Tetyana L. Vasylyeva
- Department of Pediatrics, Texas Tech University Health Sciences Center, AmarilloTX, USA
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Serum procalcitonin levels in combination with (1)H NMR spectroscopy: A rapid indicator for differentiation of urosepsis. Clin Chim Acta 2015; 453:205-14. [PMID: 26719034 DOI: 10.1016/j.cca.2015.12.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 12/01/2015] [Accepted: 12/17/2015] [Indexed: 11/20/2022]
Abstract
BACKGROUND Urosepsis, a severe form of sepsis requires immediate medical attention for prognosis. It is clinically diagnosed by estimating serum procalcitonin (PCT) levels along with time taking urine and blood cultures. We explored NMR based profiling, deriving metabolites that could potentially aid diagnosis. METHODS The proton NMR of serum and urine samples of healthy control subjects (n=32) and urosepsis cases (n=35) based on PCT levels, were analyzed. Four clinically identified non-urosepsis cases with high PCT levels were also differentiated through principal component analysis (PCA) of the serum samples. RESULTS Quantification of serum and urine through Discriminant Function Analysis (DFA) afforded 93.7% and 91.7% correct classification respectively, along with identification of malonate and urea as potential biomarkers for the disease in both urine and serum samples. The partial least square discriminant analysis (PLS-DA) showed an R(2) value of 0.97 in both biofluids with Q(2)=0.87 and 0.85 for serum and urine respectively. The training set of serum samples provided precise prediction of the test set in a small cohort through random re-sampling method, while in urine samples, the predictions were inconclusive. CONCLUSIONS Our pilot study reveals that (1)H NMR of serum metabolic profiling in combination with PCT levels may provide a rapid method for differentiation of urosepsis.
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Ahmad MS, Ashrafian H, Alsaleh M, Holmes E. Role of metabolic phenotyping in understanding obesity and related conditions in Gulf Co-operation Council countries. Clin Obes 2015; 5:302-11. [PMID: 26567983 DOI: 10.1111/cob.12121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/21/2015] [Accepted: 10/01/2015] [Indexed: 01/11/2023]
Abstract
Obesity is a major health concern in the Middle East and the incidence is rising in all sections of the population. Efforts to control obesity through diet and lifestyle interventions, and by surgical means, have had limited effect, and the gene-environment interactions underpinning the development of obesity and related pathologies such as metabolic syndrome, cardiovascular disease and certain cancers are poorly defined. Lifestyle, genetics, inflammation and the interaction between the intestinal bacteria and host metabolism have all been implicated in creating an obesogenic environment. We summarize the role of metabolic and microbial phenotyping in understanding the aetiopathogenesis of obesity and in characterizing the metabolic responses to surgical and non-surgical interventions, and explore the potential for clinical translation of this approach.
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Affiliation(s)
- M S Ahmad
- Drug Metabolism Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - H Ashrafian
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - M Alsaleh
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - E Holmes
- Drug Metabolism Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
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Montalban-Arques A, De Schryver P, Bossier P, Gorkiewicz G, Mulero V, Gatlin DM, Galindo-Villegas J. Selective Manipulation of the Gut Microbiota Improves Immune Status in Vertebrates. Front Immunol 2015; 6:512. [PMID: 26500650 PMCID: PMC4598590 DOI: 10.3389/fimmu.2015.00512] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/20/2015] [Indexed: 12/12/2022] Open
Abstract
All animals develop in association with complex microbial communities. It is now well established that commensal microbiota is essential for the correct functionality of each organ in the host. Particularly, the commensal gastro-intestinal microbiota (CGIM) is a key factor for development, immunity and nutrient conversion, rendering them bio-available for various uses. Thus, nutritional inputs generate a positive loop in maintaining host health and are essential in shaping the composition of the CGIM communities. Probiotics, which are live exogenous microorganisms, selectively provided to the host, are a promising concept for manipulating the microbiota and thus for increasing the host health status. Nevertheless, most mechanisms induced by probiotics to fortify the immune system are still a matter of debate. Alternatively, prebiotics, which are non-digestible food ingredients, can favor the growth of specific target groups of CGIM. Several metabolites are produced by the CGIM, one of the most important are the short-chain fatty acids (SCFAs), which emerge from the fermentation of complex carbohydrates. SCFAs have been recognized as key players in triggering beneficial effects elicited by simple diffusion and by specific receptors present, thus, far only in epithelial cells of higher vertebrates at different gastro-intestinal locations. However, both strategies have shown to provide resistance against pathogens during periods of high stress. In fish, knowledge about the action of pro- and prebiotics and SCFAs is still limited. Thus, in this review, we briefly summarize the mechanisms described on this topic for higher vertebrates and discuss why many of them may operate in the fish gut representing a model for different mucosal tissues
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Affiliation(s)
| | - Peter De Schryver
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University , Ghent , Belgium
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Ghent University , Ghent , Belgium
| | | | - Victoriano Mulero
- Department of Cell Biology and Histology, Faculty of Biology, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca, University of Murcia , Murcia , Spain
| | - Delbert Monroe Gatlin
- Department of Wildlife and Fisheries Sciences, College of Agriculture and Life Sciences, Texas A&M University , College Station, TX , USA
| | - Jorge Galindo-Villegas
- Department of Cell Biology and Histology, Faculty of Biology, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca, University of Murcia , Murcia , Spain
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Serrano JCE, Jove M, Gonzalo H, Pamplona R, Portero-Otin M. Nutridynamics: mechanism(s) of action of bioactive compounds and their effects. Int J Food Sci Nutr 2015; 66 Suppl 1:S22-30. [DOI: 10.3109/09637486.2015.1035231] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Pruszynska-Oszmalek E, Kolodziejski PA, Stadnicka K, Sassek M, Chalupka D, Kuston B, Nogowski L, Mackowiak P, Maiorano G, Jankowski J, Bednarczyk M. In ovo injection of prebiotics and synbiotics affects the digestive potency of the pancreas in growing chickens. Poult Sci 2015; 94:1909-16. [PMID: 26112038 DOI: 10.3382/ps/pev162] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2015] [Indexed: 12/13/2022] Open
Abstract
The purpose of the study was to examine the effect of 2 prebiotics and 2 synbiotics on the digestive potency of pancreas in 1-, 3-, 7-, 14-, 21-, and 34-day-old cockerels. Prebiotics (inulin and Bi²tos) and synbiotics (inulin + Lactococcus lactis subsp. lactis and Bi²tos + Lactococcus lactis subsp. cremoris) were injected in ovo into the air cell on the 12th d embryonic development. Their application increased the activity of amylase, lipase, and trypsin in the pancreas. The most pronounced changes were observed at the end of the investigated rearing period (d 34). The strongest stimulative effects on amylase were shown by both synbiotics, on lipase synbiotic Bi²tos + Lactococcus lactis subsp. cremoris, and on trypsin all the used prebiotics and synbiotics. Simultaneously, neither the absolute nor the relative mass of the pancreas in comparison to control group were changed. Also, the injected in ovo compounds did not cause a deterioration in the posthatching condition of the chicken liver, as determined by measurement of the activity of marker enzymes in the blood (alanine aminotransferase and aspartate aminotransferase). Treatment with the prebiotics and synbiotics did not change the feed conversion ratio but Bi²tos (galacto-oligosaccharide) and inulin (fructan) + Lactococcus lactis subsp. lactis significantly increased final BW.
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Affiliation(s)
- E Pruszynska-Oszmalek
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - P A Kolodziejski
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - K Stadnicka
- Department of Animal Biochemistry and Biotechnology, UTP University of Science and Technology, 85-084 Bydgoszcz, Poland
| | - M Sassek
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - D Chalupka
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - B Kuston
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - L Nogowski
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - P Mackowiak
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - G Maiorano
- Department of Agricultural, Environmental, and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - J Jankowski
- Department of Poultry Science, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
| | - M Bednarczyk
- Department of Animal Biochemistry and Biotechnology, UTP University of Science and Technology, 85-084 Bydgoszcz, Poland
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Biggs MB, Medlock GL, Kolling GL, Papin JA. Metabolic network modeling of microbial communities. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:317-34. [PMID: 26109480 DOI: 10.1002/wsbm.1308] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 12/15/2022]
Abstract
Genome-scale metabolic network reconstructions and constraint-based analyses are powerful methods that have the potential to make functional predictions about microbial communities. Genome-scale metabolic networks are used to characterize the metabolic functions of microbial communities via several techniques including species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the 'enzyme-soup' approach, multiscale modeling, and others. There are many challenges in the field, including a need for tools that accurately assign high-level omics signals to individual community members, the need for improved automated network reconstruction methods, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be corresponding advances in the fields of ecology, health science, and microbial community engineering.
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Affiliation(s)
- Matthew B Biggs
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Gregory L Medlock
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Glynis L Kolling
- Department of Medicine, Infectious Diseases, University of Virginia, Charlottesville, VA, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
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Verbeke KA, Boobis AR, Chiodini A, Edwards CA, Franck A, Kleerebezem M, Nauta A, Raes J, van Tol EAF, Tuohy KM. Towards microbial fermentation metabolites as markers for health benefits of prebiotics. Nutr Res Rev 2015; 28:42-66. [PMID: 26156216 PMCID: PMC4501371 DOI: 10.1017/s0954422415000037] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Available evidence on the bioactive, nutritional and putative detrimental properties of gut microbial metabolites has been evaluated to support a more integrated view of how prebiotics might affect host health throughout life. The present literature inventory targeted evidence for the physiological and nutritional effects of metabolites, for example, SCFA, the potential toxicity of other metabolites and attempted to determine normal concentration ranges. Furthermore, the biological relevance of more holistic approaches like faecal water toxicity assays and metabolomics and the limitations of faecal measurements were addressed. Existing literature indicates that protein fermentation metabolites (phenol, p-cresol, indole, ammonia), typically considered as potentially harmful, occur at concentration ranges in the colon such that no toxic effects are expected either locally or following systemic absorption. The endproducts of saccharolytic fermentation, SCFA, may have effects on colonic health, host physiology, immunity, lipid and protein metabolism and appetite control. However, measuring SCFA concentrations in faeces is insufficient to assess the dynamic processes of their nutrikinetics. Existing literature on the usefulness of faecal water toxicity measures as indicators of cancer risk seems limited. In conclusion, at present there is insufficient evidence to use changes in faecal bacterial metabolite concentrations as markers of prebiotic effectiveness. Integration of results from metabolomics and metagenomics holds promise for understanding the health implications of prebiotic microbiome modulation but adequate tools for data integration and interpretation are currently lacking. Similarly, studies measuring metabolite fluxes in different body compartments to provide a more accurate picture of their nutrikinetics are needed.
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Affiliation(s)
- Kristin A. Verbeke
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven and Leuven Food Science and Nutrition Research Center (LFoRCe), Leuven, Belgium
| | - Alan R. Boobis
- Department of Medicine, Imperial College London, London, UK
| | - Alessandro Chiodini
- Formerly ILSI Europe, Box 6, Avenue Emmanuel Mounier 83, BE-1200, Brussels, Belgium; now European Commission, Research Executive Agency (REA) Unit B2, Brussels, Belgium
| | - Christine A. Edwards
- Human Nutrition School of Medicine, College of MVLS, University of Glasgow, Glasgow, Scotland
| | | | - Michiel Kleerebezem
- Host Microbe Interactomics, Wageningen University, Wageningen, The Netherlands
| | - Arjen Nauta
- FrieslandCampina, Amersfoort, The Netherlands
| | - Jeroen Raes
- Microbiology and Immunology, Rega Institute, KU Leuven, Leuven; VIB, Leuven; DBIT, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Kieran M. Tuohy
- Nutrition and Nutrigenomics, Research and Innovation Centre-Fondazione Edmund Mach, Trento, Italy
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Yip LY, Chan ECY. Investigation of Host-Gut Microbiota Modulation of Therapeutic Outcome. Drug Metab Dispos 2015; 43:1619-31. [PMID: 25979259 DOI: 10.1124/dmd.115.063750] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/15/2015] [Indexed: 02/06/2023] Open
Abstract
A broader understanding of factors underlying interindividual variation in pharmacotherapy is important for our pursuit of "personalized medicine." Based on knowledge gleaned from the investigation of human genetics, drug-metabolizing enzymes, and transporters, clinicians and pharmacists are able to tailor pharmacotherapies according to the genotype of patients. However, human host factors only form part of the equation that accounts for heterogeneity in therapeutic outcome. Notably, the gut microbiota possesses wide-ranging metabolic activities that expand the metabolic functions of the human host beyond that encoded by the human genome. In this review, we first illustrate the mechanisms in which gut microbes modulate pharmacokinetics and therapeutic outcome. Second, we discuss the application of metabonomics in deciphering the complex host-gut microbiota interaction in pharmacotherapy. Third, we highlight an integrative approach with particular mention of the investigation of gut microbiota using culture-based and culture-independent techniques to complement the investigation of the host-gut microbiota axes in pharmaceutical research.
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Affiliation(s)
- Lian Yee Yip
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore (L.Y.Y., E.C.Y.C.); and Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore (L.Y.Y.)
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore (L.Y.Y., E.C.Y.C.); and Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), Singapore (L.Y.Y.)
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Heinken A, Thiele I. Systems biology of host-microbe metabolomics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:195-219. [PMID: 25929487 PMCID: PMC5029777 DOI: 10.1002/wsbm.1301] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/25/2015] [Accepted: 04/01/2015] [Indexed: 12/15/2022]
Abstract
The human gut microbiota performs essential functions for host and well‐being, but has also been linked to a variety of disease states, e.g., obesity and type 2 diabetes. The mammalian body fluid and tissue metabolomes are greatly influenced by the microbiota, with many health‐relevant metabolites being considered ‘mammalian–microbial co‐metabolites’. To systematically investigate this complex host–microbial co‐metabolism, a systems biology approach integrating high‐throughput data and computational network models is required. Here, we review established top‐down and bottom‐up systems biology approaches that have successfully elucidated relationships between gut microbiota‐derived metabolites and host health and disease. We focus particularly on the constraint‐based modeling and analysis approach, which enables the prediction of mechanisms behind metabolic host–microbe interactions on the molecular level. We illustrate that constraint‐based models are a useful tool for the contextualization of metabolomic measurements and can further our insight into host–microbe interactions, yielding, e.g., in potential novel drugs and biomarkers. WIREs Syst Biol Med 2015, 7:195–219. doi: 10.1002/wsbm.1301 For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article.
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Affiliation(s)
- Almut Heinken
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
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Urinary (1)H-NMR-based metabolic profiling of children with NAFLD undergoing VSL#3 treatment. Int J Obes (Lond) 2015; 39:1118-25. [PMID: 25809828 DOI: 10.1038/ijo.2015.40] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/15/2014] [Accepted: 02/08/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Nowadays, non-alcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases in children. Our recent clinical trial demonstrated that dietary and VSL#3-based interventions may improve fatty liver by ultrasound and body mass index (BMI) after 4 months. OBJECTIVES As in this short-term trial, as in others, it is impracticable to monitor response to therapy or treatment by liver biopsy, we aimed to identify a panel of potential non-invasive metabolic biomarkers by a urinary metabolic profiling. METHODS Urine samples from a group of 31 pediatric NAFLD patients, enrolled in a VSL#3 clinical trial, were analyzed by high-resolution proton nuclear magnetic resonance spectroscopy in combination with analysis of variance-Simultaneous Component Analysis model and multivariate data analyses. Urinary metabolic profiles were interpreted in terms of clinical patient feature, treatment and chronology pattern correlations. RESULTS VSL#3 treatment induced changes in NAFLD urinary metabolic phenotype mainly at level of host amino-acid metabolism (that is, valine, tyrosine, 3-amino-isobutyrate or β-aminoisobutyric acid (BAIBA)), nucleic acid degradation (pseudouridine), creatinine metabolism (methylguanidine) and secondarily at the level of gut microbial amino-acid metabolism (that is, 2-hydroxyisobutyrate from valine degradation). Furthermore, some of these metabolites correlated with clinical primary and secondary trial end points after VSL#3 treatment: tyrosine and the organic acid U4 positively with alanine aminotransferase (R=0.399, P=0.026) and BMI (R=0.36, P=0.045); BAIBA and tyrosine negatively with active glucagon-like-peptide 1 (R=-0.51, P=0.003; R=-0.41, P=0.021, respectively). CONCLUSIONS VSL#3 treatment-dependent urinary metabotypes of NAFLD children may be considered as non-invasive effective biomarkers to evaluate the response to treatment.
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