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Shtossel O, Koren O, Shai I, Rinott E, Louzoun Y. Gut microbiome-metabolome interactions predict host condition. MICROBIOME 2024; 12:24. [PMID: 38336867 PMCID: PMC10858481 DOI: 10.1186/s40168-023-01737-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 12/10/2023] [Indexed: 02/12/2024]
Abstract
BACKGROUND The effect of microbes on their human host is often mediated through changes in metabolite concentrations. As such, multiple tools have been proposed to predict metabolite concentrations from microbial taxa frequencies. Such tools typically fail to capture the dependence of the microbiome-metabolite relation on the environment. RESULTS We propose to treat the microbiome-metabolome relation as the equilibrium of a complex interaction and to relate the host condition to a latent representation of the interaction between the log concentration of the metabolome and the log frequencies of the microbiome. We develop LOCATE (Latent variables Of miCrobiome And meTabolites rElations), a machine learning tool to predict the metabolite concentration from the microbiome composition and produce a latent representation of the interaction. This representation is then used to predict the host condition. LOCATE's accuracy in predicting the metabolome is higher than all current predictors. The metabolite concentration prediction accuracy significantly decreases cross datasets, and cross conditions, especially in 16S data. LOCATE's latent representation predicts the host condition better than either the microbiome or the metabolome. This representation is strongly correlated with host demographics. A significant improvement in accuracy (0.793 vs. 0.724 average accuracy) is obtained even with a small number of metabolite samples ([Formula: see text]). CONCLUSION These results suggest that a latent representation of the microbiome-metabolome interaction leads to a better association with the host condition than any of the two separated or the simple combination of the two. Video Abstract.
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Affiliation(s)
- Oshrit Shtossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ehud Rinott
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel.
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2
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Malwe AS, Sharma VK. Application of artificial intelligence approaches to predict the metabolism of xenobiotic molecules by human gut microbiome. Front Microbiol 2023; 14:1254073. [PMID: 38116528 PMCID: PMC10728657 DOI: 10.3389/fmicb.2023.1254073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 12/21/2023] Open
Abstract
A highly complex, diverse, and dense community of more than 1,000 different gut bacterial species constitutes the human gut microbiome that harbours vast metabolic capabilities encoded by more than 300,000 bacterial enzymes to metabolise complex polysaccharides, orally administered drugs/xenobiotics, nutraceuticals, or prebiotics. One of the implications of gut microbiome mediated biotransformation is the metabolism of xenobiotics such as medicinal drugs, which lead to alteration in their pharmacological properties, loss of drug efficacy, bioavailability, may generate toxic byproducts and sometimes also help in conversion of a prodrug into its active metabolite. Given the diversity of gut microbiome and the complex interplay of the metabolic enzymes and their diverse substrates, the traditional experimental methods have limited ability to identify the gut bacterial species involved in such biotransformation, and to study the bacterial species-metabolite interactions in gut. In this scenario, computational approaches such as machine learning-based tools presents unprecedented opportunities and ability to predict the gut bacteria and enzymes that can potentially metabolise a candidate drug. Here, we have reviewed the need to identify the gut microbiome-based metabolism of xenobiotics and have provided comprehensive information on the available methods, tools, and databases to address it along with their scope and limitations.
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Affiliation(s)
| | - Vineet K. Sharma
- MetaBioSys Lab, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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3
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McCuaig B, Goto Y. Immunostimulating Commensal Bacteria and Their Potential Use as Therapeutics. Int J Mol Sci 2023; 24:15644. [PMID: 37958628 PMCID: PMC10647581 DOI: 10.3390/ijms242115644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The gut microbiome is intimately intertwined with the host immune system, having effects on the systemic immune system. Dysbiosis of the gut microbiome has been linked not only to gastrointestinal disorders but also conditions of the skin, lungs, and brain. Commensal bacteria can affect the immune status of the host through a stimulation of the innate immune system, training of the adaptive immune system, and competitive exclusion of pathogens. Commensal bacteria improve immune response through the production of immunomodulating compounds such as microbe-associated molecular patterns (MAMPs), short-chain fatty acids (SCFAs), and secondary bile acids. The microbiome, especially when in dysbiosis, is plastic and can be manipulated through the introduction of beneficial bacteria or the adjustment of nutrients to stimulate the expansion of beneficial taxa. The complex nature of the gastrointestinal tract (GIT) ecosystem complicates the use of these methods, as similar treatments have various results in individuals with different residential microbiomes and differential health statuses. A more complete understanding of the interaction between commensal species, host genetics, and the host immune system is needed for effective microbiome interventions to be developed and implemented in a clinical setting.
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Affiliation(s)
- Bonita McCuaig
- Project for Host-Microbial Interactions in Symbiosis and Pathogenesis, Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Yoshiyuki Goto
- Project for Host-Microbial Interactions in Symbiosis and Pathogenesis, Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
- Division of Pandemic and Post-Disaster Infectious Diseases, Research Institute of Disaster Medicine, Chiba University, Chiba 260-8673, Japan
- Division of Infectious Disease Vaccine R&D, Research Institute of Disaster Medicine, Chiba University, Chiba 260-8673, Japan
- Chiba University Synergy Institute for Futuristic Mucosal Vaccine Research and Development (cSIMVa), Chiba University, Chiba 260-8673, Japan
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4
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Jariyasopit N, Khoomrung S. Mass spectrometry-based analysis of gut microbial metabolites of aromatic amino acids. Comput Struct Biotechnol J 2023; 21:4777-4789. [PMID: 37841334 PMCID: PMC10570628 DOI: 10.1016/j.csbj.2023.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/24/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023] Open
Abstract
Small molecules derived from gut microbiota have been increasingly investigated to better understand the functional roles of the human gut microbiome. Microbial metabolites of aromatic amino acids (AAA) have been linked to many diseases, such as metabolic disorders, chronic kidney diseases, inflammatory bowel disease, diabetes, and cancer. Important microbial AAA metabolites are often discovered via global metabolite profiling of biological specimens collected from humans or animal models. Subsequent metabolite identity confirmation and absolute quantification using targeted analysis enable comparisons across different studies, which can lead to the establishment of threshold concentrations of potential metabolite biomarkers. Owing to their excellent selectivity and sensitivity, hyphenated mass spectrometry (MS) techniques are often employed to identify and quantify AAA metabolites in various biological matrices. Here, we summarize the developments over the past five years in MS-based methodology for analyzing gut microbiota-derived AAA. Sample preparation, method validation, analytical performance, and statistical methods for correlation analysis are discussed, along with future perspectives.
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Affiliation(s)
- Narumol Jariyasopit
- Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
| | - Sakda Khoomrung
- Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
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5
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Schoch L, Sutelman P, Suades R, Badimon L, Moreno-Indias I, Vilahur G. The gut microbiome dysbiosis is recovered by restoring a normal diet in hypercholesterolemic pigs. Eur J Clin Invest 2023; 53:e13927. [PMID: 36453873 DOI: 10.1111/eci.13927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/08/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND Gut microbiota is thought to modulate cardiovascular risk. However, the effect of cardiovascular primary prevention strategies on gut microbiota remains largely unknown. This study investigates the impact of diet and rosuvastatin interventions on gut microbiota composition in hypercholesterolemic pigs and associated potential changes in host metabolic pathways. METHODS Diet-induced hypercholesterolemic pigs (n = 32) were randomly distributed to receive one of the following 30-day interventions: (I) continued hypercholesterolemic diet (HCD; n = 9), (II) normocholesterolemic diet (NCD; n = 8), (III) continued HCD plus 40 mg rosuvastatin/daily (n = 7), or (IV) NCD plus 40 mg rosuvastatin/daily (n = 8). Faeces were collected at study endpoint for characterisation of the gut microbiome and metabolic profile prediction (PICRUSt2). TMAO levels and biochemical parameters were determined. RESULTS Principal coordinate analyses (beta-diversity) showed clear differences in the microbiota of NCD vs HCD pigs (PERMANOVA, p = .001). NCD-fed animals displayed significantly higher alpha-diversity, which inversely correlated with total cholesterol and LDL-cholesterol levels (p < .0003). NCD and HCD animals differed in the abundance of 12 genera (ANCOM; p = .001 vs HCD), and PICRUSt2 analysis revealed detrimental changes in HCD-related microbiota metabolic capacities. These latter findings were associated with a significant fivefold increase in TMAO levels in HCD-fed pigs (p < .0001 vs NCD). The addition of a 30-day rosuvastatin treatment to either of the diets exerted no effects in microbiota nor lipid profile. CONCLUSION In hypercholesterolemic animals, the ingestion of a low-fat diet for 30 days modifies gut microbiota composition in favour of alpha-diversity and towards a healthy metabolic profile, whereas rosuvastatin treatment for this period exerts no effects.
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Affiliation(s)
- Leonie Schoch
- Cardiovascular Program, Institut de Recerca, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Faculty of Medicine, University of Barcelona (UB), Barcelona, Spain
| | - Pablo Sutelman
- Cardiovascular Program, Institut de Recerca, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Rosa Suades
- Cardiovascular Program, Institut de Recerca, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- CiberCV, Institute of Health Carlos III, Madrid, Spain
| | - Lina Badimon
- Cardiovascular Program, Institut de Recerca, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- CiberCV, Institute of Health Carlos III, Madrid, Spain
- Cardiovascular Research Chair, UAB, Barcelona, Spain
| | - Isabel Moreno-Indias
- Department of Endocrinology and Nutrition, Virgen de la Victoria Hospital (IBIMA), Malaga University, Malaga, Spain
- CiberOBN, Institute of Health Carlos III, Madrid, Spain
| | - Gemma Vilahur
- Cardiovascular Program, Institut de Recerca, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- CiberCV, Institute of Health Carlos III, Madrid, Spain
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6
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Wang T, Wang XW, Lee-Sarwar KA, Litonjua AA, Weiss ST, Sun Y, Maslov S, Liu YY. Predicting metabolomic profiles from microbial composition through neural ordinary differential equations. NAT MACH INTELL 2023; 5:284-293. [PMID: 38223254 PMCID: PMC10786629 DOI: 10.1038/s42256-023-00627-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023]
Abstract
Characterizing the metabolic profile of a microbial community is crucial for understanding its biological function and its impact on the host or environment. Metabolomics experiments directly measuring these profiles are difficult and expensive, while sequencing methods quantifying the species composition of microbial communities are well-developed and relatively cost-effective. Computational methods that are capable of predicting metabolomic profiles from microbial compositions can save considerable efforts needed for metabolomic profiling experimentally. Yet, despite existing efforts, we still lack a computational method with high prediction power, general applicability, and great interpretability. Here we develop a method - mNODE (Metabolomic profile predictor using Neural Ordinary Differential Equations), based on a state-of-the-art family of deep neural network models. We show compelling evidence that mNODE outperforms existing methods in predicting the metabolomic profiles of human microbiomes and several environmental microbiomes. Moreover, in the case of human gut microbiomes, mNODE can naturally incorporate dietary information to further enhance the prediction of metabolomic profiles. Besides, susceptibility analysis of mNODE enables us to reveal microbe-metabolite interactions, which can be validated using both synthetic and real data. The presented results demonstrate that mNODE is a powerful tool to investigate the microbiome-diet-metabolome relationship, facilitating future research on precision nutrition.
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Affiliation(s)
- Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xu-Wen Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kathleen A. Lee-Sarwar
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Allergy and Clinical Immunology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Augusto A. Litonjua
- Pediatric Pulmonology, Golisano Children’s Hospital, University of Rochester, Rochester, NY 14642, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yizhou Sun
- Department of Computer Science, University of California, Los Angeles, USA
| | - Sergei Maslov
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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7
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González F, Carelli A, Komarcheuski A, Uana M, do Prado RM, Rossoni D, Gomes M, Vasconcellos R. Yeast Cell Wall Compounds on The Formation of Fermentation Products and Fecal Microbiota in Cats: An In Vivo and In Vitro Approach. Animals (Basel) 2023; 13:637. [PMID: 36830424 PMCID: PMC9951743 DOI: 10.3390/ani13040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 02/15/2023] Open
Abstract
The effects of yeast cell wall compounds (YCWs) being added to cat food on hindgut fermentation metabolites and fecal microbiota were assessed in in vivo Experiment 1 (Exp. 1) and in vitro Experiments 2 and 3 (Exp. 2 and 3). In Exp. 1, the cats' diets were supplemented with two dietary concentrations (46.2 and 92.4 ppm) of YCWs (YCW-15 and YCW-30, respectively), and a negative control diet with no compound in three groups (six cats per group) was used to assess the fecal score, pH, digestibility, fermentation products, and microbiota. In Exp. 2, feces from the cats that were not supplemented with YCWs (control) were used as an inoculum. A blend of pectin, amino acids, and cellulose was used as a substrate, and the YCW compound was added at two levels (5 and 10 mg). In Exp. 3, feces from cats fed YCWs were used as an inoculum to test three different substrates (pectin, amino acids, and cellulose). In Exp. 2 and 3, the gas production, pH, and fermentation products (ammonia, SCFAs, and BCFAs) were assessed. YCW-30 resulted in a higher digestibility coefficient of the crude protein, organic matter (OM) (p < 0.05), and energy of the diet (p < 0.10). Regarding the fermentation products, YCW-15 showed a trend toward higher concentrations of propionate, acetate, lactate, ammonia, isobutyrate, and valerate, while YCW-30 showed a trend (p < 0.10) toward higher levels of butyrate and pH values. The bacteroidia class and the genus Prevotella were increased by using YCW-30 and the control. At the gender level, decreased (p < 0.01) Megasphaera was observed with YCW inclusion. The microbiota differed (p < 0.01) among the groups in their Shannon indexes. For beta diversity, YCW-30 showed higher indexes (p = 0.008) than the control. The microbiota metabolic profile differed in the pathway CENTFERM-PWY; it was more expressed in YCW-30 compared to the control. In Exp. 2, the YCWs showed a higher ratio (p = 0.006) of the fermentation products in the treatments with additives with a trend towards a high dose of the additive (10 mg). In Exp. 3, the effects of the substrates (p < 0.001), but not of the YCWs, on the fermentation products were observed, perhaps due to the low dietary concentrations we used. However, the marked responses of the fermentation products to the substrates validated the methodology. We could conclude that the YCWs, even at low dietary concentrations, affected fecal SCFA production, reduced the fecal pH, and modulated the fecal microbiota in the cats. These responses were more pronounced under in vitro conditions.
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Affiliation(s)
- Fernando González
- Department of Internal Medicine, College of Veterinary Medicine and Animal Science, University of São Paulo (USP)—São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo 13690-970, Brazil
| | - Amanda Carelli
- Department of Animal Science, State University of Maringá, Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Alina Komarcheuski
- Department of Animal Science, State University of Maringá, Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Mayara Uana
- Department of Animal Science, State University of Maringá, Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Rodolpho Martin do Prado
- Department of Animal Science, State University of Maringá, Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Diogo Rossoni
- Department of Animal Science, State University of Maringá, Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Márcia Gomes
- Department of Internal Medicine, College of Veterinary Medicine and Animal Science, University of São Paulo (USP)—São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo 13690-970, Brazil
| | - Ricardo Vasconcellos
- Department of Animal Science, State University of Maringá, Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
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Fumagalli MR, Saro SM, Tajana M, Zapperi S, La Porta CA. Quantitative analysis of disease-related metabolic dysregulation of human microbiota. iScience 2022; 26:105868. [PMID: 36624837 PMCID: PMC9823209 DOI: 10.1016/j.isci.2022.105868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The metabolic activity of all the micro-organism composing the human microbiome interacts with the host metabolism contributing to human health and disease in a way that is not fully understood. Here, we introduce STELLA, a computational method to derive the spectrum of metabolites associated with the microbiome of an individual. STELLA integrates known information on metabolic pathways associated with each bacterial species and extracts from these the list of metabolic products of each singular reaction by means of automatic text analysis. By comparing the result obtained on a single subject with the metabolic profile data of a control set of healthy subjects, we are able to identify individual metabolic alterations. To illustrate the method, we present applications to autism spectrum disorder and multiple sclerosis.
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Affiliation(s)
- Maria Rita Fumagalli
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133 Milano, Italy
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via De Marini 6, 16149 Genova, Italy
| | - Stella Maria Saro
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
| | - Matteo Tajana
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
| | - Stefano Zapperi
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica della Materia Condensata e di Tecnologie per l’Energia, Via R. Cozzi 53, 20125 Milano, Italy
| | - Caterina A.M. La Porta
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133 Milano, Italy
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via De Marini 6, 16149 Genova, Italy
- Corresponding author
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9
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Loganathan T, Priya Doss C G. The influence of machine learning technologies in gut microbiome research and cancer studies - A review. Life Sci 2022; 311:121118. [DOI: 10.1016/j.lfs.2022.121118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022]
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10
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Bhosle A, Wang Y, Franzosa EA, Huttenhower C. Progress and opportunities in microbial community metabolomics. Curr Opin Microbiol 2022; 70:102195. [PMID: 36063685 DOI: 10.1016/j.mib.2022.102195] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 01/25/2023]
Abstract
The metabolome lies at the interface of host-microbiome crosstalk. Previous work has established links between chemically diverse microbial metabolites and a myriad of host physiological processes and diseases. Coupled with scalable and cost-effective technologies, metabolomics is thus gaining popularity as a tool for characterization of microbial communities, particularly when combined with metagenomics as a window into microbiome function. A systematic interrogation of microbial community metabolomes can uncover key microbial compounds, metabolic capabilities of the microbiome, and also provide critical mechanistic insights into microbiome-linked host phenotypes. In this review, we discuss methods and accompanying resources that have been developed for these purposes. The accomplishments of these methods demonstrate that metabolomes can be used to functionally characterize microbial communities, and that microbial properties can be used to identify and investigate chemical compounds.
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Affiliation(s)
- Amrisha Bhosle
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ya Wang
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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11
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Ravichandar JD, Rutherford E, Chow CET, Han A, Yamamoto ML, Narayan N, Kaplan GG, Beck PL, Claesson MJ, Dabbagh K, Iwai S, DeSantis TZ. Strain level and comprehensive microbiome analysis in inflammatory bowel disease via multi-technology meta-analysis identifies key bacterial influencers of disease. Front Microbiol 2022; 13:961020. [PMID: 36312950 PMCID: PMC9614153 DOI: 10.3389/fmicb.2022.961020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
Objective Inflammatory bowel disease (IBD) is a heterogenous disease in which the microbiome has been shown to play an important role. However, the precise homeostatic or pathological functions played by bacteria remain unclear. Most published studies report taxa-disease associations based on single-technology analysis of a single cohort, potentially biasing results to one clinical protocol, cohort, and molecular analysis technology. To begin to address this key question, precise identification of the bacteria implicated in IBD across cohorts is necessary. Methods We sought to take advantage of the numerous and diverse studies characterizing the microbiome in IBD to develop a multi-technology meta-analysis (MTMA) as a platform for aggregation of independently generated datasets, irrespective of DNA-profiling technique, in order to uncover the consistent microbial modulators of disease. We report the largest strain-level survey of IBD, integrating microbiome profiles from 3,407 samples from 21 datasets spanning 15 cohorts, three of which are presented for the first time in the current study, characterized using three DNA-profiling technologies, mapping all nucleotide data against known, culturable strain reference data. Results We identify several novel IBD associations with culturable strains that have so far remained elusive, including two genome-sequenced but uncharacterized Lachnospiraceae strains consistently decreased in both the gut luminal and mucosal contents of patients with IBD, and demonstrate that these strains are correlated with inflammation-related pathways that are known mechanisms targeted for treatment. Furthermore, comparative MTMA at the species versus strain level reveals that not all significant strain associations resulted in a corresponding species-level significance and conversely significant species associations are not always re-captured at the strain level. Conclusion We propose MTMA for uncovering experimentally testable strain-disease associations that, as demonstrated here, are beneficial in discovering mechanisms underpinning microbiome impact on disease or novel targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - Andrew Han
- Second Genome Inc., Brisbane, CA, United States
| | | | | | - Gilaad G. Kaplan
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Paul L. Beck
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | | | | | - Shoko Iwai
- Second Genome Inc., Brisbane, CA, United States
| | - Todd Z. DeSantis
- Second Genome Inc., Brisbane, CA, United States
- Todd Z. DeSantis,
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12
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Juarez VM, Montalbine AN, Singh A. Microbiome as an immune regulator in health, disease, and therapeutics. Adv Drug Deliv Rev 2022; 188:114400. [PMID: 35718251 PMCID: PMC10751508 DOI: 10.1016/j.addr.2022.114400] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/11/2022] [Accepted: 06/12/2022] [Indexed: 11/27/2022]
Abstract
New discoveries in drugs and drug delivery systems are focused on identifying and delivering a pharmacologically effective agent, potentially targeting a specific molecular component. However, current drug discovery and therapeutic delivery approaches do not necessarily exploit the complex regulatory network of an indispensable microbiota that has been engineered through evolutionary processes in humans or has been altered by environmental exposure or diseases. The human microbiome, in all its complexity, plays an integral role in the maintenance of host functions such as metabolism and immunity. However, dysregulation in this intricate ecosystem has been linked with a variety of diseases, ranging from inflammatory bowel disease to cancer. Therapeutics and bacteria have an undeniable effect on each other and understanding the interplay between microbes and drugs could lead to new therapies, or to changes in how existing drugs are delivered. In addition, targeting the human microbiome using engineered therapeutics has the potential to address global health challenges. Here, we present the challenges and cutting-edge developments in microbiome-immune cell interactions and outline novel targeting strategies to advance drug discovery and therapeutics, which are defining a new era of personalized and precision medicine.
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Affiliation(s)
- Valeria M Juarez
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Alyssa N Montalbine
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States
| | - Ankur Singh
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, United States; Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States.
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13
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Beale DJ, Jones OA, Bose U, Broadbent JA, Walsh TK, van de Kamp J, Bissett A. Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience. Emerg Top Life Sci 2022; 6:185-199. [PMID: 35403668 PMCID: PMC9023019 DOI: 10.1042/etls20210261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022]
Abstract
Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of 'ecosurveillance', especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.
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Affiliation(s)
- David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park QLD 4102, Australia
| | - Oliver A.H. Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, Bundoora West Campus, PO Box 71, Bundoora, VIC 3083, Australia
| | - Utpal Bose
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - James A. Broadbent
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Thomas K. Walsh
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT 2601, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
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Filardo S, Di Pietro M, Sessa R. Towards a Deeper Understanding of Chlamydia trachomatis Pathogenetic Mechanisms: Editorial to the Special Issue " Chlamydia trachomatis Pathogenicity and Disease". Int J Mol Sci 2022; 23:ijms23073943. [PMID: 35409301 PMCID: PMC8999411 DOI: 10.3390/ijms23073943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chlamydia trachomatis, an obligate intracellular Gram-negative bacterium, is characterized by a wide range of different serotypes responsible for several local or systemic human diseases, including genital tract manifestations (D-K), trachoma (A-C), and lymphogranuloma venereum (L1-3) [...].
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15
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Greenbaum J, Lin X, Su KJ, Gong R, Shen H, Shen J, Xiao HM, Deng HW. Integration of the Human Gut Microbiome and Serum Metabolome Reveals Novel Biological Factors Involved in the Regulation of Bone Mineral Density. Front Cell Infect Microbiol 2022; 12:853499. [PMID: 35372129 PMCID: PMC8966780 DOI: 10.3389/fcimb.2022.853499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
While the gut microbiome has been reported to play a role in bone metabolism, the individual species and underlying functional mechanisms have not yet been characterized. We conducted a systematic multi-omics analysis using paired metagenomic and untargeted serum metabolomic profiles from a large sample of 499 peri- and early post-menopausal women to identify the potential crosstalk between these biological factors which may be involved in the regulation of bone mineral density (BMD). Single omics association analyses identified 22 bacteria species and 17 serum metabolites for putative association with BMD. Among the identified bacteria, Bacteroidetes and Fusobacteria were negatively associated, while Firmicutes were positively associated. Several of the identified serum metabolites including 3-phenylpropanoic acid, mainly derived from dietary polyphenols, and glycolithocholic acid, a secondary bile acid, are metabolic byproducts of the microbiota. We further conducted a supervised integrative feature selection with respect to BMD and constructed the inter-omics partial correlation network. Although still requiring replication and validation in future studies, the findings from this exploratory analysis provide novel insights into the interrelationships between the gut microbiome and serum metabolome that may potentially play a role in skeletal remodeling processes.
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Affiliation(s)
- Jonathan Greenbaum
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA, United States
| | - Xu Lin
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Kuan-Jui Su
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA, United States
| | - Rui Gong
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hui Shen
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA, United States
| | - Jie Shen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hong-Mei Xiao
- Center of Systems Biology, Data Information and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, China
| | - Hong-Wen Deng
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA, United States
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16
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Noecker C, Eng A, Muller E, Borenstein E. MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. Bioinformatics 2022; 38:1615-1623. [PMID: 34999748 PMCID: PMC8896604 DOI: 10.1093/bioinformatics/btac003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION Recent technological developments have facilitated an expansion of microbiome-metabolome studies, in which samples are assayed using both genomic and metabolomic technologies to characterize the abundances of microbial taxa and metabolites. A common goal of these studies is to identify microbial species or genes that contribute to differences in metabolite levels across samples. Previous work indicated that integrating these datasets with reference knowledge on microbial metabolic capacities may enable more precise and confident inference of microbe-metabolite links. RESULTS We present MIMOSA2, an R package and web application for model-based integrative analysis of microbiome-metabolome datasets. MIMOSA2 uses genomic and metabolic reference databases to construct a community metabolic model based on microbiome data and uses this model to predict differences in metabolite levels across samples. These predictions are compared with metabolomics data to identify putative microbiome-governed metabolites and taxonomic contributors to metabolite variation. MIMOSA2 supports various input data types and customization with user-defined metabolic pathways. We establish MIMOSA2's ability to identify ground truth microbial mechanisms in simulation datasets, compare its results with experimentally inferred mechanisms in honeybee microbiota, and demonstrate its application in two human studies of inflammatory bowel disease. Overall, MIMOSA2 combines reference databases, a validated statistical framework, and a user-friendly interface to facilitate modeling and evaluating relationships between members of the microbiota and their metabolic products. AVAILABILITY AND IMPLEMENTATION MIMOSA2 is implemented in R under the GNU General Public License v3.0 and is freely available as a web server at http://elbo-spice.cs.tau.ac.il/shiny/MIMOSA2shiny/ and as an R package from http://www.borensteinlab.com/software_MIMOSA2.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Efrat Muller
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Elhanan Borenstein
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Santa Fe Institute, Santa Fe, NM 87501, USA
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17
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Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol 2022; 20:143-160. [PMID: 34552265 PMCID: PMC9578303 DOI: 10.1038/s41579-021-00621-9] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.
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Affiliation(s)
- Anelize Bauermeister
- Institute of Biomedical Science, Universidade de São Paulo, São Paulo, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Helena Mannochio-Russo
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | | | - Alan K. Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
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18
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Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care. Pathogens 2022; 11:pathogens11020121. [PMID: 35215065 PMCID: PMC8879973 DOI: 10.3390/pathogens11020121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.
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Curry KD, Nute MG, Treangen TJ. It takes guts to learn: machine learning techniques for disease detection from the gut microbiome. Emerg Top Life Sci 2021; 5:815-827. [PMID: 34779841 PMCID: PMC8786294 DOI: 10.1042/etls20210213] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 02/01/2023]
Abstract
Associations between the human gut microbiome and expression of host illness have been noted in a variety of conditions ranging from gastrointestinal dysfunctions to neurological deficits. Machine learning (ML) methods have generated promising results for disease prediction from gut metagenomic information for diseases including liver cirrhosis and irritable bowel disease, but have lacked efficacy when predicting other illnesses. Here, we review current ML methods designed for disease classification from microbiome data. We highlight the computational challenges these methods have effectively overcome and discuss the biological components that have been overlooked to offer perspectives on future work in this area.
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Affiliation(s)
- Kristen D. Curry
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Michael G. Nute
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX 77005, USA
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