151
|
Mehta S, Crane M, Leith E, Batut B, Hiltemann S, Arntzen MØ, Kunath BJ, Pope PB, Delogu F, Sajulga R, Kumar P, Johnson JE, Griffin TJ, Jagtap PD. ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Res 2021; 10:103. [PMID: 34484688 PMCID: PMC8383124 DOI: 10.12688/f1000research.28608.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.
Collapse
Affiliation(s)
- Subina Mehta
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Marie Crane
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Emma Leith
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Bérénice Batut
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
| | - Saskia Hiltemann
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | | | | | - Ray Sajulga
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Praveen Kumar
- University of Minnesota, Twin Cities, MN, 55455, USA
| | | | | | | |
Collapse
|
152
|
Mehta S, Crane M, Leith E, Batut B, Hiltemann S, Arntzen MØ, Kunath BJ, Pope PB, Delogu F, Sajulga R, Kumar P, Johnson JE, Griffin TJ, Jagtap PD. ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Res 2021; 10:103. [PMID: 34484688 PMCID: PMC8383124 DOI: 10.12688/f1000research.28608.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.
Collapse
Affiliation(s)
- Subina Mehta
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Marie Crane
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Emma Leith
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Bérénice Batut
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
| | - Saskia Hiltemann
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | | | | | - Ray Sajulga
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Praveen Kumar
- University of Minnesota, Twin Cities, MN, 55455, USA
| | | | | | | |
Collapse
|
153
|
Ginete DR, Goodrich-Blair H. From Binary Model Systems to the Human Microbiome: Factors That Drive Strain Specificity in Host-Symbiont Associations. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.614197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microbial symbionts are ubiquitous and can have significant impact on hosts. These impacts can vary in the sign (positive or negative) and degree depending on the identity of the interacting partners. Studies on host-symbiont associations indicate that subspecies (strain) genetic variation can influence interaction outcomes, making it necessary to go beyond species-level distinction to understand host-symbiont dynamics. In this review, we discuss examples of strain specificity found in host-symbiont associations, from binary model systems to the human microbiome. Although host and bacterial factors identified as mediators for specificity could be distinct at the molecular level, they generally fall into two broad functional categories: (1) those that contribute a required activity in support of the association and (2) those involved in antagonistic interactions with organisms outside of the association. We argue here based on current literature that factors from these two categories can work in concert to drive strain specificity and that this strain specificity must be considered to fully understand the molecular and ecological dynamics of host-symbiont associations, including the human microbiome.
Collapse
|
154
|
Barbuti RC, Schiavon LL, Oliveira CP, Alvares-DA-Silva MR, Sassaki LY, Passos MDCF, Farias AQ, Barros LL, Barreto BP, Albuquerque GBDMLD, Alves AM, Navarro-Rodriguez T, Bittencourt PL. GUT MICROBIOTA, PREBIOTICS, PROBIOTICS, AND SYNBIOTICS IN GASTROINTESTINAL AND LIVER DISEASES: PROCEEDINGS OF A JOINT MEETING OF THE BRAZILIAN SOCIETY OF HEPATOLOGY (SBH), BRAZILIAN NUCLEUS FOR THE STUDY OF HELICOBACTER PYLORI AND MICROBIOTA (NBEHPM), AND BRAZILIAN FEDERATION OF GASTROENTEROLOGY (FBG). ARQUIVOS DE GASTROENTEROLOGIA 2021; 57:381-398. [PMID: 33331485 DOI: 10.1590/s0004-2803.202000000-72] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023]
Abstract
Over the last years, there is growing evidence that microorganisms are involved in the maintenance of our health and are related to various diseases, both intestinal and extraintestinal. Changes in the gut microbiota appears to be a key element in the pathogenesis of hepatic and gastrointestinal disorders, including non-alcoholic fatty liver disease, alcoholic liver disease, liver cirrhosis, inflammatory bowel disease, irritable bowel syndrome, and Clostridium difficile - associated diarrhea. In 2019, the Brazilian Society of Hepatology (SBH) in cooperation with the Brazilian Nucleus for the Study of Helicobacter Pylori and Microbiota (NBEHPM), and Brazilian Federation of Gastroenterology (FBG) sponsored a joint meeting on gut microbiota and the use of prebiotics, probiotics, and synbiotics in gastrointestinal and liver diseases. This paper summarizes the proceedings of the aforementioned meeting. It is intended to provide practical information about this topic, addressing the latest discoveries and indicating areas for future studies.
Collapse
Affiliation(s)
- Ricardo Correa Barbuti
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Leonardo Lucca Schiavon
- Universidade Federal de Santa Catarina, Faculdade de Medicina, Departamento de Clínica Médica, Florianópolis, SC, Brasil
| | - Cláudia P Oliveira
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Mário Reis Alvares-DA-Silva
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Medicina Interna, Porto Alegre, RS, Brasil
| | | | | | - Alberto Queiroz Farias
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Luisa Leite Barros
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Bruno Paes Barreto
- Universidade do Estado do Pará, Centro de Ciências Biológicas e da Saúde, Belém, PA, Brasil.,Centro Universitário do Estado do Pará (CESUPA), Belém, PA, Brasil
| | | | - Amanda Mandarino Alves
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Tomás Navarro-Rodriguez
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | | |
Collapse
|
155
|
FECAL MICROBIOTES TRANSPLANTATION TECHNOLOGIES: MEDICAL, BIOTECHNOLOGICAL AND REGULATORY ASPECTS. BIOTECHNOLOGIA ACTA 2021. [DOI: 10.15407/biotech14.01.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is a treatment method based on donor's fecal solution injection into the patient's gastrointestinal tract. FMT is effectively used in the treatment of recurrent Clostridium difficile infection. There is also growing interest in the therapeutic application of the method to treat metabolic, autoimmune and other disorders that was not previously associated with intestinal microbiota. Despite the promising results of FMT use, the organizational and legal matters and that of the safety FMT application have not yet been resolved in the European and Ukrainian medical community. The purpose of this review was to summarize information on the FMT application and the regulatory aspects of its use. The analysis of the practical instructions provisions of for FMT applying in clinical practice was carried out, and the bioethical problems associated with the FMT use were investigated.
Collapse
|
156
|
Dysbiosis of gut microbiota in Polish patients with ulcerative colitis: a pilot study. Sci Rep 2021; 11:2166. [PMID: 33495479 PMCID: PMC7835370 DOI: 10.1038/s41598-021-81628-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic immune-mediated disorder, whose etiology is not fully understood and for which no effective treatment is available. Recently, research has focused on the dysbiosis of gut microbiome in UC. However, the results so far remain inconsistent and insufficient to understand the microbial component in UC pathogenesis. In this study, we determine specific changes in the gut microbial profile in Polish UC patients compared to healthy subjects for the first time. Using 16S rRNA gene-based analysis we have described the intestinal microbial community in a group of 20 individuals (10 UC patients and 10 controls). Our results after multiple hypothesis testing correction demonstrated substantially lower gut microbiome diversity in UC cases compared to the controls and considerable differences at the phylum level, as well as among 13 bacterial families and 20 bacterial genera (p < 0.05). UC samples were more abundant in Proteobacteria (8.42%), Actinobacteria (6.89%) and Candidate Division TM7 (2.88%) than those of healthy volunteers (2.57%, 2.29% and 0.012%, respectively). On the other hand, Bacteroidetes and Verrucomicrobia were presented at a lower level in UC relative to the controls (14% and 0% vs 27.97% and 4.47%, respectively). In conclusion, our results show a reduced gut microbial diversity in Polish UC patients, a reduction of taxa with an anti-inflammatory impact and an increased abundance of potentially pathogenic bacteria.
Collapse
|
157
|
Abstract
Gains and losses of large segments of genomic DNA, known as copy number variants (CNVs) gained considerable interest in clinical diagnostics lately, as particular forms may lead to inherited genetic diseases. In recent decades, researchers developed a wide variety of cytogenetic and molecular methods with different detection capabilities to detect clinically relevant CNVs. In this review, we summarize methodological progress from conventional approaches to current state of the art techniques capable of detecting CNVs from a few bases up to several megabases. Although the recent rapid progress of sequencing methods has enabled precise detection of CNVs, determining their functional effect on cellular and whole-body physiology remains a challenge. Here, we provide a comprehensive list of databases and bioinformatics tools that may serve as useful assets for researchers, laboratory diagnosticians, and clinical geneticists facing the challenge of CNV detection and interpretation.
Collapse
|
158
|
van Dongen KCW, van der Zande M, Bruyneel B, Vervoort JJM, Rietjens IMCM, Belzer C, Beekmann K. An in vitro model for microbial fructoselysine degradation shows substantial interindividual differences in metabolic capacities of human fecal slurries. Toxicol In Vitro 2021; 72:105078. [PMID: 33429044 DOI: 10.1016/j.tiv.2021.105078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Fructoselysine is formed upon heating during processing of food products, and being a key intermediate in advanced glycation end product formation considered to be potentially hazardous to human health. Human gut microbes can degrade fructoselysine to yield the short chain fatty acid butyrate. However, quantitative information on these biochemical reactions is lacking, and interindividual differences therein are not well established. Anaerobic incubations with pooled and individual human fecal slurries were optimized and applied to derive quantitative kinetic information for these biochemical reactions. Of 16 individuals tested, 11 were fructoselysine metabolizers, with Vmax, Km and kcat-values varying up to 14.6-fold, 9.5-fold, and 4.4-fold, respectively. Following fructoselysine exposure, 10 of these 11 metabolizers produced significantly increased butyrate concentrations, varying up to 8.6-fold. Bacterial taxonomic profiling of the fecal samples revealed differential abundant taxa for these reactions (e.g. families Ruminococcaceae, Christenellaceae), and Ruminococcus_1 showed the strongest correlation with fructoselysine degradation and butyrate production (ρ ≥ 0.8). This study highlights substantial interindividual differences in gut microbial degradation of fructoselysine. The presented method allows for quantification of gut microbial degradation kinetics for foodborne xenobiotics, and interindividual differences therein, which can be used to refine prediction of internal exposure.
Collapse
Affiliation(s)
- Katja C W van Dongen
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands.
| | - Meike van der Zande
- Wageningen Food Safety Research (WFSR), part of Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, the Netherlands
| | - Ben Bruyneel
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands
| | - Jacques J M Vervoort
- Laboratory of Biochemistry, Wageningen University and Research, P.O. Box 8128, 6700 ET Wageningen, the Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH Wageningen, the Netherlands
| | - Karsten Beekmann
- Division of Toxicology, Wageningen University and Research, P.O. Box 8000, 6700 EA Wageningen, the Netherlands; Wageningen Food Safety Research (WFSR), part of Wageningen University and Research, P.O. Box 230, 6700 AE Wageningen, the Netherlands
| |
Collapse
|
159
|
Carrillo-Ng H, Becerra-Goicochea L, Tarazona-Castro Y, Pinillos-Vilca L, Del Valle LJ, Aguilar-Luis MA, Tinco-Valdez C, Silva-Caso W, Martins-Luna J, Peña-Tuesta I, Aquino-Ortega R, Del Valle-Mendoza J. Variations in cervico-vaginal microbiota among HPV-positive and HPV-negative asymptomatic women in Peru. BMC Res Notes 2021; 14:4. [PMID: 33407849 PMCID: PMC7788800 DOI: 10.1186/s13104-020-05422-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
Objective To characterize the cervicovaginal microbiota of HPV-positive and HPV-negative asymptomatic Peruvian women, by identifying the presence of 13 representative bacteria genus. Results A total of 100 HPV-positive and 100 HPV-negative women were matched by age for comparison of microbiota. The following bacteria were more frequently identified in HPV-positive patients compared to HPV-negative: Eubacterium (68 vs 32%), Actinobacteria (46 vs 33%), Fusobacterium (11 vs 6%) and Bacteroides (20 vs 13%). A comparison between high-risk and low-risk genotypes was performed and differences were found in the detection of Actinobacteria (50 vs 33.33%), Bifidobacterium (50 vs 20.83%) and Enterococcus (50 vs 29.17%).
Collapse
Affiliation(s)
- Hugo Carrillo-Ng
- School of Medicine, Research and Innovation Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Av. San Marcos Cuadra 2, Chorrillos, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | | | - Yordi Tarazona-Castro
- Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru.,Escuela Profesional de Genética y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | - Luis J Del Valle
- Departament d'Enginyeria Química, EEBE, Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Miguel Angel Aguilar-Luis
- School of Medicine, Research and Innovation Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Av. San Marcos Cuadra 2, Chorrillos, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Carmen Tinco-Valdez
- School of Medicine, Research and Innovation Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Av. San Marcos Cuadra 2, Chorrillos, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Wilmer Silva-Caso
- School of Medicine, Research and Innovation Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Av. San Marcos Cuadra 2, Chorrillos, Lima, Peru. .,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru.
| | - Johanna Martins-Luna
- School of Medicine, Research and Innovation Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Av. San Marcos Cuadra 2, Chorrillos, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Isaac Peña-Tuesta
- School of Medicine, Research and Innovation Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Av. San Marcos Cuadra 2, Chorrillos, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Ronald Aquino-Ortega
- School of Medicine, Research and Innovation Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Av. San Marcos Cuadra 2, Chorrillos, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Juana Del Valle-Mendoza
- School of Medicine, Research and Innovation Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Av. San Marcos Cuadra 2, Chorrillos, Lima, Peru. .,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru.
| |
Collapse
|
160
|
Varkey J. Graft assessment for acute rejection after intestinal transplantation: current status and future perspective. Scand J Gastroenterol 2021; 56:13-19. [PMID: 33202155 DOI: 10.1080/00365521.2020.1847318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Intestinal transplantation has since its inception evolved as a lifesaving treatment option for patients with irreversible intestinal failure who can no longer be sustained on parenteral nutrition. Improvement in short-term survival after transplantation has also justified the expansion of treatment indications. Unfortunately, success is somewhat limited by a plateau observed in long-term survival. The reason for this sub-optimal long-term result experienced in this cohort may in part be attributed to the intestinal graft with the lymphoid content it carries inflicting the host with multiple complications where acute cellular rejection is one of the most common causes for graft loss. Graft monitoring is for this reason of paramount importance and detection of rejection at an early stage essential to enable early instigation of treatment and successful reversal of the pathology. Due to the challenges in diagnosing acute rejection with a noninvasive marker we are still limited to a surveillance protocol using endoscopy and biopsies for the diagnosis of rejection. The purpose of our paper is to review the adequacy of different methods in monitoring the graft for acute rejection using biomarkers, endoscopy and imaging. In conclusion, the evidence base continues to support the use of histology for the diagnosis of acute rejection. The role of biomarkers are still debatable, although markers such as calprotectin might be beneficial in excluding an ongoing process.
Collapse
Affiliation(s)
- Jonas Varkey
- Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Sahlgrenska Intestinal Failure and Transplant Centre, Gothenburg, Sweden
| |
Collapse
|
161
|
Patumcharoenpol P, Nakphaichit M, Panagiotou G, Senavonge A, Suratannon N, Vongsangnak W. MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. PLoS Comput Biol 2021; 17:e1008487. [PMID: 33406089 PMCID: PMC7787440 DOI: 10.1371/journal.pcbi.1008487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.
Collapse
Grants
- Kasetsart University Research and Development Institute (KURDI) at Kasetsart University
- Department of Zoology, Faculty of Science, Kasetsart University
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU)
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University
- International Affairs Division (IAD), Kasetsart University
- National Science and Technology Development Agency
- Ratchadapisek Research Funds
- Chulalongkorn University
- Deutsche Forschungsgemeinschaft (DFG) CRC/Transregio 124 “Pathogenic fungi and their human host: Networks of interaction”, subprojects B5 and INF
Collapse
Affiliation(s)
- Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Gianni Panagiotou
- Systems Biology & Bioinformatics Group, School of Biological Sciences, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
- Systems Biology & Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena, Germany
| | - Anchalee Senavonge
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Narissara Suratannon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| |
Collapse
|
162
|
Keck FD, Polizzi KM. Microbial interventions are an easier alternative to engineer higher organisms. Microb Biotechnol 2021; 14:26-30. [PMID: 33070407 PMCID: PMC7888442 DOI: 10.1111/1751-7915.13682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 11/27/2022] Open
Abstract
Advances in synthetic biology have made microbes easier to engineer than ever before. However, synthetic biology in animals and plants has lagged behind. Since it is now known that the phenotype of higher organisms depends largely on their microbiota, we propose that this is an easier route to achieving synthetic biology applications in these organisms.
Collapse
Affiliation(s)
- F. Dean Keck
- Department of Chemical EngineeringImperial College LondonLondonSW7 2AZUK
- Imperial College Centre for Synthetic BiologyImperial College LondonLondonSW7 2AZUK
| | - Karen M. Polizzi
- Department of Chemical EngineeringImperial College LondonLondonSW7 2AZUK
- Imperial College Centre for Synthetic BiologyImperial College LondonLondonSW7 2AZUK
| |
Collapse
|
163
|
Alkotob SS, Cannedy C, Harter K, Movassagh H, Paudel B, Prunicki M, Sampath V, Schikowski T, Smith E, Zhao Q, Traidl‐Hoffmann C, Nadeau KC. Advances and novel developments in environmental influences on the development of atopic diseases. Allergy 2020; 75:3077-3086. [PMID: 33037680 DOI: 10.1111/all.14624] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
Abstract
Although genetic factors play a role in the etiology of atopic disease, the rapid increases in the prevalence of these diseases over the last few decades suggest that environmental, rather than genetic factors are the driving force behind the increasing prevalence. In modern societies, there is increased time spent indoors, use of antibiotics, and consumption of processed foods and decreased contact with farm animals and pets, which limit exposure to environmental allergens, infectious parasitic worms, and microbes. The lack of exposure to these factors is thought to prevent proper education and training of the immune system. Increased industrialization and urbanization have brought about increases in organic and inorganic pollutants. In addition, Caesarian birth, birth order, increased use of soaps and detergents, tobacco smoke exposure and psychosomatic factors are other factors that have been associated with increased rate of allergic diseases. Here, we review current knowledge on the environmental factors that have been shown to affect the development of allergic diseases and the recent developments in the field.
Collapse
Affiliation(s)
- Shifaa Suhayl Alkotob
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Cade Cannedy
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Katharina Harter
- Chair and Institute of Environmental Medicine UNIKA‐TTechnical University of Munich and Helmholtz Zentrum München Augsburg Germany
| | - Hesam Movassagh
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Bibek Paudel
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Mary Prunicki
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Tamara Schikowski
- IUF‐Leibniz Institute for Environmental Medicine Duesseldorf Germany
| | - Eric Smith
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Qi Zhao
- IUF‐Leibniz Institute for Environmental Medicine Duesseldorf Germany
| | - Claudia Traidl‐Hoffmann
- Chair and Institute of Environmental Medicine UNIKA‐TTechnical University of Munich and Helmholtz Zentrum München Augsburg Germany
- CK‐CARE Christine Kühne Center for Allergy Research and Education Davos Switzerland
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| |
Collapse
|
164
|
Abstract
Habitual dietary intake is a major determinant of the species composition and functional output of the trillions of microorganisms residing in the human gut. Diet influences which microbes will colonise, flourish or disappear throughout life. An increase in polyphenols, oligosaccharides and fibre, which are all components found in a fruit and vegetable-rich diet, have long been associated with decreased risk of chronic diseases. Many of the benefits induced by this type of diet result from the interaction of these dietary components with the gut microbiome, where they selectively enrich specific microbial species and increase microbial diversity. Understanding the interaction of habitual dietary patterns on the gut microbiome will lead to rational dietary manipulation to improve human health through prevention and treatment of disease.
Collapse
|
165
|
Villapol S. Gastrointestinal symptoms associated with COVID-19: impact on the gut microbiome. Transl Res 2020; 226:57-69. [PMID: 32827705 PMCID: PMC7438210 DOI: 10.1016/j.trsl.2020.08.004] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the greatest worldwide pandemic since the 1918 flu. The consequences of the coronavirus disease 2019 (COVID-19) are devastating and represent the current major public health issue across the globe. At the onset, SARS-CoV-2 primarily attacks the respiratory system as it represents the main point of entry in the host, but it also can affect multiple organs. Although most of the patients do not present symptoms or are mildly symptomatic, some people infected with SARS-CoV-2 that experience more severe multiorgan dysfunction. The severity of COVID-19 is typically combined with a set of comorbidities such as hypertension, diabetes, obesity, and/or advanced age that seriously exacerbates the consequences of the infection. Also, SARS-CoV-2 can cause gastrointestinal symptoms, such as vomiting, diarrhea, or abdominal pain during the early phases of the disease. Intestinal dysfunction induces changes in intestinal microbes, and an increase in inflammatory cytokines. Thus, diagnosing gastrointestinal symptoms that precede respiratory problems during COVID-19 may be necessary for improved early detection and treatment. Uncovering the composition of the microbiota and its metabolic products in the context of COVID-19 can help determine novel biomarkers of the disease and help identify new therapeutic targets. Elucidating changes to the microbiome as reliable biomarkers in the context of COVID-19 represent an overlooked piece of the disease puzzle and requires further investigation.
Collapse
Key Words
- ards, acute respiratory distress syndrome
- ace2, angiotensin-converting enzyme ii
- cns, central nervous system
- covid-19, coronavirus disease 2019
- cpr, c-reactive protein
- h1n1, influenza a virus
- il, interleukin
- mers, middle east respiratory syndrome
- prs, proteomic risk score
- sars, severe acute respiratory syndrome
- sars-cov-2, severe acute respiratory syndrome coronavirus 2
- scfa, short-chain fatty acids
- ras, renin-angiotensin system
- ros, reactive oxygen species
- rt-pcr, reverse transcription-polymerase chain reaction
- tmprss2, transmembrane serine protease 2
- tnfα, tumor necrosis factor alpha
Collapse
Affiliation(s)
- Sonia Villapol
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, Texas; Department of Neuroscience in Neurological Surgery, Weill Cornell Medical College, New York.
| |
Collapse
|
166
|
Rashidinejad A, Bahrami A, Rehman A, Rezaei A, Babazadeh A, Singh H, Jafari SM. Co-encapsulation of probiotics with prebiotics and their application in functional/synbiotic dairy products. Crit Rev Food Sci Nutr 2020; 62:2470-2494. [PMID: 33251846 DOI: 10.1080/10408398.2020.1854169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Oral administration of live probiotics along with prebiotics has been suggested with numerous beneficial effects for several conditions including certain infectious disorders, diarrheal illnesses, some inflammatory bowel diseases, and most recently, irritable bowel syndrome. Though, delivery of such viable bacteria to the host intestine is a major challenge, due to the poor survival of the ingested probiotic bacteria during the gastric transit, especially within the stomach where the pH is highly acidic. Although microencapsulation has been known as a promising approach for improving the viability of probiotics in the human digestive tract, the success rate is not satisfactory. For this reason, co-encapsulation of probiotics with probiotics has been practised as a novel alternative approach for further improvement of the oral delivery of viable probiotics toward their targeted release in the host intestine. This paper discusses the co-encapsulation technologies used for delivery of probiotics toward better stability and viability, as well the incorporation of co-encapsulated probiotics and prebiotics in functional/synbiotic dairy foods. The common encapsulation technologies (and the materials) used for this purpose, the stability and survival of co-encapsulated probiotics in the food, and the release behavior of the co-encapsulated probiotics in the gastrointestinal tract have also been explained. Most studies reported a significant improvement particularly in the viability of bacteria associated with the presence of prebiotics. Nevertheless, the previous research has mostly been carried out in the simulated digestion, meaning that future systematic research is to be carried out to investigate the efficacy of the co-encapsulation on the survival of the bacteria in the gut in vivo.
Collapse
Affiliation(s)
- Ali Rashidinejad
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Akbar Bahrami
- Program of Applied Science and Technology, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, North Carolina, USA
| | - Abdur Rehman
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Jiangsu, People's Republic of China
| | - Atefe Rezaei
- Department of Food Science and Technology, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran.,Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Afshin Babazadeh
- Center for Motor Neuron Disease Research, Faculty of medicine, health and human sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Harjinder Singh
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Seid Mahdi Jafari
- Department of Food Materials & Process Design Engendering, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| |
Collapse
|
167
|
Abstract
Birthweight is a well-known predictor of adult-onset chronic disease. The placenta plays a necessary role in regulating fetal growth and determining birth size. Maternal stressors that affect placental function and prenatal growth include maternal overnutrition and undernutrition, toxic social stress, and exposure to toxic chemicals. These stressors lead to increased vulnerability to disease within any population. This vulnerability arises from placental and fetal exposure to stressors during fetal life. The biological drivers linking various social determinants of health to compromised placental function and fetal development have been little studied.
Collapse
|
168
|
Wróblewska B, Kaliszewska-Suchodoła A, Fuc E, Markiewicz LH, Ogrodowczyk AM, Złotkowska D, Wasilewska E. Effect of Low-Immunogenic Yogurt Drinks and Probiotic Bacteria on Immunoreactivity of Cow's Milk Proteins and Tolerance Induction-In Vitro and In Vivo Studies. Nutrients 2020; 12:E3390. [PMID: 33158132 PMCID: PMC7694189 DOI: 10.3390/nu12113390] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/28/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
There is no effective therapy for milk allergy. The role of lactic acid bacteria (LAB) and probiotics in protection against allergy-related outcomes is still under investigation. The aim of the study was to evaluate the immunomodulative and therapeutic potential of yogurt drinks in cow's milk allergy (CMA) management. We compared immunoreactivity of α-casein (α-CN), β-casein (β-CN), κ-casein (κ-CN), α-lactalbumin (α-LA), and β-lactoglobulin (β-LG) in 27 yogurt drinks fermented with different basic yogurt cultures, or yogurt cultures enriched with Lactobacillus plantarum and/or Bifidobacterium lactis strains, by competitive ELISA assay. Drinks with the lowest antigenic potential were used as allergoids for CMA therapy. BALB/c mice were sensitized via intraperitoneal injection of α-CN + β-LG mixture with aluminum adjuvant, and gavaged with increasing doses of selected low-immunogenic drinks (YM-basic, or YM-LB-enriched with L. plantarum and B. lactis) to induce tolerance. Milk- or phosphate-buffered saline (PBS)-dosed mice served as controls. Compared to milk, the immunoreactivity of proteins in drinks increased or decreased, depending on the bacterial sets applied for fermentation. Only a few sets acted synergistically in reducing immunoreactivity. The selected low-immunogenic drinks stimulated allergic mice for profiling Th2 to Th1 response and acquire tolerance, and the effect was greater with YM-LB drink, which during long-lasting interventional feeding strongly increased the secretion of regulatory cytokines, i.e., IL-10 and TGF-β, and IgA and decreased IL-4, IgE, and anti-(α-CN + β-LG) IgG1. The studies revealed variations in the potency of yogurt bacteria to change allergenicity of milk proteins and the need for their strict selection to obtain a safe product for allergy sufferers. The YM-LB drink with reduced antigenic potential may be a source of allergoids used in the immunotherapy of IgE mediated CMA, but further clinical or volunteer studies are required.
Collapse
Affiliation(s)
- Barbara Wróblewska
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10 Str., 10-748 Olsztyn, Poland; (B.W.); (E.F.); (L.H.M.); (A.M.O.); (D.Z.)
| | | | - Ewa Fuc
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10 Str., 10-748 Olsztyn, Poland; (B.W.); (E.F.); (L.H.M.); (A.M.O.); (D.Z.)
| | - Lidia Hanna Markiewicz
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10 Str., 10-748 Olsztyn, Poland; (B.W.); (E.F.); (L.H.M.); (A.M.O.); (D.Z.)
| | - Anna Maria Ogrodowczyk
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10 Str., 10-748 Olsztyn, Poland; (B.W.); (E.F.); (L.H.M.); (A.M.O.); (D.Z.)
| | - Dagmara Złotkowska
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10 Str., 10-748 Olsztyn, Poland; (B.W.); (E.F.); (L.H.M.); (A.M.O.); (D.Z.)
| | - Ewa Wasilewska
- Department of Immunology and Food Microbiology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10 Str., 10-748 Olsztyn, Poland; (B.W.); (E.F.); (L.H.M.); (A.M.O.); (D.Z.)
| |
Collapse
|
169
|
Lama S, Merlin-Zhang O, Yang C. In Vitro and In Vivo Models for Evaluating the Oral Toxicity of Nanomedicines. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2177. [PMID: 33142878 PMCID: PMC7694082 DOI: 10.3390/nano10112177] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
Toxicity studies for conventional oral drug formulations are standardized and well documented, as required by the guidelines of administrative agencies such as the US Food & Drug Administration (FDA), the European Medicines Agency (EMA) or European Medicines Evaluation Agency (EMEA), and the Japanese Pharmaceuticals and Medical Devices Agency (PMDA). Researchers tend to extrapolate these standardized protocols to evaluate nanoformulations (NFs) because standard nanotoxicity protocols are still lacking in nonclinical studies for testing orally delivered NFs. However, such strategies have generated many inconsistent results because they do not account for the specific physicochemical properties of nanomedicines. Due to their tiny size, accumulated surface charge and tension, sizeable surface-area-to-volume ratio, and high chemical/structural complexity, orally delivered NFs may generate severe topical toxicities to the gastrointestinal tract and metabolic organs, including the liver and kidney. Such toxicities involve immune responses that reflect different mechanisms than those triggered by conventional formulations. Herein, we briefly analyze the potential oral toxicity mechanisms of NFs and describe recently reported in vitro and in vivo models that attempt to address the specific oral toxicity of nanomedicines. We also discuss approaches that may be used to develop nontoxic NFs for oral drug delivery.
Collapse
Affiliation(s)
| | | | - Chunhua Yang
- Center for Diagnostics and Therapeutics, Digestive Disease Research Group, Institute for Biomedical Sciences, Petite Science Center, Suite 754, 100 Piedmont Ave SE, Georgia State University, Atlanta, GA 30303, USA; (S.L.); (O.M.-Z.)
| |
Collapse
|
170
|
The Role of the Microbiome in Oral Squamous Cell Carcinoma with Insight into the Microbiome-Treatment Axis. Int J Mol Sci 2020; 21:ijms21218061. [PMID: 33137960 PMCID: PMC7662318 DOI: 10.3390/ijms21218061] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the leading presentations of head and neck cancer (HNC). The first part of this review will describe the highlights of the oral microbiome in health and normal development while demonstrating how both the oral and gut microbiome can map OSCC development, progression, treatment and the potential side effects associated with its management. We then scope the dynamics of the various microorganisms of the oral cavity, including bacteria, mycoplasma, fungi, archaea and viruses, and describe the characteristic roles they may play in OSCC development. We also highlight how the human immunodeficiency viruses (HIV) may impinge on the host microbiome and increase the burden of oral premalignant lesions and OSCC in patients with HIV. Finally, we summarise current insights into the microbiome–treatment axis pertaining to OSCC, and show how the microbiome is affected by radiotherapy, chemotherapy, immunotherapy and also how these therapies are affected by the state of the microbiome, potentially determining the success or failure of some of these treatments.
Collapse
|
171
|
Yadav M, Chauhan NS. Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics. J Appl Microbiol 2020; 130:1425-1441. [PMID: 33022786 DOI: 10.1111/jam.14883] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022]
Abstract
Human gut microbiome is a diversified, resilient, immuno-stabilized, metabolically active and physiologically essential component of the human body. Scientific explorations have been made to seek in-depth information about human gut microbiome establishment, microbiome functioning, microbiome succession, factors influencing microbial community dynamics and the role of gut microbiome in health and diseases. Extensive investigations have proposed the microbiome therapeutics as a futuristic medicine for various physiological and metabolic disorders. A comprehensive outlook of microbial colonization, host-microbe interactions, microbial adaptation, commensal selection and immuno-survivability is still required to catalogue the essential genetic and physiological features for the commensal engagement. Evolution of a structured human gut microbiome relies on the microbial flexibility towards genetic, immunological and physiological adaptation in the human gut. Key features for commensalism could be utilized in developing tailor-made microbiome-based therapy to overcome various physiological and metabolic disorders. This review describes the key genetics and physiological traits required for host-microbe interaction and successful commensalism to institute a human gut microbiome.
Collapse
Affiliation(s)
- M Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - N S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| |
Collapse
|
172
|
Lou JM, Ren ZG, Li A, Rao BC, Yu ZJ. Fecal microbiota transplantation has therapeutic effects on chronic hepatits B patients via altering composition of gut microbiota. Hepatobiliary Pancreat Dis Int 2020; 19:486-487. [PMID: 31974041 DOI: 10.1016/j.hbpd.2019.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/27/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Jia-Min Lou
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450052, China; Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhi-Gang Ren
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450052, China; Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ang Li
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450052, China; Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ben-Chen Rao
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450052, China; Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zu-Jiang Yu
- Department of Infectious Diseases, the First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450052, China; Gene Hospital of Henan Province, Precision Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| |
Collapse
|
173
|
Paudel KR, Dharwal V, Patel VK, Galvao I, Wadhwa R, Malyla V, Shen SS, Budden KF, Hansbro NG, Vaughan A, Yang IA, Kohonen-Corish MRJ, Bebawy M, Dua K, Hansbro PM. Role of Lung Microbiome in Innate Immune Response Associated With Chronic Lung Diseases. Front Med (Lausanne) 2020; 7:554. [PMID: 33043031 PMCID: PMC7530186 DOI: 10.3389/fmed.2020.00554] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
Respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), lung fibrosis, and lung cancer, pose a huge socio-economic burden on society and are one of the leading causes of death worldwide. In the past, culture-dependent techniques could not detect bacteria in the lungs, therefore the lungs were considered a sterile environment. However, the development of culture-independent techniques, particularly 16S rRNA sequencing, allowed for the detection of commensal microbes in the lung and with further investigation, their roles in disease have since emerged. In healthy individuals, the predominant commensal microbes are of phylum Firmicutes and Bacteroidetes, including those of the genera Veillonella and Prevotella. In contrast, pathogenic microbes (Haemophilus, Streptococcus, Klebsiella, Pseudomonas) are often associated with lung diseases. There is growing evidence that microbial metabolites, structural components, and toxins from pathogenic and opportunistic bacteria have the capacity to stimulate both innate and adaptive immune responses, and therefore can contribute to the pathogenesis of lung diseases. Here we review the multiple mechanisms that are altered by pathogenic microbiomes in asthma, COPD, lung cancer, and lung fibrosis. Furthermore, we focus on the recent exciting advancements in therapies that can be used to restore altered microbiomes in the lungs.
Collapse
Affiliation(s)
- Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Vivek Dharwal
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Vyoma K Patel
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Izabela Galvao
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Ridhima Wadhwa
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Vamshikrishna Malyla
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Sj Sijie Shen
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Kurtis F Budden
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Nicole G Hansbro
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Annalicia Vaughan
- Faculty of Medicine, Thoracic Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Ian A Yang
- Faculty of Medicine, Thoracic Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Maija R J Kohonen-Corish
- Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.,Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.,School of Medicine, Western Sydney University, Sydney, NSW, Australia.,St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Mary Bebawy
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Kamal Dua
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| |
Collapse
|
174
|
Wallace RK. The Microbiome in Health and Disease from the Perspective of Modern Medicine and Ayurveda. ACTA ACUST UNITED AC 2020; 56:medicina56090462. [PMID: 32932766 PMCID: PMC7559905 DOI: 10.3390/medicina56090462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023]
Abstract
The role of the microbiome in health and disease helps to provide a scientific understanding of key concepts in Ayurveda. We now recognize that virtually every aspect of our physiology and health is influenced by the collection of microorganisms that live in various parts of our body, especially the gut microbiome. There are many external factors which influence the composition of the gut microbiome but one of the most important is diet and digestion. Ayurveda and other systems of traditional health have for thousands of years focused on diet and digestion. Recent research has helped us understand the connection between the microbiome and the many different prevention and therapeutic treatment approaches of Ayurveda.
Collapse
Affiliation(s)
- Robert Keith Wallace
- Department of Physiology and Health, Maharishi International University, Fairfield, IA 52556, USA
| |
Collapse
|
175
|
Mendez ME, Murugesh DK, Sebastian A, Hum NR, McCloy SA, Kuhn EA, Christiansen BA, Loots GG. Antibiotic Treatment Prior to Injury Improves Post-Traumatic Osteoarthritis Outcomes in Mice. Int J Mol Sci 2020; 21:E6424. [PMID: 32899361 PMCID: PMC7503363 DOI: 10.3390/ijms21176424] [Citation(s) in RCA: 12] [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: 07/24/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 12/21/2022] Open
Abstract
Osteoarthritis (OA) is a painful and debilitating disease characterized by the chronic and progressive degradation of articular cartilage. Post-traumatic OA (PTOA) is a secondary form of OA that develops in ~50% of cases of severe articular injury. Inflammation and re-occurring injury have been implicated as contributing to the progression of PTOA after the initial injury. However, there is very little known about external factors prior to injury that could affect the risk of PTOA development. To examine how the gut microbiome affects PTOA development we used a chronic antibiotic treatment regimen starting at weaning for six weeks prior to ACL rupture, in mice. A six-weeks post-injury histological examination showed more robust cartilage staining on the antibiotic (AB)-treated mice than the untreated controls (VEH), suggesting slower disease progression in AB cohorts. Injured joints also showed an increase in the presence of anti-inflammatory M2 macrophages in the AB group. Molecularly, the phenotype correlated with a significantly lower expression of inflammatory genes Tlr5, Ccl8, Cxcl13, and Foxo6 in the injured joints of AB-treated animals. Our results indicate that a reduced state of inflammation at the time of injury and a lower expression of Wnt signaling modulatory protein, Rspo1, caused by AB treatment can slow down or improve PTOA outcomes.
Collapse
Affiliation(s)
- Melanie E. Mendez
- Lawrence Livermore National Laboratories, Physical and Life Sciences Directorate, Livermore, CA 94550, USA; (M.E.M.); (D.K.M.); (A.S.); (N.R.H.); (S.A.M.); (E.A.K.)
| | - Deepa K. Murugesh
- Lawrence Livermore National Laboratories, Physical and Life Sciences Directorate, Livermore, CA 94550, USA; (M.E.M.); (D.K.M.); (A.S.); (N.R.H.); (S.A.M.); (E.A.K.)
| | - Aimy Sebastian
- Lawrence Livermore National Laboratories, Physical and Life Sciences Directorate, Livermore, CA 94550, USA; (M.E.M.); (D.K.M.); (A.S.); (N.R.H.); (S.A.M.); (E.A.K.)
| | - Nicholas R. Hum
- Lawrence Livermore National Laboratories, Physical and Life Sciences Directorate, Livermore, CA 94550, USA; (M.E.M.); (D.K.M.); (A.S.); (N.R.H.); (S.A.M.); (E.A.K.)
- UC Merced, School of Natural Sciences, Merced, CA 95343, USA
| | - Summer A. McCloy
- Lawrence Livermore National Laboratories, Physical and Life Sciences Directorate, Livermore, CA 94550, USA; (M.E.M.); (D.K.M.); (A.S.); (N.R.H.); (S.A.M.); (E.A.K.)
| | - Edward A. Kuhn
- Lawrence Livermore National Laboratories, Physical and Life Sciences Directorate, Livermore, CA 94550, USA; (M.E.M.); (D.K.M.); (A.S.); (N.R.H.); (S.A.M.); (E.A.K.)
| | | | - Gabriela G. Loots
- Lawrence Livermore National Laboratories, Physical and Life Sciences Directorate, Livermore, CA 94550, USA; (M.E.M.); (D.K.M.); (A.S.); (N.R.H.); (S.A.M.); (E.A.K.)
- UC Merced, School of Natural Sciences, Merced, CA 95343, USA
| |
Collapse
|
176
|
Griffiths JC, De Vries J, McBurney MI, Wopereis S, Serttas S, Marsman DS. Measuring health promotion: translating science into policy. Eur J Nutr 2020; 59:11-23. [PMID: 32852581 PMCID: PMC7497380 DOI: 10.1007/s00394-020-02359-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Commonly, it is the end of life when our health is deteriorating, that many will make drastic lifestyle changes to improve their quality of life. However, it is increasingly recognized that bringing good health-promoting behaviors into practice as early in life as possible has the most significant impact across the maximal healthspan. The WHO has brought clarity to health promotion over the last fifteen years, always centering on language relating to a process of enabling people to increase control over, and to improve, their physical, mental and social health. A good healthspan is not just freedom from morbidity and mortality, it is that joie de vivre ("joy of living") that should accompany every day of our lifespan. Therefore, health promotion includes not only the health sector, but also needs individual commitment to achieve that target of a healthspan aligned with the lifespan. This paper explores health promotion and health literacy, and how to design appropriate nutritional studies to characterize contributors to a positive health outcome, the role the human microbiome plays in promoting health and addressing and alleviating morbidity and diseases, and finally how to characterize phenotypic flexibility and a physiologic resilience that we must maintain as our structural and functional systems are bombarded with the insults and perturbations of life.
Collapse
Affiliation(s)
- James C Griffiths
- Council for Responsible Nutrition-International, Washington, DC, USA.
| | - Jan De Vries
- Nutrition in Transition Foundation, Gorssel, The Netherlands
| | - Michael I McBurney
- Department of Human Health & Nutritional Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Suzan Wopereis
- Research Group Microbiology and Systems Biology, Netherlands Organization for Applied Scientific Research (TNO), Utrechtseweg 48, NL-3704 HE, Zeist, The Netherlands
| | | | | |
Collapse
|
177
|
Nava Lara RA, Beltrán JA, Brizuela CA, Del Rio G. Relevant Features of Polypharmacologic Human-Target Antimicrobials Discovered by Machine-Learning Techniques. Pharmaceuticals (Basel) 2020; 13:ph13090204. [PMID: 32825532 PMCID: PMC7559829 DOI: 10.3390/ph13090204] [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: 07/11/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 11/16/2022] Open
Abstract
Polypharmacologic human-targeted antimicrobials (polyHAM) are potentially useful in the treatment of complex human diseases where the microbiome is important (e.g., diabetes, hypertension). We previously reported a machine-learning approach to identify polyHAM from FDA-approved human targeted drugs using a heterologous approach (training with peptides and non-peptide compounds). Here we discover that polyHAM are more likely to be found among antimicrobials displaying a broad-spectrum antibiotic activity and that topological, but not chemical features, are most informative to classify this activity. A heterologous machine-learning approach was trained with broad-spectrum antimicrobials and tested with human metabolites; these metabolites were labeled as antimicrobials or non-antimicrobials based on a naïve text-mining approach. Human metabolites are not commonly recognized as antimicrobials yet circulate in the human body where microbes are found and our heterologous model was able to classify those with antimicrobial activity. These results provide the basis to develop applications aimed to design human diets that purposely alter metabolic compounds proportions as a way to control human microbiome.
Collapse
Affiliation(s)
- Rodrigo A. Nava Lara
- Department of Biochemistry and Structural Biology, Instituto de Fisiologia Celular, UNAM, Mexico City 04510, Mexico;
| | - Jesús A. Beltrán
- Department of Computer Science, CICESE Research Center, Ensenada 22860, Mexico; (J.A.B.); (C.A.B.)
| | - Carlos A. Brizuela
- Department of Computer Science, CICESE Research Center, Ensenada 22860, Mexico; (J.A.B.); (C.A.B.)
| | - Gabriel Del Rio
- Department of Biochemistry and Structural Biology, Instituto de Fisiologia Celular, UNAM, Mexico City 04510, Mexico;
- Correspondence:
| |
Collapse
|
178
|
Jung Y, Tagele SB, Son H, Ibal JC, Kerfahi D, Yun H, Lee B, Park CY, Kim ES, Kim SJ, Shin JH. Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change. Microorganisms 2020; 8:microorganisms8091265. [PMID: 32825401 PMCID: PMC7569816 DOI: 10.3390/microorganisms8091265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.
Collapse
Affiliation(s)
- YeonGyun Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Setu Bazie Tagele
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Department of Applied Plant Sciences, University of Gondar, Gondar 196, Ethiopia
| | - HyunWoo Son
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Dorsaf Kerfahi
- Department of Biological Sciences, Keimyung University, Daegu 42601, Korea;
| | - Hyunju Yun
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Bora Lee
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Clara Yongjoo Park
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea;
| | - Sang-Jun Kim
- Department of Natural Sciences, Republic of Korea Naval Academy, Changwon 51702, Korea;
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Correspondence: ; Tel.: +82-53-950-5716; Fax: +82-53-953-7233
| |
Collapse
|
179
|
Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, Piro VC, García-Ferris C, Latorre A, Renard BY, Muth T. gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. NAR Genom Bioinform 2020; 2:lqaa058. [PMID: 33575609 PMCID: PMC7671378 DOI: 10.1093/nargab/lqaa058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/19/2020] [Accepted: 08/03/2020] [Indexed: 01/14/2023] Open
Abstract
The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared toward human microbiomes. Microbiota are better understood when analyzed in their biological context; that is together with their host or environment. Nevertheless, this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomics and metaproteomics in an integrative manner. The pipeline has been developed using the workflow management framework Snakemake in order to obtain an automated and reproducible pipeline. Using experimental datasets of the German cockroach Blattella germanica, a non-model organism with very complex gut microbiome, we show the capabilities of gNOMO with regard to meta-omics data integration, expression ratio comparison, taxonomic and functional analysis as well as intuitive output visualization. In conclusion, gNOMO is a bioinformatic pipeline that can easily be configured, for integrating and analyzing multiple meta-omics data types and for producing output visualizations, specifically designed for integrating paired-end sequencing data with mass spectrometry from non-model organisms.
Collapse
Affiliation(s)
- Maria Muñoz-Benavent
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC, Paterna (València) 46980, Spain
| | - Felix Hartkopf
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin 13353, Germany
| | | | - Vitor C Piro
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin 13353, Germany
| | - Carlos García-Ferris
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC, Paterna (València) 46980, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC, Paterna (València) 46980, Spain
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin 13353, Germany
| | - Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin 13353, Germany
| |
Collapse
|
180
|
Chattopadhyay I, Nandi D, Nag A. The pint- sized powerhouse: Illuminating the mighty role of the gut microbiome in improving the outcome of anti- cancer therapy. Semin Cancer Biol 2020; 70:98-111. [PMID: 32739479 DOI: 10.1016/j.semcancer.2020.07.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/20/2020] [Accepted: 07/26/2020] [Indexed: 02/06/2023]
Abstract
Cancer persists as a major health catastrophe and a leading cause of widespread mortality across every nation. Research of several decades has increased our understanding of the pivotal pathways and key players of the host during tumor development and progression, which has enabled generation of precision therapeutics with improved efficacy. Despite such tremendous advancements in our combat against this fatal disease, a majority of the cancer patients suffer from poor tumor- free survival owing to the increased incidence of recurrent tumor. This is primarily due to the development of resistance against contemporary anti- cancer strategies. Recent studies have pointed towards the involvement of the human symbiotic gut microbiota in regulating the outcome of chemotherapy and immunotherapy. It does so primarily by modulating the metabolism of the drugs and host immune response, thereby enhancing the efficacy and ameliorating the toxicity. The interactions between the therapeutic agents, microbial community and host immunity may provide a new avenue for the clinical management of cancer. In addition, consumption of dietary pro-, pre- and synbiotics has been recognized to confer protection against tumor genesis and also promote improved response to traditional tumor suppressive strategies. Naturally, the use of various combinatorial regimes containing dietary supplements that improve the gut microbiome in amalgamation with conventional cancer treatment methods may significantly augment the therapeutic outcome of cancer patients and circumnavigate the resistance mechanisms that confound traditional therapies. In this review, we have summarized the role of the gut microbiome, which is the largest assembly of commensals within the human body, in regulating the efficacy and toxicity of various existing anti- cancer therapies including chemotherapy, immunotherapy and surgery. Furthermore, we have discussed how novel strategies integrating the application of probiotics, prebiotics, synbiotics and antibiotics in combination with the aforementioned anti- cancer modules manipulate the gut microbiota and, therefore, augment their therapeutic outcome. Together, such innovative anti- tumorigenic approaches may prove highly effective in improving the prognosis of cancer patients.
Collapse
Affiliation(s)
- Indranil Chattopadhyay
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610001, India.
| | - Deeptashree Nandi
- Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India
| | - Alo Nag
- Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India.
| |
Collapse
|
181
|
Stacchiotti V, Rezzi S, Eggersdorfer M, Galli F. Metabolic and functional interplay between gut microbiota and fat-soluble vitamins. Crit Rev Food Sci Nutr 2020; 61:3211-3232. [PMID: 32715724 DOI: 10.1080/10408398.2020.1793728] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gut microbiota is a complex ecosystem seen as an extension of human genome. It represents a major metabolic interface of interaction with food components and xenobiotics in the gastrointestinal (GI) environment. In this context, the advent of modern bacterial genome sequencing technology has enabled the identification of dietary nutrients as key determinants of gut microbial ecosystem able to modulate the host-microbiome symbiotic relationship and its effects on human health. This article provides a literature review on functional and molecular interactions between a specific group of lipids and essential nutrients, e.g., fat-soluble vitamins (FSVs), and the gut microbiota. A two-way relationship appears to emerge from the available literature with important effects on human metabolism, nutrition, GI physiology and immune function. First, FSV directly or indirectly modify the microbial composition involving for example immune system-mediated and/or metabolic mechanisms of bacterial growth or inhibition. Second, the gut microbiota influences at different levels the synthesis, metabolism and transport of FSV including their bioactive metabolites that are either introduced with the diet or released in the gut via entero-hepatic circulation. A better understanding of these interactions, and of their impact on intestinal and metabolic homeostasis, will be pivotal to design new and more efficient strategies of disease prevention and therapy, and personalized nutrition.
Collapse
Affiliation(s)
- Valentina Stacchiotti
- Micronutrient Vitamins and Lipidomics Lab, Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Serge Rezzi
- Swiss Vitamin Institute, Epalinges, Switzerland
| | - Manfred Eggersdorfer
- Department of Internal Medicine, University Medical Center Groningen, Groningen, the Netherlands
| | - Francesco Galli
- Micronutrient Vitamins and Lipidomics Lab, Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| |
Collapse
|
182
|
Lim EY, Lee SY, Shin HS, Lee J, Nam YD, Lee DO, Lee JY, Yeon SH, Son RH, Park CL, Heo YH, Kim YT. The Effect of Lactobacillus acidophilus YT1 (MENOLACTO) on Improving Menopausal Symptoms: A Randomized, Double-Blinded, Placebo-Controlled Clinical Trial. J Clin Med 2020; 9:E2173. [PMID: 32660010 PMCID: PMC7408745 DOI: 10.3390/jcm9072173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
This study evaluated the efficacy of Lactobacillus acidophilus YT1 (MENOLACTO) for alleviating menopausal symptoms. This study was a multi-center, randomized, double-blinded, placebo-controlled clinical trial involving female subjects (ages: 40-60 years) with menopausal symptoms and a Kupperman index (KMI) score ≥ 20. Subjects were administered 1 × 108 CFU/day MENOLACTO or placebo, with the primary endpoint being total KMI score, and the effect of secondary endpoints on alleviating menopausal symptoms according to individual categories of the modified KMI, as well as a quality of life questionnaire (MENQOL questionnaire). After 12 weeks, total KMI scores decreased significantly, demonstrating improved menopausal symptoms relative to placebo along with improved modified KMI scores. Additionally, quality of life, according to the MENQOL questionnaire, significantly improved in all four symptoms-physical, psychosocial, vasomotor, and sexual symptoms. Moreover, we observed no significant difference between the two groups or significant changes in blood follicle-stimulating hormone and estradiol levels or endometrial thickness. These results demonstrated that MENOLACTO alleviated menopausal symptoms without notable side effects and improved quality of life, suggesting its efficacy as an alternative supplement to alleviate menopausal symptoms in women ineligible for hormonal therapy.
Collapse
Affiliation(s)
- Eun Yeong Lim
- Division of Food Functionality Research, Korea Food Research Institute, Wanju 55365, Korea; (E.Y.L.); (S.-Y.L.); (H.S.S.); (J.L.); (Y.-D.N.)
- Department of Food Biotechnology, Korea University of Science & Technology, Daejeon 34113, Korea
| | - So-Young Lee
- Division of Food Functionality Research, Korea Food Research Institute, Wanju 55365, Korea; (E.Y.L.); (S.-Y.L.); (H.S.S.); (J.L.); (Y.-D.N.)
- Department of Food Biotechnology, Korea University of Science & Technology, Daejeon 34113, Korea
| | - Hee Soon Shin
- Division of Food Functionality Research, Korea Food Research Institute, Wanju 55365, Korea; (E.Y.L.); (S.-Y.L.); (H.S.S.); (J.L.); (Y.-D.N.)
- Department of Food Biotechnology, Korea University of Science & Technology, Daejeon 34113, Korea
| | - Jaekwang Lee
- Division of Food Functionality Research, Korea Food Research Institute, Wanju 55365, Korea; (E.Y.L.); (S.-Y.L.); (H.S.S.); (J.L.); (Y.-D.N.)
| | - Young-Do Nam
- Division of Food Functionality Research, Korea Food Research Institute, Wanju 55365, Korea; (E.Y.L.); (S.-Y.L.); (H.S.S.); (J.L.); (Y.-D.N.)
- Department of Food Biotechnology, Korea University of Science & Technology, Daejeon 34113, Korea
| | - Dong Ock Lee
- Center for Gynecologic Cancer, National Cancer Center Korea, Goyang-si 10408, Korea;
| | - Ji Young Lee
- Department of Obstetrics and Gynecology, Konkuk University Hospital, Konkuk University School of Medicine, Seoul 05030, Korea;
| | - Sung Hum Yeon
- R&D Center, Huons Co., Ltd., Ansan 15588, Korea; (S.H.Y.); (R.H.S.); (C.L.P.)
| | - Rak Ho Son
- R&D Center, Huons Co., Ltd., Ansan 15588, Korea; (S.H.Y.); (R.H.S.); (C.L.P.)
| | - Chae Lee Park
- R&D Center, Huons Co., Ltd., Ansan 15588, Korea; (S.H.Y.); (R.H.S.); (C.L.P.)
| | - Yun Haeng Heo
- Clinical Operation Team, Huons Co., Ltd., Seongnam-si 13486, Korea;
| | - Yun Tai Kim
- Division of Food Functionality Research, Korea Food Research Institute, Wanju 55365, Korea; (E.Y.L.); (S.-Y.L.); (H.S.S.); (J.L.); (Y.-D.N.)
- Department of Food Biotechnology, Korea University of Science & Technology, Daejeon 34113, Korea
| |
Collapse
|
183
|
Stiemsma LT, Nakamura RE, Nguyen JG, Michels KB. Does Consumption of Fermented Foods Modify the Human Gut Microbiota? J Nutr 2020; 150:1680-1692. [PMID: 32232406 PMCID: PMC7330458 DOI: 10.1093/jn/nxaa077] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/21/2020] [Accepted: 03/02/2020] [Indexed: 01/08/2023] Open
Abstract
The human microbiota is a key contributor to many aspects of human health and its composition is largely influenced by diet. There is a growing body of scientific evidence to suggest that gut dysbiosis (microbial imbalance of the intestine) is associated with inflammatory and immune-mediated diseases (e.g., inflammatory bowel disease and asthma). Regular consumption of fermented foods (e.g., kimchi, kefir, etc.) may represent a potential avenue to counter the proinflammatory effects of gut dysbiosis. However, an assessment of the available literature in this research area is lacking. Here we provide a critical review of current human intervention studies that analyzed the effect of fermented foods on the composition and/or function of the human gut microbiota. A total of 19 human intervention studies were identified that met this search criteria. In this review, we discuss evidence that consumption of fermented foods may modify the gut microbiota in humans. Further, there is cursory evidence to suggest that gut microbiota compositional changes mediate associations between fermented food consumption and human health outcomes. Although promising, there remains considerable heterogeneity in the human populations targeted in the intervention studies we identified. Larger longitudinal feeding studies with longer follow-up are necessary to confirm and enhance the current data. Further, future studies should consider analyzing microbiota function as a means to elucidate the mechanism linking fermented food consumption with human health. This review highlights methodologic considerations for intervention trials, emphasizing an expanse of research opportunities related to fermented food consumption in humans.
Collapse
Affiliation(s)
- Leah T Stiemsma
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Reine E Nakamura
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Jennifer G Nguyen
- Department of Biology, University of California, Los Angeles, CA, USA
| | - Karin B Michels
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| |
Collapse
|
184
|
Gut microbiota and aging-A focus on centenarians. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165765. [DOI: 10.1016/j.bbadis.2020.165765] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/10/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023]
|
185
|
Aoun A, Darwish F, Hamod N. The Influence of the Gut Microbiome on Obesity in Adults and the Role of Probiotics, Prebiotics, and Synbiotics for Weight Loss. Prev Nutr Food Sci 2020; 25:113-123. [PMID: 32676461 PMCID: PMC7333005 DOI: 10.3746/pnf.2020.25.2.113] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/08/2020] [Indexed: 12/23/2022] Open
Abstract
The link between the gut microbiome and obesity is not well defined. Understanding of the role of the gut microbiome in weight and health management may lead to future revolutionary changes for treating obesity. This review examined the relationship between obesity and the gut microbiome, and the role of probiotics, prebiotics, and synbiotics for preventing and treating obesity. We used PubMed and Google Scholar to collect appropriate articles for the review. We showed that the gut microbiome has an impact on nutrient metabolism and energy expenditure. Moreover, different modalities of obesity treatment have been shown to change the diversity and composition of the gut microbiome; this raises questions about the role these changes may play in weight loss. In addition, studies have shown that supplementation with probiotics, prebiotics, and synbiotics may alter the secretion of hormones, neurotransmitters, and inflammatory factors, thus preventing food intake triggers that lead to weight gain. Further clinical studies are needed to better understand how different species of bacteria in the gut microbiome may affect weight gain, and to determine the most appropriate doses, compositions, and regimens of probiotics, prebiotics, and synbiotics supplementation for long-term weight control.
Collapse
Affiliation(s)
- Antoine Aoun
- Faculty of Nursing and Health Sciences, Notre Dame University-Louaize, Zouk Mosbeh 72, Lebanon
| | - Fatima Darwish
- Faculty of Nursing and Health Sciences, Notre Dame University-Louaize, Zouk Mosbeh 72, Lebanon
| | - Natacha Hamod
- Faculty of Nursing and Health Sciences, Notre Dame University-Louaize, Zouk Mosbeh 72, Lebanon
| |
Collapse
|
186
|
Akimbekov NS, Digel I, Sherelkhan DK, Lutfor AB, Razzaque MS. Vitamin D and the Host-Gut Microbiome: A Brief Overview. Acta Histochem Cytochem 2020; 53:33-42. [PMID: 32624628 PMCID: PMC7322162 DOI: 10.1267/ahc.20011] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
There is a growing body of evidence for the effects of vitamin D on intestinal host-microbiome interactions related to gut dysbiosis and bowel inflammation. This brief review highlights the potential links between vitamin D and gut health, emphasizing the role of vitamin D in microbiological and immunological mechanisms of inflammatory bowel diseases. A comprehensive literature search was carried out in PubMed and Google Scholar using combinations of keywords "vitamin D," "intestines," "gut microflora," "bowel inflammation". Only articles published in English and related to the study topic are included in the review. We discuss how vitamin D (a) modulates intestinal microbiome function, (b) controls antimicrobial peptide expression, and (c) has a protective effect on epithelial barriers in the gut mucosa. Vitamin D and its nuclear receptor (VDR) regulate intestinal barrier integrity, and control innate and adaptive immunity in the gut. Metabolites from the gut microbiota may also regulate expression of VDR, while vitamin D may influence the gut microbiota and exert anti-inflammatory and immune-modulating effects. The underlying mechanism of vitamin D in the pathogenesis of bowel diseases is not fully understood, but maintaining an optimal vitamin D status appears to be beneficial for gut health. Future studies will shed light on the molecular mechanisms through which vitamin D and VDR interactions affect intestinal mucosal immunity, pathogen invasion, symbiont colonization, and antimicrobial peptide expression.
Collapse
Affiliation(s)
- Nuraly S. Akimbekov
- Department of Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Ilya Digel
- Institute for Bioengineering FH Aachen University of Applied Sciences, Jülich, Germany
| | - Dinara K. Sherelkhan
- Department of Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | - Mohammed S. Razzaque
- Department of Pathology, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| |
Collapse
|
187
|
Podolich O, Kukharenko O, Zaets I, Orlovska I, Palchykovska L, Zaika L, Sysoliatin S, Zubova G, Reva O, Galkin M, Horid'ko T, Kosiakova H, Borisova T, Kravchenko V, Skoryk M, Kremenskoy M, Ghosh P, Barh D, Góes-Neto A, Azevedo V, de Vera JP, Kozyrovska N. Fitness of Outer Membrane Vesicles From Komagataeibacter intermedius Is Altered Under the Impact of Simulated Mars-like Stressors Outside the International Space Station. Front Microbiol 2020; 11:1268. [PMID: 32676055 PMCID: PMC7333525 DOI: 10.3389/fmicb.2020.01268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
Outer membrane vesicles (OMVs), produced by nonpathogenic Gram-negative bacteria, have potentially useful biotechnological applications in extraterrestrial extreme environments. However, their biological effects under the impact of various stressors have to be elucidated for safety reasons. In the spaceflight experiment, model biofilm kombucha microbial community (KMC) samples, in which Komagataeibacter intermedius was a dominant community-member, were exposed under simulated Martian factors (i.e., pressure, atmosphere, and UV-illumination) outside the International Space Station (ISS) for 1.5 years. In this study, we have determined that OMVs from post-flight K. intermedius displayed changes in membrane composition, depending on the location of the samples and some other factors. Membrane lipids such as sterols, fatty acids (FAs), and phospholipids (PLs) were modulated under the Mars-like stressors, and saturated FAs, as well as both short-chain saturated and trans FAs, appeared in the membranes of OMVs shed by both post-UV-illuminated and “dark” bacteria. The relative content of zwitterionic and anionic PLs changed, producing a change in surface properties of outer membranes, thereby resulting in a loss of interaction capability with polynucleotides. The changed composition of membranes promoted a bigger OMV size, which correlated with changes of OMV fitness. Biochemical characterization of the membrane-associated enzymes revealed an increase in their activity (DNAse, dehydrogenase) compared to wild type. Other functional membrane-associated capabilities of OMVs (e.g., proton accumulation, interaction with linear DNA, or synaptosomes) were also altered after exposure to the spaceflight stressors. Despite alterations in membranes, vesicles did not acquire endotoxicity, cytotoxicity, and neurotoxicity. Altogether, our results show that OMVs, originating from rationally selected nonpathogenic Gram-negative bacteria, can be considered as candidates in the design of postbiotics or edible mucosal vaccines for in situ production in extreme environment. Furthermore, these OMVs could also be used as promising delivery vectors for applications in Astromedicine.
Collapse
Affiliation(s)
- Olga Podolich
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Olga Kukharenko
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Iryna Zaets
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Iryna Orlovska
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Leonid Zaika
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Ganna Zubova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Oleg Reva
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Maxym Galkin
- Palladin Institute of Biochemistry of NASU, Kyiv, Ukraine
| | | | | | | | | | - Mykola Skoryk
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | | | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | | |
Collapse
|
188
|
Pandey SN, Kwatra M, Dwivedi DK, Choubey P, Lahkar M, Jangra A. 7,8-Dihydroxyflavone alleviated the high-fat diet and alcohol-induced memory impairment: behavioral, biochemical and molecular evidence. Psychopharmacology (Berl) 2020; 237:1827-1840. [PMID: 32206827 DOI: 10.1007/s00213-020-05502-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022]
Abstract
RATIONALE Alcoholism and obesity impart a deleterious impact on human health and affects the quality of life. Chronic consumption of alcohol and western diet has been reported to cause memory deficits. 7,8-dihydroxyflavone (7,8-DHF), a TrkB agonist, comprises antioxidant and anti-inflammatory properties in treating various neurological disorders. OBJECTIVES The current study was aimed to determine the protective effect and molecular mechanism of 7,8-DHF against alcohol and high-fat diet (HFD)-induced memory deficits in rats. METHODS The adult male Wistar rats were given alcohol (3-15%) and HFD ad libitum for 12 weeks in different experimental groups. 7,8-DHF (5 mg/kg) was intraperitoneally injected daily for the last 4 weeks (9th-12th week). RESULTS The alcohol and HFD administration caused cognitive impairment as evaluated through the Morris water maze (MWM) test in alcohol, HFD, and alcohol + HFD-fed animals. The last 4-week treatment of 7,8-DHF (5 mg/kg; i.p.) attenuated alcohol and HFD-induced memory loss. 7,8-DHF treatment also restored the glutathione (GSH) level along with attenuation of nitrite, malondialdehyde content (markers of oxidative and nitrosative stress), and reduction of the acetylcholinesterase activity in the hippocampus of alcohol and HFD-fed animals. Furthermore, the administration of 7,8-DHF caused downregulation of NF-κB, iNOS, and caspase-3 and upregulation of Nrf2, HO-1, and BDNF mRNA level in rat hippocampus. CONCLUSION 7,8-DHF administration conferred beneficial effects against alcohol and HFD-induced memory deficit via its unique antioxidant, anti-inflammatory, anti-apoptotic potential, along with the activation of TrkB/BDNF signaling pathway in the hippocampus.
Collapse
Affiliation(s)
- Surya Narayan Pandey
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
| | - Mohit Kwatra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
| | - Durgesh Kumar Dwivedi
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
| | - Priyansha Choubey
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India
| | - Mangala Lahkar
- Department of Pharmacology, Gauhati Medical College, Guwahati, Assam, India
| | - Ashok Jangra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, Assam, India. .,Department of Pharmacology, KIET School of Pharmacy, KIET Group of Institutions, Ghaziabad, Uttar Pradesh, India.
| |
Collapse
|
189
|
Effect of co-trimoxazole prophylaxis on morbidity and mortality of HIV-exposed, HIV-uninfected infants in South Africa: a randomised controlled, non-inferiority trial. LANCET GLOBAL HEALTH 2020; 7:e1717-e1727. [PMID: 31708152 DOI: 10.1016/s2214-109x(19)30422-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/15/2019] [Accepted: 09/19/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND WHO guidelines recommend co-trimoxazole prophylaxis for HIV-exposed, HIV-uninfected infants. These guidelines date back to an era in which HIV testing of infants was impossible and mothers had poor access to antiretroviral treatment. To determine whether this guideline requires revision in the current era of effective prevention of mother-to-child transmission and early infant diagnosis programmes, we aimed to investigate whether receiving no co-trimoxazole prophylaxis is inferior to receiving co-trimoxazole prophylaxis in the resulting incidence of grade 3 or 4 common childhood illnesses or mortality in breastfed HIV-exposed, HIV-uninfected infants. METHODS We investigated our aim in a randomised controlled, non-inferiority trial. We enrolled the HIV-negative infants of mothers living with HIV who were actively involved in transmission prevention programmes in two clinics in Durban, South Africa. Infants were included in the study if they were breastfeeding at the screening and enrolment visits, and their mother was planning to breastfeed for at least 6 months; were a singleton birth and had a birthweight of 2 kg or more; had no clinically observed genetic disorders; and had no serious illnesses and had not received antibiotics or traditional medications (such as herbal remedies). Infants were randomly assigned (1:1) to receive co-trimoxazole or no co-trimoxazole. In the co-trimoxazole group, infants received the drug until all exposure to HIV had ceased (ie, 6 weeks after last exposure to breastmilk) and the infant was confirmed to be uninfected with HIV. The drug was administered by mothers in once-daily regimens of 20 mg trimethoprim and 100 mg sulfamethoxazole orally (age <6 months or bodyweight <5 kg), or 40 mg trimethoprim and 200 mg sulfamethoxazole orally (age >6 months or bodyweight >5 kg). Clinical and laboratory staff always remained masked to group assignment, but mothers and study counsellors were not. Infants and their mothers attended study visits at ages 6 weeks (for enrolment and randomisation), 10 weeks, 14 weeks, and then monthly from 4 to 12 months. Our primary outcome was the incidence of grade 3 or 4 common childhood illnesses (pneumonia or diarrhoea) or mortality in breastfed HIV-exposed, HIV-uninfected infants by age 12 months. A non-inferiority bound of 5% was used. The study is registered with the Pan African Clinical Trials Registry, number PACTR201311000621110, and the South African National Clinical Trials Registry, number DOH-27-0614-4728. FINDINGS We screened 1570 mother-child pairs for study enrolment, from whom (78%) eligible infants were enrolled into the study between Oct 16, 2013, and May 23, 2018. Of the infants enrolled, 611 (50%) were randomly assigned to the co-trimoxazole group and 609 (50%) were randomly assigned to the no co-trimoxazole group. One (<1%) infant in the no co-trimoxazole group was excluded from the analysis of the final outcomes for having received traditional medicine (which only became apparent after randomisation); therefore, 611 (50%) infants in the co-trimoxazole group and 608 (50%) infants in the no co-trimoxazole group were included in the final intention-to-treat analysis. 136 (22%) infants in the co-trimoxazole group and 139 (23%) infants in the no co-trimoxazole group did not complete the 12-month study visit, predominantly because of loss to follow-up (93 [15%] infants in the co-trimoxazole group; 90 [15%] infants in the no co-trimoxazole group). The cumulative probability of the composite primary outcome was 0·114 (95% CI 0·076 to 0·147; 49 events) in the co-trimoxazole group versus 0·0795 (0·044 to 0·115; 39 events) in the no co-trimoxazole group. The risk difference (no co-trimoxazole group minus co-trimoxazole group) was -0·0319 (-0·075 to 0·011), meaning that the risk was around 3 percentage points lower in the no co-trimoxazole group on the additive scale. INTERPRETATION We can conclude that no co-trimoxazole is not inferior to daily co-trimoxazole among breastfed HIV-exposed, HIV-uninfected infants whose mothers are accessing a prevention of mother-to-child transmission programme in an area unaffected by malaria. We therefore believe that WHO should revise the co-trimoxazole guidelines for HIV-exposed, HIV-uninfected infants in areas unaffected by malaria. FUNDING HIV Prevention Research Unit of the South African Medical Research Council and the Family Larsson-Rosenquist Foundation.
Collapse
|
190
|
Szőke H, Kovács Z, Bókkon I, Vagedes J, Szabó AE, Hegyi G, Sterner MG, Kiss Á, Kapócs G. Gut dysbiosis and serotonin: intestinal 5-HT as a ubiquitous membrane permeability regulator in host tissues, organs, and the brain. Rev Neurosci 2020; 31:415-425. [DOI: 10.1515/revneuro-2019-0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022]
Abstract
AbstractThe microbiota and microbiome and disruption of the gut-brain axis were linked to various metabolic, immunological, physiological, neurodevelopmental, and neuropsychiatric diseases. After a brief review of the relevant literature, we present our hypothesis that intestinal serotonin, produced by intestinal enterochromaffin cells, picked up and stored by circulating platelets, participates and has an important role in the regulation of membrane permeability in the intestine, brain, and other organs. In addition, intestinal serotonin may act as a hormone-like continuous regulatory signal for the whole body, including the brain. This regulatory signal function is mediated by platelets and is primarily dependent on and reflects the intestine’s actual health condition. This hypothesis may partially explain why gut dysbiosis could be linked to various human pathological conditions as well as neurodevelopmental and neuropsychiatric disorders.
Collapse
Affiliation(s)
- Henrik Szőke
- Department of CAM, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
- Doctorate School, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Zoltán Kovács
- Doctorate School, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - István Bókkon
- Vision Research Institute, Neuroscience and Consciousness Research Department, Lowell, MA, USA
- Psychosomatic Outpatient Clinics, Budapest, Hungary
| | - Jan Vagedes
- University of Tübingen, Children’s Hospital, Tübingen, Germany
- ARCIM Institute (Academic Research in Complementary and Integrative Medicine), Filderstadt, Germany
| | | | - Gabriella Hegyi
- Department of CAM, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
- Doctorate School, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | | | - Ágnes Kiss
- Doctorate School, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Gábor Kapócs
- Buda Family-Centered Mental Health Centre, Department of Psychiatry and Psychiatric Rehabilitation, Teaching Department of Semmelweis University, New Saint John Hospital, Budapest, Hungary
- Institute for Behavioral Sciences, Semmelweis University, Budapest, Hungary
| |
Collapse
|
191
|
Nance CL, Deniskin R, Diaz VC, Paul M, Anvari S, Anagnostou A. The Role of the Microbiome in Food Allergy: A Review. CHILDREN-BASEL 2020; 7:children7060050. [PMID: 32466620 PMCID: PMC7346163 DOI: 10.3390/children7060050] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/17/2020] [Indexed: 02/06/2023]
Abstract
Food allergies are common and estimated to affect 8% of children and 11% of adults in the United States. They pose a significant burden—physical, economic and social—to those affected. There is currently no available cure for food allergies. Emerging evidence suggests that the microbiome contributes to the development and manifestations of atopic disease. According to the hygiene hypothesis, children growing up with older siblings have a lower incidence of allergic disease compared with children from smaller families, due to their early exposure to microbes in the home. Research has also demonstrated that certain environmental exposures, such as a farming environment, during early life are associated with a diverse bacterial experience and reduced risk of allergic sensitization. Dysregulation in the homeostatic interaction between the host and the microbiome or gut dysbiosis appears to precede the development of food allergy, and the timing of such dysbiosis is critical. The microbiome affects food tolerance via the secretion of microbial metabolites (e.g., short chain fatty acids) and the expression of microbial cellular components. Understanding the biology of the microbiome and how it interacts with the host to maintain gut homeostasis is helpful in developing smarter therapeutic approaches. There are ongoing trials evaluating the benefits of probiotics and prebiotics, for the prevention and treatment of atopic diseases to correct the dysbiosis. However, the routine use of probiotics as an intervention for preventing allergic disease is not currently recommended. A new approach in microbial intervention is to attempt a more general modification of the gut microbiome, such as with fecal microbiota transplantation. Developing targeted bacterial therapies for food allergy may be promising for both the treatment and prevention of food allergy. Similarly, fecal microbiota transplantation is being explored as a potentially beneficial interventional approach. Overall, targeted bacterial therapies for food allergy may be promising for both the treatment and prevention of food allergy.
Collapse
Affiliation(s)
- Christina L. Nance
- Baylor College of Medicine, Section of Pediatric Immunology, Allergy and Retrovirology, Houston, TX 77030 USA; (C.L.N.); (R.D.); (V.C.D.); (M.P.); (S.A.)
- Texas Children’s Hospital, Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Houston, TX 77030, USA
| | - Roman Deniskin
- Baylor College of Medicine, Section of Pediatric Immunology, Allergy and Retrovirology, Houston, TX 77030 USA; (C.L.N.); (R.D.); (V.C.D.); (M.P.); (S.A.)
- Texas Children’s Hospital, Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Houston, TX 77030, USA
| | - Veronica C. Diaz
- Baylor College of Medicine, Section of Pediatric Immunology, Allergy and Retrovirology, Houston, TX 77030 USA; (C.L.N.); (R.D.); (V.C.D.); (M.P.); (S.A.)
- Texas Children’s Hospital, Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Houston, TX 77030, USA
| | - Misu Paul
- Baylor College of Medicine, Section of Pediatric Immunology, Allergy and Retrovirology, Houston, TX 77030 USA; (C.L.N.); (R.D.); (V.C.D.); (M.P.); (S.A.)
- Texas Children’s Hospital, Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Houston, TX 77030, USA
| | - Sara Anvari
- Baylor College of Medicine, Section of Pediatric Immunology, Allergy and Retrovirology, Houston, TX 77030 USA; (C.L.N.); (R.D.); (V.C.D.); (M.P.); (S.A.)
- Texas Children’s Hospital, Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Houston, TX 77030, USA
| | - Aikaterini Anagnostou
- Baylor College of Medicine, Section of Pediatric Immunology, Allergy and Retrovirology, Houston, TX 77030 USA; (C.L.N.); (R.D.); (V.C.D.); (M.P.); (S.A.)
- Texas Children’s Hospital, Department of Pediatrics, Section of Immunology, Allergy and Retrovirology, Houston, TX 77030, USA
- Correspondence:
| |
Collapse
|
192
|
Boraschi D, Alijagic A, Auguste M, Barbero F, Ferrari E, Hernadi S, Mayall C, Michelini S, Navarro Pacheco NI, Prinelli A, Swart E, Swartzwelter BJ, Bastús NG, Canesi L, Drobne D, Duschl A, Ewart MA, Horejs-Hoeck J, Italiani P, Kemmerling B, Kille P, Prochazkova P, Puntes VF, Spurgeon DJ, Svendsen C, Wilde CJ, Pinsino A. Addressing Nanomaterial Immunosafety by Evaluating Innate Immunity across Living Species. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000598. [PMID: 32363795 DOI: 10.1002/smll.202000598] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
The interaction of a living organism with external foreign agents is a central issue for its survival and adaptation to the environment. Nanosafety should be considered within this perspective, and it should be examined that how different organisms interact with engineered nanomaterials (NM) by either mounting a defensive response or by physiologically adapting to them. Herein, the interaction of NM with one of the major biological systems deputed to recognition of and response to foreign challenges, i.e., the immune system, is specifically addressed. The main focus is innate immunity, the only type of immunity in plants, invertebrates, and lower vertebrates, and that coexists with adaptive immunity in higher vertebrates. Because of their presence in the majority of eukaryotic living organisms, innate immune responses can be viewed in a comparative context. In the majority of cases, the interaction of NM with living organisms results in innate immune reactions that eliminate the possible danger with mechanisms that do not lead to damage. While in some cases such interaction may lead to pathological consequences, in some other cases beneficial effects can be identified.
Collapse
Affiliation(s)
- Diana Boraschi
- Institute of Biochemistry and Cell Biology, National Research Council, Napoli, 80131, Italy
| | - Andi Alijagic
- Institute for Biomedical Research and Innovation, National Research Council, Palermo, 90146, Italy
| | - Manon Auguste
- Department of Earth, Environment and Life Sciences, University of Genova, Genova, 16126, Italy
| | - Francesco Barbero
- Institut Català de Nanosciència i Nanotecnologia (ICN2), Bellaterra, Barcelona, 08193, Spain
| | - Eleonora Ferrari
- Center for Plant Molecular Biology - ZMBP, Eberhard-Karls University Tübingen, Tübingen, 72076, Germany
| | - Szabolcs Hernadi
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Craig Mayall
- Department of Biology, Biotechnical Faculty, University of Liubljana, Ljubljana, 1000, Slovenia
| | - Sara Michelini
- Department of Biosciences, Paris-Lodron University Salzburg, Salzburg, 5020, Austria
| | | | | | - Elmer Swart
- UK Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | | | - Neus G Bastús
- Institut Català de Nanosciència i Nanotecnologia (ICN2), Bellaterra, Barcelona, 08193, Spain
| | - Laura Canesi
- Department of Earth, Environment and Life Sciences, University of Genova, Genova, 16126, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Liubljana, Ljubljana, 1000, Slovenia
| | - Albert Duschl
- Department of Biosciences, Paris-Lodron University Salzburg, Salzburg, 5020, Austria
| | | | - Jutta Horejs-Hoeck
- Department of Biosciences, Paris-Lodron University Salzburg, Salzburg, 5020, Austria
| | - Paola Italiani
- Institute of Biochemistry and Cell Biology, National Research Council, Napoli, 80131, Italy
| | - Birgit Kemmerling
- Center for Plant Molecular Biology - ZMBP, Eberhard-Karls University Tübingen, Tübingen, 72076, Germany
| | - Peter Kille
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Petra Prochazkova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, 142 20, Czech Republic
| | - Victor F Puntes
- Institut Català de Nanosciència i Nanotecnologia (ICN2), Bellaterra, Barcelona, 08193, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain
- Vall d Hebron, Institut de Recerca (VHIR), Barcelona, 08035, Spain
| | | | - Claus Svendsen
- UK Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | | | - Annalisa Pinsino
- Institute for Biomedical Research and Innovation, National Research Council, Palermo, 90146, Italy
| |
Collapse
|
193
|
Gargari G, Taverniti V, Koirala R, Gardana C, Guglielmetti S. Impact of a Multistrain Probiotic Formulation with High Bifidobacterial Content on the Fecal Bacterial Community and Short-Chain Fatty Acid Levels of Healthy Adults. Microorganisms 2020; 8:microorganisms8040492. [PMID: 32235660 PMCID: PMC7232159 DOI: 10.3390/microorganisms8040492] [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: 03/12/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 02/08/2023] Open
Abstract
The consumption of probiotic products is continually increasing, supported by growing scientific evidence of their efficacy. Considering that probiotics may primarily affect health (either positively or negatively) through gut microbiota modulation, the first aspect that should be evaluated is their impact on the intestinal microbial ecosystem. In this study, we longitudinally analyzed the bacterial taxonomic composition and organic acid levels in four fecal samples collected over the course of four weeks from 19 healthy adults who ingested one capsule a day for two weeks of a formulation containing at least 70 billion colony-forming units, consisting of 25% lactobacilli and 75% Bifidobacterium animalis subsp. lactis. We found that 16S rRNA gene profiling showed that probiotic intake only induced an increase in a single operational taxonomic unit ascribed to B. animalis, plausibly corresponding to the ingested bifidobacterial strain. Furthermore, liquid chromatography/mass spectrometry revealed a significant increase in the lactate and acetate/butyrate ratio and a trend toward a decrease in succinate following probiotic administration. The presented results indicate that the investigated probiotic formulation did not alter the intestinal bacterial ecosystem of healthy adults and suggest its potential ability to promote colonization resistance in the gut through a transient increase in fecal bifidobacteria, lactic acid, and the acetate/butyrate ratio.
Collapse
Affiliation(s)
- Giorgio Gargari
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy; (G.G.); (V.T.); (R.K.)
| | - Valentina Taverniti
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy; (G.G.); (V.T.); (R.K.)
| | - Ranjan Koirala
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy; (G.G.); (V.T.); (R.K.)
| | - Claudio Gardana
- Division of Human Nutrition, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy;
| | - Simone Guglielmetti
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133 Milan, Italy; (G.G.); (V.T.); (R.K.)
- Correspondence: ; Tel.: +39-02-5031-9136
| |
Collapse
|
194
|
Philips CA, Augustine P, Yerol PK, Ramesh GN, Ahamed R, Rajesh S, George T, Kumbar S. Modulating the Intestinal Microbiota: Therapeutic Opportunities in Liver Disease. J Clin Transl Hepatol 2020; 8:87-99. [PMID: 32274349 PMCID: PMC7132020 DOI: 10.14218/jcth.2019.00035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/11/2019] [Accepted: 10/27/2019] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota has been demonstrated to have a significant impact on the initiation, progression and development of complications associated with multiple liver diseases. Notably, nonalcoholic fatty liver diseases, including nonalcoholic steatohepatitis and cirrhosis, severe alcoholic hepatitis, primary sclerosing cholangitis and hepatic encephalopathy, have strong links to dysbiosis - or a pathobiological change in the microbiota. In this review, we provide clear and concise discussions on the human gut microbiota, methods of identifying gut microbiota and its functionality, liver diseases that are affected by the gut microbiota, including novel associations under research, and provide current evidence on the modulation of gut microbiota and its effects on specific liver disease conditions.
Collapse
Affiliation(s)
- Cyriac Abby Philips
- The Liver Unit, Monarch Liver Lab and Division of Gastroenterology, Cochin Gastroenterology Group, Ernakulam Medical Centre, Kochi, Kerala, India
| | - Philip Augustine
- The Liver Unit, Monarch Liver Lab and Division of Gastroenterology, Cochin Gastroenterology Group, Ernakulam Medical Centre, Kochi, Kerala, India
| | - Praveen Kumar Yerol
- Department of Gastroenterology, State Government Medical College, Thrissur, Kerala, India
| | | | - Rizwan Ahamed
- The Liver Unit, Monarch Liver Lab and Division of Gastroenterology, Cochin Gastroenterology Group, Ernakulam Medical Centre, Kochi, Kerala, India
| | - Sasidharan Rajesh
- The Liver Unit, Monarch Liver Lab and Division of Gastroenterology, Cochin Gastroenterology Group, Ernakulam Medical Centre, Kochi, Kerala, India
| | - Tom George
- The Liver Unit, Monarch Liver Lab and Division of Gastroenterology, Cochin Gastroenterology Group, Ernakulam Medical Centre, Kochi, Kerala, India
| | - Sandeep Kumbar
- The Liver Unit, Monarch Liver Lab and Division of Gastroenterology, Cochin Gastroenterology Group, Ernakulam Medical Centre, Kochi, Kerala, India
| |
Collapse
|
195
|
van Hensbergen VP, Wu Y, van Sorge NM, Touqui L. Type IIA Secreted Phospholipase A2 in Host Defense against Bacterial Infections. Trends Immunol 2020; 41:313-326. [PMID: 32151494 DOI: 10.1016/j.it.2020.02.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 12/13/2022]
Abstract
The enzyme type IIA secreted phospholipase A2 (sPLA2-IIA) is crucial for mammalian innate host defense against bacterial pathogens. Most studies have investigated the role of sPLA2-IIA in systemic bacterial infections, identifying molecular pathways of bacterial resistance against sPLA2-IIA-mediated killing, and providing insight into sPLA2-IIA mechanisms of action. Sensitization of (antibiotic-resistant) bacteria to sPLA2-IIA action by blocking bacterial resistance or by applying sPLA2-IIA to treat bacterial infections might represent a therapeutic option in the future. Because sPLA2-IIA is highly expressed at mucosal barriers, we also discuss how sPLA2-IIA is likely to be an important driver of microbiome composition; we anticipate that future research in this area may bring new insights into the role of sPLA2-IIA in health and disease.
Collapse
Affiliation(s)
- Vincent P van Hensbergen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Yongzheng Wu
- Unité de Biologie Cellulaire de l'infection Microbienne, CNRS UMR3691, Institut Pasteur, Paris, France
| | - Nina M van Sorge
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Lhousseine Touqui
- Mucoviscidose et Bronchopathies Chroniques, département Santé Globale; Pasteur Institute, Paris, France.
| |
Collapse
|
196
|
Cӑtoi AF, Vodnar DC, Corina A, Nikolic D, Citarrella R, Pérez-Martínez P, Rizzo M. Gut Microbiota, Obesity and Bariatric Surgery: Current Knowledge and Future Perspectives. Curr Pharm Des 2020; 25:2038-2050. [PMID: 31298152 DOI: 10.2174/1381612825666190708190437] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND There is an urgent need for a better understanding and management of obesity and obesity- associated diseases. It is known that obesity is associated with structural and functional changes in the microbiome. METHODS The purpose of this review is to present current evidence from animal and human studies, demonstrating the effects and the potential efficacy of microbiota modulation in improving obesity and associated metabolic dysfunctions. RESULTS This review discusses possible mechanisms linking gut microbiota dysbiosis and obesity, since there is a dual interaction between the two of them. Furthermore, comments on bariatric surgery, as a favourable model to understand the underlying metabolic and inflammatory effects, as well as its association with changes in the composition of the gut microbiota, are included. Also, a possible impact of anti-obesity drugs and the novel antidiabetic drugs on the gut microbiota has been briefly discussed. CONCLUSION More research is needed to better understand here discussed the association between microbiota modulation and obesity. It is expected that research in this field, in the following years, will lead to a personalized therapeutic approach considering the patient's microbiome, and also give rise to the discovery of new drugs and/or the combination therapies for the management of obesity and obesity-related co-morbidities.
Collapse
Affiliation(s)
- Adriana Florinela Cӑtoi
- Pathophysiology Department, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Dan Cristian Vodnar
- Department of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Andreea Corina
- Lipids and Atherosclerosis Research Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | - Dragana Nikolic
- PROMISE Department, University of Palermo, Italy.,Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | | | - Pablo Pérez-Martínez
- Lipids and Atherosclerosis Research Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba, Cordoba, Spain.,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | | |
Collapse
|
197
|
Donertas Ayaz B, Zubcevic J. Gut microbiota and neuroinflammation in pathogenesis of hypertension: A potential role for hydrogen sulfide. Pharmacol Res 2020; 153:104677. [PMID: 32023431 PMCID: PMC7056572 DOI: 10.1016/j.phrs.2020.104677] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/27/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
Inflammation and gut dysbiosis are hallmarks of hypertension (HTN). Hydrogen sulfide (H2S) is an important freely diffusing molecule that modulates the function of neural, cardiovascular and immune systems, and circulating levels of H2S are reduced in animals and humans with HTN. While most research to date has focused on H₂S produced endogenously by the host, H2S is also produced by the gut bacteria and may affect the host homeostasis. Here, we review an association between neuroinflammation and gut dysbiosis in HTN, with special emphasis on a potential role of H2S in this interplay.
Collapse
Affiliation(s)
- Basak Donertas Ayaz
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States; Department of Pharmacology, College of Medicine, University of Eskisehir Osmangazi, Eskisehir, Turkey
| | - Jasenka Zubcevic
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.
| |
Collapse
|
198
|
Urban-level environmental factors related to pediatric asthma. Porto Biomed J 2020; 5:e57. [PMID: 33299939 PMCID: PMC7722407 DOI: 10.1097/j.pbj.0000000000000057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/06/2020] [Indexed: 01/22/2023] Open
Abstract
During the 20th century, urbanization has increasing and represented a major demographic and environmental change in developed countries. This ever-changing urban environment has an impact on disease patterns and prevalence, namely on noncommunicable diseases, such as asthma and allergy, and poses many challenges to understand the relationship between the changing urban environment and the children health. The complex interaction between human beings and urbanization is dependent not only on individual determinants such as sex, age, social or economic resources, and lifestyles and behaviors, but also on environment, including air pollution, indoors and outdoors, land use, biodiversity, and handiness of green areas. Therefore, the assessment and identification of the impact of urban environment on children's health have become a priority and many recent studies have been conducted with the goal of better understanding the impacts related to urbanization, characterizing indoor air exposure, identifying types of neighborhoods, or characteristics of neighborhoods that promote health benefits. Thus, this review focuses on the role of urban environmental factors on pediatric asthma.
Collapse
|
199
|
Ndeh D, Baslé A, Strahl H, Yates EA, McClurgg UL, Henrissat B, Terrapon N, Cartmell A. Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus. Nat Commun 2020; 11:646. [PMID: 32005816 PMCID: PMC6994673 DOI: 10.1038/s41467-020-14509-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/10/2020] [Indexed: 01/31/2023] Open
Abstract
The human gut microbiota (HGM), which is critical to human health, utilises complex glycans as its major carbon source. Glycosaminoglycans represent an important, high priority, nutrient source for the HGM. Pathways for the metabolism of various glycosaminoglycan substrates remain ill-defined. Here we perform a biochemical, genetic and structural dissection of the genetic loci that orchestrates glycosaminoglycan metabolism in the organism Bacteroides thetaiotaomicron. Here, we report: the discovery of two previously unknown surface glycan binding proteins which facilitate glycosaminoglycan import into the periplasm; distinct kinetic and genetic specificities of various periplasmic lyases which dictate glycosaminoglycan metabolic pathways; understanding of endo sulfatase activity questioning the paradigm of how the 'sulfation problem' is handled by the HGM; and 3D crystal structures of the polysaccharide utilisation loci encoded sulfatases. Together with comparative genomic studies, our study fills major gaps in our knowledge of glycosaminoglycan metabolism by the HGM.
Collapse
Affiliation(s)
- Didier Ndeh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Urszula L McClurgg
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 23218, Saudi Arabia
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288, Marseille, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
| | - Alan Cartmell
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| |
Collapse
|
200
|
Ciobârcă D, Cătoi AF, Copăescu C, Miere D, Crișan G. Bariatric Surgery in Obesity: Effects on Gut Microbiota and Micronutrient Status. Nutrients 2020; 12:E235. [PMID: 31963247 PMCID: PMC7019602 DOI: 10.3390/nu12010235] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/30/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Obesity is associated with reduced gut microbial diversity and a high rate of micronutrient deficiency. Bariatric surgery, the therapy of choice for severe obesity, produces sustained weight loss and improvements in obesity-related comorbidities. Also, it significantly alters the gut microbiota (GM) composition and function, which might have an important impact on the micronutrient status as GM is able to synthesize certain vitamins, such as riboflavin, folate, B12, or vitamin K2. However, recent data have reported that GM is not fully restored after bariatric surgery; therefore, manipulation of GM through probiotics represents a promising therapeutic approach in bariatric patients. In this review, we discuss the latest evidence concerning the relationship between obesity, GM and micronutrients, the impact of bariatric surgery on GM in relation with micronutrients equilibrium, and the importance of the probiotics' supplementation in obese patients submitted to surgical treatment.
Collapse
Affiliation(s)
- Daniela Ciobârcă
- Department of Bromatology, Hygiene, Nutrition, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 23 Gheorghe Marinescu Street, 400337 Cluj-Napoca, Romania
| | - Adriana Florinela Cătoi
- Department of Physiopathology, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 3-4 Victor Babes Street, 400012 Cluj-Napoca, Romania
| | - Cătălin Copăescu
- General Surgery Department, Ponderas Hospital, 85A Nicolae G. Caramfil Street, 014142 Bucharest, Romania;
| | - Doina Miere
- Department of Bromatology, Hygiene, Nutrition, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 23 Gheorghe Marinescu Street, 400337 Cluj-Napoca, Romania
| | - Gianina Crișan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 23 Gheorghe Marinescu Street, 400337 Cluj-Napoca, Romania;
| |
Collapse
|