1
|
Lippincott RA, O’Connor J, Neff CP, Lozupone C, Palmer BE. Deciphering HIV-associated inflammation: microbiome's influence and experimental insights. Curr Opin HIV AIDS 2024; 19:228-233. [PMID: 38884255 PMCID: PMC11305906 DOI: 10.1097/coh.0000000000000866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
PURPOSE OF REVIEW To review novel experimental approaches for studying host:microbe interactions and their role in intestinal and systemic inflammation in people living with HIV (PLWH). RECENT FINDINGS Inflammation in PLWH is impacted by interactions between the microbiome, the intestinal epithelium, and immune cells. This complex interplay is not fully understood and requires a variety of analytical techniques to study. Using a multiomic systems biology approach provides hypothesis generating data on host:microbe interactions that can be used to guide further investigation. The direct interactions between host cells and microbes can be elucidated using peripheral blood mononuclear cells (PBMCs), lamina propria mononuclear cells (LPMC's) or human intestinal organoids (HIO). Additionally, the broader relationship between the host and the microbiome can be explored using animal models such as nonhuman primates and germ-free and double humanized mice. SUMMARY To explore complex host:microbe relationships, hypotheses are generated and investigations are guided by multiomic data, while causal components are identified using in-vitro and in-vivo assays.
Collapse
Affiliation(s)
| | - John O’Connor
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | |
Collapse
|
2
|
Lu X, Ma J, Guo L, Wu W, Li R. Associations of genetic variants contributing to gut microbiota composition in diabetic nephropathy. Front Endocrinol (Lausanne) 2023; 14:1264517. [PMID: 38189041 PMCID: PMC10771622 DOI: 10.3389/fendo.2023.1264517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/17/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The gut microbiota is strongly associated with multiple kidney diseases, and since microbial composition is heritable, we hypothesized that genetic variations controlling gut microbiota composition were associated with diabetic nephropathy susceptibility or clinical subphenotypes. Methods The genetic variations associated with gut microbiota were retrieved from the genome-wide association study database and analysed in our diabetic nephropathy susceptibility gene screening cohort. Candidate microorganisms with possible genetic associations were identified using the annotation of microbial quantitative trait loci. Finally, the candidate microorganisms were verified by 16S rDNA gene sequencing. Results There were 13 genetic variation loci associated with susceptibility to diabetic nephropathy. The TCF7L2 risk genotype was associated with a long duration of diabetes and high diastolic blood pressure, the ZCWPW2 risk genotype was associated with increased glycosylated hemoglobin, and the ZNRF3 risk genotype was associated with an increased urinary microalbumin-to-creatinine ratio. Both the ZNRF3 and SPECC1L risk genotypes were associated with the abundance of Lactococcus. 16S rDNA sequencing confirmed that there was indeed a significant difference in the Lactococcus genus between DN and DM patients. Conclusions In this study, we preliminarily confirmed that the gut microbiota of diabetic nephropathy patients is influenced by host genetics and provide a new basis for future accurate diagnosis and treatment.
Collapse
Affiliation(s)
- Xiao Lu
- Department of Nephrology, Fifth Hospital of Shanxi Medical University (Shanxi Provincial People’s Hospital), Taiyuan, China
| | - Junjun Ma
- Department of Thoracic Surgery, Fifth Hospital of Shanxi Medical University (Shanxi Provincial People’s Hospital), Taiyuan, China
| | - Lili Guo
- Shanxi Provincial Key Laboratory of Kidney Disease, Fifth Hospital of Shanxi Medical University (Shanxi Provincial People’s Hospital), Taiyuan, China
| | - Wei Wu
- Department of Clinical Laboratory, Fifth Hospital of Shanxi Medical University (Shanxi Provincial People’s Hospital), Taiyuan, China
| | - Rongshan Li
- Department of Clinical Laboratory, Fifth Hospital of Shanxi Medical University (Shanxi Provincial People’s Hospital), Taiyuan, China
| |
Collapse
|
3
|
Bensch HM, Lundin D, Tolf C, Waldenström J, Zöttl M. Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal. J Evol Biol 2023; 36:1753-1760. [PMID: 37584218 DOI: 10.1111/jeb.14208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/27/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
In social species, group members commonly show substantial similarity in gut microbiome composition. Such similarities have been hypothesized to arise either by shared environmental effects or by host relatedness. However, disentangling these factors is difficult, because group members are often related, and social groups typically share similar environmental conditions. In this study, we conducted a cross-foster experiment under controlled laboratory conditions in group-living Damaraland mole-rats (Fukomys damarensis) and used 16S amplicon sequencing to disentangle the effects of the environment and relatedness on gut microbiome similarity and diversity. Our results show that a shared environment is the main factor explaining gut microbiome similarity, overshadowing any effect of host relatedness. Together with studies in wild animal populations, our results suggest that among conspecifics environmental factors are more powerful drivers of gut microbiome composition similarity than host genetics.
Collapse
Affiliation(s)
- Hanna M Bensch
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
- Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
| | - Daniel Lundin
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Conny Tolf
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Jonas Waldenström
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Markus Zöttl
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
- Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
| |
Collapse
|
4
|
Mousavinasab F, Karimi R, Taheri S, Ahmadvand F, Sanaaee S, Najafi S, Halvaii MS, Haghgoo A, Zamany M, Majidpoor J, Khosravifar M, Baniasadi M, Talebi M, Movafagh A, Aghaei-Zarch SM, Khorram N, Farnia P, Kalhor K. Microbiome modulation in inflammatory diseases: Progress to microbiome genetic engineering. Cancer Cell Int 2023; 23:271. [PMID: 37951913 PMCID: PMC10640760 DOI: 10.1186/s12935-023-03095-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 10/07/2023] [Indexed: 11/14/2023] Open
Abstract
Recent developments in sequencing technology and analytical approaches have allowed researchers to show that the healthy gut microbiome is very varied and capable of performing a wide range of tasks. The importance of gut microbiota in controlling immunological, neurological, and endocrine function is becoming well-recognized. Thereby, numerous inflammatory diseases, including those that impact the gastrointestinal system, as well as less obvious ones, including Rheumatoid arthritis (RA), cancer, gestational diabetes (GD), type 1 diabetes (T1D), and type 2 diabetes (T2D), have been linked to dysbiotic gut microbiota. Microbiome engineering is a rapidly evolving frontier for solutions to improve human health. Microbiome engineering seeks to improve the function of an ecosystem by manipulating the composition of microbes. Thereby, generating potential therapies against metabolic, inflammatory, and immunological diseases will be possible through microbiome engineering. This essay first provides an overview of the traditional technological instruments that might be used for microbiome engineering, such as Fecal Microbiota Transplantation (FMT), prebiotics, and probiotics. Moreover, we will also discuss experimental genetic methods such as Metagenomic Alteration of Gut microbiome by In situ Conjugation (MAGIC), Bacteriophage, and Conjugative plasmids in manipulating intestinal microbiota.
Collapse
Affiliation(s)
| | - Ronika Karimi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sima Taheri
- Department of Microbiology, Shahr Qods Branch, Islamic Azad University, Tehran, Iran
| | | | - Saameh Sanaaee
- Department of New Science, Faculty of Cellular and Molecular biology, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Alireza Haghgoo
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Marzieh Zamany
- Shahid Akbarabadi Clinical Research Development Unit, Iran University of medical Science, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Mina Khosravifar
- Institute of Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mohammad Baniasadi
- Department of Basic Sciences, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Mehrdad Talebi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Abolfazl Movafagh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Nastaran Khorram
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran.
| | - Poopak Farnia
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Kambiz Kalhor
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, USA
| |
Collapse
|
5
|
Salvador AC, Huda MN, Arends D, Elsaadi AM, Gacasan CA, Brockmann GA, Valdar W, Bennett BJ, Threadgill DW. Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets. MICROBIOME 2023; 11:220. [PMID: 37784178 PMCID: PMC10546677 DOI: 10.1186/s40168-023-01588-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/01/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND The gut microbiota is modulated by a combination of diet, host genetics, and sex effects. The magnitude of these effects and interactions among them is important to understanding inter-individual variability in gut microbiota. In a previous study, mouse strain-specific responses to American and ketogenic diets were observed along with several QTLs for metabolic traits. In the current study, we searched for genetic variants underlying differences in the gut microbiota in response to American and ketogenic diets, which are high in fat and vary in carbohydrate composition, between C57BL/6 J (B6) and FVB/NJ (FVB) mouse strains. RESULTS Genetic mapping of microbial features revealed 18 loci under the QTL model (i.e., marginal effects that are not specific to diet or sex), 12 loci under the QTL by diet model, and 1 locus under the QTL by sex model. Multiple metabolic and microbial features map to the distal part of Chr 1 and Chr 16 along with eigenvectors extracted from principal coordinate analysis of measures of β-diversity. Bilophila, Ruminiclostridium 9, and Rikenella (Chr 1) were identified as sex- and diet-independent QTL candidate keystone organisms, and Parabacteroides (Chr 16) was identified as a diet-specific, candidate keystone organism in confirmatory factor analyses of traits mapping to these regions. For many microbial features, irrespective of which QTL model was used, diet or the interaction between diet and a genotype were the strongest predictors of the abundance of each microbial trait. Sex, while important to the analyses, was not as strong of a predictor for microbial abundances. CONCLUSIONS These results demonstrate that sex, diet, and genetic background have different magnitudes of effects on inter-individual differences in gut microbiota. Therefore, Precision Nutrition through the integration of genetic variation, microbiota, and sex affecting microbiota variation will be important to predict response to diets varying in carbohydrate composition. Video Abstract.
Collapse
Affiliation(s)
- Anna C Salvador
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
| | - M Nazmul Huda
- Department of Nutrition, University of California Davis, Sacramento, CA, 95616, USA
- Obesity and Metabolism Unit, Western Human Nutrition Research Center, USDA-ARS, Davis, CA, 95616, USA
| | - Danny Arends
- Albrecht Daniel Thaer-Institut, 10115, Berlin, Germany
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Ahmed M Elsaadi
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA
| | - C Anthony Gacasan
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA
| | | | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brian J Bennett
- Department of Nutrition, University of California Davis, Sacramento, CA, 95616, USA
- Obesity and Metabolism Unit, Western Human Nutrition Research Center, USDA-ARS, Davis, CA, 95616, USA
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA.
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
6
|
Nagarajan A, Scoggin K, Gupta J, Threadgill DW, Andrews-Polymenis HL. Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome. MICROBIOME 2023; 11:149. [PMID: 37420306 PMCID: PMC10329326 DOI: 10.1186/s40168-023-01552-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/18/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND The human gut microbiota is a complex community comprised of trillions of bacteria and is critical for the digestion and absorption of nutrients. Bacterial communities of the intestinal microbiota influence the development of several conditions and diseases. We studied the effect of host genetics on gut microbial composition using Collaborative Cross (CC) mice. CC mice are a panel of mice that are genetically diverse across strains, but genetically identical within a given strain allowing repetition and deeper analysis than is possible with other collections of genetically diverse mice. RESULTS 16S rRNA from the feces of 167 mice from 28 different CC strains was sequenced and analyzed using the Qiime2 pipeline. We observed a large variance in the bacterial composition across CC strains starting at the phylum level. Using bacterial composition data, we identified 17 significant Quantitative Trait Loci (QTL) linked to 14 genera on 9 different mouse chromosomes. Genes within these intervals were analyzed for significant association with pathways and the previously known human GWAS database using Enrichr analysis and Genecards database. Multiple host genes involved in obesity, glucose homeostasis, immunity, neurological diseases, and many other protein-coding genes located in these regions may play roles in determining the composition of the gut microbiota. A subset of these CC mice was infected with Salmonella Typhimurium. Using infection outcome data, an increase in abundance of genus Lachnospiraceae and decrease in genus Parasutterella correlated with positive health outcomes after infection. Machine learning classifiers accurately predicted the CC strain and the infection outcome using pre-infection bacterial composition data from the feces. CONCLUSION Our study supports the hypothesis that multiple host genes influence the gut microbiome composition and homeostasis, and that certain organisms may influence health outcomes after S. Typhimurium infection. Video Abstract.
Collapse
Affiliation(s)
- Aravindh Nagarajan
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - Kristin Scoggin
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
| | - Jyotsana Gupta
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - David W. Threadgill
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX USA
- Department of Biochemistry & Biophysics and Department of Nutrition, Texas A&M University, College Station, TX USA
| | - Helene L. Andrews-Polymenis
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| |
Collapse
|
7
|
Salvador AC, Huda MN, Arends D, Elsaadi AM, Gacasan AC, Brockmann GA, Valdar W, Bennett BJ, Threadgill DW. Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets. RESEARCH SQUARE 2023:rs.3.rs-2540322. [PMID: 36778219 PMCID: PMC9915790 DOI: 10.21203/rs.3.rs-2540322/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background The gut microbiota is modulated by a combination of diet, host genetics, and sex effects. The magnitude of these effects and interactions among them is important to understanding inter-individual variability in gut microbiota. In a previous study, mouse strain-specific responses to American and ketogenic diets were observed along with several QTL for metabolic traits. In the current study, we searched for genetic variants underlying differences in the gut microbiota in response to American and ketogenic diets, which are high in fat and vary in carbohydrate composition, between C57BL/6J (B6) and FVB/NJ (FVB) mouse strains. Results Genetic mapping of microbial features revealed 18 loci under the QTL model (i.e., marginal effects that are not specific to diet or sex), 12 loci under the QTL by diet model, and 1 locus under the QTL by sex model. Multiple metabolic and microbial features map to the distal part of Chr 1 and Chr 16 along with eigenvectors extracted from principal coordinate analysis of measures of β-diversity. Bilophila , Ruminiclostridium 9 , and Rikenella (Chr 1) were identified as sex and diet independent QTL candidate keystone organisms and Rikenelleceae RC9 Gut Group (Chr 16) was identified as a diet-specific, candidate keystone organism in confirmatory factor analyses of traits mapping to these regions. For many microbial features, irrespective of which QTL model was used, diet or the interaction between diet and a genotype were the strongest predictors of the abundance of each microbial trait. Sex, while important to the analyses, was not as strong of a predictor for microbial abundances. Conclusions These results demonstrate that sex, diet, and genetic background have different magnitudes of effects on inter-individual differences in gut microbiota. Therefore, Precision Nutrition through the integration of genetic variation, microbiota, and sex affecting microbiota variation will be important to predict response to diets varying in carbohydrate composition.
Collapse
|
8
|
Dhopatkar N, Keeler JL, Mutwalli H, Whelan K, Treasure J, Himmerich H. Gastrointestinal symptoms, gut microbiome, probiotics and prebiotics in anorexia nervosa: A review of mechanistic rationale and clinical evidence. Psychoneuroendocrinology 2023; 147:105959. [PMID: 36327759 DOI: 10.1016/j.psyneuen.2022.105959] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/22/2022] [Accepted: 10/20/2022] [Indexed: 11/27/2022]
Abstract
Recent research has revealed the pivotal role that the gut microbiota might play in psychiatric disorders. In anorexia nervosa (AN), the gut microbiota may be involved in pathophysiology as well as in the gastrointestinal (GI) symptoms commonly experienced. This review collates evidence for the potential role of gut microbiota in AN, including modulation of the immune system, the gut-brain axis and GI function. We examined studies comparing gut microbiota in AN with healthy controls as well as those looking at modifications in gut microbiota with nutritional treatment. Changes in energy intake and nutritional composition influence gut microbiota and may play a role in the evolution of the gut microbial picture in AN. Additionally, some evidence indicates that pre-morbid gut microbiota may influence risk of developing AN. There appear to be similarities in gut microbial composition, mechanisms of interaction and GI symptoms experienced in AN and other GI disorders such as inflammatory bowel disease and functional GI disorders. Probiotics and prebiotics have been studied in these disorders showing therapeutic effects of probiotics in some cases. Additionally, some evidence exists for the therapeutic benefits of probiotics in depression and anxiety, commonly seen as co-morbidities in AN. Moreover, preliminary evidence for the use of probiotics in AN has shown positive effects on immune modulation. Based on these findings, we discuss the potential therapeutic role for probiotics in ameliorating symptoms in AN.
Collapse
Affiliation(s)
- Namrata Dhopatkar
- South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road, Beckenham BR3 3BX, UK.
| | - Johanna Louise Keeler
- Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK.
| | - Hiba Mutwalli
- Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK.
| | - Kevin Whelan
- Department of Nutritional Sciences, King's College London, London SE1 9NH, UK.
| | - Janet Treasure
- South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road, Beckenham BR3 3BX, UK; Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK.
| | - Hubertus Himmerich
- South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital, Monks Orchard Road, Beckenham BR3 3BX, UK; Section of Eating Disorders, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK.
| |
Collapse
|
9
|
Evaluation of DDGS as a Low-Cost Feed Ingredient for Common Carp ( Cyprinus carpio Linneus) Cultivated in a Semi-Intensive System. Life (Basel) 2022; 12:life12101609. [PMID: 36295044 PMCID: PMC9604809 DOI: 10.3390/life12101609] [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: 09/22/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Distillers dried grains with solubles (DDGS), a coproduct from the ethanol production industry, is successfully used as an ingredient in feeding cattle and pigs due to its relatively high protein and nutrient content and low price compared to cereals. The aim of this study was to establish the optimal DDGS concentration that can be included in the diet of common carp. A seven-week experiment was performed on common carp with an initial weight of 86 g feed with three experimental diets D0 (DDGS 0%), D1 (DDGS 25%) and D2 (DDGS 35%). The chemical composition of DDGS analyzed by Fourier Transform Near-Infrared (FT-NIR) spectroscopy showed a protein content of 27.56% and oil at 6.75%. Diets with DDGS did not produce significant changes in growth parameters, flesh quality, and blood biochemical profile. Regarding the oxidative status in the muscle tissue, D1 and D2 significantly reduced, in a dose-dependent manner, the specific activity of SOD and GSH, while CAT and GPX were left unaffected. In the liver tissue, CAT, GSH, MDA and carbonylated proteins were reduced in the DDGS diets. The microbiological analysis of the intestinal contents revealed a variation in microbial density depending on the diet used. The total number of aerobic germs was between 224.2 × 104 and 69.84 × 106 (D2 > D1 > D0) and the total number of anaerobic germs was between 15.2 × 102 and 28.2 × 102 (D2 > D0 > D1).
Collapse
|
10
|
Feng Y, Liu D, Liu Y, Yang X, Zhang M, Wei F, Li D, Hu Y, Guo Y. Host-genotype-dependent cecal microbes are linked to breast muscle metabolites in Chinese chickens. iScience 2022; 25:104469. [PMID: 35707722 PMCID: PMC9189123 DOI: 10.1016/j.isci.2022.104469] [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: 10/27/2021] [Revised: 04/08/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
In chickens, the effect of host genetics on the gut microbiota is not fully understood, and the extent to which the heritable gut microbes affect chicken metabolism and physiology is still an open question. Here, we explored the interactions among chicken genetics, the cecal microbiota and metabolites in breast muscle from ten chicken breeds in China. We found that different chicken breeds displayed distinct cecal microbial community structures and functions, and 15 amplicon sequence variants (ASVs) were significantly associated with host genetics through different genetic loci, such as those related to the intestinal barrier function. We identified five heritable ASVs significantly associated with 53 chicken muscle metabolites, among which the Megamonas probably affected lipid metabolism through the production of propionate. Our study revealed that the chicken genetically associated cecal microbes may have the potential to affect the bird’s physiology and metabolism. The cecal microbiota are different among ten chicken breeds The chicken genetics influences the cecal microbiota structures and functions The chicken heritable cecal microbes are associated with muscle metabolites Megamonas may affect lipid metabolism by the production of propionate
Collapse
Affiliation(s)
- Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Dan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Xinyue Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Meihong Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Fuxiao Wei
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Depeng Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
- Corresponding author
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
- Corresponding author
| |
Collapse
|
11
|
Gut Microbial Composition of Pacific Salmonids Differs across Oregon River Basins and Hatchery Ancestry. Microorganisms 2022; 10:microorganisms10050933. [PMID: 35630377 PMCID: PMC9144809 DOI: 10.3390/microorganisms10050933] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/16/2022] [Accepted: 04/23/2022] [Indexed: 01/04/2023] Open
Abstract
The gut microbiome may represent a relatively untapped resource in the effort to manage and conserve threatened or endangered fish populations, including wild and hatchery-reared Pacific salmonids. To clarify this potential, we defined how steelhead trout gut microbiome composition varies across watersheds and as a function of ancestry. First, we measured this variation across watersheds using wild steelhead trout sampled from nine locations spanning three river basins. While gut microbial composition differs across basins, there exist bacterial clades that are ubiquitous across all populations. Correlating the phylogenetic composition of clades with geographic distance reveals 395 clades of bacteria whose ecological distribution implicates their co-diversification with steelheads. Second, we quantified how microbiome composition varies between first generation hatchery-reared steelhead and traditional hatchery-reared steelhead. Despite being subject to the same hatchery management strategies, fish bred from wild parents carry distinct microbiomes from those bred from hatchery broodstock, implicating the role of genotype on microbiome composition. Finally, we integrated all data from both studies to reveal two distinct, yet robust clusters of community composition. Collectively, our study documents for the first time how the steelhead gut microbiome varies by geography or broodstock and uncovers microbial taxa that may indicate the watershed or hatchery from which an individual was sourced.
Collapse
|
12
|
Mehrotra T, Maulik SK. Hepatic drug metabolism and gut microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 191:207-228. [DOI: 10.1016/bs.pmbts.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
13
|
Chen L, Yan S, Yang M, Yu F, Wang J, Wang X, Xu H, Shi J, Pan L, Zeng Y, Li S, Li L, You L, Peng Y. The gut microbiome is associated with bone turnover markers in postmenopausal women. Am J Transl Res 2021; 13:12601-12613. [PMID: 34956476 PMCID: PMC8661154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/05/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE The association of the gut microbiome with bone turnover markers (BTMs) in postmenopausal women is poorly understood. METHODS Fecal samples were collected from 97 Chinese postmenopausal women, and the serum CTX and P1NP were determined. Individuals with serum CTX lower or higher than the median value were divided into LCTX and P1NP groups; and individuals with serum P1NP lower or higher than the median value were grouped into LP1NP and HP1NP groups. Microbiota profiles were determined by high-throughput 16S rRNA gene sequencing. RESULTS In postmenopausal women, only Faecalibacterium showed significant alteration in the HCTX group compared with the LCTX group (P=0.004, q=0.143). Linear discriminant analysis effect size (LEfSe) analysis revealed that Clostridiaceae (P=0.015, LDA=2.89), Faecalibacterium (P=0.017, LDA=4.60), Prevotella (P=0.040, LDA=3.61) and Clostridium (P=0.007, LDA=2.79) were abundant in the LCTX group, and Facklamia (P=0.044, LDA=3.10) was enriched in the HCTX group. Peptostreptococcaceae (P=0.048, LDA=2.83) and the SMB53 (P=0.028, LDA=2.05) genus were enriched in the LPINP group, and Veillonellaceae (P=0.025, LDA=4.43) and the S24_7 (P=0.023, LDA=3.08) family were enriched in the HPINP group. Six taxa correlated with BTMs in all subjects, including Clostridium (Clostridiaceae) that was negatively correlated with serum CTX amounts significantly (r=-0.34, P<0.001). CONCLUSION This study identified taxa-specific differences in the intestinal microflora associated with BTMs, notably CTX. These findings may help in uncovering the roles of gut microbiota on bone metabolism.
Collapse
Affiliation(s)
- Lin Chen
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Shuai Yan
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Ming Yang
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Fudong Yu
- Basic Reproduction Laboratory, Shanghai Institute of Planned Parenthood Research, Fudan UniversityShanghai 200032, China
| | - Jingjing Wang
- Shanghai Key Laboratory for Pancreatic Diseases, Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Xiaoxin Wang
- Shanghai Key Laboratory for Pancreatic Diseases, Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Huanbai Xu
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Jianxia Shi
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Ling Pan
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Yuexi Zeng
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Siyu Li
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Li Li
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Li You
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Yongde Peng
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| |
Collapse
|
14
|
Vithoulkas G. An integrated perspective on transmutation of acute inflammation into chronic and the role of the microbiome. J Med Life 2021; 14:740-747. [PMID: 35126742 PMCID: PMC8811668 DOI: 10.25122/jml-2021-0375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/30/2021] [Indexed: 11/20/2022] Open
Abstract
The Continuum theory and the Levels of Health theory were separately proposed to explain the myriad responses to treatment and understand the process of health and disease in an individual. In light of accumulating evidence on the intricate relationship between the human immune system and microbiome, an attempt is made in this article to connect these two theories to explain the transmutation of the efficiently responding immune system (through the acute inflammatory response and high fever) to one involved in a low-grade chronic inflammatory process (resulting in chronic disease). There is already enough evidence to demonstrate the role of the microbiome in all chronic inflammatory diseases. In this article, we discuss the mechanism by which subjecting a healthy person to continuous drug treatment for acute inflammatory conditions (at a certain time) leads to transmutation to chronic disease. Although this hypothesis requires further experimental evidence, it calls for a reconsideration of the manner in which we treat acute infectious diseases in the population.
Collapse
Affiliation(s)
- George Vithoulkas
- University of the Aegean, Syros, Greece
- Postgraduate Doctors’ Training Institute, Health Care Ministry of the Chuvash Republic, Cheboksary, Russian Federation
| |
Collapse
|
15
|
Botta A, Barra NG, Lam NH, Chow S, Pantopoulos K, Schertzer JD, Sweeney G. Iron Reshapes the Gut Microbiome and Host Metabolism. J Lipid Atheroscler 2021; 10:160-183. [PMID: 34095010 PMCID: PMC8159756 DOI: 10.12997/jla.2021.10.2.160] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/12/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022] Open
Abstract
Compelling studies have established that the gut microbiome is a modifier of metabolic health. Changes in the composition of the gut microbiome are influenced by genetics and the environment, including diet. Iron is a potential node of crosstalk between the host-microbe relationship and metabolic disease. Although iron is well characterized as a frequent traveling companion of metabolic disease, the role of iron is underappreciated because the mechanisms of iron's influence on host metabolism are poorly characterized. Both iron deficiency and excessive amounts leading to iron overload can have detrimental effects on cardiometabolic health. Optimal iron homeostasis is critical for regulation of host immunity and metabolism in addition to regulation of commensal and pathogenic enteric bacteria. In this article we review evidence to support the notion that altering composition of the gut microbiome may be an important route via which iron impacts cardiometabolic health. We discuss reshaping of the microbiome by iron, the physiological significance and the potential for therapeutic interventions.
Collapse
Affiliation(s)
- Amy Botta
- Department of Biology, York University, Toronto, ON, Canada
| | - Nicole G. Barra
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute, Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON, Canada
| | - Nhat Hung Lam
- Department of Biology, York University, Toronto, ON, Canada
| | - Samantha Chow
- Department of Biology, York University, Toronto, ON, Canada
| | - Kostas Pantopoulos
- Lady Davis Institute for Medical Research, Jewish General Hospital and Department of Medicine, McGill University, Montreal, QC, Canada
| | - Jonathan D. Schertzer
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute, Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, ON, Canada
| | - Gary Sweeney
- Department of Biology, York University, Toronto, ON, Canada
| |
Collapse
|
16
|
Mirzaei R, Afaghi A, Babakhani S, Sohrabi MR, Hosseini-Fard SR, Babolhavaeji K, Khani Ali Akbari S, Yousefimashouf R, Karampoor S. Role of microbiota-derived short-chain fatty acids in cancer development and prevention. Biomed Pharmacother 2021; 139:111619. [PMID: 33906079 DOI: 10.1016/j.biopha.2021.111619] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/01/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
Following cancer, cells in a particular tissue can no longer respond to the factors involved in controlling cell survival, differentiation, proliferation, and death. In recent years, it has been indicated that alterations in the gut microbiota components, intestinal epithelium, and host immune system are associated with cancer incidence. Also, it has been demonstrated that the short-chain fatty acids (SCFAs) generated by gut microbiota are vitally crucial in cell homeostasis as they contribute to the modulation of histone deacetylases (HDACs), resulting effected cell attachment, immune cell immigration, cytokine production, chemotaxis, and the programmed cell death. Therefore, the manipulation of SCFA levels in the intestinal tract by alterations in the microbiota structure can be potentially taken into consideration for cancer treatment/prevention. In the current study, we will explain the most recent findings on the detrimental or protective roles of SFCA (particularly butyrate, propionate, and acetate) in several cancers, including bladder, colon, breast, stomach, liver, lung, pancreas, and prostate cancers.
Collapse
Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Azam Afaghi
- Department of Biology, Sofian Branch, Islamic Azad University, Sofian, Iran
| | - Sajad Babakhani
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Reza Sohrabi
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kiandokht Babolhavaeji
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shabnam Khani Ali Akbari
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rasoul Yousefimashouf
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
17
|
Dabee S, Passmore JAS, Heffron R, Jaspan HB. The Complex Link between the Female Genital Microbiota, Genital Infections, and Inflammation. Infect Immun 2021; 89:e00487-20. [PMID: 33558324 PMCID: PMC8091093 DOI: 10.1128/iai.00487-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The female genital tract microbiota is part of a complex ecosystem influenced by several physiological, genetic, and behavioral factors. It is uniquely linked to a woman's mucosal immunity and plays a critical role in the regulation of genital inflammation. A vaginal microbiota characterized by a high abundance of lactobacilli and low overall bacterial diversity is associated with lower inflammation. On the other hand, a more diverse microbiota is linked to high mucosal inflammation levels, a compromised genital epithelial barrier, and an increased risk of sexually transmitted infections and other conditions. Several bacterial taxa such as Gardnerella spp., Prevotella spp., Sneathia spp., and Atopobium spp. are well known to have adverse effects; however, the definitive cause of this microbial dysbiosis is yet to be fully elucidated. The aim of this review is to discuss the multiple ways in which the microbiota influences the overall genital inflammatory milieu and to explore the causes and consequences of this inflammatory response. While there is abundant evidence linking a diverse genital microbiota to elevated inflammation, understanding the risk factors and mechanisms through which it affects genital health is essential. A robust appreciation of these factors is important for identifying effective prevention and treatment strategies.
Collapse
Affiliation(s)
- Smritee Dabee
- Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jo-Ann S Passmore
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- CAPRISA Centre of Excellence in HIV Prevention, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | | | - Heather B Jaspan
- Seattle Children's Research Institute, Seattle, Washington, USA
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- University of Washington, Seattle, Washington, USA
| |
Collapse
|
18
|
Bossù G, Di Sario R, Argentiero A, Esposito S. Antimicrobial Prophylaxis and Modifications of the Gut Microbiota in Children with Cancer. Antibiotics (Basel) 2021; 10:antibiotics10020152. [PMID: 33546312 PMCID: PMC7913491 DOI: 10.3390/antibiotics10020152] [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: 12/31/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
In children with cancer, chemotherapy can produce cytotoxic effects, resulting in immunosuppression and an augmented risk of febrile neutropenia and bloodstream infections. This has led to widespread use of antibiotic prophylaxis which, combined with intensive chemotherapy treatment, could have a long-term effect on the gastrointestinal microbiome. In this review, we aimed to analyze the current literature about the widespread use of antibiotic prophylaxis in children experiencing infectious complications induced by chemotherapy and its effects on the gut microbiome. Our review of the literature shows that antimicrobial prophylaxis in children with cancer is still a trending topic and, at the moment, there are not enough data to define universal guidelines. Children with cancer experience long and painful medical treatments and side effects, which are associated with great economic and social burdens, important psychological consequences, and dysbiosis induced by antibiotics and also by chemotherapy. Considering the importance of a healthy gut microbiota, studies are needed to understand the impact of dysbiosis in response to therapy in these children and to define how to modulate the microbiome to favor a positive therapeutic outcome.
Collapse
|
19
|
Katz-Agranov N, Zandman-Goddard G. The microbiome links between aging and lupus. Autoimmun Rev 2021; 20:102765. [PMID: 33476814 DOI: 10.1016/j.autrev.2021.102765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/05/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Many forms of immune dysregulation, which lead to inflammaging and senescence, have been demonstrated in patients with systemic lupus erythematosus (SLE; lupus) and in the aging population. The discovery of the microbiome and its association with human health and pathology has led it to be the center of investigation as a major contributor to the pathogenesis of immunosenescence in both populations. Similar alterations to the microbiome in the form of dysbiosis, that are demonstrated in both aging and in lupus patients, may help explain the significant overlap in clinical manifestations seen in these groups. METHODS We performed an extensive literature review, utilizing the Pubmed search engine and Google Scholar for studies evaluating the microbiome in two groups, elderly populations and lupus patients (both murine and human models), between the years 2000-2019. We searched for the terms: microbiome, dysbiosis, lupus, elderly, aging and inflammaging, which yielded hundreds of articles, of which 114 were used for preparation of this paper. We compared the similarities between the populations. RESULTS We found that the similar processes of immune dysregulation, in both aging populations and lupus patients, extend to the microbiome, in the form of dysbiosis. Some of these similarities include loss of microbiota biodiversity, increased representation of microbes that are associated with inflammation and disease (i.e Proteobacteria, Bacteroidetes), a relative decrease in protective microbes with "anti-inflammatory" properties (i.e Firmicutes) and a subsequent compromise to the intestinal barrier, leading to leakage of proinflammatory microbial components in both groups. CONCLUSIONS We conclude that there are several similar alterations in the composition and function of the microbiome of lupus patients and aging individuals, leading to immunosenescence, which may also be a contributing mechanism in lupus. It seems in fact that the microbiome of SLE may actually be analogous to immunosenescence. This knowledge may help the continuous efforts in finding a solution for both conditions.
Collapse
Affiliation(s)
- Nurit Katz-Agranov
- Department of Medicine, Saint Elizabeth's Medical Center, Boston, MA, USA; Tufts University School of Medicine, Boston, MA, USA
| | - Gisele Zandman-Goddard
- Department of Medicine C, Wolfson Medical Center, Holon, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
20
|
Badal VD, Vaccariello ED, Murray ER, Yu KE, Knight R, Jeste DV, Nguyen TT. The Gut Microbiome, Aging, and Longevity: A Systematic Review. Nutrients 2020; 12:E3759. [PMID: 33297486 PMCID: PMC7762384 DOI: 10.3390/nu12123759] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Aging is determined by complex interactions among genetic and environmental factors. Increasing evidence suggests that the gut microbiome lies at the core of many age-associated changes, including immune system dysregulation and susceptibility to diseases. The gut microbiota undergoes extensive changes across the lifespan, and age-related processes may influence the gut microbiota and its related metabolic alterations. The aim of this systematic review was to summarize the current literature on aging-associated alterations in diversity, composition, and functional features of the gut microbiota. We identified 27 empirical human studies of normal and successful aging suitable for inclusion. Alpha diversity of microbial taxa, functional pathways, and metabolites was higher in older adults, particularly among the oldest-old adults, compared to younger individuals. Beta diversity distances significantly differed across various developmental stages and were different even between oldest-old and younger-old adults. Differences in taxonomic composition and functional potential varied across studies, but Akkermansia was most consistently reported to be relatively more abundant with aging, whereas Faecalibacterium, Bacteroidaceae, and Lachnospiraceae were relatively reduced. Older adults have reduced pathways related to carbohydrate metabolism and amino acid synthesis; however, oldest-old adults exhibited functional differences that distinguished their microbiota from that of young-old adults, such as greater potential for short-chain fatty acid production and increased butyrate derivatives. Although a definitive interpretation is limited by the cross-sectional design of published reports, we integrated findings of microbial composition and downstream functional pathways and metabolites, offering possible explanations regarding age-related processes.
Collapse
Affiliation(s)
- Varsha D. Badal
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
- Sam and Rose Stein Institute for Research on Aging, University of California San Diego, La Jolla, CA 92093, USA
| | - Eleonora D. Vaccariello
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
| | - Emily R. Murray
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
| | - Kasey E. Yu
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Dilip V. Jeste
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
- Sam and Rose Stein Institute for Research on Aging, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tanya T. Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA; (V.D.B.); (E.D.V.); (E.R.M.); (K.E.Y.); (D.V.J.)
- Sam and Rose Stein Institute for Research on Aging, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, La Jolla, CA 92161, USA
| |
Collapse
|
21
|
Garcia-Mazcorro JF, Kawas JR, Licona Cassani C, Mertens-Talcott S, Noratto G. Different analysis strategies of 16S rRNA gene data from rodent studies generate contrasting views of gut bacterial communities associated with diet, health and obesity. PeerJ 2020; 8:e10372. [PMID: 33240672 PMCID: PMC7678494 DOI: 10.7717/peerj.10372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/26/2020] [Indexed: 01/04/2023] Open
Abstract
Background One of the main functions of diet is to nurture the gut microbiota and this relationship affects the health of the host. However, different analysis strategies can generate different views on the relative abundance of each microbial taxon, which can affect our conclusions about the significance of diet to gut health in lean and obese subjects. Here we explored the impact of using different analysis strategies to study the gut microbiota in a context of diet, health and obesity. Methods Over 15 million 16S rRNA gene sequences from published studies involving dietary interventions in obese laboratory rodents were analyzed. Three strategies were used to assign the 16S sequences to Operational Taxonomic Units (OTUs) based on the GreenGenes reference OTU sequence files clustered at 97% and 99% similarity. Results Different strategies to select OTUs influenced the relative abundance of all bacterial taxa, but the magnitude of this phenomenon showed a strong study effect. Different taxa showed up to 20% difference in relative abundance within the same study, depending on the analysis strategy. Very few OTUs were shared among the samples. ANOSIM test on unweighted UniFrac distances showed that study, sequencing technique, animal model, and dietary treatment (in that order) were the most important factors explaining the differences in bacterial communities. Except for obesity status, the contribution of diet and other factors to explain the variability in bacterial communities was lower when using weighted UniFrac distances. Predicted functional profile and high-level phenotypes of the microbiota showed that each study was associated with unique features and patterns. Conclusions The results confirm previous findings showing a strong study effect on gut microbial composition and raise concerns about the impact of analysis strategies on the membership and composition of the gut microbiota. This study may be helpful to guide future research aiming to investigate the relationship between diet, health, and the gut microbiota.
Collapse
Affiliation(s)
| | - Jorge R Kawas
- Faculty of Agronomy, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo Leon, Mexico
| | | | - Susanne Mertens-Talcott
- Department of Food Science and Technology, Texas A&M University, College Station, TX, United States of America
| | - Giuliana Noratto
- Department of Food Science and Technology, Texas A&M University, College Station, TX, United States of America
| |
Collapse
|
22
|
Łoś-Rycharska E, Gołębiewski M, Grzybowski T, Rogalla-Ładniak U, Krogulska A. The microbiome and its impact on food allergy and atopic dermatitis in children. Postepy Dermatol Alergol 2020; 37:641-650. [PMID: 33240001 PMCID: PMC7675070 DOI: 10.5114/ada.2019.90120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/29/2019] [Indexed: 01/23/2023] Open
Abstract
Food allergy (FA) affects 4-10% of children, especially children with atopic dermatitis (AD). During infancy the gut microbiome may determine both the course of FA and tolerance to food allergens. Analogically, the skin microbiome changes in the course of AD. Most studies have associated FA with a lower abundance and diversity of Lactobacillales and Clostridiales, but greater numbers of Enterobacterales, while AD in children has been associated with lower numbers of Staphylococcus epidermidis and S. hominis but an abundance of S. aureus and Streptococcus species. An understanding of the impact of the microbiome on the clinical course of FA and AD may allow for the development of new models of allergy treatment and prevention.
Collapse
Affiliation(s)
- Ewa Łoś-Rycharska
- Department of Paediatrics, Allergology and Gastroenterology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Poland
| | - Marcin Gołębiewski
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, Torun, Poland
- Chair of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Torun, Poland
| | - Tomasz Grzybowski
- Chair of Forensic Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Poland
| | - Urszula Rogalla-Ładniak
- Chair of Forensic Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Poland
| | - Aneta Krogulska
- Department of Paediatrics, Allergology and Gastroenterology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Poland
| |
Collapse
|
23
|
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
|
24
|
Magne F, Gotteland M, Gauthier L, Zazueta A, Pesoa S, Navarrete P, Balamurugan R. The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? Nutrients 2020; 12:nu12051474. [PMID: 32438689 PMCID: PMC7285218 DOI: 10.3390/nu12051474] [Citation(s) in RCA: 1009] [Impact Index Per Article: 252.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
The gut microbiota is emerging as a promising target for the management or prevention of inflammatory and metabolic disorders in humans. Many of the current research efforts are focused on the identification of specific microbial signatures, more particularly for those associated with obesity, type 2 diabetes, and cardiovascular diseases. Some studies have described that the gut microbiota of obese animals and humans exhibits a higher Firmicutes/Bacteroidetes ratio compared with normal-weight individuals, proposing this ratio as an eventual biomarker. Accordingly, the Firmicutes/Bacteroidetes ratio is frequently cited in the scientific literature as a hallmark of obesity. The aim of the present review was to discuss the validity of this potential marker, based on the great amount of contradictory results reported in the literature. Such discrepancies might be explained by the existence of interpretative bias generated by methodological differences in sample processing and DNA sequence analysis, or by the generally poor characterization of the recruited subjects and, more particularly, the lack of consideration of lifestyle-associated factors known to affect microbiota composition and/or diversity. For these reasons, it is currently difficult to associate the Firmicutes/Bacteroidetes ratio with a determined health status and more specifically to consider it as a hallmark of obesity.
Collapse
Affiliation(s)
- Fabien Magne
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago 8320000, Chile;
- Correspondence: (F.M.); (M.G.); Tel.: +56-2-2978-9627 (F.M.)
| | - Martin Gotteland
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago 8320000, Chile;
- Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago 7830490, Chile;
- Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago 7830490, Chile
- Correspondence: (F.M.); (M.G.); Tel.: +56-2-2978-9627 (F.M.)
| | - Lea Gauthier
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago 8320000, Chile;
| | - Alejandra Zazueta
- Microbiology and Mycology Program, ICBM, Faculty of Medicine, University of Chile, Santiago 8320000, Chile;
| | - Susana Pesoa
- Department of Molecular Diagnosis, LACE Laboratories, Córdoba X5000, Argentina;
| | - Paola Navarrete
- Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago 7830490, Chile;
- Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago 7830490, Chile
| | | |
Collapse
|
25
|
El Bairi K, Jabi R, Trapani D, Boutallaka H, Ouled Amar Bencheikh B, Bouziane M, Amrani M, Afqir S, Maleb A. Can the microbiota predict response to systemic cancer therapy, surgical outcomes, and survival? The answer is in the gut. Expert Rev Clin Pharmacol 2020; 13:403-421. [PMID: 32308061 DOI: 10.1080/17512433.2020.1758063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The gut microbiota seems to play a key role in tumorigenesis, across various hallmarks of cancer. Recent evidence suggests its potential use as a biomarker predicting drug response and adding prognostic information, generally in the context of immuno-oncology. AREAS COVERED In this review, we focus on the modulating effects of gut microbiota dysbiosis on various anticancer molecules used in practice, including cytotoxic and immune-modulating agents, primarily immune-checkpoint inhibitors (ICI). Pubmed/Medline-based literature search was conducted to find potential original studies that discuss gut microbiota as a prognostic and predictive biomarker for cancer therapy. We also looked at the US ClinicalTrials.gov website to find additional studies particularly ongoing human clinical trials. EXPERT COMMENTARY Sequencing of stool-derived materials and tissue samples from cancer patients and animal models has shown a significant enrichment of various bacteria such as Fusobacterium nucleatum and Bacteroides fragilis were associated with resistant disease and poorer outcomes. Gut microbiota was also found to be associated with surgical outcomes and seems to play a significant role in anastomotic leak (ATL) after surgery mainly by collagen breakdown. However, this research field is just at the beginning and the current findings are not yet ready to change clinical practice.
Collapse
Affiliation(s)
- Khalid El Bairi
- Cancer Biomarkers Working Group, Mohamed Ist University , Oujda, Morocco
- Faculty of Medicine and Pharmacy, Mohamed Ist University , Oujda, Morocco
| | - Rachid Jabi
- Faculty of Medicine and Pharmacy, Mohamed Ist University , Oujda, Morocco
- Department of Visceral Surgery, Mohamed VI University Hospital , Oujda, Morocco
| | - Dario Trapani
- Department of Haematology and Oncology, European Institute of Oncology, IEO, IRCCS, University of Milano , Milan, Italy
| | - Hanae Boutallaka
- Department of Gastroenterology and Digestive Endoscopy, Mohamed V Military Teaching Hospital of Rabat, Mohamed V University , Rabat, Morocco
| | | | - Mohammed Bouziane
- Faculty of Medicine and Pharmacy, Mohamed Ist University , Oujda, Morocco
- Department of Visceral Surgery, Mohamed VI University Hospital , Oujda, Morocco
| | - Mariam Amrani
- Department of Pathology, National Institute of Oncology, Faculty of Medicine and Pharmacy, Mohamed V University , Rabat, Morocco
| | - Said Afqir
- Cancer Biomarkers Working Group, Mohamed Ist University , Oujda, Morocco
- Faculty of Medicine and Pharmacy, Mohamed Ist University , Oujda, Morocco
- Department of Medical Oncology, Mohamed VI University Hospital , Oujda, Morocco
| | - Adil Maleb
- Faculty of Medicine and Pharmacy, Mohamed Ist University , Oujda, Morocco
- Department of Microbiology, Mohamed VI University Hospital , Oujda, Morocco
| |
Collapse
|
26
|
Macke E, Callens M, Massol F, Vanoverberghe I, De Meester L, Decaestecker E. Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities. Front Microbiol 2020; 11:380. [PMID: 32256467 PMCID: PMC7090131 DOI: 10.3389/fmicb.2020.00380] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/20/2020] [Indexed: 12/04/2022] Open
Abstract
In spite of the growing interest in the role of the gut microbiome (GM) in host physiology and health, the mechanisms governing its assembly and its effects on the environment are poorly understood. In this article, we show that the host genotype and the GM of Daphnia influence the community structure of the surrounding bacterioplankton (BPK). When Daphnia genotypes were placed in an identical environment, both the GM and BPK showed a genotype and diet-dependent taxonomic composition. Overall, the GM strongly differed from the BPK in taxonomic composition and was characterized by a lower α-diversity, suggesting a selective rejecting of bacteria from the regional species pool. In a microbiome transplant experiment, the assembly of both the GM and BPK was strongly affected by the host genotype and the inoculum to which germ-free Daphnia were exposed. The combination of these results suggests a strong interaction between the host genotype, its GM and free-living microbial communities. Currently, it is generally assumed that an animal’s diet has a strong effect on the animal’s GM, but only a negligible (if any) effect on the surrounding environment. However, our results indicate that the diet/microbiome inocula have a small effect on the gut community and a large effect on the community in the surrounding environment. This structuring genotype × microbiome × environment effect is an essential prerequisite that could indicate that microbiomes play an important role in eco-evolutionary processes.
Collapse
Affiliation(s)
- Emilie Macke
- Aquatic Biology, IRF Life Sciences, KU Leuven, Kortrijk, Belgium
| | - Martijn Callens
- Aquatic Biology, IRF Life Sciences, KU Leuven, Kortrijk, Belgium.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Francois Massol
- CNRS, Lille-Sciences et Technologies, UMR 8198 Evo-Eco-Paleo, SPICI Group, Villeneuve-d'Ascq, France.,University of Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | | | - Luc De Meester
- Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | | |
Collapse
|
27
|
Dąbrowska K, Abedon ST. Pharmacologically Aware Phage Therapy: Pharmacodynamic and Pharmacokinetic Obstacles to Phage Antibacterial Action in Animal and Human Bodies. Microbiol Mol Biol Rev 2019; 83:e00012-19. [PMID: 31666296 PMCID: PMC6822990 DOI: 10.1128/mmbr.00012-19] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The use of viruses infecting bacteria (bacteriophages or phages) to treat bacterial infections has been ongoing clinically for approximately 100 years. Despite that long history, the growing international crisis of resistance to standard antibiotics, abundant anecdotal evidence of efficacy, and one successful modern clinical trial of efficacy, this phage therapy is not yet a mainstream approach in medicine. One explanation for why phage therapy has not been subject to more widespread implementation is that phage therapy research, both preclinical and clinical, can be insufficiently pharmacologically aware. Consequently, here we consider the pharmacological obstacles to phage therapy effectiveness, with phages in phage therapy explicitly being considered to serve as drug equivalents. The study of pharmacology has traditionally been differentiated into pharmacokinetic and pharmacodynamic aspects. We therefore separately consider the difficulties that phages as virions can have in traveling through body compartments toward reaching their target bacteria (pharmacokinetics) and the difficulties that phages can have in exerting antibacterial activity once they have reached those bacteria (pharmacodynamics). The latter difficulties, at least in part, are functions of phage host range and bacterial resistance to phages. Given the apparently low toxicity of phages and the minimal side effects of phage therapy as practiced, phage therapy should be successful so long as phages can reach the targeted bacteria in sufficiently high numbers, adsorb, and then kill those bacteria. Greater awareness of what obstacles to this success generally or specifically can exist, as documented in this review, should aid in the further development of phage therapy toward wider use.
Collapse
Affiliation(s)
- Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
| |
Collapse
|
28
|
Ganci M, Suleyman E, Butt H, Ball M. The role of the brain-gut-microbiota axis in psychology: The importance of considering gut microbiota in the development, perpetuation, and treatment of psychological disorders. Brain Behav 2019; 9:e01408. [PMID: 31568686 PMCID: PMC6851798 DOI: 10.1002/brb3.1408] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION The prevalence of psychological disorders remains stable despite steady increases in pharmacological treatments suggesting the need for auxiliary treatment options. Consideration of the brain-gut-microbiota axis (BGMA) has made inroads into reconceptualizing psychological illness from a more holistic perspective. While our understanding of the precise role of gut microbiota (GM) in psychological illness is in its infancy, it represents an attractive target for novel interventions. METHOD An extensive review of relevant literature was undertaken. RESULTS Gut microbiota are proposed to directly and indirectly influence mood, cognition, and behavior which are key components of mental health. This paper outlines how GM may be implicated in psychological disorders from etiology through to treatment and prevention using the Four P model of case formulation. CONCLUSION Moving forward, integration of GM into the conceptualization and treatment of psychological illness will require the discipline of psychology to undergo a significant paradigm shift. While the importance of the GM in psychological well-being must be respected, it is not proposed to be a panacea, but instead, an additional arm to a multidisciplinary approach to treatment and prevention.
Collapse
Affiliation(s)
- Michael Ganci
- Psychology Department, Institute for Health and Sport, Victoria University, Melbourne, Vic., Australia
| | - Emra Suleyman
- Psychology Department, Institute for Health and Sport, Victoria University, Melbourne, Vic., Australia
| | - Henry Butt
- Bioscreen Yarraville (Aust) Pty Ltd, Melbourne, Vic., Australia.,Melbourne University, Melbourne, Vic., Australia
| | - Michelle Ball
- Psychology Department, Institute for Health and Sport, Victoria University, Melbourne, Vic., Australia
| |
Collapse
|
29
|
Surendran Nair M, Eucker T, Martinson B, Neubauer A, Victoria J, Nicholson B, Pieters M. Influence of pig gut microbiota on Mycoplasma hyopneumoniae susceptibility. Vet Res 2019; 50:86. [PMID: 31661027 PMCID: PMC6819593 DOI: 10.1186/s13567-019-0701-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/03/2019] [Indexed: 02/07/2023] Open
Abstract
This study investigated the influence of gut microbiome composition in modulating susceptibility to Mycoplasma hyopneumoniae in pigs. Thirty-two conventional M. hyopneumoniae free piglets were randomly selected from six different litters at 3 weeks of age and were experimentally inoculated with M. hyopneumoniae at 8 weeks of age. Lung lesion scores (LS) were recorded 4 weeks post-inoculation (12 weeks of age) from piglet lungs at necropsy. Fecal bacterial community composition of piglets at 3, 8 and 12 weeks of age were targeted by amplifying the V3–V4 region of the 16S rRNA gene. The LS ranged from 0.3 to 43% with an evident clustering of the scores observed in piglets within litters. There were significant differences in species richness and alpha diversity in fecal microbiomes among piglets within litters at different time points (p < 0.05). The dissimilarity matrices indicated that at 3 weeks of age, the fecal microbiota of piglets was more dissimilar compared to those from 8 to 12 weeks of age. Specific groups of bacteria in the gut that might predict the decreased severity of M. hyopneumoniae associated lesions were identified. The microbial shift at 3 weeks of age was observed to be driven by the increase in abundance of the indicator family, Ruminococcaceae in piglets with low LS (p < 0.05). The taxa, Ruminococcus_2 having the highest richness scores, correlated significantly between litters showing stronger associations with the lowest LS (r = −0.49, p = 0.005). These findings suggest that early life gut microbiota can be a potential determinant for M. hyopneumoniae susceptibility in pigs.
Collapse
Affiliation(s)
- Meera Surendran Nair
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Tyson Eucker
- Boehringer-Ingelheim Animal Health, Duluth, GA, USA
| | | | | | | | | | - Maria Pieters
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA.
| |
Collapse
|
30
|
Zhang A, Steen TY. Gut Microbiomics-A Solution to Unloose the Gordian Knot of Biological Effects of Ionizing Radiation. J Hered 2019; 109:212-221. [PMID: 29452420 DOI: 10.1093/jhered/esx059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/05/2017] [Indexed: 12/24/2022] Open
Abstract
The Chernobyl and Fukushima nuclear accidents have called forth a growing body of research on their biological aftermaths. A variety of wild organisms, including primates, birds, fish, insects, and worms are being studied in the affected areas, with emerging morphological, physiological, and genetic aberrations ascribed to ionizing radiation. Despite the effort in surveying Chernobyl and Fukushima wildlife, little is known about the microorganisms associated with these radiation-contaminated animals. The microbiota, especially the gut commensal, plays an important role in shaping the metabolic reservoir and immune system of the host, and is sensitive to a wide array of environmental factors, including ionizing radiation. Humans and limited numbers of laboratory species have been the main subjects of microbiome studies, however, a more practical insight on host-gut microbiota dynamics under environmental impact should be explored in natural habitats. In this analysis, we introduced a working model explaining possible mechanisms of ionizing radiation on the gut microbiota, with an evaluation of the gut microbiota as a potential biomarker for exposure to ionizing radiation.
Collapse
Affiliation(s)
- Amy Zhang
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY
| | - Tomoko Y Steen
- Department of Microbiology and Immunology, School of Medicine, Georgetown University, Washington, DC
| |
Collapse
|
31
|
Ji J, Luo C, Zou X, Lv X, Xu Y, Shu D, Qu H. Association of host genetics with intestinal microbial relevant to body weight in a chicken F2 resource population. Poult Sci 2019; 98:4084-4093. [DOI: 10.3382/ps/pez199] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/27/2019] [Indexed: 12/12/2022] Open
|
32
|
Counting Oceanians of Non-European, Non-Asian Descent (ONENA) in the South Pacific to Make Them Count in Global Health. Trop Med Infect Dis 2019; 4:tropicalmed4030114. [PMID: 31405081 PMCID: PMC6789437 DOI: 10.3390/tropicalmed4030114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 01/07/2023] Open
Abstract
Several diseases and vulnerabilities associated with genetic or microbial factors are more frequent among populations of Oceanian, Non-European, Non-Asian descent (ONENA). ONENA are specific and have long been isolated geographically. To our knowledge, there are no published official, quantitative, aggregated data on the populations impacted by these excess vulnerabilities in Oceania. We searched official census reports for updated estimates of the total population for each of the Pacific Island Countries and Territories (including Australia) and the US State of Hawaii, privileging local official statistical or censual sources. We multiplied the most recent total population estimate by the cumulative percentage of the ONENA population as determined in official reports. Including Australia and the US State of Hawaii, Oceania counts 27 countries and territories, populated in 2016 by approximately 41 M inhabitants (17 M not counting Australia) among which approximately 12.5 M (11.6 M not counting Australia) consider themselves of entire or partial ONENA ancestry. Specific genetic and microbiome traits of ONENA may be unique and need further investigation to adjust risk estimates, risk prevention, diagnostic and therapeutic strategies, to the benefit of populations in the Pacific and beyond.
Collapse
|
33
|
Brown RM, Wiens GD, Salinas I. Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). FISH & SHELLFISH IMMUNOLOGY 2019; 86:497-506. [PMID: 30513381 PMCID: PMC8040288 DOI: 10.1016/j.fsi.2018.11.079] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/25/2018] [Accepted: 11/30/2018] [Indexed: 05/09/2023]
Abstract
Commensal microorganisms present at mucosal surfaces play a vital role in protecting the host organism from bacterial infection. There are multiple factors that contribute to selecting for the microbiome, including host genetics. Flavobacterium psychrophilum, the causative agent of Bacterial Cold Water Disease in salmonids, accounts for acute losses in wild and farmed rainbow trout (Oncorhynchus mykiss). The U.S. National Center for Cool and Cold Water Aquaculture has used family-based selective breeding to generate a line of rainbow trout with enhanced resistance to F. psychrophilum. The goal of this study is to determine whether selective breeding impacts the gut and gill microbiome of the F. psychrophilum-resistant as compared to a background matched susceptible trout line. Mid-gut and gill samples were collected from juvenile fish maintained at high or low stocking densities and microbial diversity assessed by 16S rDNA amplicon sequencing. Results indicate that alpha diversity was significantly higher in the mid-gut of the susceptible line compared to the resistant line, while no significant differences in alpha diversity were observed in the gills. Mycoplasma sp. was the dominant taxon in the mid-gut of both groups, although it was present at a decreased abundance in the susceptible line. We also observed an increased abundance of the potential opportunistic pathogen Brevinema andersonii in the susceptible line. Within the gills, both lines exhibited similar microbial profiles, with Candidatus Branchiomonas being the dominant taxon. Together, these results suggest that selectively bred F. psychrophilum-resistant trout may harness a more resilient gut microbiome, attributing to the disease resistant phenotype. Importantly, interactions between host genetics and environmental factors such as stocking density have a significant impact in shaping trout microbial communities.
Collapse
Affiliation(s)
- Ryan M Brown
- University of New Mexico, Department of Biology, Center for Evolutionary and Theoretical Immunology (CETI), Albuquerque, NM, USA
| | - Gregory D Wiens
- National Center for Cool and Cold Water Aquaculture, Agriculture Research Service, United States Department of Agriculture Kearneysville, WV, USA
| | - Irene Salinas
- University of New Mexico, Department of Biology, Center for Evolutionary and Theoretical Immunology (CETI), Albuquerque, NM, USA.
| |
Collapse
|
34
|
Huang E, Kang S, Park H, Park S, Ji Y, Holzapfel WH. Differences in Anxiety Levels of Various Murine Models in Relation to the Gut Microbiota Composition. Biomedicines 2018; 6:biomedicines6040113. [PMID: 30518033 PMCID: PMC6315404 DOI: 10.3390/biomedicines6040113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/09/2023] Open
Abstract
Psychobiotics are probiotic strains that confer mental health benefits to the host through the modulation of the gut microbial population. Mounting evidence shows that the gut microbiota play an important role in communication within the gut–brain axis. However, the relationship between the host genetics and the gut microbiota and their influence on anxiety are still not fully understood. Hence, in our research, we attempted to draw a connection between host genetics, microbiota composition, and anxiety by performing an elevated plus maze (EPM) test on four genetically different mice. Four different breeds of 5-week-old mice were used in this experiment: Balb/c, Orient C57BL/6N, Taconic C57BL/6N, and Taconic C57BL/6J. After 1 week of adaptation, their initial anxiety level was monitored using the EPM test via an EthoVision XT, a standardized software used for behavorial testing. Significant differences in the initial anxiety level and microbial composition were detected. Subsequently, the microbiota of each group was modulated by the administration of either a probiotic, fecal microbiota transplantation, or antibiotics. Changes were observed in host anxiety levels in correlation to the shift of the gut microbiota. Our results suggest that the microbiota, host genetics, and psychological symptoms are strongly related, yet the deeper mechanistic links need further exploration.
Collapse
Affiliation(s)
- Eunchong Huang
- Department of Advanced Green Energy and Environment, Handong Global University, Pohang-si, Gyeongbuk 37554, Korea.
| | - Shinwon Kang
- Department of Advanced Green Energy and Environment, Handong Global University, Pohang-si, Gyeongbuk 37554, Korea.
| | - Haryung Park
- Department of Advanced Green Energy and Environment, Handong Global University, Pohang-si, Gyeongbuk 37554, Korea.
| | - Soyoung Park
- Department of Advanced Green Energy and Environment, Handong Global University, Pohang-si, Gyeongbuk 37554, Korea.
| | - Yosep Ji
- Department of Advanced Green Energy and Environment, Handong Global University, Pohang-si, Gyeongbuk 37554, Korea.
| | - Wilhelm H Holzapfel
- Department of Advanced Green Energy and Environment, Handong Global University, Pohang-si, Gyeongbuk 37554, Korea.
| |
Collapse
|
35
|
Exercise and gut microbiota: clinical implications for the feasibility of Tai Chi. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2018; 15:270-281. [PMID: 28659231 DOI: 10.1016/s2095-4964(17)60342-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent studies have shown exercise is associated with changes in the gut microbiota in humans as well as in experimental animals. Tai Chi is an exercise that integrates a martial art, deep breathing and mediation, and has various beneficial effects for health. This review summarizes current knowledge and recent literature on the association between exercise and gut microbiota, and explores the feasibility of Tai Chi for improving gut microbiota composition and function. PubMed/MEDLINE was used to search the English literature for the keywords exercise and gut microbiota. Fourteen relevant studies were identified. In humans, exercise increases the gut microbial diversity. However, the evidence for this association is weak, as previous studies were small-scale, non-controlled studies of short duration or cross-sectional design. In animals, exercise alters the composition of gut microbiota, with some studies suggesting exercise increases the Bacteroidetes/Firmicutes ratio. However, these results are controversial, partly because host genetics and physical fitness also influence gut microbiota. Furthermore, the intensity of exercise may play a key role in how exercise affects gut microbiota. Tai Chi is a moderate-intensity exercise that improves immune function and inflammation of the gut. Tai Chi may also affect gut microbiota through vagal modulation and mediating the hypothalamic-pituitary-adrenal axis. However, no studies have investigated the association between Tai Chi and gut microbiota. Well designed studies exploring the effects of Tai Chi on gut microbiota are needed.
Collapse
|
36
|
Colonetti K, Roesch LF, Schwartz IVD. The microbiome and inborn errors of metabolism: Why we should look carefully at their interplay? Genet Mol Biol 2018; 41:515-532. [PMID: 30235399 PMCID: PMC6136378 DOI: 10.1590/1678-4685-gmb-2017-0235] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 01/19/2018] [Indexed: 12/26/2022] Open
Abstract
Research into the influence of the microbiome on the human body has been shedding new light on diseases long known to be multifactorial, such as obesity, mood disorders, autism, and inflammatory bowel disease. Although inborn errors of metabolism (IEMs) are monogenic diseases, genotype alone is not enough to explain the wide phenotypic variability observed in patients with these conditions. Genetics and diet exert a strong influence on the microbiome, and diet is used (alone or as an adjuvant) in the treatment of many IEMs. This review will describe how the effects of the microbiome on the host can interfere with IEM phenotypes through interactions with organs such as the liver and brain, two of the structures most commonly affected by IEMs. The relationships between treatment strategies for some IEMs and the microbiome will also be addressed. Studies on the microbiome and its influence in individuals with IEMs are still incipient, but are of the utmost importance to elucidating the phenotypic variety observed in these conditions.
Collapse
Affiliation(s)
- Karina Colonetti
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory of Basic Research and Advanced Investigations in Neurosciences (BRAIN), Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Luiz Fernando Roesch
- Interdisciplinary Research Center on Biotechnology-CIP-Biotec, Universidade Federal do Pampa, Bagé, RS, Brazil
| | - Ida Vanessa Doederlein Schwartz
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory of Basic Research and Advanced Investigations in Neurosciences (BRAIN), Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| |
Collapse
|
37
|
Abstract
Intestinal microbial flora, known as the second gene pool of the human body, play an important role in immune function, nutrient uptake, and various activities of host cells, as well as in human disease. Intestinal microorganisms are involved in a variety of mechanisms that affect bone health. Gut microbes are closely related to genetic variation, and gene regulation plays an important part in the development of bone-related diseases such as osteoporosis. Intestinal microorganisms can disrupt the balance between bone formation and resorption by indirectly stimulating or inhibiting osteoblasts and osteoclasts. In addition, intestinal microorganisms affect bone metabolism by regulating growth factors or altering bone immune status and can also alter the metabolism of serotonin, cortisol, and sex hormones, thereby affecting bone mass in mice. Moreover, probiotics, antibiotics, and diet can change the composition of the intestinal microbial flora, thus affecting bone health and also potentially helping to treat bone disease. Studying the relationship between intestinal flora and osteoblasts, osteoclasts, and bone marrow mesenchymal stem cells may provide a basis for preventing and treating bone diseases. This paper reviews recent advances in the study of the relationship between intestinal microflora and bone disease.
Collapse
Affiliation(s)
- Jian Zhang
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Ji'nan, China
- School of Medicine and Life Sciences, University of Ji'nan-Shandong Academy of Medical Sciences, Ji'nan, China
| | - Yanqin Lu
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Ji'nan, China
- School of Medicine and Life Sciences, University of Ji'nan-Shandong Academy of Medical Sciences, Ji'nan, China
- Address correspondence to:Dr. Jinxiang Han and Dr. Yanqin Lu, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Ji'nan 250062, China. E-mail: (JH); (YL)
| | - Yanzhou Wang
- Department of Paediatric Surgery, Shandong Provincial Hospital, Ji'nan, China
| | - Xiuzhi Ren
- Department of Orthopaedic Surgery, The People’s Hospital of Wuqing District, Tianjin, China
| | - Jinxiang Han
- Key Laboratory for Biotech-Drugs Ministry of Health, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, Ji'nan, China
- School of Medicine and Life Sciences, University of Ji'nan-Shandong Academy of Medical Sciences, Ji'nan, China
- Address correspondence to:Dr. Jinxiang Han and Dr. Yanqin Lu, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Ji'nan 250062, China. E-mail: (JH); (YL)
| |
Collapse
|
38
|
Pisi G, Fainardi V, Aiello M, Bertorelli G, Crisafulli E, Chetta A. The role of the microbiome in childhood asthma. Immunotherapy 2018; 9:1295-1304. [PMID: 29130800 DOI: 10.2217/imt-2017-0048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
It is now well established that the healthy bronchial tree contains a microbiome distinct from that of the upper respiratory tract and that the lung microbiome may be dysregulated in individuals with a chronic respiratory disease, such as asthma. In addition, after birth, gut microbes interact with the host tissue, especially with the lymphatic tissue, thereby guaranteeing efficient immune activation. This review focuses on the available literature on the relationships between the gut microbiome, immune function and asthma in childhood, as well as the therapeutic strategies aimed at acting on the modulation of the microbiome.
Collapse
Affiliation(s)
- Giovanna Pisi
- Cystic Fibrotic Centre, University Hospital, Parma, Italy
| | | | - Marina Aiello
- Respiratory Disease Unit, Department of Medicine & Surgery, University Hospital, Via Gramsci, 14 - 43100 Parma, Italy
| | - Giuseppina Bertorelli
- Respiratory Disease Unit, Department of Medicine & Surgery, University Hospital, Via Gramsci, 14 - 43100 Parma, Italy
| | - Ernesto Crisafulli
- Respiratory Disease Unit, Department of Medicine & Surgery, University Hospital, Via Gramsci, 14 - 43100 Parma, Italy
| | - Alfredo Chetta
- Respiratory Disease Unit, Department of Medicine & Surgery, University Hospital, Via Gramsci, 14 - 43100 Parma, Italy
| |
Collapse
|
39
|
Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y, Rook G. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1018-1038. [PMID: 29426121 DOI: 10.1016/j.scitotenv.2018.01.288] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/28/2018] [Accepted: 01/28/2018] [Indexed: 05/03/2023]
Abstract
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.
Collapse
Affiliation(s)
- Lucette Flandroy
- Federal Public Service Health, Food Chain Safety and Environment, Belgium
| | - Theofilos Poutahidis
- Laboratory of Pathology, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maria-Carlota Dao
- ICAN, Institute of Cardiometabolism and Nutrition, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; INSERM, UMRS U1166 (Eq 6) Nutriomics, Paris 6, France; UPMC, Sorbonne University, Pierre et Marie Curie-Paris 6, France
| | - Ellen Decaestecker
- Aquatic Biology, Department Biology, Science, Engineering & Technology Group, KU Leuven, Campus Kortrijk. E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Eeva Furman
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Finland
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, University of Liège, Passage des deportes, 2, 5030 Gembloux, Belgium
| | - Hubert Plovier
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Graham Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, UK.
| |
Collapse
|
40
|
Exploring the diversity-stability paradigm using sponge microbial communities. Sci Rep 2018; 8:8425. [PMID: 29849034 PMCID: PMC5976656 DOI: 10.1038/s41598-018-26641-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
A key concept in theoretical ecology is the positive correlation between biodiversity and ecosystem stability. When applying this diversity-stability concept to host-associated microbiomes, the following questions emerge: (1) Does microbial diversity influence the stability of microbiomes upon environmental fluctuations? (2) Do hosts that harbor high versus low microbial diversity differ in their stress response? To test the diversity-stability concept in host-associated microbiomes, we exposed six marine sponge species with varying levels of microbial diversity to non-lethal salinity disturbances and followed their microbial composition over time using 16S rRNA gene amplicon sequencing. No signs of sponge stress were evident following salinity amendment and microbiomes exhibited compositional resistance irrespective of their microbial diversity. Compositional stability of the sponge microbiome manifests itself at distinct host taxonomic and host microbial diversity groups, with (1) stable host genotype-specific microbiomes at oligotype-level; (2) stable host species-specific microbiomes at genus-level; and (3) stable and specific microbiomes at phylum-level for hosts with high versus low microbial diversity. The resistance of sponge microbiomes together with the overall stability of sponge holobionts upon salinity fluctuations suggest that the stability-diversity concept does not appear to hold for sponge microbiomes and provides further evidence for the widely recognized environmental tolerance of sponges.
Collapse
|
41
|
Mullaney JA, Stephens JE, Costello ME, Fong C, Geeling BE, Gavin PG, Wright CM, Spector TD, Brown MA, Hamilton-Williams EE. Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota. MICROBIOME 2018; 6:35. [PMID: 29454391 PMCID: PMC5816355 DOI: 10.1186/s40168-018-0417-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/26/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Dysbiosis of the gut microbiota has been implicated in the pathogenesis of many autoimmune conditions including type 1 diabetes (T1D). It is unknown whether changes in the gut microbiota observed in T1D are due to environmental drivers, genetic risk factors, or both. Here, we have performed an analysis of associations between the gut microbiota and T1D genetic risk using the non-obese diabetic (NOD) mouse model of T1D and the TwinsUK cohort. RESULTS Through the analysis of five separate colonies of T1D susceptible NOD mice, we identified similarities in NOD microbiome that were independent of animal facility. Introduction of disease protective alleles at the Idd3 and Idd5 loci (IL2, Ctla4, Slc11a1, and Acadl) resulted in significant alterations in the NOD microbiome. Disease-protected strains exhibited a restoration of immune regulatory pathways within the gut which could also be reestablished using IL-2 therapy. Increased T1D disease risk from IL-2 pathway loci in the TwinsUK cohort of human subjects resulted in some similar microbiota changes to those observed in the NOD mouse. CONCLUSIONS These findings demonstrate for the first time that type 1 diabetes-associated genetic variants that restore immune tolerance to islet antigens also result in functional changes in the gut immune system and resultant changes in the microbiota.
Collapse
Affiliation(s)
- Jane A. Mullaney
- Translational Research Institute, The University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD Australia
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Juliette E. Stephens
- Translational Research Institute, The University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD Australia
| | - Mary-Ellen Costello
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, QLD Australia
| | - Cai Fong
- Translational Research Institute, The University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD Australia
| | - Brooke E. Geeling
- Translational Research Institute, The University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD Australia
| | - Patrick G. Gavin
- Translational Research Institute, The University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD Australia
| | - Casey M. Wright
- Translational Research Institute, The University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD Australia
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Matthew A. Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, QLD Australia
| | - Emma E. Hamilton-Williams
- Translational Research Institute, The University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD Australia
- Translational Research Institute, The University of Queensland Diamantina Institute, 37 Kent St, Woolloongabba, QLD 4102 Australia
| |
Collapse
|
42
|
Abstract
Over the last decade, biologists have come to appreciate that the human body is inhabited by thousands of bacterial species in diverse communities unique to each body site. Moreover, due to high-throughput sequencing methods for microbial characterization in a culture-independent manner, it is becoming evident that the microbiome plays an important role in human health and disease. This chapter focuses on the most common form of bacterial microbiome profiling, targeted amplicon sequencing of the 16S ribosomal RNA (rRNA) subunit encoded by 16S rDNA. We discuss important features for designing and performing microbiome experiments on human specimens, including experimental design, sample collection, DNA preparation, and selection of the 16S rDNA sequencing target. We also provide details for designing fusion primers required for targeted amplicon sequencing and selecting the most appropriate high-throughput sequencing platform. We conclude with a review of the fundamental concepts of data analysis and interpretation for these kinds of experiments. Our goal is to provide the reader with the essential knowledge needed to undertake microbiome experiments for application to human disease research questions.
Collapse
Affiliation(s)
- Rebecca M Davidson
- Department of Biomedical Research, Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA.
| | - L Elaine Epperson
- Department of Biomedical Research, Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| |
Collapse
|
43
|
Abstract
Though seemingly distinct and autonomous, emerging evidence suggests there is a bidirectional interaction between the intestinal microbiota and the brain. This crosstalk may play a substantial role in neurologic diseases, including anxiety, depression, autism, multiple sclerosis, Parkinson's disease, and, potentially, Alzheimer's disease. Long hypothesized by Metchnikoff and others well over 100 years ago, investigations into the mind-microbe axis is now seeing a rapid resurgence of research. If specific pathways and mechanisms of interaction are understood, it could have broad therapeutic potential, as the microbiome is environmentally acquired and can be modified to promote health. This review will discuss immune, endocrine, and neural system pathways that interconnect the gut microbiota to central nervous system and discuss how these findings might be applied to neurologic disease.
Collapse
Affiliation(s)
- Laura M Cox
- Ann Romney Center for Neurologic Diseases, Brigham & Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA, 02446, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Brigham & Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA, 02446, USA.
| |
Collapse
|
44
|
Jayasinghe TN, Hilton C, Tsai P, Apple B, Shepherd P, Cutfield WS, O'Sullivan JM. Long-term stability in the gut microbiome over 46 years in the life of Billy Apple®. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.humic.2017.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
45
|
Bai J, Behera M, Bruner DW. The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review. Support Care Cancer 2017; 26:427-439. [PMID: 29168036 DOI: 10.1007/s00520-017-3982-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022]
Abstract
PURPOSE The gut microbiome plays a critical role in maintaining children's health and in preventing and treating children's disease. Current application of the gut microbiome in childhood cancer is still lacking. This study aimed to systematically review the following: (1) alternations in the gut microbiome throughout cancer treatment trajectories in children, (2) the associations between the gut microbiome and gastrointestinal (GI) symptoms and psychoneurological symptoms (PNS), and (3) the efficacy of therapeutic interventions in the gut microbiome in children with cancer. METHODS PubMed, EMBASE, the Cochrane Library, and the American Society of Clinical Oncology abstract were searched. Eligible studies included all study types in which the gut microbiome was primarily reported in children with cancer. The Mixed Methods Assessment Tool was used to evaluate the methodology quality of included studies. Seven studies met our eligibility criteria, including two cohort studies, two case-control studies, and three randomized controlled trails. RESULTS The findings showed that the diversity estimates of the gut microbiome in children with cancer were lower than those of healthy controls both pre- and post-treatment. Children with cancer showed a significantly lower relative abundance of healthy gut microbiome (e.g., Clostridium XIVa and Bifidobacterium) during and after cancer treatment. No adequate literature was identified to support the associations between dysbiosis of the gut microbiome and GI symptoms/PNS. The use of prebiotics (fructooligosaccharides) and probiotics (Bifidobacterium or Lactobacilli) appears to improve the microenvironment of the gut around 1 month (4-5 weeks) during chemotherapy rather than at the beginning of treatment. Data also suggest that both prebiotic and probiotic interventions decrease clinical side effects (e.g., infection and morbidity risk) in children with cancer. CONCLUSIONS This study adds to the evidence that dysbiosis of the gut microbiome can be improved using prebiotic and probiotic supplementations in children with cancer. More well-designed experimental studies are needed to confirm this conclusion. Further studies are needed to examine the associations between the gut microbiome and GI symptoms/PNS in childhood cancer.
Collapse
Affiliation(s)
- Jinbing Bai
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA.
| | - Madhusmita Behera
- Department of Hematology and Oncology, School of Medicine, Emory University, Atlanta, GA, USA.,Winship Research Informatics, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Deborah Watkins Bruner
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA.,Education and Training, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| |
Collapse
|
46
|
Xu X, Jia X, Mo L, Liu C, Zheng L, Yuan Q, Zhou X. Intestinal microbiota: a potential target for the treatment of postmenopausal osteoporosis. Bone Res 2017; 5:17046. [PMID: 28983411 PMCID: PMC5627629 DOI: 10.1038/boneres.2017.46] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 07/24/2017] [Indexed: 02/08/2023] Open
Abstract
Postmenopausal osteoporosis (PMO) is a prevalent metabolic bone disease characterized by bone loss and structural destruction, which increases the risk of fracture in postmenopausal women. Owing to the high morbidity and serious complications of PMO, many efforts have been devoted to its prophylaxis and treatment. The intestinal microbiota is the complex community of microorganisms colonizing the gastrointestinal tract. Probiotics, which are dietary or medical supplements consisting of beneficial intestinal bacteria, work in concert with endogenous intestinal microorganisms to maintain host health. Recent studies have revealed that bone loss in PMO is closely related to host immunity, which is influenced by the intestinal microbiota. The curative effects of probiotics on metabolic bone diseases have also been demonstrated. The effects of the intestinal microbiota on bone metabolism suggest a promising target for PMO management. This review seeks to summarize the critical effects of the intestinal microbiota and probiotics on PMO, with a focus on the molecular mechanisms underlying the pathogenic relationship between bacteria and host, and to define the possible treatment options.
Collapse
Affiliation(s)
- Xin Xu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaoyue Jia
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Longyi Mo
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Liwei Zheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Dental Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
47
|
Vaiserman AM, Koliada AK, Marotta F. Gut microbiota: A player in aging and a target for anti-aging intervention. Ageing Res Rev 2017; 35:36-45. [PMID: 28109835 DOI: 10.1016/j.arr.2017.01.001] [Citation(s) in RCA: 277] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 02/07/2023]
Abstract
Aging-associated alterations in composition, diversity and functional features of intestinal microbiota are well-described in the modern literature. They are suggested to be caused by an age-related decline in immune system functioning (immunosenescence) and a low-grade chronic inflammation (inflammaging), which accompany many aging-associated pathologies. The microbiota-targeted dietary and probiotic interventions have been shown to favorably affect the host health and aging by an enhancement of antioxidant activity, improving immune homeostasis, suppression of chronic inflammation, regulation of fat deposition and metabolism and prevention of insulin resistance. Recently, a high effectiveness and safety of novel therapeutic application such as fecal microbiota transplantation in the prevention and treatment of age-related pathological conditions including atherosclerosis, type 2 diabetes and Parkinson's disease has been demonstrated. In this review, recent research findings are summarized on the role of gut micribiota in aging processes with emphasis on therapeutic potential of microbiome-targeted interventions in anti-aging medicine.
Collapse
Affiliation(s)
| | | | - Francesco Marotta
- ReGenera Research Group for Aging-Intervention & Montenapoleone Clinic, Healthy Aging Unit, Milano, Italy
| |
Collapse
|
48
|
Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet? Nat Rev Gastroenterol Hepatol 2017; 14:315-320. [PMID: 28356581 DOI: 10.1038/nrgastro.2017.29] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Spurred on by ever-evolving developments in analytical methodology, the microbiome, and the gut microbiome in particular, has become the hot topic in biomedical research. Ingenious experiments in animal models have revealed the extent to which the gut microbiota sustains health and how its disruption might contribute to disease pathogenesis. Not surprisingly, associations between the microbiota and disease states in humans have been the subject of considerable interest and many links proposed. However, with rare exceptions, the incrimination of an altered microbiota in disease pathogenesis seems premature at this time given our incomplete understanding of the composition of the gut microbiota in health and the effect of many confounding factors in the interpretation of supposedly abnormal microbial signatures. Future studies must account for these variables and the bidirectionality of host-microorganism interactions in health and disease. In this Perspectives, the status of microbiota signatures in the clinical arena (for facilitating diagnosis or refining prognosis) will be critically assessed and guidance toward future progress provided.
Collapse
|
49
|
Garcia-Mazcorro JF, Barcenas-Walls JR, Suchodolski JS, Steiner JM. Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing. PeerJ 2017; 5:e3184. [PMID: 28439463 PMCID: PMC5398277 DOI: 10.7717/peerj.3184] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/14/2017] [Indexed: 01/18/2023] Open
Abstract
Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics have not been well studied with regard to the changes they trigger on the composition of the gut microbiota. This study evaluated the effect of a commercially available nutraceutical containing fructo-oligosaccharides (FOS) and inulin on the fecal microbiota of healthy cats and dogs when administered for 16 days. Fecal samples were collected at two time points before and at two time points during prebiotic administration. Total genomic DNA was obtained from fecal samples and 454-pyrosequencing was used for 16S rRNA gene bacterial profiling. The linear discriminant analysis (LDA) effect size (LEfSe) method was used for detecting bacterial taxa that may respond (i.e., increase or decrease in its relative abundance) to prebiotic administration. Prebiotic administration was associated with a good acceptance and no side effects (e.g., diarrhea) were reported by the owners. A low dose of prebiotics (50 mL total regardless of body weight with the end product containing 0.45% of prebiotics) revealed a lower abundance of Gammaproteobacteria and a higher abundance of Veillonellaceae during prebiotic administration in cats, while Staphylococcaceae showed a higher abundance during prebiotic administration in dogs. These differences were not sufficient to separate bacterial communities as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal bacterial metagenome using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) also did not reveal differences between the period before and during prebiotic administration. A second trial using a higher dose of prebiotics (3.2 mL/kg body weight with the end product containing 3.1% of prebiotics) was tested in dogs and revealed a lower abundance of Dorea (family Clostridiaceae) and a higher abundance of Megamonas and other (unknown) members of Veillonellaceae during prebiotic administration. Again, these changes were not sufficient to separate bacterial communities or predicted metabolic profiles according to treatment. A closer analysis of bacterial communities at all time-points revealed highly individualized patterns of variation. This study shows a high interindividual variation of fecal bacterial communities from pet cats and dogs, that these communities are relatively stable over time, and that some of this variation can be attributable to prebiotic administration, a phenomenon that may be affected by the amount of the prebiotic administered in the formulation. This study also provides insights into the response of gut bacterial communities in pet cats and dogs during administration of commercially available products containing prebiotics. More studies are needed to explore potentially beneficial effects on host health beyond changes in bacterial communities.
Collapse
Affiliation(s)
- Jose F Garcia-Mazcorro
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States.,Faculty of Veterinary Medicine, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo Leon, Mexico
| | - Jose R Barcenas-Walls
- Center for Research and Development in Health Sciences (CIDICS), Genomics Unit, Universidad Autónoma de Nuevo León, Monterrey, Nuevo Leon, Mexico
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Jörg M Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| |
Collapse
|
50
|
Kaput J, Perozzi G, Radonjic M, Virgili F. Propelling the paradigm shift from reductionism to systems nutrition. GENES & NUTRITION 2017; 12:3. [PMID: 28138347 PMCID: PMC5264346 DOI: 10.1186/s12263-016-0549-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
The complex physiology of living organisms represents a challenge for mechanistic understanding of the action of dietary bioactives in the human body and of their possible role in health and disease. Animal, cell, and microbial models have been extensively used to address questions that could not be pursued experimentally in humans, posing an additional level of complexity in translation of the results to healthy and diseased metabolism. The past few decades have witnessed a surge in development of increasingly sensitive molecular techniques and bioinformatic tools for storing, managing, and analyzing increasingly large datasets. Application of such powerful means to molecular nutrition research led to a major leap in study designs and experimental approaches yielding experimental data connecting dietary components to human health. Scientific journals bear major responsibilities in the advancement of science. As primary actors of dissemination to the scientific community, journals can impose rigid criteria for publishing only sound, reliable, and reproducible data. Journal policies are meant to guide potential authors to adopt the most updated standardization guidelines and shared best practices. Such policies evolve in parallel with the evolution of novel approaches and emerging challenges and therefore require constant updating. We highlight in this manuscript the major scientific issues that led to formulating new, updated journal policies for Genes & Nutrition, a journal which targets the growing field of nutritional systems biology interfacing personalized nutrition and preventive medicine, with the ultimate goal of promoting health and preventing or treating disease. We focus here on relevant issues requiring standardization in nutrition research. We also introduce new sections on human genetic variation and nutritional bioinformatics which follow the evolution of nutritional science into the twenty-first century.
Collapse
Affiliation(s)
- Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | | | | | - Fabio Virgili
- CREA-NUT, Food & Nutrition Research Centre, Rome, Italy
| |
Collapse
|