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Qiao F, Tan F, Li LY, Lv HB, Chen L, Du ZY, Zhang ML. Alteration and the Function of Intestinal Microbiota in High-Fat-Diet- or Genetics-Induced Lipid Accumulation. Front Microbiol 2021; 12:741616. [PMID: 34603270 PMCID: PMC8484964 DOI: 10.3389/fmicb.2021.741616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
Diet and host genetics influence the composition of intestinal microbiota, yet few studies have compared the function of intestinal microbiota in the diet- or genotype-induced lipid deposition, which limits our understanding of the role of intestinal bacteria in metabolic disorders. The lipid accumulation in wild-type zebrafish fed with control (CON) or high-fat (HF) diet and two gene-knockout zebrafish lines (cpt1b–/– or pparab–/–) fed with control diet was measured after a 4-week feeding experiment. The intestinal microbiota composition of these groups was investigated using 16S ribosomal RNA (rRNA) gene sequencing (DNA-based) and 16S rRNA sequencing (RNA-based). The HF diet or deficiency of two genes induced more weight gain and higher triglyceride content in the liver compared with their control group. 16S rRNA gene sequencing (DNA-based) indicated the decreased abundance of Proteobacteria in the HF group compared with CON, but there was no significant difference in bacterial α diversity among treatments. 16S rRNA sequencing (RNA-based) confirmed the decreased abundance of Proteobacteria and the bacterial α diversity in the HF group compared with CON. Deficiency of cpt1b or pparab showed less change in microbiota composition compared with their wild-type group. Intestinal microbiota of each group was transferred to germ-free zebrafish, and the quantification of Nile red staining indicated that the intestinal microbiota of the HF group induced more lipid accumulation compared with CON, whereas intestinal microbiota of cpt1b–/– and pparab–/– zebrafish did not. The results showed that RNA-based bacterial sequencing revealed more bacterial alteration than DNA-based bacterial sequencing. HF diet had a more dominant role in shaping gut microbiota composition to induce lipid accumulation compared with the gene-knockout of cpt1b or pparab in zebrafish, and the transplant of intestinal microbiota from HF-fed fish induced more lipid deposition in germ-free zebrafish. Together, these data suggested that a high-fat diet exerted a more dominant role over the deletion of cpt1b or pparab on the intestinal bacterial composition, which corresponded to lipid accumulation.
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Affiliation(s)
- Fang Qiao
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Fang Tan
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Ling-Yu Li
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Hong-Bo Lv
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Liqiao Chen
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhen-Yu Du
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
| | - Mei-Ling Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, China
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52
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Xu J, Zhang JN, Sun BH, Liu Q, Ma J, Zhang Q, Liu YX, Chen N, Chen F. The role of genotype and diet in shaping gut microbiome in a genetic vitamin A deficient mouse model. J Genet Genomics 2021; 49:155-164. [PMID: 34537414 DOI: 10.1016/j.jgg.2021.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/26/2022]
Abstract
Multifactors have been reported to affect the gut microbiome, including genotype, age, diet, and nutrition. However, few reports have investigated the relative capacity of different factors to shape the gut microbiome in a single study. Our design used a genetic vitamin A-deficient mouse model, the Rbp4-/- mouse, feeding with the low vitamin A diets at different ages of initiation (4 or 7 weeks) for 28 days. Fecal samples were collected for bacterial profiling at seven time points after diet controlling. With RBP4 depletion, Akkermansia decreased and Bacteroides increased, whereas Desulfovibrio, Barnesiella, Clostridium_XlVa, and Lactobacillus fluctuated. The bacterial community swiftly adjusted with the vitamin A-deficient diet administration and gradually changed (e.g., decrease of Barnesiella and increase of Desulfovibrio). Age exerted a relatively weaker but long-last influence. At an earlier age to feed a vitamin A-deficient diet, a higher microbial dysbiosis index will be valued. Of note, the shaping effects of diet and age on the bacterial community varied with the difference of genotype, which might indicate a greater role of genotype than diet and age in shaping the gut microbiome.
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Affiliation(s)
- Jun Xu
- Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China; Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing 100044, China; Institute of Clinical Molecular Biology & Central Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Jie-Ni Zhang
- Department of Orthodontics, Peking University School of Stomatology, Beijing 100081, China
| | - Bo-Hui Sun
- Department of Orthodontics, Peking University School of Stomatology, Beijing 100081, China
| | - Qing Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China; Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing 100044, China
| | - Juan Ma
- Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China; Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing 100044, China
| | - Qian Zhang
- Central Laboratory, Peking University School of Stomatology, Beijing 100081, China
| | - Yong-Xin Liu
- CAS Center for Excellence in Biotic Interactions, Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Chen
- Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China; Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing 100044, China.
| | - Feng Chen
- Department of Orthodontics, Peking University School of Stomatology, Beijing 100081, China; Central Laboratory, Peking University School of Stomatology, Beijing 100081, China.
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53
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Lobo AK, Traeger LL, Keller MP, Attie AD, Rey FE, Broman KW. Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice. G3-GENES GENOMES GENETICS 2021; 11:6362887. [PMID: 34499168 PMCID: PMC8527510 DOI: 10.1093/g3journal/jkab308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/26/2021] [Indexed: 11/14/2022]
Abstract
In a Diversity Outbred mouse project with genotype data on 500 mice, including 297 with microbiome data, we identified three sets of sample mix-ups (two pairs and one trio) as well as at least 15 microbiome samples that appear to be mixtures of pairs of mice. The microbiome data consisted of shotgun sequencing reads from fecal DNA, used to characterize the gut microbial communities present in these mice. These sequence reads included sufficient reads derived from the host mouse to identify the individual. A number of microbiome samples appeared to contain a mixture of DNA from two mice. We describe a method for identifying sample mix-ups in such microbiome data, as well as a method for evaluating sample mixtures in this context.
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Affiliation(s)
- Alexandra K Lobo
- Departments of *Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
| | - Lindsay L Traeger
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Mark P Keller
- Departments of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
| | - Alan D Attie
- Departments of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706, USA
| | - Karl W Broman
- Departments of *Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
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54
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El-Sayed A, Aleya L, Kamel M. Microbiota and epigenetics: promising therapeutic approaches? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:49343-49361. [PMID: 34319520 PMCID: PMC8316543 DOI: 10.1007/s11356-021-15623-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/20/2021] [Indexed: 04/15/2023]
Abstract
The direct/indirect responsibility of the gut microbiome in disease induction in and outside the digestive tract is well studied. These results are usually from the overpopulation of certain species on the cost of others, interaction with beneficial microflora, interference with normal epigenetic control mechanisms, or suppression of the immune system. Consequently, it is theoretically possible to cure such disorders by rebalancing the microbiome inside our bodies. This can be achieved by changing the lifestyle pattern and diet or by supplementation with beneficial bacteria or their metabolites. Various approaches have been explored to manipulate the normal microbial inhabitants, including nutraceutical, supplementations with prebiotics, probiotics, postbiotics, synbiotics, and antibiotics, or through microbiome transplantation (fecal, skin, or vaginal microbiome transplantation). In the present review, the interaction between the microbiome and epigenetics and their role in disease induction is discussed. Possible future therapeutic approaches via the reestablishment of equilibrium in our internal micro-ecosystem are also highlighted.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, F-25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
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55
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Salamone D, Rivellese AA, Vetrani C. The relationship between gut microbiota, short-chain fatty acids and type 2 diabetes mellitus: the possible role of dietary fibre. Acta Diabetol 2021; 58:1131-1138. [PMID: 33970303 PMCID: PMC8316221 DOI: 10.1007/s00592-021-01727-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Gut microbiota and its metabolites have been shown to influence multiple physiological mechanisms related to human health. Among microbial metabolites, short-chain fatty acids (SCFA) are modulators of different metabolic pathways. On the other hand, several studies suggested that diet might influence gut microbiota composition and activity thus modulating the risk of metabolic disease, i.e. obesity, insulin resistance and type 2 diabetes. Among dietary component, dietary fibre may play a pivotal role by virtue of its prebiotic effect on fibre-fermenting bacteria, that may increase SCFA production. The aim of this review was to summarize and discuss current knowledge on the impact of dietary fibre as modulator of the relationship between glucose metabolism and microbiota composition in humans. More specifically, we analysed evidence from observational studies and randomized nutritional intervention investigating the relationship between gut microbiota, short-chain fatty acids and glucose metabolism. The possible mechanisms behind this association were also discussed.
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Affiliation(s)
- Dominic Salamone
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 5 Sergio Pansini, 80131, Naples, Italy
| | - Angela Albarosa Rivellese
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 5 Sergio Pansini, 80131, Naples, Italy.
- Task Force On Microbiome Studies, University of Naples "Federico II", Naples, Italy.
| | - Claudia Vetrani
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 5 Sergio Pansini, 80131, Naples, Italy
- Task Force On Microbiome Studies, University of Naples "Federico II", Naples, Italy
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56
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El-Sayed A, Aleya L, Kamel M. Microbiota's role in health and diseases. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:36967-36983. [PMID: 34043164 PMCID: PMC8155182 DOI: 10.1007/s11356-021-14593-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/24/2021] [Indexed: 05/06/2023]
Abstract
The microbiome is a term that usually refers to the community of various microorganisms that inhabit/live inside human/animal bodies or on their skin. It forms a complex ecosystem that includes trillions of commensals, symbiotics, and even pathogenic microorganisms. The external environment, diet, and lifestyle are the major determinants influencing the microbiome's composition and vitality. Recent studies have indicated the tremendous influence of the microbiome on health and disease. Their number, constitution, variation, and viability are dynamic. All these elements are responsible for the induction, development, and treatment of many health disorders. Serious diseases such as cancer, metabolic disorders, cardiovascular diseases, and even psychological disorders such as schizophrenia are influenced directly or indirectly by microbiota. In addition, in the last few weeks, accumulating data about the link between COVID-19 and the microbiota were published. In the present work, the role of the microbiome in health and disease is discussed. A deep understanding of the exact role of microbiota in disease induction enables the prevention of diseases and the development of new therapeutic concepts for most diseases through the correction of diet and lifestyle. The present review brings together evidence from the most recent works and discusses suggested nutraceutical approaches for the management of COVID-19 pandemic.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, F-25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
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57
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Long LL, Svenson KL, Mourino AJ, Michaud M, Fahey JR, Waterman L, Vandegrift KL, Adams MD. Shared and distinctive features of the gut microbiome of C57BL/6 mice from different vendors and production sites, and in response to a new vivarium. Lab Anim (NY) 2021; 50:185-195. [PMID: 34127866 DOI: 10.1038/s41684-021-00777-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
Abstract
Animal models play a critical role in establishing causal relationships between gut microbiota and disease. The laboratory mouse is widely used to study the role of microbes in various disorders; however, differences between mouse vendors, genetic lineages and husbandry protocols have been shown to contribute to variation in phenotypes and to non-reproducibility of experimental results. We sought to understand how gut microbiome profiles of mice vary by vendor, vendor production facility and health status upon receipt into an academic facility and how they change over 12 weeks in the new environment. C57BL/6 mice were sourced from two different production sites for each of three different vendors. Mice were shipped to an academic research vivarium, and fresh-catch stool samples were collected from mice immediately from the shipping box upon receipt, and again after 2, 6 and 12 weeks in the new facility. Substantial variation in bacterial proportional abundance was observed among mice from each vendor at the time of receipt, but shared microbes accounted for most sequence reads. Vendor-specific microbes were generally of low abundance. Microbial profiles of mice from all vendors exhibited shifts over time, highlighting the importance of environmental conditions on microbial dynamics. Our results emphasize the need for continued efforts to account for sources of variation in animal models and understand how they contribute to experimental reproducibility.
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Affiliation(s)
- Lauren L Long
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Karen L Svenson
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Michael Michaud
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - James R Fahey
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Linda Waterman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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58
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Kim M, Huda MN, O'Connor A, Albright J, Durbin-Johnson B, Bennett BJ. Hepatic transcriptional profile reveals the role of diet and genetic backgrounds on metabolic traits in female progenitor strains of the Collaborative Cross. Physiol Genomics 2021; 53:173-192. [PMID: 33818129 PMCID: PMC8424536 DOI: 10.1152/physiolgenomics.00140.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/28/2022] Open
Abstract
Mice have provided critical mechanistic understandings of clinical traits underlying metabolic syndrome (MetSyn) and susceptibility to MetSyn in mice is known to vary among inbred strains. We investigated the diet- and strain-dependent effects on metabolic traits in the eight Collaborative Cross (CC) founder strains (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HILtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ). Liver transcriptomics analysis showed that both atherogenic diet and host genetics have profound effects on the liver transcriptome, which may be related to differences in metabolic traits observed between strains. We found strain differences in circulating trimethylamine N-oxide (TMAO) concentration and liver triglyceride content, both of which are traits associated with metabolic diseases. Using a network approach, we identified a module of transcripts associated with TMAO and liver triglyceride content, which was enriched in functional pathways. Interrogation of the module related to metabolic traits identified NADPH oxidase 4 (Nox4), a gene for a key enzyme in the production of reactive oxygen species, which showed a strong association with plasma TMAO and liver triglyceride. Interestingly, Nox4 was identified as the highest expressed in the C57BL/6J and NZO/HILtJ strains and the lowest expressed in the CAST/EiJ strain. Based on these results, we suggest that there may be genetic variation in the contribution of Nox4 to the regulation of plasma TMAO and liver triglyceride content. In summary, we show that liver transcriptomic analysis identified diet- or strain-specific pathways for metabolic traits in the Collaborative Cross (CC) founder strains.
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Affiliation(s)
- Myungsuk Kim
- Department of Nutrition, University of California, Davis, California
- USDA-ARS-Western Human Nutrition Research Center, Davis, California
| | - M Nazmul Huda
- Department of Nutrition, University of California, Davis, California
- USDA-ARS-Western Human Nutrition Research Center, Davis, California
| | - Annalouise O'Connor
- Nutrition Research Institute, University of North Carolina, Kannapolis, North Carolina
| | - Jody Albright
- Nutrition Research Institute, University of North Carolina, Kannapolis, North Carolina
| | | | - Brian J Bennett
- Department of Nutrition, University of California, Davis, California
- USDA-ARS-Western Human Nutrition Research Center, Davis, California
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59
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Catania F, Baedke J, Fábregas-Tejeda A, Nieves Delgado A, Vitali V, Long LAN. Global climate change, diet, and the complex relationship between human host and microbiome: Towards an integrated picture. Bioessays 2021; 43:e2100049. [PMID: 33829521 DOI: 10.1002/bies.202100049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023]
Abstract
Dietary changes can alter the human microbiome with potential detrimental consequences for health. Given that environment, health, and evolution are interconnected, we ask: Could diet-driven microbiome perturbations have consequences that extend beyond their immediate impact on human health? We address this question in the context of the urgent health challenges posed by global climate change. Drawing on recent studies, we propose that not only can diet-driven microbiome changes lead to dysbiosis, they can also shape life-history traits and fuel human evolution. We posit that dietary shifts prompt mismatched microbiome-host genetics configurations that modulate human longevity and reproductive success. These mismatches can also induce a heritable intra-holobiont stress response, which encourages the holobiont to re-establish equilibrium within the changed nutritional environment. Thus, while mismatches between climate change-related genetic and epigenetic configurations within the holobiont increase the risk and severity of diseases, they may also affect life-history traits and facilitate adaptive responses. These propositions form a framework that can help systematize and address climate-related dietary challenges for policy and health interventions.
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Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jan Baedke
- Department of Philosophy I, Ruhr University Bochum, Bochum, Germany
| | | | - Abigail Nieves Delgado
- Knowledge, Technology & Innovation, Wageningen University, Wageningen, The Netherlands.,Freudenthal Institute, Utrecht University, Utrecht, The Netherlands
| | - Valerio Vitali
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Le Anh Nguyen Long
- Department of Public Administration, University of Twente, Enschede, The Netherlands
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60
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Mims TS, Abdallah QA, Stewart JD, Watts SP, White CT, Rousselle TV, Gosain A, Bajwa A, Han JC, Willis KA, Pierre JF. The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet. Commun Biol 2021; 4:281. [PMID: 33674757 PMCID: PMC7935979 DOI: 10.1038/s42003-021-01820-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
As an active interface between the host and their diet, the gut microbiota influences host metabolic adaptation; however, the contributions of fungi have been overlooked. Here, we investigate whether variations in gut mycobiome abundance and composition correlate with key features of host metabolism. We obtained animals from four commercial sources in parallel to test if differing starting mycobiomes can shape host adaptation in response to processed diets. We show that the gut mycobiome of healthy mice is shaped by the environment, including diet, and significantly correlates with metabolic outcomes. We demonstrate that exposure to processed diet leads to persistent differences in fungal communities that significantly associate with differential deposition of body mass in male mice compared to mice fed standardized diet. Fat deposition in the liver, transcriptional adaptation of metabolically active tissues and serum metabolic biomarker levels are linked with alterations in fungal community diversity and composition. Specifically, variation in fungi from the genera Thermomyces and Saccharomyces most strongly associate with metabolic disturbance and weight gain. These data suggest that host-microbe metabolic interactions may be influenced by variability in the mycobiome. This work highlights the potential significance of the gut mycobiome in health and has implications for human and experimental metabolic studies.
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Affiliation(s)
- Tahliyah S Mims
- Department of Pediatrics, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Qusai Al Abdallah
- Department of Pediatrics, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Justin D Stewart
- Department of Geography and the Environment, Villanova University, Radnor, PA, USA
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sydney P Watts
- Department of Pediatrics, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Catrina T White
- Department of Pediatrics, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Thomas V Rousselle
- Department of Surgery, Transplant Research Institute, James D. Eason Transplant Institute, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ankush Gosain
- Division of Pediatric Surgery, Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amandeep Bajwa
- Department of Surgery, Transplant Research Institute, James D. Eason Transplant Institute, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Joan C Han
- Department of Pediatrics, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kent A Willis
- Department of Pediatrics, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA.
- Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Joseph F Pierre
- Department of Pediatrics, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA.
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA.
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61
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Adriansjach J, Baum ST, Lefkowitz EJ, Van Der Pol WJ, Buford TW, Colman RJ. Age-Related Differences in the Gut Microbiome of Rhesus Macaques. J Gerontol A Biol Sci Med Sci 2021; 75:1293-1298. [PMID: 32052009 DOI: 10.1093/gerona/glaa048] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Aging is a multifactorial process characterized by progressive changes in gut physiology and the intestinal mucosal immune system. These changes, along with alterations in lifestyle, diet, nutrition, inflammation and immune function alter both composition and stability of the gut microbiota. Given the impact of environmental influences on the gut microbiota, animal models are particularly useful in this field. To understand the relationship between the gut microbiota and aging in nonhuman primates, we collected fecal samples from 20 male and 20 female rhesus macaques (Macaca mulatta), across the natural macaque age range, for 16S rRNA gene analyses. Operational taxonomic units were then grouped together to summarize taxon abundance at different hierarchical levels of classification and alpha- and beta-diversity were calculated. There were no age or sex differences in alpha diversity. At the phylum level, relative abundance of Proteobacteria and Firmicutes and Firmicutes to Bacteriodetes ratio were different between age groups though significance disappeared after correction for multiple comparisons. At the class level, relative abundance of Firmicutes_Bacilli decreased and Proteobacteria_Alphaproteobacteria and Proteobacteria_Betaproteobacteria increased with each successively older group. Only differences in Firmicutes_Bacilli remained significant after correction for multiple comparisons. No sex differences were identified in relative abundances after correction for multiple comparisons. Our results are not surprising given the known impact of environmental factors on the gut microbiota.
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Affiliation(s)
- Julie Adriansjach
- Wisconsin National Primate Research Center, University of Wisconsin, Madison
| | - Scott T Baum
- Wisconsin National Primate Research Center, University of Wisconsin, Madison
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Madison
| | - William J Van Der Pol
- Biomedical Informatics, Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Madison
| | - Thomas W Buford
- Department of Medicine, University of Alabama at Birmingham, Madison
| | - Ricki J Colman
- Wisconsin National Primate Research Center, University of Wisconsin, Madison.,Department of Cell and Regenerative Biology, University of Wisconsin, Madison
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62
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Abstract
Blood glucose and insulin homeostasis is disrupted during the progression of type 2 diabetes. Insulin levels and action are regulated by both peripheral and central responses that involve the intestine and microbiome. The intestine and its microbiota process nutrients and generate molecules that influence blood glucose and insulin. Peripheral insulin regulation is regulated by gut-segment-dependent nutrient sensing and microbial factors such as short-chain fatty acids and bile acids that engage G-protein-coupled receptors. Innate immune sensing of gut-derived bacterial cell wall components and lipopolysaccharides also alter insulin homeostasis. These bacterial metabolites and postbiotics influence insulin secretion and insulin clearance in part by altering endocrine responses such as glucagon-like peptide-1. Gut-derived bacterial factors can promote inflammation and insulin resistance, but other postbiotics can be insulin sensitizers. In parallel, activation of small intestinal sirtuin 1 increases insulin sensitivity by reversing high fat-induced hypothalamic insulin resistance through a gut-brain neuronal axis, whereas high fat-feeding alters small intestinal microbiome and increases taurochenodeoxycholic acid in the plasma and the dorsal vagal complex to induce insulin resistance. In summary, emerging evidence indicates that intestinal molecular signaling involving nutrient sensing and the host-microbe symbiosis alters insulin homeostasis and action. Gut-derived host endocrine and paracrine factors as well as microbial metabolites act on the liver, pancreas, and the brain, and in parallel on the gut-brain neuronal axis. Understanding common nodes of peripheral and central insulin homeostasis and action may reveal new ways to target the intestinal host-microbe relationship in obesity, metabolic disease, and type 2 diabetes.
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Affiliation(s)
- 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, Ontario, Canada
| | - Tony K T Lam
- Toronto General Hospital Research Institute, UHN, Toronto, Ontario, Canada
- Departments of Physiology and Medicine, University of Toronto, Toronto, Ontario, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, Ontario, Canada
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Modulation of Short-Chain Fatty Acids as Potential Therapy Method for Type 2 Diabetes Mellitus. ACTA ACUST UNITED AC 2021; 2021:6632266. [PMID: 33488888 PMCID: PMC7801078 DOI: 10.1155/2021/6632266] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 12/25/2022]
Abstract
In recent years, the relationship between intestinal microbiota (IM) and the pathogenesis of type 2 diabetes mellitus (T2DM) has attracted much attention. The beneficial effects of IM on the metabolic phenotype of the host are often considered to be mediated by short-chain fatty acids (SCFAs), mainly acetate, butyrate, and propionate, the small-molecule metabolites derived from microbial fermentation of indigestible carbohydrates. SCFAs not only have an essential role in intestinal health but might also enter the systemic circulation as signaling molecules affecting the host's metabolism. In this review, we summarize the effects of SCFAs on glucose homeostasis and energy homeostasis and the mechanism through which SCFAs regulate the function of metabolically active organs (brain, liver, adipose tissue, skeletal muscle, and pancreas) and discuss the potential role of modulation of SCFAs as a therapeutic method for T2DM.
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64
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Bombin A, Cunneely O, Eickman K, Bombin S, Ruesy A, Su M, Myers A, Cowan R, Reed L. Influence of Lab Adapted Natural Diet and Microbiota on Life History and Metabolic Phenotype of Drosophila melanogaster. Microorganisms 2020; 8:E1972. [PMID: 33322411 PMCID: PMC7763083 DOI: 10.3390/microorganisms8121972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 01/14/2023] Open
Abstract
Symbiotic microbiota can help its host to overcome nutritional challenges, which is consistent with a holobiont theory of evolution. Our project investigated the effects produced by the microbiota community, acquired from the environment and horizontal transfer, on metabolic traits related to obesity. The study applied a novel approach of raising Drosophila melanogaster, from ten wild-derived genetic lines on naturally fermented peaches, preserving genuine microbial conditions. Larvae raised on the natural and standard lab diets were significantly different in every tested phenotype. Frozen peach food provided nutritional conditions similar to the natural ones and preserved key microbial taxa necessary for survival and development. On the peach diet, the presence of parental microbiota increased the weight and development rate. Larvae raised on each tested diet formed microbial communities distinct from each other. The effect that individual microbial taxa produced on the host varied significantly with changing environmental and genetic conditions, occasionally to the degree of opposite correlations.
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Affiliation(s)
- Andrei Bombin
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA; (O.C.); (K.E.); (S.B.); (A.R.); (M.S.); (A.M.); (R.C.)
| | | | | | | | | | | | | | | | - Laura Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA; (O.C.); (K.E.); (S.B.); (A.R.); (M.S.); (A.M.); (R.C.)
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65
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Peri-operative antibiotics acutely and significantly impact intestinal microbiota following bariatric surgery. Sci Rep 2020; 10:20340. [PMID: 33230230 PMCID: PMC7684314 DOI: 10.1038/s41598-020-77285-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Bariatric surgery is the most effective treatment for weight loss. Vertical sleeve gastrectomy (VSG) involves the resection of ~ 80% of the stomach and was conceived to purely restrict oral intake. However, evidence suggests more complex mechanisms, particularly postoperative changes in gut microbiota, in facilitating weight loss and resolving associated comorbidities. VSG in humans is a complex procedure and includes peri-operative antibiotics and caloric restriction in addition to the altered anatomy. The impact of each of these factors on the intestinal microbiota have not been evaluated. The aim of this study was to determine the relative contributions of each of these factors on intestinal microbiota composition following VSG prior to substantial weight loss. Thirty-two obese patients underwent one of three treatments: (1) VSG plus routine intravenous peri-operative antibiotics (n = 12), (2) VSG with intravenous vancomycin chosen for its low intestinal penetrance (n = 12), and (3) caloric restriction (n = 8). Fecal samples were evaluated for bacterial composition prior to and 7 days following each intervention. Only patients undergoing VSG with routine peri-operative antibiotics showed a significant shift in community composition. Our data support the single dose of routine peri-operative antibiotics as the most influential factor of intestinal microbial composition acutely following VSG.
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66
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Wang Y, Shao T, Wang J, Huang X, Deng X, Cao Y, Zhou M, Zhao C. An update on potential biomarkers for diagnosing diabetic foot ulcer at early stage. Biomed Pharmacother 2020; 133:110991. [PMID: 33227713 DOI: 10.1016/j.biopha.2020.110991] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 01/01/2023] Open
Abstract
As one of major chronic complications of diabetes, diabetic foot ulcer (DFU) is the main cause of disability and death. The clinical diagnosis and prognosis of DFU is inadequate. For clinicians, if the risk stratification of DFU can be obtained earlier in diabetic patients, the hospitalization, disability and mortality rate will be reduced. In addition to the inflammatory biomarkers that have been widely concerned and used, e.g., procalcitonin, pentraxin-3, C-reactive protein (CRP), interleukins (ILs), and tumor necrosis factor-α (TNF-α), etc., a more comprehensive prediction of the risk and severity of DFU is needed to reflect new biomarkers for therapeutic intervention effects. Along with the development of systems biology technology, genomics, proteomics, metabolomics and microbiome have been used in the studies on DFU for better understanding of the disease. In this review, new biomarkers that are expected to assist in the accurate diagnosis and risk stratification of DFU will be discussed and summarized in detail.
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Affiliation(s)
- Yuqing Wang
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China; Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Tengteng Shao
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China; Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jialin Wang
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China; Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiaoting Huang
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China; Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiaofei Deng
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China
| | - Yemin Cao
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China
| | - Mingmei Zhou
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China; Center for Chinese Medicine Therapy and Systems Biology, Institute for Interdisciplinary Medicine Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Cheng Zhao
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China.
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Cammarota G, Ianiro G, Ahern A, Carbone C, Temko A, Claesson MJ, Gasbarrini A, Tortora G. Gut microbiome, big data and machine learning to promote precision medicine for cancer. Nat Rev Gastroenterol Hepatol 2020; 17:635-648. [PMID: 32647386 DOI: 10.1038/s41575-020-0327-3] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
The gut microbiome has been implicated in cancer in several ways, as specific microbial signatures are known to promote cancer development and influence safety, tolerability and efficacy of therapies. The 'omics' technologies used for microbiome analysis continuously evolve and, although much of the research is still at an early stage, large-scale datasets of ever increasing size and complexity are being produced. However, there are varying levels of difficulty in realizing the full potential of these new tools, which limit our ability to critically analyse much of the available data. In this Perspective, we provide a brief overview on the role of gut microbiome in cancer and focus on the need, role and limitations of a machine learning-driven approach to analyse large amounts of complex health-care information in the era of big data. We also discuss the potential application of microbiome-based big data aimed at promoting precision medicine in cancer.
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Affiliation(s)
- Giovanni Cammarota
- Gastroenterology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Gianluca Ianiro
- Gastroenterology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Anna Ahern
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Carmine Carbone
- Oncology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andriy Temko
- School of Engineering, University College Cork, Cork, Ireland.,Qualcomm ML R&D, Cork, Ireland
| | - Marcus J Claesson
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Antonio Gasbarrini
- Gastroenterology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giampaolo Tortora
- Oncology Department, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
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68
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Ma L, Li H, Hu J, Zheng J, Zhou J, Botchlett R, Matthews D, Zeng T, Chen L, Xiao X, Athrey G, Threadgill D, Li Q, Glaser S, Francis H, Meng F, Li Q, Alpini G, Wu C. Indole Alleviates Diet-Induced Hepatic Steatosis and Inflammation in a Manner Involving Myeloid Cell 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3. Hepatology 2020; 72:1191-1203. [PMID: 31953865 PMCID: PMC7365739 DOI: 10.1002/hep.31115] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Indole is a microbiota metabolite that exerts anti-inflammatory responses. However, the relevance of indole to human non-alcoholic fatty liver disease (NAFLD) is not clear. It also remains largely unknown whether and how indole acts to protect against NAFLD. The present study sought to examine the association between the circulating levels of indole and liver fat content in human subjects and explore the mechanisms underlying indole actions in mice with diet-induced NAFLD. APPROACH AND RESULTS In a cohort of 137 subjects, the circulating levels of indole were reversely correlated with body mass index. In addition, the circulating levels of indole in obese subjects were significantly lower than those in lean subjects and were accompanied with increased liver fat content. At the whole-animal level, treatment of high-fat diet (HFD)-fed C57BL/6J mice with indole caused significant decreases in the severity of hepatic steatosis and inflammation. In cultured cells, indole treatment stimulated the expression of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), a master regulatory gene of glycolysis, and suppressed macrophage proinflammatory activation in a PFKFB3-dependent manner. Moreover, myeloid cell-specific PFKFB3 disruption exacerbated the severity of HFD-induced hepatic steatosis and inflammation and blunted the effect of indole on alleviating diet-induced NAFLD phenotype. CONCLUSIONS Taken together, our results demonstrate that indole is relevant to human NAFLD and capable of alleviating diet-induced NAFLD phenotypes in mice in a myeloid cell PFKFB3-dependent manner. Therefore, indole mimetic and/or macrophage-specific PFKFB3 activation may be the viable preventive and/or therapeutic approaches for inflammation-associated diseases including NAFLD.
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Affiliation(s)
- Linqiang Ma
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA, Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China, Laboratory of Lipid & Glucose Metabolism, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Honggui Li
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA
| | - Jinbo Hu
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Juan Zheng
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jing Zhou
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA
| | - Rachel Botchlett
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA
| | - Destiny Matthews
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA
| | - Tianshu Zeng
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Lulu Chen
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Xiaoqiu Xiao
- Laboratory of Lipid & Glucose Metabolism, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Giri Athrey
- Department of Poultry Science, Texas A&M University, College Station, TX 77843, USA
| | - David Threadgill
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Shannon Glaser
- Department of Medical Physiology, Texas A&M University College of Medicine, Temple, TX, 76504, USA
| | - Heather Francis
- Indiana Center for Liver Research, Richard L. Roudebush VA Medical Center, and Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Fanyin Meng
- Indiana Center for Liver Research, Richard L. Roudebush VA Medical Center, and Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Qifu Li
- Department of Endocrinology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China, Corresponding addresses: Chaodong Wu, MD, PhD, College Station, TX 77843, ; Gianfranco Alpini, PhD, Indianapolis, IN 46202, ; or Qifu Li, MD, PhD, Chongqing 400016, China,
| | - Gianfranco Alpini
- Indiana Center for Liver Research, Richard L. Roudebush VA Medical Center, and Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202., Corresponding addresses: Chaodong Wu, MD, PhD, College Station, TX 77843, ; Gianfranco Alpini, PhD, Indianapolis, IN 46202, ; or Qifu Li, MD, PhD, Chongqing 400016, China,
| | - Chaodong Wu
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX 77843, USA, Corresponding addresses: Chaodong Wu, MD, PhD, College Station, TX 77843, ; Gianfranco Alpini, PhD, Indianapolis, IN 46202, ; or Qifu Li, MD, PhD, Chongqing 400016, China,
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69
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Sailani MR, Metwally AA, Zhou W, Rose SMSF, Ahadi S, Contrepois K, Mishra T, Zhang MJ, Kidziński Ł, Chu TJ, Snyder MP. Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. Nat Commun 2020; 11:4933. [PMID: 33004787 PMCID: PMC7529769 DOI: 10.1038/s41467-020-18758-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
The influence of seasons on biological processes is poorly understood. In order to identify biological seasonal patterns based on diverse molecular data, rather than calendar dates, we performed a deep longitudinal multiomics profiling of 105 individuals over 4 years. Here, we report more than 1000 seasonal variations in omics analytes and clinical measures. The different molecules group into two major seasonal patterns which correlate with peaks in late spring and late fall/early winter in California. The two patterns are enriched for molecules involved in human biological processes such as inflammation, immunity, cardiovascular health, as well as neurological and psychiatric conditions. Lastly, we identify molecules and microbes that demonstrate different seasonal patterns in insulin sensitive and insulin resistant individuals. The results of our study have important implications in healthcare and highlight the value of considering seasonality when assessing population wide health risk and management.
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Affiliation(s)
- M Reza Sailani
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Ahmed A Metwally
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | | | - Sara Ahadi
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Contrepois
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Tejaswini Mishra
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Martin Jinye Zhang
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Łukasz Kidziński
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Theodore J Chu
- Department of Pediatrics, Division of Allergy and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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Sublette MG, Cross TWL, Korcarz CE, Hansen KM, Murga-Garrido SM, Hazen SL, Wang Z, Oguss MK, Rey FE, Stein JH. Effects of Smoking and Smoking Cessation on the Intestinal Microbiota. J Clin Med 2020; 9:jcm9092963. [PMID: 32937839 PMCID: PMC7564179 DOI: 10.3390/jcm9092963] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
We evaluated associations of smoking heaviness markers and the effects of smoking cessation on the intestinal microbiota and cardiovascular disease risk factors in current smokers undertaking a quit attempt. Participants were current smokers enrolled in a prospective randomized clinical trial of smoking cessation therapies with visits at baseline, 2, and 12 weeks. Genomic DNA was extracted from fecal samples followed by 16S rRNA gene sequencing and analysis using the QIIME2 software workflow. Relative abundances of bacterial taxa and alpha- and beta-diversity measures were used for comparisons. The 36 smokers were (mean (standard deviation)) 51.5 (11.1) years old (42% male) and smoked 15.1 (6.4) cigarettes per day for 22.7 (11.9) pack-years. Relative abundances of the phylum Actinobacteria correlated with pack-years (rho = −0.44, p = 0.008) and Cyanobacteria correlated with CO levels (rho = 0.39, p = 0.021). After 12 weeks, relative abundances of the phylum Bacteroidetes increased (pANCOVA = 0.048) and Firmicutes decreased (pANCOVA = 0.036) among abstainers compared to continuing smokers. Increases in alpha-diversity were associated with heart rates (rho = −0.59, p = 0.037), systolic blood pressures (rho = −0.58, p = 0.043), and C-reactive protein (rho = −0.60, p = 0.034). Smoking cessation led to minor changes in the intestinal microbiota. It is unclear if the proven health benefits of smoking cessation lead to salutary changes in the intestinal microbiota.
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Affiliation(s)
- Marcus G. Sublette
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (M.G.S.); (C.E.K.); (K.M.H.); (M.K.O.)
| | - Tzu-Wen L. Cross
- Department of Nutrition Science, Purdue University, West Lafayette, Indiana, 47907, USA;
| | - Claudia E. Korcarz
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (M.G.S.); (C.E.K.); (K.M.H.); (M.K.O.)
| | - Kristin M. Hansen
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (M.G.S.); (C.E.K.); (K.M.H.); (M.K.O.)
| | - Sofia M. Murga-Garrido
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA; (S.M.M.-G.); (S.L.H.); (F.E.R.)
| | - Stanley L. Hazen
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA; (S.M.M.-G.); (S.L.H.); (F.E.R.)
| | - Zeneng Wang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Madeline K. Oguss
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (M.G.S.); (C.E.K.); (K.M.H.); (M.K.O.)
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA; (S.M.M.-G.); (S.L.H.); (F.E.R.)
| | - James H. Stein
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; (M.G.S.); (C.E.K.); (K.M.H.); (M.K.O.)
- Correspondence:
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71
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Foley KP, Zlitni S, Duggan BM, Barra NG, Anhê FF, Cavallari JF, Henriksbo BD, Chen CY, Huang M, Lau TC, Plante R, Schwab M, Marette A, Schertzer JD. Gut microbiota impairs insulin clearance in obese mice. Mol Metab 2020; 42:101067. [PMID: 32860984 PMCID: PMC7522491 DOI: 10.1016/j.molmet.2020.101067] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Objective Hyperinsulinemia can be both a cause and consequence of obesity and insulin resistance. Hyperinsulinemia can result from increased insulin secretion and/or reduced insulin clearance. While many studies have focused on mechanisms triggering insulin secretion during obesity, the triggers for changes in insulin clearance during obesity are less defined. In this study, we investigated the role of the microbiota in regulating insulin clearance during diet-induced obesity. Methods Blood glucose and insulin clearance were tested in conventional male mice treated with antibiotics and germ-free mice colonized with microbes from mice that were fed a control (chow) diet or an obesogenic high-fat diet (HFD). The composition of the fecal microbiota was analyzed using 16S rRNA sequencing. Results Short-term HFD feeding and aging did not alter insulin clearance in the mice. Oral antibiotics mitigated impaired blood insulin clearance in the mice fed an HFD for 12 weeks or longer. Germ-free mice colonized with microbes from HFD-fed donor mice had impaired insulin but not C-peptide clearance. Microbe-transmissible insulin clearance impairment was only observed in germ-free mice after more than 6 weeks post-colonization upon HFD feeding. Five bacterial taxa predicted >90% of the variance in insulin clearance. Mechanistically, impaired insulin clearance was associated with lower levels of hepatic Ceacam-1 but increased liver and skeletal muscle insulin-degrading enzyme (IDE) activity. Conclusions Gut microbes regulate insulin clearance during diet-induced obesity. A small cluster of microbes or their metabolites may be targeted for mitigating defects in insulin clearance and hyperinsulinemia during the progression of obesity and type 2 diabetes. Obesity impairs insulin clearance in mice, which is mitigated by antibiotics. The gut microbiota contributes to impaired insulin but not C-peptide clearance. The gut microbiota is a stand-alone factor that impairs insulin clearance. A cluster of related bacteria predict >90% of the variance in insulin clearance. Impaired insulin clearance is associated with lower hepatic Ceacam-1.
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Affiliation(s)
- Kevin P Foley
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Soumaya Zlitni
- Departments of Genetics and Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Brittany M Duggan
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Nicole G Barra
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Fernando F Anhê
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Joseph F Cavallari
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Brandyn D Henriksbo
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Cassandra Y Chen
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Michael Huang
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Trevor C Lau
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
| | - Roxanne Plante
- Quebec Heart and Lung Institute Research Center, Faculty of Medicine, Laval University, Quebec City, Quebec, G1V 4G5, Canada
| | - Michael Schwab
- Quebec Heart and Lung Institute Research Center, Faculty of Medicine, Laval University, Quebec City, Quebec, G1V 4G5, Canada
| | - André Marette
- Quebec Heart and Lung Institute Research Center, Faculty of Medicine, Laval University, Quebec City, Quebec, G1V 4G5, Canada
| | - Jonathan D Schertzer
- Department of Biochemistry and Biomedical Sciences, Farncombe Family Digestive Health Research Institute McMaster University, Hamilton, Ontario, L8N 3Z5, Canada.
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72
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Deal AW, Seshie O, Lenzo A, Cooper N, Ozimek N, Solberg Woods LC. High-fat diet negatively impacts both metabolic and behavioral health in outbred heterogeneous stock rats. Physiol Genomics 2020; 52:379-390. [PMID: 32687430 PMCID: PMC7509248 DOI: 10.1152/physiolgenomics.00018.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Obesity is influenced by genetics and diet and has wide ranging comorbidities, including anxiety and depressive disorders. Outbred heterogeneous stock (HS) rats are used for fine-genetic mapping of complex traits and may be useful for understanding gene by diet interactions. In this study, HS rats were fed diets containing 60% kcal from fat (high-fat diet, HFD) or 10% kcal from fat (low-fat diet, LFD) and tested for metabolic (study 1) and behavioral (study 2) outcomes. In study 1, we measured glucose tolerance, fasting glucose and insulin, fat pad weights and despair-like behavior in the forced swim test (FST). In study 2, we assessed anxiety-like (elevated plus maze, EPM; open field test, OFT) and despair-like/coping (splash test, SpT; and FST) behaviors. Body weight and food intake were measured weekly in both studies. We found negative effects of HFD on metabolic outcomes, including increased body weight and fat pad weights, decreased glucose tolerance, and increased fasting insulin. We also found negative effects of HFD on despair-like/coping and anxiety-like behaviors. These include increased immobility in the FST, decreased open arm time in the EPM, and increased movement and rest episodes and decreased rearing in the OFT. The diet-induced changes in EPM and OFT were independent of overall locomotion. Additionally, diet-induced changes in OFT behaviors were independent of adiposity, while adiposity was a confounding factor for EPM and FST behavior. This work establishes the HS as a model to study gene by diet interactions affecting metabolic and behavioral health.
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Affiliation(s)
- Aaron W Deal
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Osborne Seshie
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Anne Lenzo
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Nicholas Cooper
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Noelle Ozimek
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Leah C Solberg Woods
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
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73
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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Verdugo-Meza A, Ye J, Dadlani H, Ghosh S, Gibson DL. Connecting the Dots Between Inflammatory Bowel Disease and Metabolic Syndrome: A Focus on Gut-Derived Metabolites. Nutrients 2020; 12:E1434. [PMID: 32429195 PMCID: PMC7285036 DOI: 10.3390/nu12051434] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
The role of the microbiome in health and disease has gained considerable attention and shed light on the etiology of complex diseases like inflammatory bowel disease (IBD) and metabolic syndrome (MetS). Since the microorganisms inhabiting the gut can confer either protective or harmful signals, understanding the functional network between the gut microbes and the host provides a comprehensive picture of health and disease status. In IBD, disruption of the gut barrier enhances microbe infiltration into the submucosae, which enhances the probability that gut-derived metabolites are translocated from the gut to the liver and pancreas. Considering inflammation and the gut microbiome can trigger intestinal barrier dysfunction, risk factors of metabolic diseases such as insulin resistance may have common roots with IBD. In this review, we focus on the overlap between IBD and MetS, and we explore the role of common metabolites in each disease in an attempt to connect a common origin, the gut microbiome and derived metabolites that affect the gut, liver and pancreas.
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Affiliation(s)
- Andrea Verdugo-Meza
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, BC V6T 1Z4, Canada; (A.V.-M.); (J.Y.); (H.D.)
| | - Jiayu Ye
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, BC V6T 1Z4, Canada; (A.V.-M.); (J.Y.); (H.D.)
| | - Hansika Dadlani
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, BC V6T 1Z4, Canada; (A.V.-M.); (J.Y.); (H.D.)
| | - Sanjoy Ghosh
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, BC V6T 1Z4, Canada; (A.V.-M.); (J.Y.); (H.D.)
| | - Deanna L. Gibson
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, BC V6T 1Z4, Canada; (A.V.-M.); (J.Y.); (H.D.)
- Department of Medicine, University of British Columbia, Okanagan campus, Kelowna, BC V1V 1V7, Canada
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Zhang X, Dong L, Jia X, Liu L, Chi J, Huang F, Ma Q, Zhang M, Zhang R. Bound Phenolics Ensure the Antihyperglycemic Effect of Rice Bran Dietary Fiber in db/ db Mice via Activating the Insulin Signaling Pathway in Skeletal Muscle and Altering Gut Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4387-4398. [PMID: 32197570 DOI: 10.1021/acs.jafc.0c00584] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Whole-grain dietary fiber intake is beneficial in the prevention of metabolic syndrome. Considering rich in bound phenolics being a special characteristic of whole-grain dietary fiber, the aim of this study was to evaluate the effects of the presence or absence of bound phenolics in rice bran dietary fiber (RBDF) on regulating glucose metabolism in diabetic db/db mice. In comparison to phenolics-removed RBDF (PR-RBDF) intervention without an antihyperglycemic effect, RBDF and formulated RBDF (F-RBDF, obtained by mixing PR-RBDF and hydrolyzed-bound phenolics) significantly reduced fasting blood glucose levels after 1 and 5 weeks of interventions, respectively. The presence of bound phenolics interventions could activate the IRS1/AKT/GLUT4 insulin signaling pathway in skeletal muscle and alter gut microbiota by modulating gut microbiota dysbiosis and enriching the butyric-acid-producing bacteria genera of the families Lachnospiraceae and Ruminococcaceae, thus leading to the reduction of blood glucose levels. These findings indicate that bound phenolics ensure the antihyperglycemic effect of RBDF.
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Affiliation(s)
- Xinwen Zhang
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Lihong Dong
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
| | - Xuchao Jia
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
| | - Lei Liu
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
| | - Jianwei Chi
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
| | - Fei Huang
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
| | - Qin Ma
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
| | - Mingwei Zhang
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Ruifen Zhang
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou, Guangdong 510610, People's Republic of China
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76
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Zou XH, Sun LH, Yang W, Li BJ, Cui RJ. Potential role of insulin on the pathogenesis of depression. Cell Prolif 2020; 53:e12806. [PMID: 32281722 PMCID: PMC7260070 DOI: 10.1111/cpr.12806] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/22/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
The regulation of insulin on depression and depression-like behaviour has been widely reported. Insulin and activation of its receptor can promote learning and memory, affect the hypothalamic-pituitary-adrenal axis (HPA) balance, regulate the secretion of neurotrophic factors and neurotransmitters, interact with gastrointestinal microbiome, exert neuroprotective effects and have an impact on depression. However, the role of insulin on depression remains largely unclear. Therefore, in this review, we summarized the potential role of insulin on depression. It may provide new insight for clarifying role of insulin on the pathogenesis of depression.
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Affiliation(s)
- Xiao Han Zou
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, China
| | - Li Hua Sun
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, China
| | - Wei Yang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, China
| | - Bing Jin Li
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, China
| | - Ran Ji Cui
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, China
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77
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Fitzgerald DM, Spence RJ, Stewart ZK, Prentis PJ, Sillence MN, de Laat MA. The effect of diet change and insulin dysregulation on the faecal microbiome of ponies. J Exp Biol 2020; 223:jeb219154. [PMID: 32098884 DOI: 10.1242/jeb.219154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/12/2020] [Indexed: 12/16/2022]
Abstract
The equine microbiome can change in response to dietary alteration and may play a role in insulin dysregulation. The aim of this study was to determine the effect of adding pasture to a hay diet on the faecal bacterial microbiome of both healthy and insulin-dysregulated ponies. Faecal samples were collected from 16 ponies before and after dietary change to enable bacterial 16S rRNA sequencing of the V3-V4 region. The dominant phyla in all samples were the Firmicutes and Bacteroidetes. The evenness of the bacterial populations decreased after grazing pasture, and when a pony was moderately insulin dysregulated (P=0.001). Evenness scores negatively correlated with post-prandial glucagon-like peptide-1 concentration after a hay-only diet (r²=-0.7, P=0.001). A change in diet explained 3% of faecal microbiome variability. We conclude that metabolically healthy ponies have greater microbial stability when challenged with a subtle dietary change, compared with moderately insulin-dysregulated ponies.
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Affiliation(s)
- Danielle M Fitzgerald
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Robert J Spence
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Zachary K Stewart
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Peter J Prentis
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Martin N Sillence
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Melody A de Laat
- Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia
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78
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Morrison PK, Newbold CJ, Jones E, Worgan HJ, Grove-White DH, Dugdale AH, Barfoot C, Harris PA, Argo CM. The equine gastrointestinal microbiome: impacts of weight-loss. BMC Vet Res 2020; 16:78. [PMID: 32131835 PMCID: PMC7057583 DOI: 10.1186/s12917-020-02295-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Background Obesity is an important equine welfare issue. Whilst dietary restriction is the most effective weight-loss tool, individual animals range in their weight-loss propensity. Gastrointestinal-derived bacteria play a fundamental role in host-health and have been associated with obesity and weight-loss in other species. This study evaluated the faecal microbiome (next-generation sequencing of 16S rRNA genes) of 15 obese Welsh Mountain pony mares, in the same 11-week period across 2 years (n = 8 Year 1; n = 7 Year 2). Following a 4-week acclimation period (pre-diet phase) during which time individuals were fed the same hay to maintenance (2% body mass (BM) as daily dry matter (DM) intake), animals underwent a 7-week period of dietary restriction (1% BM hay as daily DM intake). Faeces were sampled on the final 3 days of the pre-diet phase and the final 3 days of the dietary restriction phase. Bacterial communities were determined using Next Generation Sequencing of amplified V1-V2 hypervariable regions of bacterial 16S rRNA. Results Losses in body mass ranged from 7.11 to 11.59%. Changes in the faecal microbiome composition following weight-loss included a reduction in the relative abundance of Firmicutes and Tenericutes and a reduction in indices of bacterial diversity. Pre-diet diversity was negatively associated with weight-loss. Pre-diet faecal acetate concentration was a strong predictor of subsequent weight-loss and negatively associated with Sphaerochaeta (Spirochaetes phylum) abundance. When animals were divided into 3 groups (high, mid, low) based overall weight loss, pre-diet bacterial community structure was found to have the greatest divergence between the high and low weight-loss groups (R = 0.67, p < 0.01), following PERMANOVA and ANOSIM analysis. Conclusions Weight-loss in this group of ponies was associated with lower pre-diet faecal bacterial diversity and greater pre-diet acetate concentration. Overall, these data support a role for the faecal microbiome in weight-loss propensity in ponies and provide a baseline for research evaluating elements of the faecal microbiome in predicting weight-loss success in larger cohorts.
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Affiliation(s)
| | | | - Eleanor Jones
- Aberystwyth University, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Hilary J Worgan
- Aberystwyth University, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dai H Grove-White
- University of Liverpool, Faculty of Health and Life Sciences, Leahurst Campus, Chester High Road, Neston, Wirral, UK
| | | | - Clare Barfoot
- MARS Horsecare UK Ltd, Old Wolverton, Buckinghamshire, UK
| | - Patricia A Harris
- WALTHAM Petcare Science Institute, Freeby lane, Waltham-on-the-Wolds, Leicestershire, UK
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79
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Safari Z, Bruneau A, Monnoye M, Mariadassou M, Philippe C, Zatloukal K, Gérard P. Murine Genetic Background Overcomes Gut Microbiota Changes to Explain Metabolic Response to High-Fat Diet. Nutrients 2020; 12:E287. [PMID: 31973214 PMCID: PMC7071469 DOI: 10.3390/nu12020287] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 12/23/2022] Open
Abstract
Interactions of diet, gut microbiota, and host genetics play essential roles in the development of metabolic diseases. A/J and C57BL/6J (C57) are two mouse strains known to display different susceptibilities to metabolic disorders. In this context, we analyzed gut microbiota composition in A/J and C57 mice, and assessed its responses to high-fat diet (HFD) and antibiotic (AB) treatment. We also exchanged the gut microbiota between the two strains following AB treatment to evaluate its impact on the metabolism. We showed that A/J and C57 mice have different microbiome structure and composition at baseline. Moreover, A/J and C57 microbiomes responded differently to HFD and AB treatments. Exchange of the gut microbiota between the two strains was successful as recipients' microbiota resembled donor-strain microbiota. Seven weeks after inoculation, the differences between recipients persisted and were still closer from the donor-strain microbiota. Despite effective microbiota transplants, the response to HFD was not markedly modified in C57 and A/J mice. Particularly, body weight gain and glucose intolerance in response to HFD remained different in the two mouse strains whatever the changes in microbiome composition. This indicated that genetic background has a much stronger impact on metabolic responses to HFD than gut microbiome composition.
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Affiliation(s)
- Zahra Safari
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (Z.S.); (A.B.); (M.M.); (C.P.)
- Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Aurélia Bruneau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (Z.S.); (A.B.); (M.M.); (C.P.)
| | - Magali Monnoye
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (Z.S.); (A.B.); (M.M.); (C.P.)
| | | | - Catherine Philippe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (Z.S.); (A.B.); (M.M.); (C.P.)
| | - Kurt Zatloukal
- Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Philippe Gérard
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (Z.S.); (A.B.); (M.M.); (C.P.)
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Affiliation(s)
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | | | - Sasha G. Tetu
- Department of Molecular Sciences Macquarie University North Ryde NSW Australia
| | - Michael R. Gillings
- Department of Biological Sciences Macquarie University North Ryde NSW Australia
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81
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Wang W, Zhai S, Xia Y, Wang H, Ruan D, Zhou T, Zhu Y, Zhang H, Zhang M, Ye H, Ren W, Yang L. Ochratoxin A induces liver inflammation: involvement of intestinal microbiota. MICROBIOME 2019; 7:151. [PMID: 31779704 PMCID: PMC6883682 DOI: 10.1186/s40168-019-0761-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 10/17/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Ochratoxin A (OTA) is a widespread mycotoxin and induces liver inflammation to human and various species of animals. The intestinal microbiota has critical importance in liver inflammation; however, it remains to know whether intestinal microbiota mediates the liver inflammation induced by OTA. Here, we treated ducklings with oral gavage of OTA (235 μg/kg body weight) for 2 weeks. Then, the microbiota in the cecum and liver were analyzed with 16S rRNA sequencing, and the inflammation in the liver was analyzed. To explore the role of intestinal microbiota in OTA-induced liver inflammation, intestinal microbiota was cleared with antibiotics and fecal microbiota transplantation was conducted. RESULTS Here, we find that OTA treatment in ducks altered the intestinal microbiota composition and structure [e.g., increasing the relative abundance of lipopolysaccharides (LPS)-producing Bacteroides], and induced the accumulation of LPS and inflammation in the liver. Intriguingly, in antibiotic-treated ducks, OTA failed to induce these alterations in the liver. Notably, with the fecal microbiota transplantation (FMT) program, in which ducks were colonized with intestinal microbiota from control or OTA-treated ducks, we elucidated the involvement of intestinal microbiota, especially Bacteroides, in liver inflammation induced by OTA. CONCLUSIONS These results highlight the role of gut microbiota in OTA-induced liver inflammation and open a new window for novel preventative or therapeutic intervention for mycotoxicosis.
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Affiliation(s)
- Wence Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shuangshuang Zhai
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoyao Xia
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Hao Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Dong Ruan
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou, 510640, China
| | - Ting Zhou
- Guelph Food Research Center, Agriculture and Agri-Food Canada, Guelph, N1G 5C9, Canada
| | - Yongwen Zhu
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Minhong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hui Ye
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wenkai Ren
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Lin Yang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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Li Y, Liu Y, Liang J, Wang T, Sun M, Zhang Z. Gymnemic Acid Ameliorates Hyperglycemia through PI3K/AKT- and AMPK-Mediated Signaling Pathways in Type 2 Diabetes Mellitus Rats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13051-13060. [PMID: 31609623 DOI: 10.1021/acs.jafc.9b04931] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Gymnemic acid (GA) isolated from Gymnema sylvestre (Retz.) Schult. has been shown to have antihyperglycemic activity; however, the molecular mechanisms governing these effects are unclear. In this study, GA (40 and 80 mg kg-1 day-1) was evaluated by type 2 diabetes mellitus (T2DM) rats to explore its hypoglycemic activity and underlying mechanisms of action. The results indicated that GA decreased fasting blood glucose (FBG) concentrations by 26.7% and lowered insulin concentrations by 16.1% after oral administration of GA at a dose of 80 mg kg-1 day-1 for 6 weeks in T2DM rats. Our data showed that real-time polymerase chain reaction and western blot indicated that GA upregulated the level of phosphatidylinositol-3-kinase (PI3K) and glycogen synthesis (GS) and promoted the phosphorylation of protein kinase B (Akt) while downregulated the expression of glycogen synthesis kinase-3β (GSK-3β) in T2DM rats. In addition, key proteins involved in adenosine monophosphate (AMP)-activated protein kinase (AMPK)-mediated gluconeogenesis [such as phosphoenolpyruvate carboxy kinase (PEPCK) and glucose-6-phosphatase (G6Pase)] were downregulated in GA-treated T2DM rats. In summary, the hypoglycemic mechanisms of GA may be related to promoting insulin signal transduction and activating PI3K/Akt- and AMPK-mediated signaling pathways in T2DM rats.
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Affiliation(s)
- Yumeng Li
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology) , Ministry of Education , Tianjin 300457 , People's Republic of China
| | - Yaping Liu
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology) , Ministry of Education , Tianjin 300457 , People's Republic of China
| | - Junjie Liang
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology) , Ministry of Education , Tianjin 300457 , People's Republic of China
| | - Tianxin Wang
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology) , Ministry of Education , Tianjin 300457 , People's Republic of China
| | - Mingzhe Sun
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology) , Ministry of Education , Tianjin 300457 , People's Republic of China
| | - Zesheng Zhang
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology) , Ministry of Education , Tianjin 300457 , People's Republic of China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center , Tianjin 300457 , People's Republic of China
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83
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Hughes RL, Kable ME, Marco M, Keim NL. The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models. Part II: Results. Adv Nutr 2019; 10:979-998. [PMID: 31225587 PMCID: PMC6855959 DOI: 10.1093/advances/nmz049] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/28/2019] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
The gut microbiota is increasingly implicated in the health and metabolism of its human host. The host's diet is a major component influencing the composition and function of the gut microbiota, and mounting evidence suggests that the composition and function of the gut microbiota influence the host's metabolic response to diet. This effect of the gut microbiota on personalized dietary response is a growing focus of precision nutrition research and may inform the effort to tailor dietary advice to the individual. Because the gut microbiota has been shown to be malleable to some extent, it may also allow for therapeutic alterations of the gut microbiota in order to alter response to certain dietary components. This article is the second in a 2-part review of the current research in the field of precision nutrition incorporating the gut microbiota into studies investigating interindividual variability in response to diet. Part I reviews the methods used by researchers to design and carry out such studies as well as analyze the results subsequently obtained. Part II reviews the findings of these studies and discusses the gaps in our current knowledge and directions for future research. The studies reviewed provide the current understanding in this field of research and a foundation from which we may build, utilizing and expanding upon the methods and results they present to inform future studies.
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Affiliation(s)
- Riley L Hughes
- Departments of Nutrition, Food Science & Technology, University of California, Davis, CA
| | - Mary E Kable
- Departments of Nutrition, Food Science & Technology, University of California, Davis, CA,Departments of Immunity and Disease Prevention, Obesity and Metabolism, Western Human Nutrition Research Center, Agricultural Research Service, USDA, Davis, CA
| | - Maria Marco
- Food Science & Technology, University of California, Davis, CA
| | - Nancy L Keim
- Departments of Nutrition, Food Science & Technology, University of California, Davis, CA,Obesity and Metabolism, Western Human Nutrition Research Center, Agricultural Research Service, USDA, Davis, CA,Address correspondence to NLK (e-mail: )
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84
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Hughes RL, Marco ML, Hughes JP, Keim NL, Kable ME. The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models-Part I: Overview of Current Methods. Adv Nutr 2019; 10:953-978. [PMID: 31225589 PMCID: PMC6855943 DOI: 10.1093/advances/nmz022] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/06/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022] Open
Abstract
Health care is increasingly focused on health at the individual level. In the rapidly evolving field of precision nutrition, researchers aim to identify how genetics, epigenetics, and the microbiome interact to shape an individual's response to diet. With this understanding, personalized responses can be predicted and dietary advice can be tailored to the individual. With the integration of these complex sources of data, an important aspect of precision nutrition research is the methodology used for studying interindividual variability in response to diet. This article stands as the first in a 2-part review of current research investigating the contribution of the gut microbiota to interindividual variability in response to diet. Part I reviews the methods used by researchers to design and carry out such studies as well as the statistical and bioinformatic methods used to analyze results. Part II reviews the findings of these studies, discusses gaps in our current knowledge, and summarizes directions for future research. Taken together, these reviews summarize the current state of knowledge and provide a foundation for future research on the role of the gut microbiome in precision nutrition.
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Affiliation(s)
- Riley L Hughes
- Departments of Nutrition, Food Science and Technology, University of California, Davis, Davis, CA
| | - Maria L Marco
- Food Science and Technology, University of California, Davis, Davis, CA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Nancy L Keim
- Departments of Nutrition, Food Science and Technology, University of California, Davis, Davis, CA,Obesity and Metabolism, Western Human Nutrition Research Center, Agricultural Research Service, USDA, Davis, CA
| | - Mary E Kable
- Departments of Nutrition, Food Science and Technology, University of California, Davis, Davis, CA,Immunity and Disease Prevention, Western Human Nutrition Research Center, Agricultural Research Service, USDA, Davis, CA,Address correspondence to MEK (e-mail: )
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85
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Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis. Animal 2019; 14:706-715. [PMID: 31619307 DOI: 10.1017/s1751731119002428] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Exploring the composition and structure of the faecal microbial community improves the understanding of the role of the gut microbiota in the gastrointestinal function and the egg-laying performance of hens. Therefore, detection of hen-microbial interactions can explore a new breeding marker for the selection of egg production due to the important role of the gut microbiome in the host's metabolism and health. Recently, the gut microbiota has been recognised as a regulator of host performance, which has led to investigations of the productive effects of changes in the faecal microbiome in various animals. In the present study, a metagenomics analysis was applied to characterise the composition and structural diversity of faecal microbial communities under two selections of egg-laying performance, high (H, n = 30) and low (L, n = 30), using 16S rRNA-based metagenomic association analysis. The most abundant bacterial compositions were estimated based on the operational classification units among samples and between the groups from metagenomic data sets. The results indicated that Firmicutes phylum has higher significant (P < 0.01) in the H group than in the L group. In addition, higher relative abundance phyla of Bacteroides and Fusobacteria were estimated in the H group than the L group, contrasting the phyla of Actinobacteria, Cyanobacteria and Proteobacteria were more relative abundance in the L group. The families (Lactobacillus, Bifidobacterium, Acinetobacter, Flavobacteriaceae, Lachnoclostridum and Rhodococcus) were more abundant in the H group based on the comparison between the H and L groups. Meanwhile, three types of phyla (Proteobacteria, Actinobacteria and Cyanobacteria) and six families (Acinetobacter, Avibacterium, Clostridium, Corynebacterium, Helicobacter and Peptoclostridium) were more abundant in the L group (P < 0.01). Overall, the selection of genotypes has enriched a relationship between the gut microbiota and the egg-laying performance. These findings suggest that the faecal microbiomes of chickens with high egg-laying performance have more diverse activities than those of chickens with low egg-laying performance, which may be related to the metabolism and health of the host and egg production variation.
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86
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Björk JR, Dasari M, Grieneisen L, Archie EA. Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research. Am J Primatol 2019; 81:e22970. [PMID: 30941803 PMCID: PMC7193701 DOI: 10.1002/ajp.22970] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/05/2019] [Accepted: 03/07/2019] [Indexed: 12/16/2022]
Abstract
To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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87
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Kemis JH, Linke V, Barrett KL, Boehm FJ, Traeger LL, Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Churchill GA, Amador-Noguez D, Russell JD, Yandell BS, Broman KW, Coon JJ, Attie AD, Rey FE. Genetic determinants of gut microbiota composition and bile acid profiles in mice. PLoS Genet 2019; 15:e1008073. [PMID: 31465442 PMCID: PMC6715156 DOI: 10.1371/journal.pgen.1008073] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/14/2019] [Indexed: 02/03/2023] Open
Abstract
The microbial communities that inhabit the distal gut of humans and other mammals exhibit large inter-individual variation. While host genetics is a known factor that influences gut microbiota composition, the mechanisms underlying this variation remain largely unknown. Bile acids (BAs) are hormones that are produced by the host and chemically modified by gut bacteria. BAs serve as environmental cues and nutrients to microbes, but they can also have antibacterial effects. We hypothesized that host genetic variation in BA metabolism and homeostasis influence gut microbiota composition. To address this, we used the Diversity Outbred (DO) stock, a population of genetically distinct mice derived from eight founder strains. We characterized the fecal microbiota composition and plasma and cecal BA profiles from 400 DO mice maintained on a high-fat high-sucrose diet for ~22 weeks. Using quantitative trait locus (QTL) analysis, we identified several genomic regions associated with variations in both bacterial and BA profiles. Notably, we found overlapping QTL for Turicibacter sp. and plasma cholic acid, which mapped to a locus containing the gene for the ileal bile acid transporter, Slc10a2. Mediation analysis and subsequent follow-up validation experiments suggest that differences in Slc10a2 gene expression associated with the different strains influences levels of both traits and revealed novel interactions between Turicibacter and BAs. This work illustrates how systems genetics can be utilized to generate testable hypotheses and provide insight into host-microbe interactions.
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Affiliation(s)
- Julia H. Kemis
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Vanessa Linke
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Kelsey L. Barrett
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Frederick J. Boehm
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Lindsay L. Traeger
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mary E. Rabaglia
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Kathryn L. Schueler
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Donald S. Stapleton
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Daniel M. Gatti
- Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jason D. Russell
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Brian S. Yandell
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Karl W. Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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88
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Gut Microbiota, Muscle Mass and Function in Aging: A Focus on Physical Frailty and Sarcopenia. Nutrients 2019; 11:nu11071633. [PMID: 31319564 PMCID: PMC6683074 DOI: 10.3390/nu11071633] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023] Open
Abstract
Human gut microbiota is able to influence the host physiology by regulating multiple processes, including nutrient absorption, inflammation, oxidative stress, immune function, and anabolic balance. Aging is associated with reduced microbiota biodiversity, increased inter-individual variability, and over-representation of pathobionts, and these phenomena may have great relevance for skeletal muscle mass and function. For this reason, the presence of a gut-muscle axis regulating the onset and progression of age-related physical frailty and sarcopenia has been recently hypothesized. In this narrative review, we summarize the studies supporting a possible association between gut microbiota-related parameters with measures of muscle mass, muscle function, and physical performance in animal models and humans. Reduced muscle mass has been associated with distinct microbiota composition and reduced fermentative capacity in mice, and the administration of probiotics or butyrate to mouse models of muscle wasting has been associated with improved muscle mass. However, no studies have targeted the human microbiome associated with sarcopenia. Limited evidence from human studies shows an association between microbiota composition, involving key taxa such as Faecalibacterium and Bifidobacterium, and grip strength. Similarly, few studies conducted on patients with parkinsonism showed a trend towards a different microbiota composition in those with reduced gait speed. No studies have assessed the association of fecal microbiota with other measures of physical performance. However, several studies, mainly with a cross-sectional design, suggest an association between microbiota composition and frailty, mostly assessed according to the deficit accumulation model. Namely, frailty was associated with reduced microbiota biodiversity, and lower representation of butyrate-producing bacteria. Therefore, we conclude that the causal link between microbiota and physical fitness is still uncertain due to the lack of targeted studies and the influence of a large number of covariates, including diet, exercise, multimorbidity, and polypharmacy, on both microbiota composition and physical function in older age. However, the relationship between gut microbiota and physical function remains a very promising area of research for the future.
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89
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Li T, Qi M, Gatesoupe FJ, Tian D, Jin W, Li J, Lin Q, Wu S, Li H. Adaptation to Fasting in Crucian Carp (Carassius auratus): Gut Microbiota and Its Correlative Relationship with Immune Function. MICROBIAL ECOLOGY 2019; 78:6-19. [PMID: 30343437 DOI: 10.1007/s00248-018-1275-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
Fasting influences the overall physiology of fish, and the knowledge how the gut microbiota, growth performances, and immune function in response to intermittent and long-term fasting is still insufficient. Here, we characterized the effects of fasting on the host-gut microbiota in crucian carp, which would enhance our insight into physiological adaptation to fasting. To achieve this, we investigated the gut microbial communities of crucian carp with different fasting stress, and corresponding immune and growth parameters. The gut microbial communities were structured into four clusters according to different fasting stress, namely one control group (feed regularly), two intermittent fasting groups (fasting period and re-feeding period, respectively), and one long-term fasting group. Intermittent fasting significantly improved the activity of superoxide dismutase (SOD) and lysozyme (LZM) (ANOVA, p < 0.05) and significantly increased alpha diversity and ecosystem stability of gut microbiota (ANOVA, p < 0.05). Gut length (GL) and condition factor (CF) showed no significant difference between the control group (CG) and intermittent fasting group under re-feeding period (RIF) (ANOVA, p = 0.11), but relative gut length (RGL) in group RIF was higher than that in the CG (ANOVA, p = 0.00). The bacterial genera Bacteroides, Akkermansia, and Erysipelotrichaceae were enriched in fishes under intermittent fasting. Two Bacteroides OTUs (OTU50 and OTU1292) correlated positively with immune (SOD, complement, and LZM) and growth (GL and RGL) parameters. These results highlight the possible interplay between growth performances, immune function, and gut microbiota in response to fasting.
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Affiliation(s)
- Tongtong Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Mengting Qi
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | | | - Dongcan Tian
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Weihua Jin
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jun Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Shijin Wu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Huan Li
- Institute of Occupational Health and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China.
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90
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Lew KN, Starkweather A, Cong X, Judge M. A Mechanistic Model of Gut-Brain Axis Perturbation and High-Fat Diet Pathways to Gut Microbiome Homeostatic Disruption, Systemic Inflammation, and Type 2 Diabetes. Biol Res Nurs 2019; 21:384-399. [PMID: 31113222 DOI: 10.1177/1099800419849109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Type 2 diabetes (T2D) is a highly prevalent metabolic disease, affecting nearly 10% of the American population. Although the etiopathogenesis of T2D remains poorly understood, advances in DNA sequencing technologies have allowed for sophisticated interrogation of the human microbiome, providing insight into the role of the gut microbiome in the development and progression of T2D. An emerging body of research reveals that gut-brain axis (GBA) perturbations and a high-fat diet (HFD), along with other modifiable and nonmodifiable risk factors, contribute to gut microbiome homeostatic imbalance. Homeostatic imbalance or disruption increases gut wall permeability and facilitates translocation of endotoxins (lipopolysaccharides) into the circulation with resultant systemic inflammation. Chronic, low-grade systemic inflammation ensues with pro-inflammatory pathways activated, contributing to obesity, insulin resistance (IR), pancreatic β-cell decline, and, thereby, T2D. While GBA perturbations and HFD are implicated in provoking these conditions, prior mechanistic models have tended to examine HFD and GBA pathways exclusively without considering their shared pathways to T2D. Addressing this gap, this article proposes a mechanistic model informed by animal and human studies to advance scientific understanding of (1) modifiable and nonmodifiable risk factors for gut microbiome homeostatic disruption, (2) HFD and GBA pathways contributing to homeostatic disruption, and (3) shared GBA and HFD pro-inflammatory pathways to obesity, IR, β-cell decline, and T2D. The proposed mechanistic model, based on the extant literature, proposes a framework for studying the complex relationships of the gut microbiome to T2D to advance study in this promising area of research.
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Affiliation(s)
| | | | - Xiaomei Cong
- 1 School of Nursing, University of Connecticut, Storrs, CT, USA
| | - Michelle Judge
- 1 School of Nursing, University of Connecticut, Storrs, CT, USA
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91
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Cluster partitions and fitness landscapes of the Drosophila fly microbiome. J Math Biol 2019; 79:861-899. [PMID: 31101975 DOI: 10.1007/s00285-019-01381-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 05/03/2019] [Indexed: 01/29/2023]
Abstract
The concept of genetic epistasis defines an interaction between two genetic loci as the degree of non-additivity in their phenotypes. A fitness landscape describes the phenotypes over many genetic loci, and the shape of this landscape can be used to predict evolutionary trajectories. Epistasis in a fitness landscape makes prediction of evolutionary trajectories more complex because the interactions between loci can produce local fitness peaks or troughs, which changes the likelihood of different paths. While various mathematical frameworks have been proposed to investigate properties of fitness landscapes, Beerenwinkel et al. (Stat Sin 17(4):1317-1342, 2007a) suggested studying regular subdivisions of convex polytopes. In this sense, each locus provides one dimension, so that the genotypes form a cube with the number of dimensions equal to the number of genetic loci considered. The fitness landscape is a height function on the coordinates of the cube. Here, we propose cluster partitions and cluster filtrations of fitness landscapes as a new mathematical tool, which provides a concise combinatorial way of processing metric information from epistatic interactions. Furthermore, we extend the calculation of genetic interactions to consider interactions between microbial taxa in the gut microbiome of Drosophila fruit flies. We demonstrate similarities with and differences to the previous approach. As one outcome we locate interesting epistatic information on the fitness landscape where the previous approach is less conclusive.
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92
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Onos KD, Uyar A, Keezer KJ, Jackson HM, Preuss C, Acklin CJ, O’Rourke R, Buchanan R, Cossette TL, Sukoff Rizzo SJ, Soto I, Carter GW, Howell GR. Enhancing face validity of mouse models of Alzheimer's disease with natural genetic variation. PLoS Genet 2019; 15:e1008155. [PMID: 31150388 PMCID: PMC6576791 DOI: 10.1371/journal.pgen.1008155] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 06/17/2019] [Accepted: 04/24/2019] [Indexed: 01/01/2023] Open
Abstract
Classical laboratory strains show limited genetic diversity and do not harness natural genetic variation. Mouse models relevant to Alzheimer's disease (AD) have largely been developed using these classical laboratory strains, such as C57BL/6J (B6), and this has likely contributed to the failure of translation of findings from mice to the clinic. Therefore, here we test the potential for natural genetic variation to enhance the translatability of AD mouse models. Two widely used AD-relevant transgenes, APPswe and PS1de9 (APP/PS1), were backcrossed from B6 to three wild-derived strains CAST/EiJ, WSB/EiJ, PWK/PhJ, representative of three Mus musculus subspecies. These new AD strains were characterized using metabolic, functional, neuropathological and transcriptional assays. Strain-, sex- and genotype-specific differences were observed in cognitive ability, neurodegeneration, plaque load, cerebrovascular health and cerebral amyloid angiopathy. Analyses of brain transcriptional data showed strain was the greatest driver of variation. We identified significant variation in myeloid cell numbers in wild type mice of different strains as well as significant differences in plaque-associated myeloid responses in APP/PS1 mice between the strains. Collectively, these data support the use of wild-derived strains to better model the complexity of human AD.
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Affiliation(s)
- Kristen D. Onos
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Asli Uyar
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Kelly J. Keezer
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Christoph Preuss
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Casey J. Acklin
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Rita O’Rourke
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Rebecca Buchanan
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | | | - Ileana Soto
- Department of Biomedical and Translational Sciences, Rowan University, Glassboro, New Jersey, United States of America
| | - Gregory W. Carter
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, United States of America
| | - Gareth R. Howell
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, United States of America
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93
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Grieneisen LE, Charpentier MJE, Alberts SC, Blekhman R, Bradburd G, Tung J, Archie EA. Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proc Biol Sci 2019; 286:20190431. [PMID: 31014219 PMCID: PMC6501927 DOI: 10.1098/rspb.2019.0431] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/02/2019] [Indexed: 12/19/2022] Open
Abstract
Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host-population FST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.
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Affiliation(s)
- Laura E. Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biology, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Marie J. E. Charpentier
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Susan C. Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Institute for Primate Research, National Museums of Kenya, Nairobi 00502, Kenya
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gideon Bradburd
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Institute for Primate Research, National Museums of Kenya, Nairobi 00502, Kenya
| | - Elizabeth A. Archie
- Department of Biology, University of Notre Dame, Notre Dame, IN 46556, USA
- Institute for Primate Research, National Museums of Kenya, Nairobi 00502, Kenya
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94
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Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, Võsa U, Mujagic Z, Masclee AAM, Jonkers DMAE, Oosting M, Joosten LAB, Netea MG, Franke L, Zhernakova A, Fu J, Wijmenga C, McCarthy MI. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nat Genet 2019; 51:600-605. [PMID: 30778224 PMCID: PMC6441384 DOI: 10.1038/s41588-019-0350-x] [Citation(s) in RCA: 840] [Impact Index Per Article: 168.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Microbiome-wide association studies on large population cohorts have highlighted associations between the gut microbiome and complex traits, including type 2 diabetes (T2D) and obesity1. However, the causal relationships remain largely unresolved. We leveraged information from 952 normoglycemic individuals for whom genome-wide genotyping, gut metagenomic sequence and fecal short-chain fatty acid (SCFA) levels were available2, then combined this information with genome-wide-association summary statistics for 17 metabolic and anthropometric traits. Using bidirectional Mendelian randomization (MR) analyses to assess causality3, we found that the host-genetic-driven increase in gut production of the SCFA butyrate was associated with improved insulin response after an oral glucose-tolerance test (P = 9.8 × 10-5), whereas abnormalities in the production or absorption of another SCFA, propionate, were causally related to an increased risk of T2D (P = 0.004). These data provide evidence of a causal effect of the gut microbiome on metabolic traits and support the use of MR as a means to elucidate causal relationships from microbiome-wide association findings.
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Affiliation(s)
- Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Natalie R van Zuydam
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes Endocrinology and Metabolism, Churchill Hospital, University of Oxford, Oxford, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes Endocrinology and Metabolism, Churchill Hospital, University of Oxford, Oxford, UK
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Zlatan Mujagic
- Maastricht University Medical Center, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Ad A M Masclee
- Maastricht University Medical Center, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Daisy M A E Jonkers
- Maastricht University Medical Center, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Oxford Centre for Diabetes Endocrinology and Metabolism, Churchill Hospital, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.
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95
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Mendes-Soares H, Raveh-Sadka T, Azulay S, Edens K, Ben-Shlomo Y, Cohen Y, Ofek T, Bachrach D, Stevens J, Colibaseanu D, Segal L, Kashyap P, Nelson H. Assessment of a Personalized Approach to Predicting Postprandial Glycemic Responses to Food Among Individuals Without Diabetes. JAMA Netw Open 2019; 2:e188102. [PMID: 30735238 PMCID: PMC6484621 DOI: 10.1001/jamanetworkopen.2018.8102] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
IMPORTANCE Emerging evidence suggests that postprandial glycemic responses (PPGRs) to food may be influenced by and predicted according to characteristics unique to each individual, including anthropometric and microbiome variables. Interindividual diversity in PPGRs to food requires a personalized approach for the maintenance of healthy glycemic levels. OBJECTIVES To describe and predict the glycemic responses of individuals to a diverse array of foods using a model that considers the physiology and microbiome of the individual in addition to the characteristics of the foods consumed. DESIGN, SETTING, AND PARTICIPANTS This cohort study using a personalized predictive model enrolled 327 individuals without diabetes from October 11, 2016, to December 13, 2017, in Minnesota and Florida to be part of a study lasting 6 days. The study measured anthropometric variables, described the gut microbial composition, and assessed blood glucose levels every 5 minutes using a continuous glucose monitor. Participants logged their food and activity information for the duration of the study. A predictive model of individualized PPGRs to a diverse array of foods was trained and applied. MAIN OUTCOMES AND MEASURES Glycemic responses to food consumed over 6 days for each participant. The predictive model of personalized PPGRs considered individual features, including the microbiome, in addition to the features of the foods consumed. RESULTS Postprandial response to the same foods varied across 327 individuals (mean [SD] age, 45 [12] years; 78.0% female). A model predicting each individual's responses to food that considers several individual factors in addition to food features had better overall performance (R = 0.62) than current standard-of-care approaches using nutritional content alone (R = 0.34 for calories and R = 0.40 for carbohydrates) to control postprandial glycemic levels. CONCLUSIONS AND RELEVANCE Across the cohort of adults without diabetes who were examined, a personalized predictive model that considers unique features of the individual, such as clinical characteristics, physiological variables, and the microbiome, in addition to nutrient content was more predictive than current dietary approaches that focus only on the calorie or carbohydrate content of foods. Providing individuals with tools to manage their glycemic responses to food based on personalized predictions of their PPGRs may allow them to maintain their blood glucose levels within limits associated with good health.
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Affiliation(s)
- Helena Mendes-Soares
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | | | | | - Kim Edens
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | | | | | | | - Purna Kashyap
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Gastroenterology, Mayo Clinic, Rochester, Minnesota
| | - Heidi Nelson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
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96
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Wang Q, Wang K, Wu W, Giannoulatou E, Ho JWK, Li L. Host and microbiome multi-omics integration: applications and methodologies. Biophys Rev 2019; 11:55-65. [PMID: 30627872 PMCID: PMC6381360 DOI: 10.1007/s12551-018-0491-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Our review summarises the application of integrating host omics with microbiome as well as the analytical methods and related tools applied in these studies. In addition, potential future directions are discussed.
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Affiliation(s)
- Qing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Kaicen Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Wenrui Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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97
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Pak HH, Cummings NE, Green CL, Brinkman JA, Yu D, Tomasiewicz JL, Yang SE, Boyle C, Konon EN, Ong IM, Lamming DW. The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome. Sci Rep 2019; 9:67. [PMID: 30635612 PMCID: PMC6329753 DOI: 10.1038/s41598-018-37177-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/28/2018] [Indexed: 12/22/2022] Open
Abstract
Obesity and type 2 diabetes are increasing in prevalence around the world, and there is a clear need for new and effective strategies to promote metabolic health. A low protein (LP) diet improves metabolic health in both rodents and humans, but the mechanisms that underlie this effect remain unknown. The gut microbiome has recently emerged as a potent regulator of host metabolism and the response to diet. Here, we demonstrate that a LP diet significantly alters the taxonomic composition of the gut microbiome at the phylum level, altering the relative abundance of Actinobacteria, Bacteroidetes, and Firmicutes. Transcriptional profiling suggested that any impact of the microbiome on liver metabolism was likely independent of the microbiome-farnesoid X receptor (FXR) axis. We therefore tested the ability of a LP diet to improve metabolic health following antibiotic ablation of the gut microbiota. We found that a LP diet promotes leanness, increases energy expenditure, and improves glycemic control equally well in mice treated with antibiotics as in untreated control animals. Our results demonstrate that the beneficial effects of a LP diet on glucose homeostasis, energy balance, and body composition are unlikely to be mediated by diet-induced changes in the taxonomic composition of the gut microbiome.
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Affiliation(s)
- Heidi H Pak
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Interdisciplinary Graduate Program in Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicole E Cummings
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Endocrinology and Reproductive Physiology Graduate Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Cara L Green
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacqueline A Brinkman
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Deyang Yu
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Shany E Yang
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Colin Boyle
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth N Konon
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Irene M Ong
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Dudley W Lamming
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA.
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.
- Interdisciplinary Graduate Program in Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Endocrinology and Reproductive Physiology Graduate Training Program, University of Wisconsin-Madison, Madison, WI, USA.
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, WI, USA.
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin, Madison, WI, USA.
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98
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Abstract
Since the renaissance of microbiome research in the past decade, much insight has accumulated in comprehending forces shaping the architecture and functionality of resident microorganisms in the human gut. Of the multiple host-endogenous and host-exogenous factors involved, diet emerges as a pivotal determinant of gut microbiota community structure and function. By introducing dietary signals into the nexus between the host and its microbiota, nutrition sustains homeostasis or contributes to disease susceptibility. Herein, we summarize major concepts related to the effect of dietary constituents on the gut microbiota, highlighting chief principles in the diet-microbiota crosstalk. We then discuss the health benefits and detrimental consequences that the interactions between dietary and microbial factors elicit in the host. Finally, we present the promises and challenges that arise when seeking to incorporate microbiome data in dietary planning and portray the anticipated revolution that the field of nutrition is facing upon adopting these novel concepts.
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Affiliation(s)
- Niv Zmora
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.,Gastroenterology Unit, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jotham Suez
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
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99
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Cuevas-Sierra A, Ramos-Lopez O, Riezu-Boj JI, Milagro FI, Martinez JA. Diet, Gut Microbiota, and Obesity: Links with Host Genetics and Epigenetics and Potential Applications. Adv Nutr 2019; 10:S17-S30. [PMID: 30721960 PMCID: PMC6363528 DOI: 10.1093/advances/nmy078] [Citation(s) in RCA: 237] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/16/2018] [Indexed: 12/15/2022] Open
Abstract
Diverse evidence suggests that the gut microbiota is involved in the development of obesity and associated comorbidities. It has been reported that the composition of the gut microbiota differs in obese and lean subjects, suggesting that microbiota dysbiosis can contribute to changes in body weight. However, the mechanisms by which the gut microbiota participates in energy homeostasis are unclear. Gut microbiota can be modulated positively or negatively by different lifestyle and dietary factors. Interestingly, complex interactions between genetic background, gut microbiota, and diet have also been reported concerning the risk of developing obesity and metabolic syndrome features. Moreover, microbial metabolites can induce epigenetic modifications (i.e., changes in DNA methylation and micro-RNA expression), with potential implications for health status and susceptibility to obesity. Also, microbial products, such as short-chain fatty acids or membrane proteins, may affect host metabolism by regulating appetite, lipogenesis, gluconeogenesis, inflammation, and other functions. Metabolomic approaches are being used to identify new postbiotics with biological activity in the host, allowing discovery of new targets and tools for incorporation into personalized therapies. This review summarizes the current understanding of the relations between the human gut microbiota and the onset and development of obesity. These scientific insights are paving the way to understanding the complex relation between obesity and microbiota. Among novel approaches, prebiotics, probiotics, postbiotics, and fecal microbiome transplantation could be useful to restore gut dysbiosis.
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Affiliation(s)
- Amanda Cuevas-Sierra
- Department of Nutrition, Food Science, and Physiology and Center for Nutrition Research, University of Navarra, Pamplona, Spain
| | - Omar Ramos-Lopez
- Department of Nutrition, Food Science, and Physiology and Center for Nutrition Research, University of Navarra, Pamplona, Spain
| | - Jose I Riezu-Boj
- Department of Nutrition, Food Science, and Physiology and Center for Nutrition Research, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Fermin I Milagro
- Department of Nutrition, Food Science, and Physiology and Center for Nutrition Research, University of Navarra, Pamplona, Spain
- Centro de Investigacion Biomedica en Red Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - J Alfredo Martinez
- Department of Nutrition, Food Science, and Physiology and Center for Nutrition Research, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigacion Biomedica en Red Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Madrid Institute of Advanced Studies (IMDEA Food), Madrid, Spain
- Address correspondence to JAM (e-mail: )
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100
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The relationship between vitamin C status, the gut-liver axis, and metabolic syndrome. Redox Biol 2018; 21:101091. [PMID: 30640128 PMCID: PMC6327911 DOI: 10.1016/j.redox.2018.101091] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/13/2022] Open
Abstract
Metabolic syndrome (MetS) is a constellation of cardiometabolic risk factors, which together predict increased risk of more serious chronic diseases. We propose that one consequence of dietary overnutrition is increased abundance of Gram-negative bacteria in the gut that cause increased inflammation, impaired gut function, and endotoxemia that further dysregulate the already compromised antioxidant vitamin status in MetS. This discussion is timely because "healthy" individuals are no longer the societal norm and specialized dietary requirements are needed for the growing prevalence of MetS. Further, these lines of evidence provide the foundational basis for investigation that poor vitamin C status promotes endotoxemia, leading to metabolic dysfunction that impairs vitamin E trafficking through a mechanism involving the gut-liver axis. This report will establish a critical need for translational research aimed at validating therapeutic approaches to manage endotoxemia-an early, but inflammation-inducing phenomenon, which not only occurs in MetS, but is also prognostic of more advanced metabolic disorders including type 2 diabetes mellitus, as well as the increasing severity of nonalcoholic fatty liver diseases.
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