101
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Ervin SM, Li H, Lim L, Roberts LR, Liang X, Mani S, Redinbo MR. Gut microbial β-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens. J Biol Chem 2019; 294:18586-18599. [PMID: 31636122 DOI: 10.1074/jbc.ra119.010950] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Gut microbial β-glucuronidase (GUS) enzymes have been suggested to be involved in the estrobolome, the collection of microbial reactions involving estrogens. Furthermore, bacterial GUS enzymes within the gastrointestinal tract have been postulated to be a contributing factor in hormone-driven cancers. However, to date, there has been no experimental evidence to support these hypotheses. Here we provide the first in vitro analysis of the ability of 35 human gut microbial GUS enzymes to reactivate two distinct estrogen glucuronides, estrone-3-glucuronide and estradiol-17-glucuronide, to estrone and estradiol, respectively. We show that certain members within the Loop 1, mini-Loop 1, and FMN-binding classes of gut microbial GUS enzymes can reactivate estrogens from their inactive glucuronides. We provide molecular details of key interactions that facilitate these catalytic processes and present the structures of two novel human gut microbial GUS enzymes related to the estrobolome. Further, we demonstrate that estrogen reactivation by Loop 1 bacterial GUS enzymes can be inhibited both in purified enzymes and in fecal preparations of mixed murine fecal microbiota. Finally, however, despite these in vitro and ex vivo data, we show that a Loop 1 GUS-specific inhibitor is not capable of reducing the development of tumors in the PyMT mouse model of breast cancer. These findings validate that gut microbial GUS enzymes participate in the estrobolome but also suggest that the estrobolome is a multidimensional set of processes on-going within the mammalian gastrointestinal tract that likely involves many enzymes, including several distinct types of GUS proteins.
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Affiliation(s)
- Samantha M Ervin
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Hao Li
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Lauren Lim
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lee R Roberts
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141
| | - Xue Liang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141
| | - Sridhar Mani
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599; Integrated Program for Biological and Genome Sciences and Departments of Biochemistry and Microbiology, University of North Carolina, Chapel Hill, North Carolina 27599.
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102
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Wang G, Huang S, Wang Y, Cai S, Yu H, Liu H, Zeng X, Zhang G, Qiao S. Bridging intestinal immunity and gut microbiota by metabolites. Cell Mol Life Sci 2019; 76:3917-3937. [PMID: 31250035 PMCID: PMC6785585 DOI: 10.1007/s00018-019-03190-6] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023]
Abstract
The gastrointestinal tract is the site of nutrient digestion and absorption and is also colonized by diverse, highly mutualistic microbes. The intestinal microbiota has diverse effects on the development and function of the gut-specific immune system, and provides some protection from infectious pathogens. However, interactions between intestinal immunity and microorganisms are very complex, and recent studies have revealed that this intimate crosstalk may depend on the production and sensing abilities of multiple bioactive small molecule metabolites originating from direct produced by the gut microbiota or by the metabolism of dietary components. Here, we review the interplay between the host immune system and the microbiota, how commensal bacteria regulate the production of metabolites, and how these microbiota-derived products influence the function of several major innate and adaptive immune cells involved in modulating host immune homeostasis.
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Affiliation(s)
- Gang Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing, 100193, China
| | - Shuo Huang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing, 100193, China
| | - Yuming Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing, 100193, China
| | - Shuang Cai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing, 100193, China
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing, 100193, China
| | - Hongbing Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing, 100193, China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing, 100193, China
| | - Guolong Zhang
- Department of Animal Science, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing, 100193, China.
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103
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New and Preliminary Evidence on Altered Oral and Gut Microbiota in Individuals with Autism Spectrum Disorder (ASD): Implications for ASD Diagnosis and Subtyping Based on Microbial Biomarkers. Nutrients 2019; 11:nu11092128. [PMID: 31489949 PMCID: PMC6770733 DOI: 10.3390/nu11092128] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/16/2019] [Accepted: 08/23/2019] [Indexed: 02/06/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a complex neurological and developmental disorder characterized by behavioral and social impairments as well as multiple co-occurring conditions, such as gastrointestinal abnormalities, dental/periodontal diseases, and allergies. The etiology of ASD likely involves interaction between genetic and environmental factors. Recent studies suggest that oral and gut microbiome play important roles in the pathogenesis of inflammation, immune dysfunction, and disruption of the gut–brain axis, which may contribute to ASD pathophysiology. The majority of previous studies used unrelated neurotypical individuals as controls, and they focused on the gut microbiome, with little attention paid to the oral flora. In this pilot study, we used a first degree-relative matched design combined with high fidelity 16S rRNA (ribosomal RNA) gene amplicon sequencing in order to characterize the oral and gut microbiotas of patients with ASD compared to neurotypical individuals, and explored the utility of microbiome markers for ASD diagnosis and subtyping of clinical comorbid conditions. Additionally, we aimed to develop microbiome biomarkers to monitor responses to a subsequent clinical trial using probiotics supplementation. We identified distinct features of gut and salivary microbiota that differed between ASD patients and neurotypical controls. We next explored the utility of some differentially enriched markers for ASD diagnosis and examined the association between the oral and gut microbiomes using network analysis. Due to the tremendous clinical heterogeneity of the ASD population, we explored the relationship between microbiome and clinical indices as an attempt to extract microbiome signatures assocociated with clinical subtypes, including allergies, abdominal pain, and abnormal dietary habits. The diagnosis of ASD currently relies on psychological testing with potentially high subjectivity. Given the emerging role that the oral and gut microbiome plays in systemic diseases, our study will provide preliminary evidence for developing microbial markers that can be used to diagnose or guide treatment of ASD and comorbid conditions. These preliminary results also serve as a starting point to test whether altering the oral and gut microbiome could improve co-morbid conditions in patients with ASD and further modify the core symptoms of ASD.
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104
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Cui J, Lian Y, Zhao C, Du H, Han Y, Gao W, Xiao H, Zheng J. Dietary Fibers from Fruits and Vegetables and Their Health Benefits via Modulation of Gut Microbiota. Compr Rev Food Sci Food Saf 2019; 18:1514-1532. [DOI: 10.1111/1541-4337.12489] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/13/2019] [Accepted: 07/10/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Jiefen Cui
- Inst. of Food Science and TechnologyChinese Academy of Agricultural Sciences Beijing 100193 China
| | - Yunhe Lian
- Research and Development Dept.Chenguang Biotech Group Co., Ltd. Hebei 057250 China
| | - Chengying Zhao
- Inst. of Food Science and TechnologyChinese Academy of Agricultural Sciences Beijing 100193 China
| | - Hengjun Du
- Dept. of Food ScienceUniv. of Massachusetts Amherst MA 01003 U.S.A
| | - Yanhui Han
- Dept. of Food ScienceUniv. of Massachusetts Amherst MA 01003 U.S.A
| | - Wei Gao
- Research and Development Dept.Chenguang Biotech Group Co., Ltd. Hebei 057250 China
| | - Hang Xiao
- Dept. of Food ScienceUniv. of Massachusetts Amherst MA 01003 U.S.A
| | - Jinkai Zheng
- Inst. of Food Science and TechnologyChinese Academy of Agricultural Sciences Beijing 100193 China
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105
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Aguilera-Correa JJ, Madrazo-Clemente P, Martínez-Cuesta MDC, Peláez C, Ortiz A, Sánchez-Niño MD, Esteban J, Requena T. Lyso-Gb3 modulates the gut microbiota and decreases butyrate production. Sci Rep 2019; 9:12010. [PMID: 31427622 PMCID: PMC6700068 DOI: 10.1038/s41598-019-48426-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/31/2019] [Indexed: 02/08/2023] Open
Abstract
Fabry disease is a rare X-linked lysosomal storage disorder resulting from deficient activity of α-galactosidase A, leading to the accumulation of glycosphingolipids such as globotriaosylsphingosine (lyso-Gb3). The gastrointestinal symptoms of this disease may be disabling, and the life expectancy of affected patients is shortened by kidney and heart disease. Our hypothesis was that lyso-Gb3 may modify the gut microbiota. The impact of a clinically relevant concentration of lyso-Gb3 on mono- or multispecies bacterial biofilms were evaluated. A complex bacterial community from the simulated transverse colon microbiota was studied using quantitative PCR to estimate different bacterial group concentrations and a HPLC was used to estimate short-chain fatty acids concentrations. We found that lyso-Gb3 increased the biofilm-forming capacity of several individual bacteria, including Bacteroides fragilis and significantly increased the growth of B. fragilis in a multispecies biofilm. Lyso-Gb3 also modified the bacterial composition of the human colon microbiota suspension, increasing bacterial counts of B. fragilis, among others. Finally, lyso-Gb3 modified the formation of short-chain fatty acids, leading to a striking decrease in butyrate concentration. Lyso-Gb3 modifies the biology of gut bacteria, favoring the production of biofilms and altering the composition and short-chain fatty-acid profile of the gut microbiota.
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Affiliation(s)
- John-Jairo Aguilera-Correa
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, UAM. Av. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Patricia Madrazo-Clemente
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, UAM. Av. Reyes Católicos, 2, 28040, Madrid, Spain
| | - María Del Carmen Martínez-Cuesta
- Department of Food Biotechnology and Microbiology, Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), Nicolás Cabrera, 9, 28049, Madrid, Spain
| | - Carmen Peláez
- Department of Food Biotechnology and Microbiology, Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), Nicolás Cabrera, 9, 28049, Madrid, Spain
| | - Alberto Ortiz
- Nephrology Department. IIS-Fundación Jiménez Díaz, UAM. Av. Reyes Católicos, 2, 28040, Madrid, Spain
| | | | - Jaime Esteban
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, UAM. Av. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Teresa Requena
- Department of Food Biotechnology and Microbiology, Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), Nicolás Cabrera, 9, 28049, Madrid, Spain
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106
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Toward an accessible and robust in vitro approach to evaluate bacterial viability in the upper gastro-intestinal tract: A Gastro-Intestinal Digestive Simulator (GIDS) combined with alternative methods to plating. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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107
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Ketogenic Diet and Microbiota: Friends or Enemies? Genes (Basel) 2019; 10:genes10070534. [PMID: 31311141 PMCID: PMC6678592 DOI: 10.3390/genes10070534] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/06/2019] [Accepted: 07/10/2019] [Indexed: 12/12/2022] Open
Abstract
Over the last years, a growing body of evidence suggests that gut microbial communities play a fundamental role in many aspects of human health and diseases. The gut microbiota is a very dynamic entity influenced by environment and nutritional behaviors. Considering the influence of such a microbial community on human health and its multiple mechanisms of action as the production of bioactive compounds, pathogens protection, energy homeostasis, nutrients metabolism and regulation of immunity, establishing the influences of different nutritional approach is of pivotal importance. The very low carbohydrate ketogenic diet is a very popular dietary approach used for different aims: from weight loss to neurological diseases. The aim of this review is to dissect the complex interactions between ketogenic diet and gut microbiota and how this large network may influence human health.
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108
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Metabolism, bioenergetics and thermal physiology: influences of the human intestinal microbiota. Nutr Res Rev 2019; 32:205-217. [PMID: 31258100 DOI: 10.1017/s0954422419000076] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The micro-organisms which inhabit the human gut (i.e. the intestinal microbiota) influence numerous human biochemical pathways and physiological functions. The present review focuses on two questions, 'Are intestinal microbiota effects measurable and meaningful?' and 'What research methods and variables are influenced by intestinal microbiota effects?'. These questions are considered with respect to doubly labelled water measurements of energy expenditure, heat balance calculations and models, measurements of RMR via indirect calorimetry, and diet-induced energy expenditure. Several lines of evidence suggest that the intestinal microbiota introduces measurement variability and measurement errors which have been overlooked in research studies involving nutrition, bioenergetics, physiology and temperature regulation. Therefore, we recommend that present conceptual models and research techniques be updated via future experiments, to account for the metabolic processes and regulatory influences of the intestinal microbiota.
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109
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Ding M, Qi C, Yang Z, Jiang S, Bi Y, Lai J, Sun J. Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China. Food Funct 2019; 10:554-564. [PMID: 30681124 DOI: 10.1039/c8fo02182a] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Breast milk bacteria play an important role in the early development of the gut microbiota and the immune system. Dominant living bacteria of 89 healthy Chinese women from 11 cities in five regions were analysed by broad-range yeast extract, casitone, and fatty acid and de Man, Rogosa, and Sharpe-based culturing coupled with 16S rRNA sequence and quantitative polymerase chain reaction. Principal coordinate analysis showed that human breast milk samples were classified into three groups, driven by Enterococcus (abundance in group 1, 63.13%), Streptococcus (abundance in group 2, 68.16%) and Staphylococcus (abundance in group 3, 55.17%). The microbiota profile was highly region-specific. Samples from the Northwest and North of China showed higher alpha diversity compared to other regions (p < 0.05). Staphylococcus, Streptococcus, and Enterococcus were the dominant genera in all samples. Lactobacillus had a high occurrence in samples from the Northwest and North, dominated by Lactobacillus reuteri and Lactobacillus gasseri. Samples of mothers with a high postpartum body mass index showed more Staphylococcus and less Lactobacillus and Streptococcus. Staphylococcus was negatively correlated with Lactobacillus and Streptococcus. The mode of delivery also affected the composition of microbiota, even after culture. These findings indicate differences between the North and South, provide effective information for collection of samples in which Lactobacillus is the predominant genus, and lower the detection limit for small amounts of bacteria.
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Affiliation(s)
- Mengfan Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.
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110
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Abstract
Aim:to review available data confirming the pathogenetic role of the intestinal microbiota in the formation of irritable bowel syndrome (IBS).Key findings.Changes in the intestinal biotope cause the development of visceral hypersensitivity and impaired intestinal motor activity, as well as neuroimmune transmission. This article discusses the main aspects of the biological properties of probiotic bacteria in terms of their action within the “brain — intestine — microbiota” chain. The results of experimental and clinical studies elucidating the mechanisms of action of probiotic cultures have been generalized. The understanding of these mechanisms allows practitioners to make informed decisions in prescribing probiotics to IBS patients. Key concepts concerning fecal microbiota transplantation, as well as the prospects and difficulties of implementing this approach are considered.Conclusions.The term “microbiota — intestine — brain” clearly demonstrates the correlation between the main functional components of IBS. Meta-analyses and systematic reviews confirm the efficacy of probiotics in IBS. However, further research into probiotic therapy options is needed to identify specific bacterial strains with proven clinical efficacy. The fecal microbiota transplantation method also requires further research, since many issues associated with this approach remain unclear.
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111
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Davani-Davari D, Negahdaripour M, Karimzadeh I, Seifan M, Mohkam M, Masoumi SJ, Berenjian A, Ghasemi Y. Prebiotics: Definition, Types, Sources, Mechanisms, and Clinical Applications. Foods 2019; 8:E92. [PMID: 30857316 PMCID: PMC6463098 DOI: 10.3390/foods8030092] [Citation(s) in RCA: 585] [Impact Index Per Article: 117.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/20/2022] Open
Abstract
Prebiotics are a group of nutrients that are degraded by gut microbiota. Their relationship with human overall health has been an area of increasing interest in recent years. They can feed the intestinal microbiota, and their degradation products are short-chain fatty acids that are released into blood circulation, consequently, affecting not only the gastrointestinal tracts but also other distant organs. Fructo-oligosaccharides and galacto-oligosaccharides are the two important groups of prebiotics with beneficial effects on human health. Since low quantities of fructo-oligosaccharides and galacto-oligosaccharides naturally exist in foods, scientists are attempting to produce prebiotics on an industrial scale. Considering the health benefits of prebiotics and their safety, as well as their production and storage advantages compared to probiotics, they seem to be fascinating candidates for promoting human health condition as a replacement or in association with probiotics. This review discusses different aspects of prebiotics, including their crucial role in human well-being.
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Affiliation(s)
- Dorna Davani-Davari
- Pharmaceutical Biotechnology Incubator, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
| | - Iman Karimzadeh
- Department of Clinical Pharmacy, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
| | - Mostafa Seifan
- Faculty of Science and Engineering, University of Waikato, Hamilton 3216, New Zealand.
| | - Milad Mohkam
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
| | - Seyed Jalil Masoumi
- Nutrition Research Center, Department of Clinical Nutrition, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
| | - Aydin Berenjian
- Faculty of Science and Engineering, University of Waikato, Hamilton 3216, New Zealand.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
- Nutrition Research Center, Department of Clinical Nutrition, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz 71348, Iran.
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112
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Sorndech W, Rodtong S, Blennow A, Tongta S. Impact of Resistant Maltodextrins and Resistant Starch on Human Gut Microbiota and Organic Acids Production. STARCH-STARKE 2019. [DOI: 10.1002/star.201800231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Waraporn Sorndech
- School of Food Technology; Institute of Agricultural Technology; Suranaree University of Technology; Nakhon Ratchasima 30000 Thailand
| | - Sureelak Rodtong
- School of Preclinic; Institute of Science; Suranaree University of Technology; Nakhon Ratchasima 30000 Thailand
| | - Andreas Blennow
- Department of Plant and Environmental Sciences; Faculty of Sciences; University of Copenhagen; C 1871 Frederiksberg Denmark
| | - Sunanta Tongta
- School of Food Technology; Institute of Agricultural Technology; Suranaree University of Technology; Nakhon Ratchasima 30000 Thailand
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113
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Shin W, Wu A, Massidda MW, Foster C, Thomas N, Lee DW, Koh H, Ju Y, Kim J, Kim HJ. A Robust Longitudinal Co-culture of Obligate Anaerobic Gut Microbiome With Human Intestinal Epithelium in an Anoxic-Oxic Interface-on-a-Chip. Front Bioeng Biotechnol 2019; 7:13. [PMID: 30792981 PMCID: PMC6374617 DOI: 10.3389/fbioe.2019.00013] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/18/2019] [Indexed: 01/01/2023] Open
Abstract
The majority of human gut microbiome is comprised of obligate anaerobic bacteria that exert essential metabolic functions in the human colon. These anaerobic gut bacteria constantly crosstalk with the colonic epithelium in a mucosal anoxic-oxic interface (AOI). However, in vitro recreation of the metabolically mismatched colonic AOI has been technically challenging. Furthermore, stable co-culture of the obligate anaerobic commensal microbiome and epithelial cells in a mechanically dynamic condition is essential for demonstrating the host-gut microbiome crosstalk. Here, we developed an anoxic-oxic interface-on-a-chip (AOI Chip) by leveraging a modified human gut-on-a-chip to demonstrate a controlled oxygen gradient in the lumen-capillary transepithelial interface by flowing anoxic and oxic culture medium at various physiological milieus. Computational simulation and experimental results revealed that the presence of the epithelial cell layer and the flow-dependent conditioning in the lumen microchannel is necessary and sufficient to create the steady-state vertical oxygen gradient in the AOI Chip. We confirmed that the created AOI does not compromise the viability, barrier function, mucin production, and the expression and localization of tight junction proteins in the 3D intestinal epithelial layer. Two obligate anaerobic commensal gut microbiome, Bifidobacterium adolescentis and Eubacterium hallii, that exert metabolic cross-feeding in vivo, were independently co-cultured with epithelial cells in the AOI Chip for up to a week without compromising any cell viability. Our new protocol for creating an AOI in a microfluidic gut-on-a-chip may enable to demonstrate the key physiological interactions of obligate anaerobic gut microbiome with the host cells associated with intestinal metabolism, homeostasis, and immune regulation.
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Affiliation(s)
- Woojung Shin
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Alexander Wu
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Miles W Massidda
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Charles Foster
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Newin Thomas
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States
| | - Dong-Woo Lee
- Department of Biotechnology, College of Life Science and Technology, Yonsei University, Seoul, South Korea
| | - Hong Koh
- Department of Pediatrics, Severance Fecal Microbiota Transplantation Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Youngwon Ju
- Department of Chemistry, Research Institute for Basic Sciences, Kyung Hee University, Seoul, South Korea
| | - Joohoon Kim
- Department of Chemistry, Research Institute for Basic Sciences, Kyung Hee University, Seoul, South Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, South Korea
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin Austin, TX, United States.,Department of Medical Engineering, Yonsei University College of Medicine, Seoul, South Korea
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114
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The microbiome and immunodeficiencies: Lessons from rare diseases. J Autoimmun 2019; 98:132-148. [PMID: 30704941 DOI: 10.1016/j.jaut.2019.01.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are inherited disorders of the immune system, associated with a considerable increase in susceptibility to infections. PIDs can also predispose to malignancy, inflammation and autoimmunity. There is increasing awareness that some aspects of the immune dysregulation in PIDs may be linked to intestinal microbiota. Indeed, the gut microbiota and its metabolites have been shown to influence immune functions and immune homeostasis both locally and systemically. Recent studies have indicated that genetic defects causing PIDs lead to perturbations in the conventional mechanisms underlying homeostasis in the gut, resulting in poor immune surveillance at the intestinal barrier, which associates with altered intestinal permeability and bacterial translocation. Consistently, a substantial proportion of PID patients presents with clinically challenging IBD-like pathology. Here, we describe the current body of literature reporting on dysbiosis of the gut microbiota in different PIDs and how this can be either the result or cause of immune dysregulation. Further, we report how infections in PIDs enhance pathobionts colonization and speculate how, in turn, pathobionts may be responsible for increased disease susceptibility and secondary infections in these patients. The potential relationship between the microbial composition in the intestine and other sites, such as the oral cavity and skin, is also highlighted. Finally, we provide evidence, in preclinical models of PIDs, for the efficacy of microbiota manipulation to ameliorate disease complications, and suggest that the potential use of dietary intervention to correct dysbiotic flora in PID patients may hold promise.
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115
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Wang FG, Bai RX, Yan WM, Yan M, Dong LY, Song MM. Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients. Exp Ther Med 2019; 17:2268-2278. [PMID: 30867711 PMCID: PMC6395995 DOI: 10.3892/etm.2019.7200] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 12/31/2018] [Indexed: 12/17/2022] Open
Abstract
The modulation of the gut microbiota was recently deemed one of the mechanisms responsible for the excellent outcomes of bariatric surgery. However, to date, only few studies have assessed this, and they have high heterogeneity. In the present study, next-generation 16S ribosomal DNA amplicon sequencing was used to characterize the gut microbiota of healthy volunteers, as well as patients prior to and after sleeve gastrectomy (SG) or Roux-en-Y gastric bypass (RYGB). Significant differences in α diversity, β diversity and species were identified between the different groups/time-points. The results demonstrated excellent outcomes of SG and RYGB. The β diversity was lower in healthy volunteers compared with that in morbidly obese patients with or without type 2 diabetes mellitus. At 3 months after SG, the α diversity was increased and the β diversity was decreased. The abundance of certain species changed significantly after SG and RYGB. It was also revealed that the abundance of certain microbes was significantly correlated with the body mass index, fasting blood glucose and glycosylated haemoglobin. It may be concluded that bariatric surgery may cause obvious alterations in the gut microbiota and compared with healthy volunteers and obese patients without bariatric surgery, the microbiota composition of post-bariatric surgery has unique characteristics. However, studies with a larger cohort and longer follow-up may be required to confirm these results.
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Affiliation(s)
- Fu-Gang Wang
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Ri-Xing Bai
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Wen-Mao Yan
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Ming Yan
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Ling-Yue Dong
- Department of Cell Biology, Basic Medical College, Capital Medical University, Beijing 100069, P.R. China
| | - Mao-Min Song
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
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116
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De Paepe K, Verspreet J, Rezaei MN, Martinez SH, Meysman F, Van de Walle D, Dewettinck K, Courtin CM, Van de Wiele T. Modification of wheat bran particle size and tissue composition affects colonisation and metabolism by human faecal microbiota. Food Funct 2019; 10:379-396. [DOI: 10.1039/c8fo01272e] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Six wheat bran products, varying in particle size, histological and chemical composition differentially affected thein vitrofermentation activity and composition of human faecal microbiota of ten individuals.
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Affiliation(s)
- Kim De Paepe
- Center for Microbial Ecology and Technology (CMET)
- Department of Biotechnology
- Faculty of Bioscience Engineering
- Ghent University
- Ghent
| | - Joran Verspreet
- Laboratory of Food Chemistry and Biochemistry
- Leuven Food Science and Nutrition Research Centre (LFoRCe)
- Faculty of Bioscience Engineering
- KU Leuven
- Heverlee
| | - Mohammad Naser Rezaei
- Laboratory of Food Chemistry and Biochemistry
- Leuven Food Science and Nutrition Research Centre (LFoRCe)
- Faculty of Bioscience Engineering
- KU Leuven
- Heverlee
| | - Silvia Hidalgo Martinez
- Ecosystem Management Research Group (ECOBE)
- Department of Biology
- Faculty of Sciences
- Universiteit Antwerpen
- Antwerp
| | - Filip Meysman
- Ecosystem Management Research Group (ECOBE)
- Department of Biology
- Faculty of Sciences
- Universiteit Antwerpen
- Antwerp
| | - Davy Van de Walle
- Laboratory of Food Technology and Engineering (FTE)
- Department of Food technology
- Safety and Health
- Faculty of Bioscience Engineering
- Ghent University
| | - Koen Dewettinck
- Laboratory of Food Technology and Engineering (FTE)
- Department of Food technology
- Safety and Health
- Faculty of Bioscience Engineering
- Ghent University
| | - Christophe M. Courtin
- Laboratory of Food Chemistry and Biochemistry
- Leuven Food Science and Nutrition Research Centre (LFoRCe)
- Faculty of Bioscience Engineering
- KU Leuven
- Heverlee
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET)
- Department of Biotechnology
- Faculty of Bioscience Engineering
- Ghent University
- Ghent
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117
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Sorini C, Cardoso RF, Gagliani N, Villablanca EJ. Commensal Bacteria-Specific CD4 + T Cell Responses in Health and Disease. Front Immunol 2018; 9:2667. [PMID: 30524431 PMCID: PMC6256970 DOI: 10.3389/fimmu.2018.02667] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Over the course of evolution, mammalian body surfaces have adapted their complex immune system to allow a harmless coexistence with the commensal microbiota. The adaptive immune response, in particular CD4+ T cell-mediated, is crucial to maintain intestinal immune homeostasis by discriminating between harmless (e.g., dietary compounds and intestinal microbes) and harmful stimuli (e.g., pathogens). To tolerate food molecules and microbial components, CD4+ T cells establish a finely tuned crosstalk with the environment whereas breakdown of these mechanisms might lead to chronic disease associated with mucosal barriers and beyond. How commensal-specific immune responses are regulated and how these molecular and cellular mechanisms can be manipulated to treat chronic disorders is yet poorly understood. In this review, we discuss current knowledge of the regulation of commensal bacteria-specific CD4+ T cells. We place particular focus on the key role of commensal-specific CD4+ T cells in maintaining tolerance while efficiently eradicating local and systemic infections, with a focus on factors that trigger their aberrant activation.
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Affiliation(s)
- Chiara Sorini
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Rebeca F. Cardoso
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Nicola Gagliani
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eduardo J. Villablanca
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
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118
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Cox LA, Olivier M, Spradling-Reeves K, Karere GM, Comuzzie AG, VandeBerg JL. Nonhuman Primates and Translational Research-Cardiovascular Disease. ILAR J 2018; 58:235-250. [PMID: 28985395 DOI: 10.1093/ilar/ilx025] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 12/18/2022] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of morbidity and mortality in the United States. Human epidemiological studies provide challenges for understanding mechanisms that regulate initiation and progression of CVD due to variation in lifestyle, diet, and other environmental factors. Studies describing metabolic and physiologic aspects of CVD, and those investigating genetic and epigenetic mechanisms influencing CVD initiation and progression, have been conducted in multiple Old World nonhuman primate (NHP) species. Major advantages of NHPs as models for understanding CVD are their genetic, metabolic, and physiologic similarities with humans, and the ability to control diet, environment, and breeding. These NHP species are also genetically and phenotypically heterogeneous, providing opportunities to study gene by environment interactions that are not feasible in inbred animal models. Each Old World NHP species included in this review brings unique strengths as models to better understand human CVD. All develop CVD without genetic manipulation providing multiple models to discover genetic variants that influence CVD risk. In addition, as each of these NHP species age, their age-related comorbidities such as dyslipidemia and diabetes are accelerated proportionally 3 to 4 times faster than in humans.In this review, we discuss current CVD-related research in NHPs focusing on selected aspects of CVD for which nonprimate model organism studies have left gaps in our understanding of human disease. We include studies on current knowledge of genetics, epigenetics, calorie restriction, maternal calorie restriction and offspring health, maternal obesity and offspring health, nonalcoholic steatohepatitis and steatosis, Chagas disease, microbiome, stem cells, and prevention of CVD.
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Affiliation(s)
- Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas.,Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas
| | | | - Genesio M Karere
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas
| | - John L VandeBerg
- South Texas Diabetes and Obesity Center, School of Medicine, University of Texas Rio Grande Valley, Edinburg/Harlingen/Brownsville, Texas
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119
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Pham HTT, Boger MCL, Dijkhuizen L, van Leeuwen SS. Stimulatory effects of novel glucosylated lactose derivatives GL34 on growth of selected gut bacteria. Appl Microbiol Biotechnol 2018; 103:707-718. [PMID: 30406451 PMCID: PMC6373440 DOI: 10.1007/s00253-018-9473-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
Previously we structurally characterized five glucosylated lactose derivatives (F1-F5) with a degree of polymerization (DP) of 3-4 (GL34), products of Lactobacillus reuteri glucansucrases, with lactose and sucrose as substrates. Here, we show that these GL34 compounds are largely resistant to the hydrolytic activities of common carbohydrate-degrading enzymes. Also, the ability of single strains of gut bacteria, bifidobacteria, lactobacilli, and commensal bacteria, to ferment the GL34 compounds was studied. Bifidobacteria clearly grew better on the GL34 mixture than lactobacilli and commensal bacteria. Lactobacilli and the commensal bacteria Escherichia coli Nissle and Bacteroides thetaiotaomicron only degraded the F2 compound α-D-Glcp-(1 → 2)-[β-D-Galp-(1 → 4)-]D-Glcp, constituting around 30% w/w of GL34. Bifidobacteria digested more than one compound from the GL34 mixture, varying with the specific strain tested. Bifidobacterium adolescentis was most effective, completely degrading four of the five GL34 compounds, leaving only one minor constituent. GL34 thus represents a novel oligosaccharide mixture with (potential) synbiotic properties towards B. adolescentis, synthesized from cheap and abundantly available lactose and sucrose.
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Affiliation(s)
- Hien T T Pham
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Markus C L Boger
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. .,CarbExplore Research B.V, Zernikepark 12, 9747 AN, Groningen, The Netherlands.
| | - Sander S van Leeuwen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
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120
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Preparation, characterization and improvement in intestinal function of polysaccharide fractions from okra. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.09.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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121
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Henson MA, Phalak P. Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota. PLoS Comput Biol 2018; 14:e1006558. [PMID: 30376571 PMCID: PMC6226200 DOI: 10.1371/journal.pcbi.1006558] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/09/2018] [Accepted: 10/09/2018] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota represent a highly complex ecosystem comprised of approximately 1000 species that forms a mutualistic relationship with the human host. A critical attribute of the microbiota is high species diversity, which provides system robustness through overlapping and redundant metabolic capabilities. The gradual loss of bacterial diversity has been associated with a broad array of gut pathologies and diseases including malnutrition, obesity, diabetes and inflammatory bowel disease. We formulated an in silico community model of the gut microbiota by combining genome-scale metabolic reconstructions of 28 representative species to explore the relationship between species diversity and community growth. While the individual species offered a broad range of metabolic capabilities, communities optimized for maximal growth on simulated Western and high-fiber diets had low diversities and imbalances in short-chain fatty acid (SCFA) synthesis characterized by acetate overproduction. Community flux variability analysis performed with the 28-species model and a reduced 20-species model suggested that enhanced species diversity and more balanced SCFA production were achievable at suboptimal growth rates. We developed a simple method for constraining species abundances to sample the growth-diversity tradeoff and used the 20-species model to show that tradeoff curves for Western and high-fiber diets resembled Pareto-optimal surfaces. Compared to maximal growth solutions, suboptimal growth solutions were characterized by higher species diversity, more balanced SCFA synthesis and lower exchange rates of crossfed metabolites between more species. We hypothesized that modulation of crossfeeding relationships through host-microbiota interactions could be an important means for maintaining species diversity and suggest that community metabolic modeling approaches that allow multiobjective optimization of growth and diversity are needed for more realistic simulation of complex communities.
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Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts, USA
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA
- * E-mail:
| | - Poonam Phalak
- Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts, USA
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA
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122
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Impact of Diet-Modulated Butyrate Production on Intestinal Barrier Function and Inflammation. Nutrients 2018; 10:nu10101499. [PMID: 30322146 PMCID: PMC6213552 DOI: 10.3390/nu10101499] [Citation(s) in RCA: 306] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 02/07/2023] Open
Abstract
A major challenge in affluent societies is the increase in disorders related to gut and metabolic health. Chronic over nutrition by unhealthy foods high in energy, fat, and sugar, and low in dietary fibre is a key environmental factor responsible for this development, which may cause local and systemic inflammation. A low intake of dietary fibre is a limiting factor for maintaining a viable and diverse microbiota and production of short-chain fatty acids in the gut. A suppressed production of butyrate is crucial, as this short-chain fatty acid (SCFA) can play a key role not only in colonic health and function but also at the systemic level. At both sites, the mode of action is through mediation of signalling pathways involving nuclear NF-κB and inhibition of histone deacetylase. The intake and composition of dietary fibre modulate production of butyrate in the large intestine. While butyrate production is easily adjustable it is more variable how it influences gut barrier function and inflammatory markers in the gut and periphery. The effect of butyrate seems generally to be more consistent and positive on inflammatory markers related to the gut than on inflammatory markers in the peripheral tissue. This discrepancy may be explained by differences in butyrate concentrations in the gut compared with the much lower concentration at more remote sites.
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123
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Kuntal BK, Chandrakar P, Sadhu S, Mande SS. 'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets. ISME JOURNAL 2018; 13:442-454. [PMID: 30287886 DOI: 10.1038/s41396-018-0291-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/05/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease. Additionally, we devise a score to identify important microbial taxa which serve as 'drivers' from the healthy to disease. We demonstrate the validity of our score on a number of scenarios and apply our methodology on two real world metagenomic datasets. The 'NetShift' methodology is also implemented as a web-based application available at https://web.rniapps.net/netshift.
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Affiliation(s)
- Bhusan K Kuntal
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory Campus, Pune, 411 008, India
| | - Pranjal Chandrakar
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.,Decision Sciences, Indian Institute of Management Bangalore, Bannerghatta Road, Bengaluru, Karnataka, 560076, India
| | - Sudipta Sadhu
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune, 411 013, India.
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124
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Li X, Yin J, Zhu Y, Wang X, Hu X, Bao W, Huang Y, Chen L, Chen S, Yang W, Shan Z, Liu L. Effects of Whole Milk Supplementation on Gut Microbiota and Cardiometabolic Biomarkers in Subjects with and without Lactose Malabsorption. Nutrients 2018; 10:nu10101403. [PMID: 30279333 PMCID: PMC6213503 DOI: 10.3390/nu10101403] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/09/2018] [Accepted: 09/21/2018] [Indexed: 01/07/2023] Open
Abstract
The aim of this study was to compare the impact of whole milk supplementation on gut microbiota and cardiometabolic biomarkers between lactose malabsorbers (LM) and absorbers (LA). We performed a pair-wise intervention study of 31 LM and 31 LA, 1:1 matched by age, sex, body mass index, and daily dairy intake. Subjects were required to add 250 mL/day whole milk for four weeks in their routine diet. At the beginning and the end of the intervention period, we collected data on gut microbiota and cardiometabolic biomarkers. Whole milk supplementation significantly increased Actinobacteria (P < 0.01), Bifidobacterium (P < 0.01), Anaerostipe (P < 0.01), and Blautia (P = 0.04), and decreased Megamonas (P = 0.04) in LM, but not LA. Microbial richness and diversity were not affected. The fecal levels of short-chain fatty acids (SCFAs) remained stable throughout the study. Body fat mass (P < 0.01) and body fat percentage (P < 0.01) reduced in both groups, but the changes did not differ between groups. No significant differences in other cardiometabolic markers were found between LM and LA. When compared with LA, whole milk supplementation could alter the intestinal microbiota composition in LM, without significant changes in fecal SCFAs and cardiometabolic biomarkers.
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Affiliation(s)
- Xiaoqin Li
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jiawei Yin
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yalun Zhu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xiaoqian Wang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xiaoli Hu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Wei Bao
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA 52242, USA.
| | - Yue Huang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Liangkai Chen
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Sijing Chen
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Wei Yang
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Zhilei Shan
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Departments of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Liegang Liu
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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125
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Pretreatment and treatment with fructo-oligosaccharides attenuate intestinal mucositis induced by 5-FU in mice. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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126
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De Paepe K, Verspreet J, Verbeke K, Raes J, Courtin CM, Van de Wiele T. Introducing insoluble wheat bran as a gut microbiota niche in an in vitro
dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community. Environ Microbiol 2018; 20:3406-3426. [DOI: 10.1111/1462-2920.14381] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/03/2018] [Accepted: 08/09/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Kim De Paepe
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering; Ghent University; Ghent Belgium
| | - Joran Verspreet
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), Faculty of Bioscience Engineering; KU Leuven; Leuven Belgium
| | - Kristin Verbeke
- Translational Research in Gastrointestinal Disorders; KU Leuven; Leuven Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology; KU Leuven, Rega Institute; Leuven Belgium
- VIB, Center for the Biology of Disease; Leuven Belgium
- Faculty of Sciences and Bioengineering Sciences; Microbiology Unit, Vrije Universiteit Brussel; Brussels Belgium
| | - Christophe M. Courtin
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), Faculty of Bioscience Engineering; KU Leuven; Leuven Belgium
| | - Tom Van de Wiele
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering; Ghent University; Ghent Belgium
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127
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Dohi M, Mougi A. A coexistence theory in microbial communities. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180476. [PMID: 30839701 PMCID: PMC6170546 DOI: 10.1098/rsos.180476] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/21/2018] [Indexed: 06/05/2023]
Abstract
Microbes are widespread in natural ecosystems where they create complex communities. Understanding the functions and dynamics of such microbial communities is a very important theme not only for ecology but also for humankind because microbes can play major roles in our health. Yet, it remains unclear how such complex ecosystems are maintained. Here, we present a simple theory on the dynamics of a microbial community. Bacteria preferring a particular pH in their environment indirectly inhibit the growth of the other types of bacteria by changing the pH to their optimum value. This pH-driven interaction always causes a state of bistability involving different types of bacteria that can be more or less abundant. Furthermore, a moderate abundance ratio of different types of bacteria can confer enhanced resilience to a specific equilibrium state, particularly when a trade-off relationship exists between growth and the ability of bacteria to change the pH of their environment. These results suggest that the balance of the composition of microbiota plays a critical role in maintaining microbial communities.
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128
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Clinical trials of kimchi intakes on the regulation of metabolic parameters and colon health in healthy Korean young adults. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.05.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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129
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Duszka K, Wahli W. Enteric Microbiota⁻Gut⁻Brain Axis from the Perspective of Nuclear Receptors. Int J Mol Sci 2018; 19:ijms19082210. [PMID: 30060580 PMCID: PMC6121494 DOI: 10.3390/ijms19082210] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Nuclear receptors (NRs) play a key role in regulating virtually all body functions, thus maintaining a healthy operating body with all its complex systems. Recently, gut microbiota emerged as major factor contributing to the health of the whole organism. Enteric bacteria have multiple ways to influence their host and several of them involve communication with the brain. Mounting evidence of cooperation between gut flora and NRs is already available. However, the full potential of the microbiota interconnection with NRs remains to be uncovered. Herewith, we present the current state of knowledge on the multifaceted roles of NRs in the enteric microbiota–gut–brain axis.
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Affiliation(s)
- Kalina Duszka
- Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
| | - Walter Wahli
- Lee Kong Chian School of Medicine, Nanyang Technological, 11 Mandalay Road, Singapore 308232, Singapore.
- Center for Integrative Genomics, University of Lausanne, Génopode, CH-1015 Lausanne, Switzerland.
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130
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Huang CH, Yu X, Liao WB. The Expensive-Tissue Hypothesis in Vertebrates: Gut Microbiota Effect, a Review. Int J Mol Sci 2018; 19:E1792. [PMID: 29914188 PMCID: PMC6032294 DOI: 10.3390/ijms19061792] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/28/2018] [Accepted: 06/12/2018] [Indexed: 02/08/2023] Open
Abstract
The gut microbiota is integral to an organism’s digestive structure and has been shown to play an important role in producing substrates for gluconeogenesis and energy production, vasodilator, and gut motility. Numerous studies have demonstrated that variation in diet types is associated with the abundance and diversity of the gut microbiota, a relationship that plays a significant role in nutrient absorption and affects gut size. The Expensive-Tissue Hypothesis states (ETH) that the metabolic requirement of relatively large brains is offset by a corresponding reduction of the other tissues, such as gut size. However, how the trade-off between gut size and brain size in vertebrates is associated with the gut microbiota through metabolic requirements still remains unexplored. Here, we review research relating to and discuss the potential influence of gut microbiota on the ETH.
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Affiliation(s)
- Chun Hua Huang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan, China.
- Institute of Eco-adaptation in Amphibians and Reptiles, China West Normal University, Nanchong 637009, Sichuan, China.
| | - Xin Yu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan, China.
- Institute of Eco-adaptation in Amphibians and Reptiles, China West Normal University, Nanchong 637009, Sichuan, China.
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan, China.
- Institute of Eco-adaptation in Amphibians and Reptiles, China West Normal University, Nanchong 637009, Sichuan, China.
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131
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Mente E, Nikouli E, Antonopoulou E, Martin SAM, Kormas KA. Core versus diet-associated and postprandial bacterial communities of the rainbow trout ( Oncorhynchus mykiss) midgut and faeces. Biol Open 2018; 7:bio.034397. [PMID: 29776922 PMCID: PMC6031335 DOI: 10.1242/bio.034397] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study investigated the impact of different dietary ingredients, with different protein/lipid sources, on midgut and faeces bacteria community structures just before feeding and 3 h after feeding a single meal to individual rainbow trout (Oncorhynchus mykiss). Fish were kept in experimental rearing facilities and fed ad libitum twice daily for 5 weeks. Fish were fed three different commercial diets, which contained variations of high or low marine fishmeal/fish oil content. DNA was extracted from midgut and faeces samples for analysis of their bacterial 16S rRNA gene diversity by targeting the V3-V4 region with 454 pyrosequencing. A total of 332 unique bacterial operational taxonomic units (OTUs) were revealed in all samples. However, each sample was dominated (>80% relative abundance) by 2–14 OTUs, with the single most dominant OTU having >30% dominance, indicating that only a few bacteria were fundamental in terms of relative abundance in each treatment. Fifteen OTUs occurred in all samples (core microbiota). The majority of these OTUs belonged to the Proteobacteria, Firmicutes or Tenericutes, and were associated with other animal gut environments. The faecal material and the midgut samples had few overlaps in their shared OTUs. A postprandial response in the gut bacterial community structure 3 h after feeding highlights how dietary stimulation induces structural changes in the microbiota profiles in the established gut bacteria. This study showed that feeding O. mykiss different diets and even single meals lead to perturbations in the established gut bacteria of O. mykiss. Summary: The gut bacterial microbiome of rainbow trout contains a few core bacterial taxa and has little overlap with its faeces. Bacterial communities can change even 3 h after feeding.
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Affiliation(s)
- Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece.,School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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132
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Yang J, Shimogonya Y, Ishikawa T. What causes the spatial heterogeneity of bacterial flora in the intestine of zebrafish larvae? J Theor Biol 2018. [PMID: 29526663 DOI: 10.1016/j.jtbi.2018.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Microbial flora in the intestine has been thoroughly investigated, as it plays an important role in the health of the host. Jemielita et al. (2014) showed experimentally that Aeromonas bacteria in the intestine of zebrafish larvae have a heterogeneous spatial distribution. Although bacterial aggregation is important biologically and clinically, there is no mathematical model describing the phenomenon and its mechanism remains largely unknown. In this study, we developed a computational model to describe the heterogeneous distribution of bacteria in the intestine of zebrafish larvae. The results showed that biological taxis could cause the bacterial aggregation. Intestinal peristalsis had the effect of reducing bacterial aggregation through mixing function. Using a scaling argument, we showed that the taxis velocity of bacteria must be larger than the sum of the diffusive velocity and background bulk flow velocity to induce bacterial aggregation. Our model and findings will be useful to further the scientific understanding of intestinal microbial flora.
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Affiliation(s)
- Jinyou Yang
- Department of Biomedical Engineering, Graduate School of Biomedical Engineering, Tohoku University, 6-6-01 Aoba, Sendai 980-8579, Japan; School of Fundamental Sciences, China Medical University, Shenyang 110122, China.
| | - Yuji Shimogonya
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aoba, Sendai 980-8578, Japan
| | - Takuji Ishikawa
- Department of Biomedical Engineering, Graduate School of Biomedical Engineering, Tohoku University, 6-6-01 Aoba, Sendai 980-8579, Japan; Department of Finemechanics, Graduate School of Engineering, Tohoku University, 6-6-01 Aoba, Sendai 980-8579, Japan
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133
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Abstract
The gut microbiota has been recognized as an important factor in the development of metabolic diseases such as obesity and is considered an endocrine organ involved in the maintenance of energy homeostasis and host immunity. Dysbiosis can change the functioning of the intestinal barrier and the gut-associated lymphoid tissues (GALT) by allowing the passage of structural components of bacteria, such as lipopolysaccharides (LPS), which activate inflammatory pathways that may contribute to the development of insulin resistance. Furthermore, intestinal dysbiosis can alter the production of gastrointestinal peptides related to satiety, resulting in an increased food intake. In obese people, this dysbiosis seems be related to increases of the phylum Firmicutes, the genus Clostridium, and the species Eubacterium rectale, Clostridium coccoides, Lactobacillus reuteri, Akkermansia muciniphila, Clostridium histolyticum, and Staphylococcus aureus.
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Affiliation(s)
- Aline Corado Gomes
- Clinical and Sports Nutrition Research Laboratory (LABINCE), Faculty of Nutrition, Goiás Federal University, Goiânia, Goiás, Brazil,CONTACT Dra. Aline Corado Gomes Clinical and Sports Nutrition Research Laboratory (LABINCE), Faculty of Nutrition, Goiás Federal University, Setor Leste Universitário, Goiânia, St. 227, Block 68, Goiânia GO, Brazil
| | - Christian Hoffmann
- Department of Food Sciences and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - João Felipe Mota
- Clinical and Sports Nutrition Research Laboratory (LABINCE), Faculty of Nutrition, Goiás Federal University, Goiânia, Goiás, Brazil
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134
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Fang S, Zhuo Z, Yu X, Wang H, Feng J. Oral administration of liquid iron preparation containing excess iron induces intestine and liver injury, impairs intestinal barrier function and alters the gut microbiota in rats. J Trace Elem Med Biol 2018; 47:12-20. [PMID: 29544798 DOI: 10.1016/j.jtemb.2018.01.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 12/26/2017] [Accepted: 01/09/2018] [Indexed: 12/21/2022]
Abstract
The aim of this study was to determine the toxicological effects of excess iron in a liquid iron preparation (especially on intestinal barrier function) and the possible etiology of side effects or diseases caused by the excess iron. In study 1, forty male Sprague-Dawley rats (4-5 wk old) were subjected to oral gavage with 1 ml vehicle (0.01 mol/L HCl) or 1 ml liquid iron preparation containing 8 mg, 16 mg or 24 mg of iron for 30 d. Iron status, oxidative stress, histology (H&E staining), ultrastructure (electron microscopy) and apoptosis (TUNEL assay) in the intestines and liver were assessed. The cecal microbiota was evaluated by 16S rRNA sequencing. In study 2, twenty rats with the same profile as above were subjected to oral gavage with 1 ml vehicle or 24 mg Fe for 30 d. The intestinal barrier function was determined by in vivo studies and an Ussing chamber assay; tight junction proteins and serum pro-inflammatory cytokines were observed by enzyme-linked immunosorbent assay. In study 1, the intestinal mucosa and liver showed apparent oxidative stress. In addition, iron concentration-dependent ultrastructural alterations to duodenal enterocytes and hepatocytes and histological damage to the colonic mucosa were detected. Notably, apoptosis was increased in duodenal enterocytes and hepatocytes. Impaired intestinal barrier function and lower expression of intestinal tight junction proteins were observed, and the phenotype was more severe in the colon than in the duodenum. A trend toward higher expression of serum pro-inflammatory cytokines might indicate systemic inflammation. Furthermore, the caecal microbiota showed a significant change, with increased Defluviitaleaceae, Ruminococcaceae, and Coprococcus and reduced Lachnospiraceae and Allobaculum, which could mediate the detrimental effects of excess iron on gut health. We concluded that excessive iron exposure from liquid iron preparation induces oxidative stress and histopathological alterations in the intestine and liver. Impaired intestinal barrier function could increase iron transportation, and inflammation along with oxidative stress-enhanced liver iron deposition may cause further liver injury in a vicious circle. These effects were accompanied by lower intestinal segment damage and altered gut microbial composition of rats toward a profile with an increased risk of gut disease.
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Affiliation(s)
- Shenglin Fang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zhao Zhuo
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xiaonan Yu
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Haichao Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jie Feng
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences, Zhejiang University, Hangzhou, China.
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135
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Bacterial diversity in the feces of dogs with CPV infection. Microb Pathog 2018; 121:70-76. [PMID: 29709688 DOI: 10.1016/j.micpath.2018.04.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/04/2018] [Accepted: 04/23/2018] [Indexed: 01/14/2023]
Abstract
Canine parvovirus (CPV) is a contagious disease in dogs that has high morbidity and mortality. In cases of infection, the pups tend to have a higher mortality and more severe clinical symptoms than the adult dogs because the dehydration is difficult for pups to bear. Following the natural infection, there is a rapid antibody response neutralizing the extracellular virus. As a result, virus titers in tissue and feces become markedly reduced. Hence, it is important to have an effective symptomatic therapy of supporting animals to survive in the early stages of CPV infection. Furthermore, the co-infection with bacteria could increase the severity of lesions and clinical signs as well. In this paper, we obtained the bacterial diversity in feces of CPV infected dogs with the enrichment of five bacteria genera (Shigella, Peptoclostridium, Peptostreptococcus, Streptococcus, Fusobacterium). These microorganisms may partly result in the intestinal pathology of the infection. In summary, the discussion of the bacterial biodiversity in feces of CPV infected dogs provides further insights into the pathology of CPV disease and the targets of developing more effective treatment strategies.
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136
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Healey GR, Murphy R, Brough L, Butts CA, Coad J. Interindividual variability in gut microbiota and host response to dietary interventions. Nutr Rev 2018; 75:1059-1080. [PMID: 29190368 DOI: 10.1093/nutrit/nux062] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dysbiosis is linked to human disease; therefore, gut microbiota modulation strategies provide an attractive means of correcting microbial imbalance to enhance human health. Because diet has a major influence on the composition, diversity, and metabolic capacity of the gut microbiota, numerous dietary intervention studies have been conducted to manipulate the gut microbiota to improve host outcomes and reduce disease risk. Emerging evidence suggests that interindividual variability in gut microbiota and host responsiveness exists, making it difficult to predict gut microbiota and host response to a given dietary intervention. This may, in turn, have implications on the consistency of results among studies and the perceived success or true efficacy of a dietary intervention in eliciting beneficial changes to the gut microbiota and human health.
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Affiliation(s)
- Genelle R Healey
- Massey Institute of Food Science and Technology, School of Food and Nutrition, Massey University, Palmerston North, New Zealand
- Food, Nutrition & Health Group, New Zealand Institute for Plant & Food Research Limited, Palmerston North, New Zealand
| | - Rinki Murphy
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Louise Brough
- Massey Institute of Food Science and Technology, School of Food and Nutrition, Massey University, Palmerston North, New Zealand
| | - Christine A Butts
- Food, Nutrition & Health Group, New Zealand Institute for Plant & Food Research Limited, Palmerston North, New Zealand
| | - Jane Coad
- Massey Institute of Food Science and Technology, School of Food and Nutrition, Massey University, Palmerston North, New Zealand
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137
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Bircher L, Geirnaert A, Hammes F, Lacroix C, Schwab C. Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes. Microb Biotechnol 2018; 11:721-733. [PMID: 29663668 PMCID: PMC6011992 DOI: 10.1111/1751-7915.13265] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/22/2018] [Accepted: 03/08/2018] [Indexed: 01/22/2023] Open
Abstract
Strict anaerobic gut microbes have been suggested as ‘next‐generation probiotics’ for treating several intestinal disorders. The development of preservation techniques is of major importance for therapeutic application. This study investigated cryopreservation (−80°C) and lyophilization survival and storage stability (4°C for 3 months) of the strict anaerobic gut microbes Bacteroides thetaiotaomicron, Faecalibacterium prausnitzii, Roseburia intestinalis, Anaerostipes caccae, Eubacterium hallii and Blautia obeum. To improve preservation survival, protectants sucrose and inulin (both 5% w/v) were added for lyophilization and were also combined with glycerol (15% v/v) for cryopreservation. Bacterial fitness, evaluated by maximum growth rate and lag phase, viability and membrane integrity were determined using a standardized growth assay and by flow cytometry as markers for preservation resistance. Lyophilization was more detrimental to viability and fitness than cryopreservation, but led to better storage stability. Adding sucrose and inulin enhanced viability and the proportion of intact cells during lyophilization of all strains. Viability of protectant‐free B. thetaiotaomicron, A. caccae and F. prausnitzii was above 50% after cryopreservation and storage and increased to above 80% if protectants were present. The addition of glycerol, sucrose and inulin strongly enhanced the viability of B. obeum, E. hallii and R. intestinalis from 0.03–2% in protectant‐free cultures to 11–37%. This is the first study that quantitatively compared the effect of cryopreservation and lyophilization and the addition of selected protectants on viability and fitness of six strict anaerobic gut microbes. Our results suggest that efficiency of protectants is process‐ and species‐specific.
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Affiliation(s)
- Lea Bircher
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092, Zürich, Switzerland
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138
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Mayta-Apaza AC, Pottgen E, De Bodt J, Papp N, Marasini D, Howard L, Abranko L, Van de Wiele T, Lee SO, Carbonero F. Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo. J Nutr Biochem 2018; 59:160-172. [PMID: 30055451 DOI: 10.1016/j.jnutbio.2018.04.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 03/19/2018] [Accepted: 04/04/2018] [Indexed: 12/11/2022]
Abstract
Tart cherries have been reported to exert potential health benefits attributed to their specific and abundant polyphenol content. However, there is a need to study the impact and fate of tart cherries polyphenols in the gut microbiota. Here, tart cherries, pure polyphenols (and apricots) were submitted to in vitro bacterial fermentation assays and assessed through 16S rRNA gene sequence sequencing and metabolomics. A short-term (5 days, 8 oz. daily) human dietary intervention study was also conducted for microbiota analyses. Tart cherry concentrate juices were found to contain expected abundances of anthocyanins (cyanidin-glycosylrutinoside) and flavonoids (quercetin-rutinoside) and high amounts of chlorogenic and neochlorogenic acids. Targeted metabolomics confirmed that gut microbes were able to degrade those polyphenols mainly to 4-hydroxyphenylpropionic acids and to lower amounts of epicatechin and 4-hydroxybenzoic acids. Tart cherries were found to induce a large increase of Bacteroides in vitro, likely due to the input of polysaccharides, but prebiotic effect was also suggested by Bifidobacterium increase from chlorogenic acid. In the human study, two distinct and inverse responses to tart cherry consumption were associated with initial levels of Bacteroides. High-Bacteroides individuals responded with a decrease in Bacteroides and Bifidobacterium, and an increase of Lachnospiraceae, Ruminococcus and Collinsella. Low-Bacteroides individuals responded with an increase in Bacteroides or Prevotella and Bifidobacterium, and a decrease of Lachnospiraceae, Ruminococcus and Collinsella. These data confirm that gut microbiota metabolism, in particular the potential existence of different metabotypes, needs to be considered in studies attempting to link tart cherries consumption and health.
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Affiliation(s)
| | - Ellen Pottgen
- Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Jana De Bodt
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of BioScience Engineering, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nora Papp
- Faculty of Food Science, Department of Applied Chemistry, Szent István University, 1118 Budapest, Hungary
| | - Daya Marasini
- Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Luke Howard
- Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Laszlo Abranko
- Faculty of Food Science, Department of Applied Chemistry, Szent István University, 1118 Budapest, Hungary
| | - Tom Van de Wiele
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of BioScience Engineering, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Sun-Ok Lee
- Food Science, University of Arkansas, Fayetteville, AR, United States; Center for Human Nutrition, Division of Agriculture, University of Arkansas, United States
| | - Franck Carbonero
- Food Science, University of Arkansas, Fayetteville, AR, United States; Center for Human Nutrition, Division of Agriculture, University of Arkansas, United States.
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139
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Abstract
Microbes usually exist in communities consisting of myriad different but interacting species. These interactions are typically mediated through environmental modifications; microbes change the environment by taking up resources and excreting metabolites, which affects the growth of both themselves and also other microbes. We show here that the way microbes modify their environment and react to it sets the interactions within single-species populations and also between different species. A very common environmental modification is a change of the environmental pH. We find experimentally that these pH changes create feedback loops that can determine the fate of bacterial populations; they can either facilitate or inhibit growth, and in extreme cases will cause extinction of the bacterial population. Understanding how single species change the pH and react to these changes allowed us to estimate their pairwise interaction outcomes. Those interactions lead to a set of generic interaction motifs—bistability, successive growth, extended suicide, and stabilization—that may be independent of which environmental parameter is modified and thus may reoccur in different microbial systems. Microbes typically live alongside many other species in complex communities. These microbial communities are very important for us because they also live in and on our bodies and can determine our health and well-being. The composition and function of these communities, such as who is part of such a community and who is excluded, are decided by the interactions between the microbes. These microbial interactions can be driven by many different factors such as resource competition or toxin production. Although these factors are all different, the interactions are typically mediated through the environment; the microbes modify the environment, and they and other microbes have to live in this new environment. We show here that by understanding how microbes change and react to the environment, it is possible to understand and even predict their interactions. We believe that this way of thinking about microbial interactions will lead to a better understanding of more complex communities that are so important for our well-being.
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Affiliation(s)
- Christoph Ratzke
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (CR); (JG)
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (CR); (JG)
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140
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Brown K, Abbott DW, Uwiera RRE, Inglis GD. Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice. Gut Microbes 2018; 9:218-235. [PMID: 29227180 PMCID: PMC6291264 DOI: 10.1080/19490976.2017.1408763] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The murine cecum is a major site of fermentation of dietary materials, and production of short chain fatty acids (SCFAs). To examine the role that the cecum plays in acute bacterial infection in mice, the cecum was surgically removed, and changes in bacterial communities and production of SCFAs were analyzed relative to surgical sham animals. To incite bacterial colitis, mice were orally challenged with Citrobacter rodentium. The impact of butyrate administered directly into the colon was also examined. Concentrations of SCFAs in feces were substantially lower in mice with an excised cecum. Bacterial communities were also less diverse in cecectomized mice, and densities of major SCFA-producing taxa including bacteria within the Ruminococcaceae and Lachnospiraceae families were reduced. Colonization of the intestine by C. rodentium was not affected by removal of the cecum, and the bacterium equally incited acute colitis in mice with and without a cecum. However, cecectomized mice exhibited lower body weights at later stages of infection indicating an impaired ability to recover following challenge with C. rodentium. Furthermore, removal of the cecum altered immune and inflammatory responses to infection including increased inflammatory markers in the proximal colon (Tnfα, Il10, βd1), and heightened inflammatory response in the proximal and distal colon (Ifnγ, Tnfα, Relmβ). Exogenous administration of butyrate was insufficient to normalize responses to C. rodentium in cecectomized mice. The murine cecum plays a critical role in maintaining intestinal health, and the murine cecectomy model may be a useful tool in elucidating key aspects of intestine-pathogen-microbiota interactions.
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Affiliation(s)
- Kirsty Brown
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - D. Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Richard R. E. Uwiera
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - G. Douglas Inglis
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada,CONTACT G. Douglas Inglis Agriculture and Agri-Food Canada, 5403-1st Avenue S, Lethbridge, AB, T1J 4B1
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141
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Racing to Stay Put: How Resident Microbiota Stimulate Intestinal Epithelial Cell Proliferation. CURRENT PATHOBIOLOGY REPORTS 2018. [DOI: 10.1007/s40139-018-0163-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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142
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Davison KM, Temple NJ. Cereal fiber, fruit fiber, and type 2 diabetes: Explaining the paradox. J Diabetes Complications 2018; 32:240-245. [PMID: 29191432 DOI: 10.1016/j.jdiacomp.2017.11.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 10/10/2017] [Accepted: 11/03/2017] [Indexed: 12/20/2022]
Abstract
While the relationship between dietary fiber and type 2 diabetes mellitus (T2DM) has been much studied, the evidence about its role in the prevention and control of this condition has been conflicting. We critically evaluate prospective cohort studies and randomized controlled trials (RCTs) that examined insoluble/nonviscous/cereal fiber and soluble/viscous/fruit fiber in relation to risk of T2DM. Taken as a whole this evidence indicates that, in the quantities typically eaten, cereal fiber is protective against T2DM while fruit fiber gives little protection. We argue that the protective action of cereal fiber may be explained by the modulating effects of gut microbiota through mechanisms such as: 1) improving glucose tolerance via energy metabolism pathways (colonic fermentation and generation of short-chain fatty acids); 2) reducing inflammation; and 3) altering the immune response. By gaining more knowledge of specific host and gut microbial functional pathways involved in T2DM development and the potential role of cereal fiber, appropriate disease prevention and intervention strategies may be developed.
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Affiliation(s)
- Karen M Davison
- Health Science Program, Department of Biology, Kwantlen Polytechnic University, Surrey, British Columbia, Canada.
| | - Norman J Temple
- Centre for Science, Athabasca University, Athabasca, Alberta T9S 3A3, Canada.
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143
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Wu SH, Huang BH, Huang CL, Li G, Liao PC. The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions. MICROBIAL ECOLOGY 2018; 75:434-446. [PMID: 28765980 DOI: 10.1007/s00248-017-1050-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils. The nonsignificant rhizosphere effect suggested other undetermined factors or stochastic processes accounted for microbial diversity in the rhizosphere. More significant microbe-microbe interactions were observed in forest and rhizosphere soils relative to the grassland soils. The elevated number of positive correlations for relative abundances in forest soil implied beneficial associations being common among bacteria, in particular within the rhizosphere environment. The particular soil properties generated by root exudates also alter the physicochemical properties of soil such as K and pH value, and might in turn favor the adoption of teamwork-cooperation strategies for microbe-microbe interactions, represented as large clusters of positive associations among bacterial taxa. Specific biological interactions differentiated the microbiomes within forest soils. Thus, the environmental selection pressure of aboveground vegetation accounts for differences between soil microbiomes while biotic factors are responsible for fine-scale differences of the microbial community in forest soils.
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Affiliation(s)
- Shu-Hong Wu
- School of Nature Conservation, Beijing Forestry University, No.35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan
| | - Gang Li
- School of Nature Conservation, Beijing Forestry University, No.35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan.
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144
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Fat, Sugar, Whole Grains and Heart Disease: 50 Years of Confusion. Nutrients 2018; 10:nu10010039. [PMID: 29300309 PMCID: PMC5793267 DOI: 10.3390/nu10010039] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 12/26/2017] [Accepted: 12/29/2017] [Indexed: 12/22/2022] Open
Abstract
During the 1970s some investigators proposed that refined carbohydrates, especially sugar and a low intake of dietary fiber, were major factors in coronary heart disease (CHD). This suggestion was eclipsed by the belief that an excess intake of saturated fatty acids (SFA) was the key dietary factor, a view that prevailed from roughly 1974 to 2014. Findings that have accumulated since 1990 inform us that the role of SFA in the causation of CHD has been much exaggerated. A switch from SFA to refined carbohydrates does not lower the ratio of total cholesterol to HDL-cholesterol in the blood and therefore does not prevent CHD. A reduced intake of SFA combined with an increased intake of polyunsaturated fatty acids lowers the ratio of total cholesterol to HDL-cholesterol; this may reduce the risk of CHD. The evidence linking carbohydrate-rich foods with CHD has been steadily strengthening. Refined carbohydrates, especially sugar-sweetened beverages, increase the risk of CHD. Conversely, whole grains and cereal fiber are protective. An extra one or 2 servings per day of these foods increases or decreases risk by approximately 10% to 20%.
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145
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Abstract
The gastrointestinal (GI) tract is a highly efficient organ system with specialized structures to facilitate digestion and absorption of nutrients to meet the body's needs. The presence of nutrients in the GI tract supports optimal structure and function, stimulates regulatory hormones, and supports the microbiota, the population of microorganisms residing in the GI tract. A lack of enteral nutrition (EN) results in impaired GI integrity and serious patient complications, making EN a priority. Normal GI physiology is reviewed, and the regulatory impact of luminal nutrients on GI function is discussed.
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146
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Menon R, Ramanan V, Korolev KS. Interactions between species introduce spurious associations in microbiome studies. PLoS Comput Biol 2018; 14:e1005939. [PMID: 29338008 PMCID: PMC5786326 DOI: 10.1371/journal.pcbi.1005939] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/26/2018] [Accepted: 12/21/2017] [Indexed: 12/30/2022] Open
Abstract
Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease.
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Affiliation(s)
- Rajita Menon
- Department of Physics, Boston University, Boston, Massachusetts, United States of America
| | - Vivek Ramanan
- BRITE Bioinformatics REU Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biology and Computer Science, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Kirill S. Korolev
- Department of Physics, Boston University, Boston, Massachusetts, United States of America
- Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
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147
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Hillman ET, Lu H, Yao T, Nakatsu CH. Microbial Ecology along the Gastrointestinal Tract. Microbes Environ 2017; 32:300-313. [PMID: 29129876 PMCID: PMC5745014 DOI: 10.1264/jsme2.me17017] [Citation(s) in RCA: 313] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/19/2017] [Indexed: 02/06/2023] Open
Abstract
The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem. Furthermore, due to the challenges associated with collecting samples directly from the inside of humans, many studies are still exploratory, with a primary focus on the composition of microbiomes. Thus, mechanistic studies to investigate functions are conducted using animal models. However, differences in physiology and microbiomes need to be clarified in order to aid in the translation of animal model findings into the context of humans. This review will highlight Bacteria, Archaea, Fungi, and Viruses, discuss differences along the GI tract of healthy humans, and perform comparisons with three common animal models: rats, mice, and pigs.
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Affiliation(s)
- Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Hang Lu
- Department of Animal Science, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Tianming Yao
- Department of Food Science, Purdue UniversityWest Lafayette, Indiana 47907USA
| | - Cindy H. Nakatsu
- Department of Agronomy, Purdue UniversityWest Lafayette, Indiana 47907USA
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148
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Liu P, Zhao J, Guo P, Lu W, Geng Z, Levesque CL, Johnston LJ, Wang C, Liu L, Zhang J, Ma N, Qiao S, Ma X. Dietary Corn Bran Fermented by Bacillus subtilis MA139 Decreased Gut Cellulolytic Bacteria and Microbiota Diversity in Finishing Pigs. Front Cell Infect Microbiol 2017; 7:526. [PMID: 29312900 PMCID: PMC5744180 DOI: 10.3389/fcimb.2017.00526] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/12/2017] [Indexed: 01/29/2023] Open
Abstract
Solid-state fermentation of feedstuffs by Bacillus subtilis MA139 can reduce insoluble dietary fiber content in vitro and improve growth performance in pigs. This study was conducted to investigate the effects of dietary corn bran (CB) fermented by B. subtilis on growth performance and gut microbiota composition in finishing pigs. A total of 60 finishing pigs were allocated to 3 dietary treatments consisting of a control (CON) diet, a 10% CB diet, and a 10% fermented CB (FCB) diet in a 21 d feeding trial. Growth performance and nutrient digestibility were evaluated. Fecal samples were determined for bacterial community diversity by 16S rRNA gene amplicon sequencing. The dietary CB and FCB did not affect growth performance of finishing pigs. The digestibility of organic matter was decreased in both CB and FCB treatments compared with CON group (P < 0.05). The α-diversity for bacterial community analysis of Chao 1 in FCB treatment was lower than CON treatment (P < 0.05). The Fibrobacteres phylum belongs to cellulolytic bacteria was isolated, and their relative abundance in CB group showed no difference between CON and FCB treatments. The abundance of Lachnospiraceae_NK4A136_group in CB treatment was higher than CON and FCB groups (P < 0.05), whereas the population of norank_f_Prevotellaceae was higher in FCB group compared to CON and CB groups (P < 0.05). In conclusion, dietary FCB decreased the abundance of bacterial communities, particularly the population of bacteria related to cellulolytic degradation.
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Affiliation(s)
- Ping Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinbiao Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Pingting Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wenqing Lu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengying Geng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Crystal L Levesque
- Department of Animal Sciences, South Dakota State University, Brookings, SD, United States
| | - Lee J Johnston
- Swine Nutrition and Production, West Central Research and Outreach Center, University of Minnesota, Morris, MN, United States
| | - Chunlin Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ling Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jie Zhang
- Department of Animal Husbandry and Veterinary Medicine, Beijing Vocational College of Agriculture, Beijing, China
| | - Ning Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Internal Medicine, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
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149
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Harkey MA, Villagran AM, Venkataraman GM, Leisenring WM, Hullar MAJ, Torok-Storb BJ. Associations between gastric dilatation-volvulus in Great Danes and specific alleles of the canine immune-system genes DLA88, DRB1, and TLR5. Am J Vet Res 2017; 78:934-945. [PMID: 28738011 DOI: 10.2460/ajvr.78.8.934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether specific alleles of candidate genes of the major histocompatibility complex (MHC) and innate immune system were associated with gastric dilatation-volvulus (GDV) in Great Danes. ANIMALS 42 healthy Great Danes (control group) and 39 Great Danes with ≥ 1 GDV episode. PROCEDURES Variable regions of the 2 most polymorphic MHC genes (DLA88 and DRB1) were amplified and sequenced from the dogs in each group. Similarly, regions of 3 genes associated with the innate immune system (TLR5, NOD2, and ATG16L1), which have been linked to inflammatory bowel disease, were amplified and sequenced. Alleles were evaluated for associations with GDV, controlling for age and dog family. RESULTS Specific alleles of genes DLA88, DRB1, and TLR5 were significantly associated with GDV. One allele of each gene had an OR > 2 in the unadjusted univariate analyses and retained a hazard ratio > 2 after controlling for temperament, age, and familial association in the multivariate analysis. CONCLUSIONS AND CLINICAL RELEVANCE The 3 GDV-associated alleles identified in this study may serve as diagnostic markers for identification of Great Danes at risk for GDV. Additional research is needed to determine whether other dog breeds have the same genetic associations. These findings also provided a new target for research into the etiology of, and potential treatments for, GDV in dogs.
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150
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Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists. mBio 2017; 8:mBio.01620-17. [PMID: 29184014 PMCID: PMC5705916 DOI: 10.1128/mbio.01620-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional, from the producer to the recipient. This is likely true when a producer’s waste, such as a fermentation product, has value only for a recipient. However, in some cases the cross-fed nutrient holds value for both the producer and the recipient. In such cases, there is potential for nutrient reacquisition by producer cells in a population, leading to competition against recipients. Here, we investigated the consequences of interpartner competition for cross-fed nutrients on mutualism dynamics by using an anaerobic coculture pairing fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris. In this coculture, E. coli excretes waste organic acids that provide a carbon source for R. palustris. In return, R. palustris cross-feeds E. coli ammonium (NH4+), a compound that both species value. To explore the potential for interpartner competition, we first used a kinetic model to simulate cocultures with varied affinities for NH4+ in each species. The model predicted that interpartner competition for NH4+ could profoundly impact population dynamics. We then experimentally tested the predictions by culturing mutants lacking NH4+ transporters in both NH4+ competition assays and mutualistic cocultures. Both theoretical and experimental results indicated that the recipient must have a competitive advantage in acquiring cross-fed NH4+ to sustain the mutualism. This recipient-biased competitive advantage is predicted to be crucial, particularly when the communally valuable nutrient is generated intracellularly. Thus, the very metabolites that form the basis for mutualistic cross-feeding can also be subject to competition between mutualistic partners. Mutualistic relationships, particularly those based on nutrient cross-feeding, promote stability of diverse ecosystems and drive global biogeochemical cycles. Cross-fed nutrients within these systems can be either waste products valued by only one partner or nutrients valued by both partners. Here, we explored how interpartner competition for a communally valuable cross-fed nutrient impacts mutualism dynamics. We discovered that mutualism stability necessitates that the recipient have a competitive advantage against the producer in obtaining the cross-fed nutrient, provided that the nutrient is generated intracellularly. We propose that the requirement for recipient-biased competition is a general rule for mutualistic coexistence based on the transfer of intracellularly generated, communally valuable resources.
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