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ASSMAR M, KEYPOUR M, ROHANI M, MOSTAFAVI E, DANESHVAR FARHUD D. The Resistance to Plague Infection among Meriones persicus from Endemic and Non-endemic Regions in Iran: The Role of Gut Microbiota. IRANIAN JOURNAL OF PUBLIC HEALTH 2018; 47:86-94. [PMID: 29318122 PMCID: PMC5756605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/21/2017] [Indexed: 12/02/2022]
Abstract
BACKGROUND The present study was conducted approximately 40 years ago, but its results have not been released. At the time of this study, the importance of the gut microbiota was not fully understood. METHODS Meriones persicus rodents, as one of the major reservoirs of Yersinia pestis bacterium in Iran, were compared in a disease endemic area (Akanlu, Hamadan, western Iran) and a non-endemic zone (Telo, Tehran, Iran) from 1977 to 1981. RESULTS This study was able to transmit the resistance to Y. pestis to other rodents creatively by using and transferring gut microbiota. CONCLUSION The study indicated for the first time that the gut microbiota could affect the sensitivity to plague in Meriones in Telo.
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Affiliation(s)
- Mehdi ASSMAR
- Dept. of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Marjan KEYPOUR
- Dept. of Epidemiology and Biostatistics, Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Hamadan, Iran
| | - Mehdi ROHANI
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Hamadan, Iran
- Dept. of Microbiology, Pasteur Institute of Iran, Tehran, Iran
| | - Ehsan MOSTAFAVI
- Dept. of Epidemiology and Biostatistics, Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Hamadan, Iran
| | - Dariush DANESHVAR FARHUD
- School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Dept. of Basic Sciences/Ethics, Iranian Academy of Medical Sciences, Tehran, Iran
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252
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Chen L, Brar MS, Leung FCC, Hsiao WLW. Triterpenoid herbal saponins enhance beneficial bacteria, decrease sulfate-reducing bacteria, modulate inflammatory intestinal microenvironment and exert cancer preventive effects in ApcMin/+ mice. Oncotarget 2017; 7:31226-42. [PMID: 27121311 PMCID: PMC5058752 DOI: 10.18632/oncotarget.8886] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/02/2016] [Indexed: 12/26/2022] Open
Abstract
Saponins derived from medicinal plants have raised considerable interest for their preventive roles in various diseases. Here, we investigated the impacts of triterpenoid saponins isolated from Gynostemma pentaphyllum (GpS) on gut microbiome, mucosal environment, and the preventive effect on tumor growth. Six-week old ApcMin/+ mice and their wild-type littermates were fed either with vehicle or GpS daily for the duration of 8 weeks. The fecal microbiome was analyzed by enterobacterial repetitive intergenic consensus (ERIC)-PCR and 16S rRNA gene pyrosequencing. Study showed that GpS treatment significantly reduced the number of intestinal polyps in a preventive mode. More importantly, GpS feeding strikingly reduced the sulfate-reducing bacteria lineage, which are known to produce hydrogen sulfide and contribute to damage the intestinal epithelium or even promote cancer progression. Meanwhile, GpS also boosted the beneficial microbes. In the gut barrier of the ApcMin/+ mice, GpS treatment increased Paneth and goblet cells, up-regulated E-cadherin and down-regulated N-cadherin. In addition, GpS decreased the pro-oncogenic β-catenin, p-Src and the p-STAT3. Furthermore, GpS might also improve the inflamed gut epithelium of the ApcMin/+ mice by upregulating the anti-inflammatory cytokine IL-4, while downregulating pro-inflammatory cytokines TNF-α, IL-1β and IL-18. Intriguingly, GpS markedly stimulated M2 and suppressed M1 macrophage markers, indicating that GpS altered mucosal cytokine profile in favor of the M1 to M2 macrophages switching, facilitating intestinal tissue repair. In conclusion, GpS might reverse the host's inflammatory phenotype by increasing beneficial bacteria, decreasing sulfate-reducing bacteria, and alleviating intestinal inflammatory gut environment, which might contribute to its cancer preventive effects.
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Affiliation(s)
- Lei Chen
- Center for Cancer & Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Manreetpal S Brar
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Frederick C C Leung
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - W L Wendy Hsiao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China
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253
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Affiliation(s)
- Tao Wang
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyu Zhao
- Department of Biostatistics, Yale University, New Haven, CT
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254
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Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota. mSystems 2017; 2:mSystems00107-17. [PMID: 29085914 PMCID: PMC5655592 DOI: 10.1128/msystems.00107-17] [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] [Received: 08/28/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023] Open
Abstract
Multiple host pathways were affected by its adaptation to the microbiota. We have found significant transcriptome-proteome discordance caused by the microbiota. This discovery leads to the definite conclusion that transcript-level analysis is not sufficient to predict protein levels and their influence on the function of many specific cellular pathways, so only analysis of combinations of the quantitative data determined at different levels will lead to a complete understanding of the complex relationships between the host and the microbiota. Therefore, our results demonstrate the importance of using an integrative approach to study host-microbiota interaction at the molecular level. The bodies of mammals are hosts to vast microbial communities composed of trillions of bacteria from thousands of species, whose effects on health and development have begun to be appreciated only recently. In this investigation, an integrated analysis combining proteomics and transcriptomics was used to quantitatively compare the terminal ilia from conventional and germfree mice. Female and male mice responded similarly to the microbiota, but C57BL/10A mice responded more strongly than BALB/c mice at both the transcriptome and proteome levels. The microbiota primarily caused upregulation of immunological pathways and downregulation of metabolic pathways in the conventional mice. Many of the affected pathways were altered only at either the transcriptome or proteome level. Of the pathways that were affected at both levels, most were affected concordantly. The discordant pathways were not principally involved in the immune system but instead were related to metabolism, oxidative phosphorylation, protein translation, transport, and turnover. To broaden the discovery of affected host pathways, a meta-analysis was performed using intestinal transcriptomics data from previously published studies of germfree versus conventional mice with diverse microbiota populations. Similar transcript-level responses to the microbiota were found, and many additional affected host pathways were discovered. IMPORTANCE Multiple host pathways were affected by its adaptation to the microbiota. We have found significant transcriptome-proteome discordance caused by the microbiota. This discovery leads to the definite conclusion that transcript-level analysis is not sufficient to predict protein levels and their influence on the function of many specific cellular pathways, so only analysis of combinations of the quantitative data determined at different levels will lead to a complete understanding of the complex relationships between the host and the microbiota. Therefore, our results demonstrate the importance of using an integrative approach to study host-microbiota interaction at the molecular level.
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255
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Abstract
The high affinity leukotriene B4 receptor, BLT1 mediates chemotaxis of diverse leukocyte subsets to the sites of infection or inflammation. Whereas the pathological functions of LTB4/BLT1 axis in allergy, autoimmunity and cardiovascular disorders are well established; its role in cancer is only beginning to emerge. In this review, we summarize recent findings on LTB4/BLT1 axis enabling distinct outcomes toward tumor progression. In a mouse lung tumor model promoted by silicosis-induced inflammation, genetic deletion of BLT1 attenuated neutrophilic inflammation and tumor promotion. In contrast, in a spontaneous model of intestinal tumorigenesis, absence of BLT1 led to defective mucosal host response, altered microbiota and bacteria dependent colon tumor progression. Furthermore, BLT1 mediated CD8+ T cell recruitment was shown to be essential for initiating anti-tumor immunity in number of xenograft models and is critical for effective PD1 based immunotherapy. BLT2 mediated chemotherapy resistance, tumor promotion and metastasis are also discussed. This new information points to a paradigm shift in our understanding of the LTB4 pathways in cancer.
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256
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Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017; 111:118-131. [DOI: 10.1016/j.micpath.2017.08.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/12/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
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257
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Wang L, Zhu Q, Lu A, Liu X, Zhang L, Xu C, Liu X, Li H, Yang T. Sodium butyrate suppresses angiotensin II-induced hypertension by inhibition of renal (pro)renin receptor and intrarenal renin-angiotensin system. J Hypertens 2017; 35:1899-1908. [PMID: 28509726 PMCID: PMC11157961 DOI: 10.1097/hjh.0000000000001378] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVES Butyrate, a short-chain fatty acid, is the end product of the fermentation of complex carbohydrates by the gut microbiota. Recently, sodium butyrate (NaBu) has been found to play a protective role in a number of chronic diseases. However, it is still unclear whether NaBu has a therapeutic potential in hypertension. The present study was aimed to investigate the role of NaBu in angiotensin II (Ang II)-induced hypertension and to further explore the underlying mechanism. METHODS Ang II was infused into uninephrectomized Sprague-Dawley rats with or without intramedullary infusion of NaBu for 14 days. Mean arterial blood pressure was recorded by the telemetry system. Renal tissues, serum samples, and 24-h urine samples were collected to examine renal injury and the regulation of the (pro)renin receptor (PRR) and renin. RESULTS Intramedullary infusion of NaBu in Sprague-Dawley rats lowered the Ang II-induced mean arterial pressure from 129 ± 6 mmHg to 108 ± 4 mmHg (P < 0.01). This corresponded with an improvement in Ang II-induced renal injury, including urinary albumin, glomerulosclerosis, and renal fibrosis, as well as the expression of inflammatory mediators tumor necrosis factor α, interleukin 6. The renal expression of PRR, angiotensinogen, angiotensin I-converting enzyme and the urinary excretion of soluble PRR, renin, and angiotensinogen were all increased by Ang II infusion but decreased by NaBu treatment. In cultured innermedullary collecting duct cells, NaBu treatment attenuated Ang II-induced expression of PRR and renin. CONCLUSION These results demonstrate that NaBu exerts an antihypertensive action, likely by suppressing the PRR-mediated intrarenal renin-angiotensin system.
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Affiliation(s)
- Lei Wang
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
| | - Qing Zhu
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
| | - Aihua Lu
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
| | - Xiaofen Liu
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
| | - Linlin Zhang
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
| | - Chuanming Xu
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
| | - Xiyang Liu
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
| | - Haobo Li
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
| | - Tianxin Yang
- Institute of Hypertension, Sun Yat-sen University School of Medicine, Guangzhou, China
- Veterans Affairs Medical Center, University of Utah, Salt Lake City, Utah, USA
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258
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Vishwakarma VK, Upadhyay PK, Gupta JK, Yadav HN. Pathophysiologic role of ischemia reperfusion injury: A review. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.jicc.2017.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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259
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Patel CJ, Kerr J, Thomas DC, Mukherjee B, Ritz B, Chatterjee N, Jankowska M, Madan J, Karagas MR, McAllister KA, Mechanic LE, Fallin MD, Ladd-Acosta C, Blair IA, Teitelbaum SL, Amos CI. Opportunities and Challenges for Environmental Exposure Assessment in Population-Based Studies. Cancer Epidemiol Biomarkers Prev 2017; 26:1370-1380. [PMID: 28710076 PMCID: PMC5581729 DOI: 10.1158/1055-9965.epi-17-0459] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/14/2017] [Accepted: 06/22/2017] [Indexed: 12/15/2022] Open
Abstract
A growing number and increasing diversity of factors are available for epidemiological studies. These measures provide new avenues for discovery and prevention, yet they also raise many challenges for adoption in epidemiological investigations. Here, we evaluate 1) designs to investigate diseases that consider heterogeneous and multidimensional indicators of exposure and behavior, 2) the implementation of numerous methods to capture indicators of exposure, and 3) the analytical methods required for discovery and validation. We find that case-control studies have provided insights into genetic susceptibility but are insufficient for characterizing complex effects of environmental factors on disease development. Prospective and two-phase designs are required but must balance extended data collection with follow-up of study participants. We discuss innovations in assessments including the microbiome; mass spectrometry and metabolomics; behavioral assessment; dietary, physical activity, and occupational exposure assessment; air pollution monitoring; and global positioning and individual sensors. We claim the the availability of extensive correlated data raises new challenges in disentangling specific exposures that influence cancer risk from among extensive and often correlated exposures. In conclusion, new high-dimensional exposure assessments offer many new opportunities for environmental assessment in cancer development. Cancer Epidemiol Biomarkers Prev; 26(9); 1370-80. ©2017 AACR.
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Affiliation(s)
- Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts.
| | - Jacqueline Kerr
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California
| | - Duncan C Thomas
- Department of Preventive Medicine, University of Southern California, Los Angeles, California
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California
| | - Nilanjan Chatterjee
- Department of Biostatistics and Department of Oncology, Johns Hopkins University, Baltimore, Maryland
| | - Marta Jankowska
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California
| | - Juliette Madan
- Division of Neonatology, Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire
| | - Kimberly A McAllister
- Susceptibility and Population Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Leah E Mechanic
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, Maryland
| | - M Daniele Fallin
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Ian A Blair
- Center of Excellence in Environmental Toxicology and Penn SRP Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan L Teitelbaum
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire.
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260
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Greenhalgh K, Meyer KM, Aagaard KM, Wilmes P. The human gut microbiome in health: establishment and resilience of microbiota over a lifetime. Environ Microbiol 2017; 18:2103-16. [PMID: 27059297 PMCID: PMC7387106 DOI: 10.1111/1462-2920.13318] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With technological advances in culture-independent molecular methods, we are uncovering a new facet of our natural history by accounting for the vast diversity of microbial life which colonizes the human body. The human microbiome contributes functional genes and metabolites which affect human physiology and are, therefore, considered an important factor for maintaining health. Much has been described in the past decade based primarily on 16S rRNA gene amplicon sequencing regarding the diversity, structure, stability and dynamics of human microbiota in their various body habitats, most notably within the gastrointestinal tract (GIT). Relatively high levels of variation have been described across different stages of life and geographical locations for the GIT microbiome. These observations may prove helpful for the future contextualization of patterns in other body habitats especially in relation to identifying generalizable trends over human lifetime. Given the large degree of complexity and variability, a key challenge will be how to define baseline healthy microbiomes and how to identify features which reflect deviations therefrom in the future. In this context, metagenomics and functional omics will likely play a central role as they will allow resolution of microbiome-conferred functionalities associated with health. Such information will be vital for formulating therapeutic interventions aimed at managing microbiota-mediated health particularly in the GIT over the course of a human lifetime.
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Affiliation(s)
- Kacy Greenhalgh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Kristen M Meyer
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Kjersti M Aagaard
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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261
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Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome. mSystems 2017; 2:mSystems00006-17. [PMID: 28845459 PMCID: PMC5566786 DOI: 10.1128/msystems.00006-17] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/25/2017] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome is known to have a complex yet vital relationship with host health. While both exercise and the gut microbiome have been shown to impact human health independently, the direct effects of moderate exercise on the intestinal microbiota remain unclear. In this study, we compared gut microbial diversity and changes in inflammatory markers associated with exercise over an 8-week period in mice that performed either voluntary exercise (VE) (n = 10) or moderate forced exercise (FE) (n = 11) and mice that did not perform any exercise (n = 21). VE mice, but not FE mice, had increased food intake and lean body mass compared to sedentary mice. The levels of inflammatory markers associated with exercise were similar for mice in all three groups. Traditional microbial profiles comparing operational taxonomic units (OTUs) in samples (P > 0.1) and multivariate analysis of beta diversity via Adonis testing (P > 0.1) did not identify significantly altered taxonomic profiles in the voluntary or forced exercise group compared to the sedentary controls. However, a random forests machine learning model, which takes into account the relationships between bacteria in a community, classified voluntary exercisers and nonexercisers with 97% accuracy at 8 weeks. The top bacteria used by the model allowed us to identify known taxa (Bacteroides, S24-7, and Lactobacillus) and novel taxa (Rikenellaceae and Lachnospiraceae) associated with exercise. Although aerobic exercise in mice did not result in significant changes of abundance in gut microbes or in host inflammatory response, more sophisticated computational methods could identify some microbial shifts. More study is needed on the effects of various exercise intensities and their impact on the gut microbiome. IMPORTANCE The bacteria that live in our gut have a complex yet vital relationship with our health. Environmental factors that influence the gut microbiome are of great interest, as recent research demonstrates that these microbes, mostly bacteria, are important for normal host physiology. Diseases such as obesity, diabetes, inflammatory bowel disease, and colon cancer have also been linked to shifts in the microbiome. Exercise is known to have beneficial effects on these diseases; however, much less is known about its direct impact on the gut microbiome. Our results illustrate that exercise has a moderate but measurable effect on gut microbial communities in mice. These methods can be used to provide important insight into other factors affecting the microbiome and our health.
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262
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Jala VR, Maturu P, Bodduluri SR, Krishnan E, Mathis S, Subbarao K, Wang M, Jenson AB, Proctor ML, Rouchka EC, Knight R, Haribabu B. Leukotriene B 4-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progression. Oncoimmunology 2017; 6:e1361593. [PMID: 29209564 DOI: 10.1080/2162402x.2017.1361593] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/24/2017] [Accepted: 07/26/2017] [Indexed: 02/07/2023] Open
Abstract
Inflammation and infection are key promoters of colon cancer but the molecular interplay between these events is largely unknown. Mice deficient in leukotriene B4 receptor1 (BLT1) are protected in inflammatory disease models of arthritis, asthma and atherosclerosis. In this study, we show that BLT1-/- mice when bred onto a spontaneous tumor (ApcMin/+) model displayed an increase in the rate of intestinal tumor development and mortality. A paradoxical increase in inflammation in the tumors from the BLT1-/-ApcMin/+ mice is coincidental with defective host response to infection. Germ-free BLT1-/-ApcMin/+ mice are free from colon tumors that reappeared upon fecal transplantation. Analysis of microbiota showed defective host response in BLT1-/- ApcMin/+ mice reshapes the gut microbiota to promote colon tumor development. The BLT1-/-MyD88-/- double deficient mice are susceptible to lethal neonatal infections. Broad-spectrum antibiotic treatment eliminated neonatal lethality in BLT1-/-MyD88-/- mice and the BLT1-/-MyD88-/-ApcMin+ mice are protected from colon tumor development. These results identify a novel interplay between the Toll-like receptor mediated microbial sensing mechanisms and BLT1-mediated host response in the control of colon tumor development.
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Affiliation(s)
- Venkatakrishna R Jala
- James Graham Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY, USA.,Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Paramahamsa Maturu
- James Graham Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY, USA.,Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Sobha R Bodduluri
- James Graham Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY, USA.,Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Elangovan Krishnan
- James Graham Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY, USA.,Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Steven Mathis
- James Graham Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY, USA.,Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Krishnaprasad Subbarao
- James Graham Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY, USA.,Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Min Wang
- James Graham Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY, USA.,Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Alfred B Jenson
- Department of Pathology, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Mary L Proctor
- Research Resources Center, University of Louisville Health Sciences Center, Louisville, KY, USA
| | - Eric C Rouchka
- Department of Computer Engineering & Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Bodduluri Haribabu
- James Graham Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY, USA.,Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY, USA
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263
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Rysz J, Gluba-Brzózka A, Franczyk B, Jabłonowski Z, Ciałkowska-Rysz A. Novel Biomarkers in the Diagnosis of Chronic Kidney Disease and the Prediction of Its Outcome. Int J Mol Sci 2017; 18:E1702. [PMID: 28777303 PMCID: PMC5578092 DOI: 10.3390/ijms18081702] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 02/07/2023] Open
Abstract
In its early stages, symptoms of chronic kidney disease (CKD) are usually not apparent. Significant reduction of the kidney function is the first obvious sign of disease. If diagnosed early (stages 1 to 3), the progression of CKD can be altered and complications reduced. In stages 4 and 5 extensive kidney damage is observed, which usually results in end-stage renal failure. Currently, the diagnosis of CKD is made usually on the levels of blood urea and serum creatinine (sCr), however, sCr has been shown to be lacking high predictive value. Due to the development of genomics, epigenetics, transcriptomics, proteomics, and metabolomics, the introduction of novel techniques will allow for the identification of novel biomarkers in renal diseases. This review presents some new possible biomarkers in the diagnosis of CKD and in the prediction of outcome, including asymmetric dimethylarginine (ADMA), symmetric dimethylarginine (SDMA), uromodulin, kidney injury molecule-1 (KIM-1), neutrophil gelatinase-associated lipocalin (NGAL), miRNA, ncRNA, and lincRNA biomarkers and proteomic and metabolomic biomarkers. Complicated pathomechanisms of CKD development and progression require not a single marker but their combination in order to mirror all types of alterations occurring in the course of this disease. It seems that in the not so distant future, conventional markers may be exchanged for new ones, however, confirmation of their efficacy, sensitivity and specificity as well as the reduction of analysis costs are required.
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Affiliation(s)
- Jacek Rysz
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, Zeromskiego 113, 90-549 Lodz, Poland.
| | - Anna Gluba-Brzózka
- Department of Nephrology, Hypertension and Family Medicine, WAM Teaching Hospital, Zeromskiego 113, 90-549 Lodz, Poland.
| | - Beata Franczyk
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, Zeromskiego 113, 90-549 Lodz, Poland.
| | - Zbigniew Jabłonowski
- I Department of Urology, Medical University of Lodz, Zeromskiego 113, 90-549 Lodz, Poland.
| | - Aleksandra Ciałkowska-Rysz
- Palliative Medicine Unit, Chair of Oncology, Medical University of Lodz, Zeromskiego 113, 90-549 Lodz, Poland.
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264
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Lee H, Ko G. New perspectives regarding the antiviral effect of vitamin A on norovirus using modulation of gut microbiota. Gut Microbes 2017; 8:616-620. [PMID: 28727498 PMCID: PMC5730389 DOI: 10.1080/19490976.2017.1353842] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Gut microbiota has been revealed to play an important role in various health conditions, and recent studies have suggested the modulation of gut microbiota as a therapeutic strategy. There is no effective treatment of norovirus infection, though vitamin A has been suggested to have an antiviral effect in an epidemiological study. We demonstrated that vitamin A significantly inhibited murine norovirus replication. Vitamin A supplementation significantly increased the abundance of Lactobacillus sp. during norovirus infection, which played a crucial role in antiviral efficacy, inhibiting murine norovirus. Therefore, we elaborated the antiviral effect of vitamin A via modulation of gut microbiota. Furthermore, we suggest a novel strategy, using potential probiotics, as having a protective and therapeutic effect on noroviral infection.
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Affiliation(s)
- Heetae Lee
- College of Pharmacy, Sahmyook University, Seoul, Korea
| | - GwangPyo Ko
- Center for Human and Environmental Microbiome, Institute of Health and Environment, School of Public Health, Seoul National University, Seoul, Korea,CONTACT GwangPyo Ko School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
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265
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Abstract
The human gut contains trillions of bacteria (microbiome) that play a major role in maintaining a healthy state for the host. Perturbation of this healthy gut microbiome might be an important environmental factor in the pathogenesis of inflammatory autoimmune diseases such as multiple sclerosis (MS). Others and we have recently reported that MS patients have gut microbial dysbiosis (altered microbiota) with the depletion of some and enrichment of other bacteria. However, the significance of gut bacteria that show lower or higher abundance in MS is unclear. The majority of gut bacteria are associated with certain metabolic pathways, which in turn help in the maintenance of immune homeostasis of the host. Here we discuss recent MS microbiome studies and the possible mechanisms through which gut microbiome might contribute to the pathogenesis of MS.
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Affiliation(s)
- Shailesh K. Shahi
- Department of Pathology, Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Samantha N. Freedman
- Department of Pathology, Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ashutosh K. Mangalam
- Department of Pathology, Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA,CONTACT Ashutosh K. Mangalam, Ph.D. Department of Pathology, University of Iowa Carver College of Medicine, 25 S. Grand Avenue, 1080A ML Iowa City, IA 52242
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266
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Stevens CH, Croft DP, Paull GC, Tyler CR. Stress and welfare in ornamental fishes: what can be learned from aquaculture? JOURNAL OF FISH BIOLOGY 2017; 91:409-428. [PMID: 28691234 DOI: 10.1111/jfb.13377] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 06/05/2017] [Indexed: 06/07/2023]
Abstract
The ornamental fish trade is estimated to handle up to 1·5 billion fishes. Transportation and handling of fishes imposes a range of stressors that can result in mortality at rates of up to 73%. These rates vary hugely, however, and can be as low as 2%, because they are generally estimated rather than based on experimental work. Given the numbers of ornamental fishes traded, any of the estimated mortality rates potentially incur significant financial losses and serious welfare issues. Industry bodies, such as the Ornamental Aquatic Trade Association (OATA), have established standards and codes of best practice for handling fishes, but little scientific research has been conducted to understand the links between stress, health and welfare in ornamental species. In aquaculture, many of the same stressors occur as those in the ornamental trade, including poor water quality, handling, transportation, confinement, poor social and physical environment and disease and in this sector directed research and some resulting interventions have resulted in improved welfare standards. This review considers the concept of welfare in fishes and evaluates reported rates of mortality in the ornamental trade. It assesses how the stress response can be quantified and used as a welfare indicator in fishes. It then analyses whether lessons from aquaculture can be usefully applied to the ornamental fish industry to improve welfare. Finally, this analysis is used to suggest how future research might be directed to help improve welfare in the ornamental trade.
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Affiliation(s)
- C H Stevens
- Centre for Research in Animal Behaviour, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, U.K
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, U.K
| | - D P Croft
- Centre for Research in Animal Behaviour, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, U.K
| | - G C Paull
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, U.K
| | - C R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, U.K
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267
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Dai D, Prussin AJ, Marr LC, Vikesland PJ, Edwards MA, Pruden A. Factors Shaping the Human Exposome in the Built Environment: Opportunities for Engineering Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7759-7774. [PMID: 28677960 DOI: 10.1021/acs.est.7b01097] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The "exposome" is a term describing the summation of one's lifetime exposure to microbes and chemicals. Such exposures are now recognized as major drivers of human health and disease. Because humans spend ∼90% of their time indoors, the built environment exposome merits particular attention. Herein we utilize an engineering perspective to advance understanding of the factors that shape the built environment exposome and its influence on human wellness and disease, while simultaneously informing development of a framework for intentionally controlling the exposome to protect public health. Historically, engineers have been focused on controlling chemical and physical contaminants and on eradicating microbes; however, there is a growing awareness of the role of "beneficial" microbes. Here we consider the potential to selectively control the materials and chemistry of the built environment to positively influence the microbial and chemical components of the indoor exposome. Finally, we discuss research gaps that must be addressed to enable intentional engineering design, including the need to define a "healthy" built environment exposome and how to control it.
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Affiliation(s)
- Dongjuan Dai
- Via Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University , Blacksburg Virginia 24061, United States
| | - Aaron J Prussin
- Via Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University , Blacksburg Virginia 24061, United States
| | - Linsey C Marr
- Via Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University , Blacksburg Virginia 24061, United States
| | - Peter J Vikesland
- Via Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University , Blacksburg Virginia 24061, United States
| | - Marc A Edwards
- Via Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University , Blacksburg Virginia 24061, United States
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University , Blacksburg Virginia 24061, United States
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268
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Borbón-García A, Reyes A, Vives-Flórez M, Caballero S. Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance. Front Microbiol 2017; 8:1316. [PMID: 28751883 PMCID: PMC5507997 DOI: 10.3389/fmicb.2017.01316] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/29/2017] [Indexed: 12/31/2022] Open
Abstract
The Andean bear is an endemic species of the tropical Andes who has an almost exclusively plant-based diet. Since herbivorous mammals do not carry enzymes for fiber degradation, the establishment of symbiosis with cellulolytic microorganisms in their gastrointestinal (GI) tract is necessary to help them fulfill their nutritional needs. Furthermore, as described for other mammals, a stable, diverse, and balanced gut microbial composition is an indicator of a healthy status of the host; under disturbances this balance can be lost, leading to potential diseases of the host. The goal of this study was to describe the gut microbiota of wild and captive Andean bears and determine how habitat status influences the composition and diversity of the gut symbiotic community. Fecal samples from wild (n = 28) and captive (n = 8) Andean bears were collected in "Reserva Pantano de Martos" and "Fundación Bioandina", Colombia. Composition and diversity analyses were performed using amplicons from the V4 region of the 16S rDNA gene sequenced using the Ion PGM platform. PICRUSt algorithm was applied to predict the gene content of the gut microbiome of wild and captive Andean bears. A total of 5,411 and 838 OTUs were identified for wild and captive bears, respectively. Captive bears contained a lower number of bacterial phyla (n = 7) compared to wild individuals (n = 9). Proteobacteria (59.03%) and Firmicutes (14.03%) were the phyla that contributed the most to differences between wild and captive bears (overall dissimilarity = 87.72%). At family level, Enterobacteriaceae drove the main differences between the two groups (13.7%). PICRUSt metagenomics predictions suggested a similar pattern of relative abundance of gene families associated with the metabolism of carbohydrates across samples in wild individuals, despite the taxonomic differences of their gut microbiota. Captivity alters the availability and diversity of food resources, which likely reduces microbiota richness and diversity compared to wild individuals. Further considerations should be taken into account for nutritional schemes improving ex-situ conservation and its potential as a surveillance tool of endangered populations of wild Andean bears.
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Affiliation(s)
- Andrea Borbón-García
- Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia.,Max Planck Tandem Group in Computational Biology, Universidad de los AndesBogotá, Colombia.,Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
| | - Alejandro Reyes
- Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia.,Max Planck Tandem Group in Computational Biology, Universidad de los AndesBogotá, Colombia.,Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint LouisMO, United States
| | - Martha Vives-Flórez
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
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269
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Hoffman JB, Hennig B. Protective influence of healthful nutrition on mechanisms of environmental pollutant toxicity and disease risks. Ann N Y Acad Sci 2017; 1398:99-107. [PMID: 28574588 DOI: 10.1111/nyas.13365] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 03/29/2017] [Accepted: 04/06/2017] [Indexed: 12/21/2022]
Abstract
Human exposures to environmental contaminants around the world contribute to the global burden of disease and thus require urgent attention. Exploring preventive measures against environmental exposure and disease risk is essential. While a sedentary lifestyle and/or poor dietary habits can exacerbate the deleterious effects resulting from exposure to toxic chemicals, much emerging evidence suggests that positive lifestyle changes (e.g., healthful nutrition) can modulate and/or reduce the toxicity of environmental pollutants. Our work has shown that diets high in anti-inflammatory bioactive food components (e.g., phytochemicals or polyphenols) are possible strategies for modulating and reducing the disease risks associated with exposure to toxic pollutants in the environment. Thus, consuming healthy diets rich in plant-derived bioactive nutrients may reduce the vulnerability to diseases linked to environmental toxic insults. This nutritional paradigm in environmental toxicology requires further study in order to improve our understanding of the relationships between nutrition and other lifestyle modifications and toxicant-induced diseases.
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Affiliation(s)
- Jessie B Hoffman
- Superfund Research Center, University of Kentucky, Lexington, Kentucky.,Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky
| | - Bernhard Hennig
- Superfund Research Center, University of Kentucky, Lexington, Kentucky.,Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky
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270
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Kim D, Zeng MY, Núñez G. The interplay between host immune cells and gut microbiota in chronic inflammatory diseases. Exp Mol Med 2017; 49:e339. [PMID: 28546562 PMCID: PMC5454439 DOI: 10.1038/emm.2017.24] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 01/02/2017] [Indexed: 02/08/2023] Open
Abstract
Many benefits provided by the gut microbiota to the host rely on its intricate interactions with host cells. Perturbations of the gut microbiota, termed gut dysbiosis, affect the interplay between the gut microbiota and host cells, resulting in dysregulation of inflammation that contributes to the pathogenesis of chronic inflammatory diseases, including inflammatory bowel disease, multiple sclerosis, allergic asthma and rheumatoid arthritis. In this review, we provide an overview of how gut bacteria modulates host metabolic and immune functions, summarize studies that examined the roles of gut dysbiosis in chronic inflammatory diseases, and finally discuss measures to correct gut dysbiosis as potential therapeutics for chronic inflammatory diseases.
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Affiliation(s)
- Donghyun Kim
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea, Seoul, Korea
| | - Melody Y Zeng
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gabriel Núñez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
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271
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Galla S, Chakraborty S, Mell B, Vijay-Kumar M, Joe B. Microbiotal-Host Interactions and Hypertension. Physiology (Bethesda) 2017; 32:224-233. [PMID: 28404738 DOI: 10.1152/physiol.00003.2017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/24/2017] [Accepted: 02/24/2017] [Indexed: 12/12/2022] Open
Abstract
Hypertension, or elevated blood pressure (BP), has been extensively researched over decades and clearly demonstrated to be caused due to a combination of host genetic and environmental factors. Although much research remains to be conducted to pin-point the precise genetic elements on the host genome that control BP, new lines of evidence are emerging to indicate that, besides the host genome, the genomes of all indigenous commensal micro-organisms, collectively referred to as the microbial metagenome or microbiome, are important, but largely understudied, determinants of BP. Unlike the rigid host genome, the microbiome or the "second genome" can be altered by diet or microbiotal transplantation in the host. This possibility is attractive from the perspective of exploiting the microbiotal composition for clinical management of inherited hypertension. Thus, focusing on the limited current literature supporting a role for the microbiome in BP regulation, this review highlights the need to further explore the role of the co-existence of host and the microbiota as an organized biological unit called the "holobiont" in the context of BP regulation.
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Affiliation(s)
- Sarah Galla
- Physiological Genomics Laboratory, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; and
| | - Saroj Chakraborty
- Physiological Genomics Laboratory, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; and
| | - Blair Mell
- Physiological Genomics Laboratory, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; and
| | - Matam Vijay-Kumar
- Department of Nutritional Sciences and Medicine, The Pennsylvania State University, University Park, Pennsylvania
| | - Bina Joe
- Physiological Genomics Laboratory, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; and
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272
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Hoffman JB, Petriello MC, Hennig B. Impact of nutrition on pollutant toxicity: an update with new insights into epigenetic regulation. REVIEWS ON ENVIRONMENTAL HEALTH 2017; 32:65-72. [PMID: 28076319 PMCID: PMC5489226 DOI: 10.1515/reveh-2016-0041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/09/2016] [Indexed: 05/03/2023]
Abstract
Exposure to environmental pollutants is a global health problem and is associated with the development of many chronic diseases, including cardiovascular disease, diabetes and metabolic syndrome. There is a growing body of evidence that nutrition can both positively and negatively modulate the toxic effects of pollutant exposure. Diets high in proinflammatory fats, such as linoleic acid, can exacerbate pollutant toxicity, whereas diets rich in bioactive and anti-inflammatory food components, including omega-3 fatty acids and polyphenols, can attenuate toxicant-associated inflammation. Previously, researchers have elucidated direct mechanisms of nutritional modulation, including alteration of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, but recently, increased focus has been given to the ways in which nutrition and pollutants affect epigenetics. Nutrition has been demonstrated to modulate epigenetic markers that have been linked either to increased disease risks or to protection against diseases. Overnutrition (i.e. obesity) and undernutrition (i.e. famine) have been observed to alter prenatal epigenetic tags that may increase the risk of offspring developing disease later in life. Conversely, bioactive food components, including curcumin, have been shown to alter epigenetic markers that suppress the activation of NF-κB, thus reducing inflammatory responses. Exposure to pollutants also alters epigenetic markers and may contribute to inflammation and disease. It has been demonstrated that pollutants, via epigenetic modulations, can increase the activation of NF-κB and upregulate microRNAs associated with inflammation, cardiac injury and oxidative damage. Importantly, recent evidence suggests that nutritional components, including epigallocatechin gallate (EGCG), can protect against pollutant-induced inflammation through epigenetic regulation of proinflammatory target genes of NF-κB. Further research is needed to better understand how nutrition can modulate pollutant toxicity through epigenetic regulation. Therefore, the objective of this review is to elucidate the current evidence linking epigenetic changes to pollutant-induced diseases and how this regulation may be modulated by nutrients allowing for the development of future personalized lifestyle interventions.
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Affiliation(s)
- Jessie B Hoffman
- Superfund Research Center, University of Kentucky, Lexington, KY 40536
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY 40536
| | - Michael C Petriello
- Superfund Research Center, University of Kentucky, Lexington, KY 40536
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40536
| | - Bernhard Hennig
- Superfund Research Center, University of Kentucky, Lexington, KY 40536
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40536
- Correspondence should be directed to: Bernhard Hennig, 900 S. Limestone Street, Superfund Research Center, University of Kentucky, Lexington, KY 40536, USA. Tel.: +1 859-218-1343; fax: +1 859-257-1811;
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273
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Investigation of the microbiota of the reproductive tract in women undergoing a total hysterectomy and bilateral salpingo-oopherectomy. Fertil Steril 2017; 107:813-820.e1. [DOI: 10.1016/j.fertnstert.2016.11.028] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/29/2016] [Accepted: 11/29/2016] [Indexed: 11/24/2022]
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274
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The Oral β-Lactamase SYN-004 (Ribaxamase) Degrades Ceftriaxone Excreted into the Intestine in Phase 2a Clinical Studies. Antimicrob Agents Chemother 2017; 61:AAC.02197-16. [PMID: 28052855 PMCID: PMC5328510 DOI: 10.1128/aac.02197-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/20/2016] [Indexed: 12/28/2022] Open
Abstract
SYN-004 (ribaxamase) is a β-lactamase designed to be orally administered concurrently with intravenous β-lactam antibiotics, including most penicillins and cephalosporins. Ribaxamase's anticipated mechanism of action is to degrade excess β-lactam antibiotic that is excreted into the small intestine. This enzymatic inactivation of excreted antibiotic is expected to protect the gut microbiome from disruption and thus prevent undesirable side effects, including secondary infections such as Clostridium difficile infections, as well as other antibiotic-associated diarrheas. In phase 1 clinical studies, ribaxamase was well tolerated compared to a placebo group and displayed negligible systemic absorption. The two phase 2a clinical studies described here were performed to confirm the mechanism of action of ribaxamase, degradation of β-lactam antibiotics in the human intestine, and were therefore conducted in subjects with functioning ileostomies to allow serial sampling of their intestinal chyme. Ribaxamase fully degraded ceftriaxone to below the level of quantitation in the intestines of all subjects in both studies. Coadministration of oral ribaxamase with intravenous ceftriaxone was also well tolerated, and the plasma pharmacokinetics of ceftriaxone were unchanged by ribaxamase administration. Since ribaxamase is formulated as a pH-dependent, delayed-release formulation, the activity of ribaxamase in the presence of the proton pump inhibitor esomeprazole was examined in the second study; coadministration of these drugs did not adversely affect ribaxamase's ability to degrade ceftriaxone excreted into the intestine. These studies have confirmed the in vivo mechanism of action of ribaxamase, degradation of β-lactam antibiotics in the human intestine (registered at ClinicalTrials.gov under NCT02419001 and NCT02473640).
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275
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Gupta RS, Nanda A, Khadka B. Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales. PLoS One 2017; 12:e0172176. [PMID: 28212383 PMCID: PMC5315409 DOI: 10.1371/journal.pone.0172176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/12/2017] [Indexed: 12/23/2022] Open
Abstract
Members from the order Bifidobacteriales, which include many species exhibiting health promoting effects, differ from all other organisms in using a unique pathway for carbohydrate metabolism, known as the "bifid shunt", which utilizes the enzyme phosphoketolase (PK) to carry out the phosphorolysis of both fructose-6-phosphate (F6P) and xylulose-5-phosphate (X5P). In contrast to bifidobacteria, the PKs found in other organisms (referred to XPK) are able to metabolize primarily X5P and show very little activity towards F6P. Presently, very little is known about the molecular or biochemical basis of the differences in the two forms of PKs. Comparative analyses of PK sequences from different organisms reported here have identified multiple high-specific sequence features in the forms of conserved signature inserts and deletions (CSIs) in the PK sequences that clearly distinguish the X5P/F6P phosphoketolases (XFPK) of bifidobacteria from the XPK homologs found in most other organisms. Interestingly, most of the molecular signatures that are specific for the XFPK from bifidobacteria are also shared by the PK homologs from the Coriobacteriales order of Actinobacteria. Similarly to the Bifidobacteriales, the order Coriobacteriales is also made up of commensal organisms, that are saccharolytic and able to metabolize wide variety of carbohydrates, producing lactate and other metabolites. Phylogenetic studies provide evidence that the XFPK from bifidobacteria are specifically related to those found in the Coriobacteriales and suggest that the gene for PK (XFPK) was horizontally transferred between these two groups. A number of the identified CSIs in the XFPK sequence, which serve to distinguish the XFPK homologs from XPK homologs, are located at the subunit interface in the structure of the XFPK dimer protein. The results of protein modelling and subunit docking studies indicate that these CSIs are involved in the formation/stabilization of the protein dimer. The significance of these observations regarding the differences in the activities of the XFPK and XPK homologs are discussed. Additionally, this work also discusses the significance of the XFPK-like homologs, similar to those found in bifidobacteria, in the order Coriobacteriales.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Anish Nanda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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276
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Nakayama J, Yamamoto A, Palermo-Conde LA, Higashi K, Sonomoto K, Tan J, Lee YK. Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island. Front Microbiol 2017; 8:197. [PMID: 28261164 PMCID: PMC5306386 DOI: 10.3389/fmicb.2017.00197] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 01/26/2017] [Indexed: 12/25/2022] Open
Abstract
Urbanization has changed life styles of the children in some towns and cities on Leyte island in the Philippines. To evaluate the impact of modernization in dietary habits on gut microbiota, we compared fecal microbiota of 7 to 9-year-old children from rural Baybay city (n = 24) and urban Ormoc city (n = 19), and assessed the correlation between bacterial composition and diet. A dietary survey indicated that Ormoc children consumed fast food frequently and more meat and confectionary than Baybay children, suggesting modernization/westernization of dietary habits. Fat intake accounted for 27.2% of the total energy intake in Ormoc children; this was remarkably higher than in their Baybay counterparts (18.1%) and close to the upper limit (30%) recommended by the World Health Organization. Their fecal microbiota were analyzed by high-throughput 16S rRNA gene sequencing in conjunction with a dataset from five other Asian countries. Their microbiota were classified into two enterotype-like clusters with the other countries' children, each defined by high abundance of either Prevotellaceae (P-type) or Bacteroidaceae (BB-type), respectively. Baybay and Ormoc children mainly harbored P-type and BB-type, respectively. Redundancy analysis showed that P-type favored carbohydrates whereas BB-type preferred fats. Fat intake correlated positively with the Firmicutes-to-Bacteroidetes (F/B) ratio and negatively with the relative abundance of the family Prevotellaceae/genus Prevotella. A species-level analysis suggested that dietary fat positively correlated with an Oscillibacter species as well as a series of Bacteroides/Parabacteroides species, whereas dietary carbohydrate positively correlated with Dialister succinatiphilus known as succinate-utilizing bacteria and some succinate-producing species of family Prevotellaceae, Veillonellaceae, and Erysipelotrichaceae. We also found that a Succinivibrio species was overrepresented in the P-type community, suggesting the syntroph via hydrogen and succinate. Predicted metagenomics suggests that BB-type microbiota is well nourished and metabolically more active with simple sugars, amino acids, and lipids, while P-type community is more involved in digestion of complex carbohydrates. Overweight and obese children living in Ormoc, who consumed a high-fat diet, harbored microbiota with higher F/B ratio and low abundance of Prevotella. The altered gut microbiota may be a sign of a modern diet-associated obesity among children in developing areas.
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Affiliation(s)
- Jiro Nakayama
- Laboratory of Microbial Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Azusa Yamamoto
- Laboratory of Microbial Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | | | - Kanako Higashi
- Laboratory of Microbial Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Julie Tan
- PhilRootcrops, Visayas State University Baybay, Philippines
| | - Yuan-Kun Lee
- Department of Microbiology, National University of Singapore Singapore, Singapore
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277
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Manor O, Borenstein E. Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome. Cell Host Microbe 2017; 21:254-267. [PMID: 28111203 PMCID: PMC5316541 DOI: 10.1016/j.chom.2016.12.014] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 10/24/2016] [Accepted: 12/28/2016] [Indexed: 01/06/2023]
Abstract
Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity.
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Affiliation(s)
- Ohad Manor
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Santa Fe Institute, Santa Fe, NM 87501, USA.
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278
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Cho CE, Caudill MA. Trimethylamine-N-Oxide: Friend, Foe, or Simply Caught in the Cross-Fire? Trends Endocrinol Metab 2017; 28:121-130. [PMID: 27825547 DOI: 10.1016/j.tem.2016.10.005] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/05/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022]
Abstract
Trimethylamine-N-oxide (TMAO), a gut-derived metabolite, has recently emerged as a candidate risk factor for cardiovascular disease and other adverse health outcomes. However, the relation between TMAO and chronic disease can be confounded by several factors, including kidney function, the gut microbiome, and flavin-containing monooxygenase 3 (FMO3) genotype. Thus, whether TMAO is a causative agent in human disease development and progression, or simply a marker of an underlying pathology, remains inconclusive. Importantly, dietary sources of TMAO have beneficial health effects and provide nutrients that have critical roles in many biological functions. Pre-emptive dietary strategies to restrict TMAO-generating nutrients as a means to improve human health warrant careful consideration and may not be justified at this time.
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Affiliation(s)
- Clara E Cho
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT 84322, USA
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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279
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Drosophila Genotype Influences Commensal Bacterial Levels. PLoS One 2017; 12:e0170332. [PMID: 28095502 PMCID: PMC5240971 DOI: 10.1371/journal.pone.0170332] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/03/2017] [Indexed: 02/04/2023] Open
Abstract
Host genotype can influence the composition of the commensal bacterial community in some organisms. Composition, however, is only one parameter describing a microbial community. Here, we test whether a second parameter—abundance of bacteria—is a heritable trait by quantifying the presence of four commensal bacterial strains within 36 gnotobiotic inbred lines of Drosophila melanogaster. We find that D. melanogaster genotype exerts a significant effect on microbial levels within the fly. When introduced as monocultures into axenic flies, three of the four bacterial strains were reliably detected within the fly. The amounts of these different strains are strongly correlated, suggesting that the host regulates commensal bacteria through general, not bacteria-specific, means. While the correlation does not appear to be driven by simple variation in overall gut dimensions, a genetic association study suggests that variation in commensal bacterial load may largely be attributed to physical aspects of host cell growth and development.
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280
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Prentice AM, Mendoza YA, Pereira D, Cerami C, Wegmuller R, Constable A, Spieldenner J. Dietary strategies for improving iron status: balancing safety and efficacy. Nutr Rev 2017; 75:49-60. [PMID: 27974599 PMCID: PMC5155616 DOI: 10.1093/nutrit/nuw055] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In light of evidence that high-dose iron supplements lead to a range of adverse events in low-income settings, the safety and efficacy of lower doses of iron provided through biological or industrial fortification of foodstuffs is reviewed. First, strategies for point-of-manufacture chemical fortification are compared with biofortification achieved through plant breeding. Recent insights into the mechanisms of human iron absorption and regulation, the mechanisms by which iron can promote malaria and bacterial infections, and the role of iron in modifying the gut microbiota are summarized. There is strong evidence that supplemental iron given in nonphysiological amounts can increase the risk of bacterial and protozoal infections (especially malaria), but the use of lower quantities of iron provided within a food matrix, ie, fortified food, should be safer in most cases and represents a more logical strategy for a sustained reduction of the risk of deficiency by providing the best balance of risk and benefits. Further research into iron compounds that would minimize the availability of unabsorbed iron to the gut microbiota is warranted.
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Affiliation(s)
- Andrew M Prentice
- A.M. Prentice, D. Pereira, C. Cerami, and R. Wegmuller are with the Medical Research Council (MRC) Unit The Gambia, Fajara, Banjul, The Gambia. A.M. Prentice and R. Wegmuller are with the MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, United Kingdom. Y.A. Mendoza, A. Constable, and J. Spieldenner are with the Nestlé Research Centre, Lausanne, Switzerland. D. Pereira is with the Department of Pathology, University of Cambridge, Cambridge, United Kingdom. C. Cerami is with the Division of Infectious Diseases, Institute for Global Health & Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
| | - Yery A Mendoza
- A.M. Prentice, D. Pereira, C. Cerami, and R. Wegmuller are with the Medical Research Council (MRC) Unit The Gambia, Fajara, Banjul, The Gambia. A.M. Prentice and R. Wegmuller are with the MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, United Kingdom. Y.A. Mendoza, A. Constable, and J. Spieldenner are with the Nestlé Research Centre, Lausanne, Switzerland. D. Pereira is with the Department of Pathology, University of Cambridge, Cambridge, United Kingdom. C. Cerami is with the Division of Infectious Diseases, Institute for Global Health & Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Dora Pereira
- A.M. Prentice, D. Pereira, C. Cerami, and R. Wegmuller are with the Medical Research Council (MRC) Unit The Gambia, Fajara, Banjul, The Gambia. A.M. Prentice and R. Wegmuller are with the MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, United Kingdom. Y.A. Mendoza, A. Constable, and J. Spieldenner are with the Nestlé Research Centre, Lausanne, Switzerland. D. Pereira is with the Department of Pathology, University of Cambridge, Cambridge, United Kingdom. C. Cerami is with the Division of Infectious Diseases, Institute for Global Health & Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Carla Cerami
- A.M. Prentice, D. Pereira, C. Cerami, and R. Wegmuller are with the Medical Research Council (MRC) Unit The Gambia, Fajara, Banjul, The Gambia. A.M. Prentice and R. Wegmuller are with the MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, United Kingdom. Y.A. Mendoza, A. Constable, and J. Spieldenner are with the Nestlé Research Centre, Lausanne, Switzerland. D. Pereira is with the Department of Pathology, University of Cambridge, Cambridge, United Kingdom. C. Cerami is with the Division of Infectious Diseases, Institute for Global Health & Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Rita Wegmuller
- A.M. Prentice, D. Pereira, C. Cerami, and R. Wegmuller are with the Medical Research Council (MRC) Unit The Gambia, Fajara, Banjul, The Gambia. A.M. Prentice and R. Wegmuller are with the MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, United Kingdom. Y.A. Mendoza, A. Constable, and J. Spieldenner are with the Nestlé Research Centre, Lausanne, Switzerland. D. Pereira is with the Department of Pathology, University of Cambridge, Cambridge, United Kingdom. C. Cerami is with the Division of Infectious Diseases, Institute for Global Health & Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Anne Constable
- A.M. Prentice, D. Pereira, C. Cerami, and R. Wegmuller are with the Medical Research Council (MRC) Unit The Gambia, Fajara, Banjul, The Gambia. A.M. Prentice and R. Wegmuller are with the MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, United Kingdom. Y.A. Mendoza, A. Constable, and J. Spieldenner are with the Nestlé Research Centre, Lausanne, Switzerland. D. Pereira is with the Department of Pathology, University of Cambridge, Cambridge, United Kingdom. C. Cerami is with the Division of Infectious Diseases, Institute for Global Health & Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jörg Spieldenner
- A.M. Prentice, D. Pereira, C. Cerami, and R. Wegmuller are with the Medical Research Council (MRC) Unit The Gambia, Fajara, Banjul, The Gambia. A.M. Prentice and R. Wegmuller are with the MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, United Kingdom. Y.A. Mendoza, A. Constable, and J. Spieldenner are with the Nestlé Research Centre, Lausanne, Switzerland. D. Pereira is with the Department of Pathology, University of Cambridge, Cambridge, United Kingdom. C. Cerami is with the Division of Infectious Diseases, Institute for Global Health & Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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Taylor M, Wood HM, Halloran SP, Quirke P. Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing. J Clin Pathol 2016; 70:600-606. [DOI: 10.1136/jclinpath-2016-204165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 01/19/2023]
Abstract
AimsWith a growing interest in the influence the gut microbiome has on the development of colorectal cancer (CRC), we investigated the feasibility and stability of isolating and typing microbial DNA from guaiac faecal occult blood test (gFOBt) cards. This has the future potential to screen the microbial populations present in confirmed colorectal neoplasia cases with aims to predict the presence and development of CRC.MethodsFresh stool samples from three healthy volunteers were applied to gFOBt cards. DNA was extracted from both the cards and fresh stool samples. A series of additional cards were prepared from one volunteer, and extracted at time points between 2 weeks and 3 years. The V4 region of the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq at 2×250 bp read lengths. Data were analysed using QIIME software.ResultsSamples were grouped both by volunteer and by type (fresh or gFOBt), and compared a variety of ways: visual inspection of taxa, α and β diversity, intraclass correlation. In all comparisons, samples grouped by volunteer, and not by sample type. The different time points showed no appreciable differences with increased storage time.ConclusionsThis study has demonstrated that there is good concordance between microbial DNA isolated from fresh stool sample, and from the matched gFOBt card. Samples stored for up to 3 years showed no detrimental effect on measureable microbial DNA. This study has important future implications for investigating microbial influence on CRC development and other pathologies.
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282
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Vryzas Z. The Plant as Metaorganism and Research on Next-Generation Systemic Pesticides - Prospects and Challenges. Front Microbiol 2016; 7:1968. [PMID: 28018306 PMCID: PMC5161002 DOI: 10.3389/fmicb.2016.01968] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/24/2016] [Indexed: 12/14/2022] Open
Abstract
Systemic pesticides (SPs) are usually recommended for soil treatments and as seed coating agents and are taken up from the soil by involving various plant-mediated processes, physiological, and morphological attributes of the root systems. Microscopic insights and next-generation sequencing combined with bioinformatics allow us now to identify new functions and interactions of plant-associated bacteria and perceive plants as meta-organisms. Host symbiotic, rhizo-epiphytic, endophytic microorganisms and their functions on plants have not been studied yet in accordance with uptake, tanslocation and action of pesticides. Root tips exudates mediated by rhizobacteria could modify the uptake of specific pesticides while bacterial ligands and enzymes can affect metabolism and fate of pesticide within plant. Over expression of specific proteins in cell membrane can also modify pesticide influx in roots. Moreover, proteins and other membrane compartments are usually involved in pesticide modes of action and resistance development. In this article it is discussed what is known of the physiological attributes including apoplastic, symplastic, and trans-membrane transport of SPs in accordance with the intercommunication dictated by plant-microbe, cell to cell and intracellular signaling. Prospects and challenges for uptake, translocation, storage, exudation, metabolism, and action of SPs are given through the prism of new insights of plant microbiome. Interactions of soil applied pesticides with physiological processes, plant root exudates and plant microbiome are summarized to scrutinize challenges for the next-generation pesticides.
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Affiliation(s)
- Zisis Vryzas
- Laboratory of Agricultural Pharmacology and Ecotoxicology, Department of Agricultural Development, Democritus University of ThraceOrestias, Greece
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283
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Abstract
Ischemic disorders, such as myocardial infarction, stroke, and peripheral vascular disease, are the most common causes of debilitating disease and death in westernized cultures. The extent of tissue injury relates directly to the extent of blood flow reduction and to the length of the ischemic period, which influence the levels to which cellular ATP and intracellular pH are reduced. By impairing ATPase-dependent ion transport, ischemia causes intracellular and mitochondrial calcium levels to increase (calcium overload). Cell volume regulatory mechanisms are also disrupted by the lack of ATP, which can induce lysis of organelle and plasma membranes. Reperfusion, although required to salvage oxygen-starved tissues, produces paradoxical tissue responses that fuel the production of reactive oxygen species (oxygen paradox), sequestration of proinflammatory immunocytes in ischemic tissues, endoplasmic reticulum stress, and development of postischemic capillary no-reflow, which amplify tissue injury. These pathologic events culminate in opening of mitochondrial permeability transition pores as a common end-effector of ischemia/reperfusion (I/R)-induced cell lysis and death. Emerging concepts include the influence of the intestinal microbiome, fetal programming, epigenetic changes, and microparticles in the pathogenesis of I/R. The overall goal of this review is to describe these and other mechanisms that contribute to I/R injury. Because so many different deleterious events participate in I/R, it is clear that therapeutic approaches will be effective only when multiple pathologic processes are targeted. In addition, the translational significance of I/R research will be enhanced by much wider use of animal models that incorporate the complicating effects of risk factors for cardiovascular disease. © 2017 American Physiological Society. Compr Physiol 7:113-170, 2017.
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Affiliation(s)
- Theodore Kalogeris
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Christopher P. Baines
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, Missouri, USA
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
- Department of Biomedical Sciences, University of Missouri College of Veterinary Medicine, Columbia, Missouri, USA
| | - Maike Krenz
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, Missouri, USA
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
| | - Ronald J. Korthuis
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, Missouri, USA
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
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284
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Oki K, Toyama M, Banno T, Chonan O, Benno Y, Watanabe K. Comprehensive analysis of the fecal microbiota of healthy Japanese adults reveals a new bacterial lineage associated with a phenotype characterized by a high frequency of bowel movements and a lean body type. BMC Microbiol 2016; 16:284. [PMID: 27894251 PMCID: PMC5127096 DOI: 10.1186/s12866-016-0898-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/15/2016] [Indexed: 12/18/2022] Open
Abstract
Background In Japan, a variety of traditional dietary habits and daily routines have developed in many regions. The effects of these behaviors, and the regional differences in the composition of the gut microbiota, are yet to be sufficiently studied. To characterize the Japanese gut microbiota and identify the factors shaping its composition, we conducted 16S metagenomics analysis of fecal samples collected from healthy Japanese adults residing in various regions of Japan. Each participant also completed a 94-question lifestyle questionnaire. Results We collected fecal samples from 516 healthy Japanese adults (325 females, 191 males; age, 21–88). Heatmap and biplot analyses based on the bacterial family composition of the fecal microbiota showed that subjects’ region of residence or gender were not strongly correlated with the general composition of the fecal microbiota. Although clustering analysis for the whole cohort did not reveal any distinct clusters, two enterotype-like clusters were observed in the male, but not the female, subjects. In the whole subject population, the scores for bowel movement frequency were significantly correlated with the abundances of Christensenellaceae, Mogibacteriaceae, and Rikenellaceae in the fecal microbiota (P < 0.001). These three bacterial families were also significantly more abundant (P < 0.05 or 0.01) in lean subjects (body mass index (BMI) < 25) than in obese subjects (BMI > 30), which is consistent with previously published results. However, a previously reported correlation between BMI and bowel movement frequency was not observed. In addition, the abundances of these three families were positively correlated with each other and comprised a correlative network with 14 other bacterial families. Conclusions The present study showed that the composition of the fecal microbiota of healthy Japanese adults at the national level was not strongly correlated with subjects’ area of residence or gender. In addition, enterotype partitioning was ambiguous in this cohort of healthy Japanese adults. Finally, the results implied that the abundances of Christensenellaceae, Mogibacteriaceae, and Rikenellaceae, along with several other bacterial components that together comprised a correlative network, contributed to a phenotype characterized by a high frequency of bowel movements and a lean body type. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0898-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaihei Oki
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo, 186-8650, Japan.
| | - Mutsumi Toyama
- Benno Laboratory, RIKEN Innovation Center, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Taihei Banno
- Benno Laboratory, RIKEN Innovation Center, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Osamu Chonan
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo, 186-8650, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Koichi Watanabe
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo, 186-8650, Japan
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285
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Khan F, Oloketuyi SF. A future perspective on neurodegenerative diseases: nasopharyngeal and gut microbiota. J Appl Microbiol 2016; 122:306-320. [PMID: 27740729 DOI: 10.1111/jam.13327] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/23/2016] [Accepted: 10/08/2016] [Indexed: 12/11/2022]
Abstract
Neurodegenerative diseases are considered a serious life-threatening issue regardless of age. Resulting nerve damage progressively affects important activities, such as movement, coordination, balance, breathing, speech and the functioning of vital organs. Reports on the subject have concluded that neurodegenerative disease can be caused by mutations of susceptible genes, alcohol consumption, toxins, chemicals and other unknown environmental factors. Although several diagnostic techniques can be used to determine aetiologies, the process is difficult and often fails. Research shows that nasopharyngeal and gut microbiota play important roles in brain to spinal cord coordination. However, no conclusive epidemiologic evidence is available on the roles played by respiratory and gut microbiota in the development of neurodegenerative diseases. Thus, understanding the connection between respiratory and gut microbiota and the nervous system could provide information on causal links. The present review describes future perspectives on the role played by nasopharyngeal and gut microbiota in the development of neurodegenerative diseases.
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Affiliation(s)
- F Khan
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, UP, India
| | - S F Oloketuyi
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, UP, India
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286
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Zhou X, Nardini C. A method for automated pathogenic content estimation with application to rheumatoid arthritis. BMC SYSTEMS BIOLOGY 2016; 10:107. [PMID: 27846901 PMCID: PMC5111251 DOI: 10.1186/s12918-016-0344-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/13/2016] [Indexed: 11/29/2022]
Abstract
Background Sequencing technologies applied to mammals’ microbiomes have revolutionized our understanding of health and disease. Hence, to assess diseases’ progression as well as therapies longterm effects, the impact of maladies and drugs on the gut-intestinal (GI) microbiome has to be evaluated. Typical metagenomic analyses are run to associate to a condition (disease, therapy, diet) a pool of bacteria, whose eubiotic/dysbiotic potential is assessed either by α-diversity, a measure of the varieties populating the microbiome, or by Firmicutes to Bacteroides ratio, associated to systemic inflammation, and finally by manual and direct inspection of bacteria’s biological functions, when known. These approaches lead to results sometimes difficult to interpret in terms of the evolution towards a specific microbial composition, harmed by large areas of unknown. Results We propose to additionally evaluate a microbiome based on its global composition, by automatic annotation of pathogenic genera and statistical assessment of the net varied frequency of harmless versus harmful organisms. This application is intuitive, quantitative and computationally efficient and designed to cope with the currently incomplete species’ functional knowledge. Our results, applied to human GI-microbiome data exemplify how this layer of information provides additional insights into treatments’ impact on the GI microbiome, allowing to characterize a more physiologic effects of Prednisone versus Methotrexate, two treatments for rheumatoid arthritis (RA) a complex autoimmune systemic disease. Conclusions Our quantitative analysis integrates with previous approaches offering an additional systemic level of interpretation here applied, for its potential to translate into clinically relevant information, to the therapies for RA. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0344-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoyuan Zhou
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Christine Nardini
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, People's Republic of China. .,Personalgenomics, Verona, Italy.
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287
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Abstract
CVD accounted for 27 % of all deaths in the UK in 2014, and was responsible for 1·7 million hospital admissions in 2013/2014. This condition becomes increasingly prevalent with age, affecting 34·1 and 29·8 % of males and females over 75 years of age respectively in 2011. The dysregulation of cholesterol metabolism with age, often observed as a rise in LDL-cholesterol, has been associated with the pathogenesis of CVD. To compound this problem, it is estimated by 2050, 22 % of the world's population will be over 60 years of age, in culmination with a growing resistance and intolerance to pre-existing cholesterol regulating drugs such as statins. Therefore, it is apparent research into additional therapies for hypercholesterolaemia and CVD prevention is a growing necessity. However, it is also imperative to recognise this complex biological system cannot be studied using a reductionist approach; rather its biological uniqueness necessitates a more integrated methodology, such as that offered by systems biology. In this review, we firstly discuss cholesterol metabolism and how it is affected by diet and the ageing process. Next, we describe therapeutic strategies for hypercholesterolaemia, and finally how the systems biology paradigm can be utilised to investigate how ageing interacts with complex systems such as cholesterol metabolism. We conclude by emphasising the need for nutritionists to work in parallel with the systems biology community, to develop novel approaches to studying cholesterol metabolism and its interaction with ageing.
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288
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Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies. FEMS Microbiol Ecol 2016; 92:fiw182. [PMID: 27559027 DOI: 10.1093/femsec/fiw182] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2016] [Indexed: 11/15/2022] Open
Abstract
Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Gino Fornaciari
- Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa 56126, Italy Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy
| | - Stefania Luciani
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Scot E Dowd
- Molecular Research LP (MR DNA), Shallowater, Texas 79363, USA
| | - Gary A Toranzos
- Department of Biology, University of Puerto Rico, Julio Garcia Diaz Building, San Juan 00931, Puerto Rico
| | - Isolina Marota
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Raul J Cano
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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289
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016. [PMID: 27507964 DOI: 10.3389/fmicb.2016.01144]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy; Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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290
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016. [PMID: 27507964 DOI: 10.3389/fmicb.2016.01144] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy; Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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291
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016; 7:1144. [PMID: 27507964 PMCID: PMC4960240 DOI: 10.3389/fmicb.2016.01144] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/08/2016] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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292
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Kuno T, Hirayama-Kurogi M, Ito S, Ohtsuki S. Effect of Intestinal Flora on Protein Expression of Drug-Metabolizing Enzymes and Transporters in the Liver and Kidney of Germ-Free and Antibiotics-Treated Mice. Mol Pharm 2016; 13:2691-701. [DOI: 10.1021/acs.molpharmaceut.6b00259] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Takuya Kuno
- Department
of Pharmaceutical Microbiology, Graduate School of Pharmaceutical
Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department
of Drug Metabolism and Pharmacokinetics, Drug Safety Research Center,
Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., 463-10 Kagasuno, Kawauchi-cho, Tokushima, Tokushima 771-0192, Japan
| | - Mio Hirayama-Kurogi
- Department
of Pharmaceutical Microbiology, Graduate School of Pharmaceutical
Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department
of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- AMED-CREST, Japan
Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda, Tokyo 100-0004, Japan
| | - Shingo Ito
- Department
of Pharmaceutical Microbiology, Graduate School of Pharmaceutical
Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department
of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- AMED-CREST, Japan
Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda, Tokyo 100-0004, Japan
| | - Sumio Ohtsuki
- Department
of Pharmaceutical Microbiology, Graduate School of Pharmaceutical
Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department
of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- AMED-CREST, Japan
Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda, Tokyo 100-0004, Japan
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293
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Adam E, Groenenboom AE, Kurm V, Rajewska M, Schmidt R, Tyc O, Weidner S, Berg G, de Boer W, Falcão Salles J. Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut. Front Microbiol 2016; 7:1079. [PMID: 27468279 PMCID: PMC4942455 DOI: 10.3389/fmicb.2016.01079] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/27/2016] [Indexed: 12/22/2022] Open
Affiliation(s)
- Eveline Adam
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | | | - Viola Kurm
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
| | - Magdalena Rajewska
- Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of GdańskGdańsk, Poland
| | - Ruth Schmidt
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Simone Weidner
- Department of Biology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Joana Falcão Salles
- Institute of Evolutionary Life sciences, Groningen UniversityGroningen, Netherlands
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294
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Saha P, Yeoh BS, Singh R, Chandrasekar B, Vemula PK, Haribabu B, Vijay-Kumar M, Jala VR. Gut Microbiota Conversion of Dietary Ellagic Acid into Bioactive Phytoceutical Urolithin A Inhibits Heme Peroxidases. PLoS One 2016; 11:e0156811. [PMID: 27254317 PMCID: PMC4890745 DOI: 10.1371/journal.pone.0156811] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/19/2016] [Indexed: 12/15/2022] Open
Abstract
Numerous studies signify that diets rich in phytochemicals offer many beneficial functions specifically during pathologic conditions, yet their effects are often not uniform due to inter-individual variation. The host indigenous gut microbiota and their modifications of dietary phytochemicals have emerged as factors that greatly influence the efficacy of phytoceutical-based intervention. Here, we investigated the biological activities of one such active microbial metabolite, Urolithin A (UA or 3,8-dihydroxybenzo[c]chromen-6-one), which is derived from the ellagic acid (EA). Our study demonstrates that UA potently inhibits heme peroxidases i.e. myeloperoxidase (MPO) and lactoperoxidase (LPO) when compared to the parent compound EA. In addition, chrome azurol S (CAS) assay suggests that EA, but not UA, is capable of binding to Fe3+, due to its catechol-like structure, although its modest heme peroxidase inhibitory activity is abrogated upon Fe3+-binding. Interestingly, UA-mediated MPO and LPO inhibition can be prevented by innate immune protein human NGAL or its murine ortholog lipocalin 2 (Lcn2), implying the complex nature of host innate immunity-microbiota interactions. Spectral analysis indicates that UA inhibits heme peroxidase-catalyzed reaction by reverting the peroxidase back to its inactive native state. In support of these in vitro results, UA significantly reduced phorbol myristate acetate (PMA)-induced superoxide generation in neutrophils, however, EA failed to block the superoxide generation. Treatment with UA significantly reduced PMA-induced mouse ear edema and MPO activity compared to EA treated mice. Collectively, our results demonstrate that microbiota-mediated conversion of EA to UA is advantageous to both host and microbiota i.e. UA-mediated inhibition of pro-oxidant enzymes reduce tissue inflammation, mitigate non-specific killing of gut bacteria, and abrogate iron-binding property of EA, thus providing a competitive edge to the microbiota in acquiring limiting nutrient iron and thrive in the gut.
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Affiliation(s)
- Piu Saha
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Beng San Yeoh
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Rajbir Singh
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Bhargavi Chandrasekar
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), UAS-GKVK Campus, Bellary Road, Bangalore, Karnataka, India
| | - Praveen Kumar Vemula
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), UAS-GKVK Campus, Bellary Road, Bangalore, Karnataka, India
- Ramalingaswami ReEntry Fellow, Dept. of Biotechnology, Govt. of India
| | - Bodduluri Haribabu
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Matam Vijay-Kumar
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Medicine, The Pennsylvania State University Medical Center, Hershey, Pennsylvania, United States of America
- * E-mail: (MVK); (VRJ)
| | - Venkatakrishna R. Jala
- Department of Microbiology and Immunology, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail: (MVK); (VRJ)
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295
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Biggs MB, Papin JA. Metabolic network-guided binning of metagenomic sequence fragments. Bioinformatics 2016; 32:867-74. [PMID: 26568626 PMCID: PMC6169484 DOI: 10.1093/bioinformatics/btv671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/16/2015] [Accepted: 11/09/2015] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health. RESULTS We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score. We successfully demonstrate proof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the variables that impact reaction assignment accuracy. We further demonstrate the integration of SONEC with existing approaches (such as cross-sample scaffold abundance profile clustering) on a set of 94 metagenomic samples from the Human Microbiome Project. We show that not only does SONEC aid in reconstructing species-level genomes, but it also improves functional predictions made with the resulting metabolic networks. AVAILABILITY AND IMPLEMENTATION The datasets and code presented in this work are available at: https://bitbucket.org/mattbiggs/sorting_by_network_completion/ CONTACT papin@virginia.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew B Biggs
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903 USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903 USA
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296
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Wang BG, Xu HB, Xu F, Zeng ZL, Wei H. Efficacy of oral Bifidobacterium bifidum ATCC 29521 on microflora and antioxidant in mice. Can J Microbiol 2016; 62:249-62. [DOI: 10.1139/cjm-2015-0685] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study aimed to examine whether Bifidobacterium bifidum ATCC 29521, a species of colonic microflora in humans, is involved in the intestinal tract of mice. This study was also conducted to determine the antioxidant activity of this species by evaluating different microbial populations and reactive oxygen species isolated from feces and intestinal contents for 28 days of oral administration. Microbial diversities were assessed through bacterial culture techniques, PCR–DGGE, and real-time PCR. This study showed that the intake of B. bifidum ATCC 29521 significantly (p < 0.05) improved the ecosystem of the intestinal tract of BALB/c mice by increasing the amount of probiotics (Lactobacillus intestinalis and Lactobacillus crispatus) and by reducing unwanted bacterial populations (Enterobacter, Escherichia coli). Antioxidative activities of incubated cell-free extracts were evaluated through various assays, including the scavenging ability of DPPH radical (64.5% and 67.54% (p < 0.05), respectively, at 21 days in nutrients and 28 days in MRS broth), superoxide anion, and hydroxyl radical (85% and 61.5% (p < 0.05), respectively, at intestinal contents in nutrients and 21 days in MRS broth). Total reducing power (231.5 μmol/L (p < 0.05), 14 days in MRS broth) and mRNA level of genes related to oxidative stress were also determined. Results indicated that B. bifidum ATCC 29521 elicits a beneficial effect on murine gut microbiota and antioxidant activities compared with the control samples. This species can be considered as a potential bioresource antioxidant to promote health. Bifidobacterium bifidum ATCC 29521 may also be used as a promising material in microbiological and food applications.
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Affiliation(s)
- Bao-gui Wang
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, People’s Republic of China
| | - Hai-bo Xu
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Department of Health and Exercise Science, Tianjin University of Sport, Tianjin 300381, People’s Republic of China
| | - Feng Xu
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, People’s Republic of China
| | - Zhe-ling Zeng
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, People’s Republic of China
| | - Hua Wei
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, People’s Republic of China
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297
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Watkins RR, Mukherjee PK, Chandra J, Retuerto MA, Guidry C, Haller N, Paranjape C, Ghannoum MA. Admission to the Intensive Care Unit is Associated With Changes in the Oral Mycobiome. J Intensive Care Med 2016; 32:278-282. [PMID: 26893317 DOI: 10.1177/0885066615627757] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A prospective exploratory study was conducted to characterize the oral mycobiome at baseline and determine whether changes occur after admission to the intensive care unit (ICU). We found that ICU admission is associated with alterations in the oral mycobiome, including an overall increase in Candida albicans.
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Affiliation(s)
- Richard R Watkins
- 1 Department of Internal Medicine, Northeast Ohio Medical University, Rootstown, OH, USA.,2 Division of Infectious Diseases, Akron General Medical Center, Akron, OH, USA
| | - Pranab K Mukherjee
- 3 Department of Dermatology, Center for Medical Mycology, University Hospitals Case Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Jyotsna Chandra
- 3 Department of Dermatology, Center for Medical Mycology, University Hospitals Case Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Mauricio A Retuerto
- 4 OHARA/ACTG Mycology Unit, Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Chrissy Guidry
- 5 Department of Surgery, Akron General Medical Center, Akron, OH, USA
| | - Nairmeen Haller
- 6 Department of Research, Akron General Medical Center, Akron, OH, USA
| | | | - Mahmoud A Ghannoum
- 7 Department of Dermatology, Center for Medical Microbiology, Case Western Reserve University School of Medicine, University Hospitals Case Medical Center, Cleveland, OH, USA
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298
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Ravcheev DA, Thiele I. Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. Front Microbiol 2016; 7:128. [PMID: 26904004 PMCID: PMC4746308 DOI: 10.3389/fmicb.2016.00128] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/25/2016] [Indexed: 02/06/2023] Open
Abstract
Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that are essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes can synthesize both quinones. So far, most of the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis of individual HGM genomes to the identification of ubiquinone and menaquinone biosynthetic pathways. In our opinion, the shift from metagenomics to analysis of individual genomes is a pivotal milestone in investigation of bacterial communities, including the HGM. The key results of this study are as follows. (i) The distribution of the canonical pathways in the HGM genomes was consistent with previous reports and with the distribution of the quinone-dependent reductases for electron acceptors. (ii) The comparative genomics analysis identified four alternative forms of the previously known enzymes for quinone biosynthesis. (iii) Genes for the previously unknown part of the futalosine pathway were identified, and the corresponding biochemical reactions were proposed. We discuss the remaining gaps in the menaquinone and ubiquinone pathways in some of the microbes, which indicate the existence of further alternate genes or routes. Together, these findings provide further insight into the biosynthesis of quinones in bacteria and the physiology of the HGM.
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Affiliation(s)
- Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
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299
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Abstract
Sepsis is a complex syndrome triggered by infection and characterized by systemic deregulation of immune and inflammatory pathways. It is a major cause of death worldwide and results in the widespread use of antibiotics and substantial health care costs. In a vicious circle, sepsis treatment promotes the emergence of highly virulent and resistant pathogens and devastating nosocomial infections. Sepsis is a heterogeneous disease affecting many people worldwide. Because individual patients have different inflammatory responses and unique profiles of immune activation against pathogens, the most effective way to advance the treatment of sepsis is probably through a tailored approach. The advent of high-throughput technologies and the remarkable progress in the field of bioinformatics has allowed the subclassification of many pathological conditions. This has potential to provide better understanding of life-threatening infections in people. The study of host factors, however, needs to be integrated with studies on bacterial signaling in both symbiotic and pathogenic bacteria. Sepsis is certainly the sum of multiple host-microbial interactions and the metagenome should be extensively investigated. Personalized medicine is probably the only strategy able to deconstruct and reassemble our knowledge about sepsis, and its use should allow us to understand and manipulate sepsis as a wide, interconnected phenomenon with myriad variables and peculiarities. In this study, the recent advances in this area, the major challenges that remain, and the reasons why the septic patient should be approached as a superorganism are discussed.
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300
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Gut Microbiota Dysbiosis as Risk and Premorbid Factors of IBD and IBS Along the Childhood-Adulthood Transition. Inflamm Bowel Dis 2016; 22:487-504. [PMID: 26588090 DOI: 10.1097/mib.0000000000000602] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastrointestinal disorders, although clinically heterogeneous, share pathogenic mechanisms, including genetic susceptibility, impaired gut barrier function, altered microbiota, and environmental triggers (infections, social and behavioral factors, epigenetic control, and diet). Gut microbiota has been studied for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) in either children or adults, while modifiable gut microbiota features, acting as risk and premorbid factors along the childhood-adulthood transition, have not been thoroughly investigated so far. Indeed, the relationship between variations of the entire host/microbiota/environmental scenario and clinical phenotypes is still not fully understood. In this respect, tracking gut dysbiosis grading may help deciphering host phenotype-genotype associations and microbiota shifts in an integrated top-down omics-based approach within large-scale pediatric and adult case-control cohorts. Large-scale gut microbiota signatures and host inflammation patterns may be integrated with dietary habits, under genetic and epigenetic constraints, providing gut dysbiosis profiles acting as risk predictors of IBD or IBS in preclinical cases. Tracking dysbiosis supports new personalized/stratified IBD and IBS prevention programmes, generating Decision Support System tools. They include (1) high risk or flare-up recurrence -omics-based dysbiosis profiles; (2) microbial and molecular biomarkers of health and disease; (3) -omics-based pipelines for laboratory medicine diagnostics; (4) health apps for self-management of score-based dietary profiles, which can be shared with clinicians for nutritional habit and lifestyle amendment; (5) -omics profiling data warehousing and public repositories for IBD and IBS profile consultation. Dysbiosis-related indexes can represent novel laboratory and clinical medicine tools preventing or postponing the disease, finally interfering with its natural history.
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