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Romero-Miguel D, Casquero-Veiga M, Fernández J, Lamanna-Rama N, Gómez-Rangel V, Gálvez-Robleño C, Santa-Marta C, Villar CJ, Lombó F, Abalo R, Desco M, Soto-Montenegro ML. Maternal Supplementation with N-Acetylcysteine Modulates the Microbiota-Gut-Brain Axis in Offspring of the Poly I:C Rat Model of Schizophrenia. Antioxidants (Basel) 2023; 12:antiox12040970. [PMID: 37107344 PMCID: PMC10136134 DOI: 10.3390/antiox12040970] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
The microbiota-gut-brain axis is a complex interconnected system altered in schizophrenia. The antioxidant N-acetylcysteine (NAC) has been proposed as an adjunctive therapy to antipsychotics in clinical trials, but its role in the microbiota-gut-brain axis has not been sufficiently explored. We aimed to describe the effect of NAC administration during pregnancy on the gut-brain axis in the offspring from the maternal immune stimulation (MIS) animal model of schizophrenia. Pregnant Wistar rats were treated with PolyI:C/Saline. Six groups of animals were studied according to the study factors: phenotype (Saline, MIS) and treatment (no NAC, NAC 7 days, NAC 21 days). Offspring were subjected to the novel object recognition test and were scanned using MRI. Caecum contents were used for metagenomics 16S rRNA sequencing. NAC treatment prevented hippocampal volume reduction and long-term memory deficits in MIS-offspring. In addition, MIS-animals showed lower bacterial richness, which was prevented by NAC. Moreover, NAC7/NAC21 treatments resulted in a reduction of proinflammatory taxons in MIS-animals and an increase in taxa known to produce anti-inflammatory metabolites. Early approaches, like this one, with anti-inflammatory/anti-oxidative compounds, especially in neurodevelopmental disorders with an inflammatory/oxidative basis, may be useful in modulating bacterial microbiota, hippocampal size, as well as hippocampal-based memory impairments.
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Grants
- project number PI17/01766, and grant number BA21/00030 Ministerio de Ciencia e Innovación, Instituto de Salud Carlos III, co-financed by the European Regional Development Fund (ERDF), "A way to make Europe"
- project PID2021-128862OB-I00 MCIN /AEI /10.13039/501100011033 / FEDER, UE
- project number CB07/09/0031 CIBER de Salud Mental - Instituto de Salud Carlos III
- project numbers 2017/085, 2022/008917 Delegación del Gobierno para el Plan Nacional sobre Drogas
- 2016/01 Fundación Alicia Koplowitz
- grant, PEJD-2018-PRE/BMD-7899 Consejería de Educación e investigación, Comunidad de Madrid, co-funded by the European Social Fund "Investing in your future"
- "Programa Intramural de Impulso a la I+D+I 2019" Instituto de investigación Sanitaria Gregorio Marañón
- PT20/00044 Ministerio de Ciencia e Innovación, Instituto de Salud Carlos III
- x The CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Ministerio de Ciencia e Innovación (MCIN) and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505)
- Contrato Intramural Postdoctoral FINBA
- SV-PA-21-AYUD/2021/51347 Ayudas para grupos de investigación de organismos del Principado de Asturias
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Affiliation(s)
| | | | - Javier Fernández
- Grupo de Investigación "Biotechnology in Nutraceuticals and Bioactive Compounds-BIONUC", Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Nicolás Lamanna-Rama
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, 28911 Madrid, Spain
| | | | - Carlos Gálvez-Robleño
- Grupo de Investigación de Alto Rendimiento en Fisiopatología y Farmacología del Sistema Digestivo (NeuGut-URJC), Universidad Rey Juan Carlos, 28922 Alcorcón, Spain
- Departamento de Ciencias Básicas de la Salud, Universidad Rey Juan Carlos (URJC), 28922 Alcorcón, Spain
| | - Cristina Santa-Marta
- Departamento de Física Matemática y de Fluidos, Universidad Nacional de Educación a Distancia (UNED), 28040 Madrid, Spain
| | - Claudio J Villar
- Grupo de Investigación "Biotechnology in Nutraceuticals and Bioactive Compounds-BIONUC", Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Felipe Lombó
- Grupo de Investigación "Biotechnology in Nutraceuticals and Bioactive Compounds-BIONUC", Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Raquel Abalo
- Grupo de Investigación de Alto Rendimiento en Fisiopatología y Farmacología del Sistema Digestivo (NeuGut-URJC), Universidad Rey Juan Carlos, 28922 Alcorcón, Spain
- Departamento de Ciencias Básicas de la Salud, Universidad Rey Juan Carlos (URJC), 28922 Alcorcón, Spain
- Grupo de Trabajo de Ciencias Básicas en Dolor y Analgesia, Sociedad Española del Dolor (SED), 28046 Madrid, Spain
- Grupo de Trabajo de Cannabinoides, Sociedad Española del Dolor (SED), 28046 Madrid, Spain
- Unidad Asociada I+D+i del Instituto de Química Medica (IQM), Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Manuel Desco
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, 28911 Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - María Luisa Soto-Montenegro
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- Grupo de Investigación de Alto Rendimiento en Fisiopatología y Farmacología del Sistema Digestivo (NeuGut-URJC), Universidad Rey Juan Carlos, 28922 Alcorcón, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029 Madrid, Spain
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Ling X, Peng S, Zhong J, Guo L, Xu Y, Jin X, Chu F. Effects of Chang-Kang-Fang Formula on the Microbiota-Gut-Brain Axis in Rats With Irritable Bowel Syndrome. Front Pharmacol 2022; 13:778032. [PMID: 35614949 PMCID: PMC9125359 DOI: 10.3389/fphar.2022.778032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Chang-Kang-Fang formula (CKF), a multi-herb traditional Chinese medicine, has been used in clinical settings to treat irritable bowel syndrome (IBS). Recent studies show that 5.0 g/kg/d CKF can alleviate the symptoms of IBS rats by modulating the brain-gut axis through the production of brain-gut peptides (BGPs), thus relieving pain, and reversing the effects of intestinal propulsion disorders. However, the exact mechanisms underlying the therapeutic effects of CKF in IBS remain unclear. The microbiota-gut-brain axis (MGBA) is central to the pathogenesis of IBS, regulating BGPs, depression-like behaviors, and gut microbiota. Given that CKF ameliorates IBS via the MGBA, we performed metabolomic analyses, evaluated the gut microbiota, and system pharmacology to elucidate the mechanisms of action of CKF. The results of intestinal tract motility, abdominal withdrawal reflex (AWR), sucrose preference test (SPT), and the forced swimming test (FST) showed that the male Sprague-Dawley rats subjected to chronic acute combining stress (CACS) for 22 days exhibited altered intestinal motility, visceral hypersensitivity, and depression-like behaviors. Treatment of IBS rats with CKF normalized dysfunctions of CACS-induced central and peripheral nervous system. CKF regulated BDNF and 5-HT levels in the colon and hippocampus as well as the expressions of the related BGP pathway genes. Moreover, the system pharmacology assays were used to assess the physiological targets involved in the action of CKF, with results suggesting that CKF putatively functioned through the 5-HT-PKA-CREB-BDNF pathway. LC-MS-based metabolomics identified the significantly altered 5-HT pathway-related metabolites in the CKF treatment group, and thus, the CKF-related signaling pathways were further examined. After pyrosequencing-based analysis of bacterial 16S rRNA (V3 + V4 region) using rat feces, the Lefse analysis of gut microbiota suggested that CKF treatment could induce structural changes in the gut microbiota, thereby regulating it by decreasing Clostridiales, and the F-B ratio while increasing the levels of Lactobacillus. Furthermore, the integrated analysis showed a correlation of CKF-associated microbes with metabolites. These findings showed that CKF effectively alleviated IBS, which was associated with the altered features of the metabolite profiles and the gut microbiota through a bidirectional communication along the microbiota-gut-brain axis.
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Affiliation(s)
- Xiwen Ling
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangzhou Higher Education Mega Center, Guangdong Pharmaceutical University, Guangzhou, China
| | - Siyuan Peng
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangzhou Higher Education Mega Center, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jingbin Zhong
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Lirong Guo
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangzhou Higher Education Mega Center, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yaqin Xu
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangzhou Higher Education Mega Center, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaobao Jin
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangzhou Higher Education Mega Center, Guangdong Pharmaceutical University, Guangzhou, China
| | - Fujiang Chu
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangzhou Higher Education Mega Center, Guangdong Pharmaceutical University, Guangzhou, China
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Kim M, Benayoun BA. The microbiome: an emerging key player in aging and longevity. TRANSLATIONAL MEDICINE OF AGING 2020; 4:103-116. [PMID: 32832742 PMCID: PMC7437988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023] Open
Abstract
Revolutionary advancements of high-throughput sequencing and metagenomic tools have provided new insights to microbiome function, including a bidirectional relationship between the microbiome and host aging. The intestinal tract is the largest surface in the human body that directly interacts with foreign antigens - it is covered with extremely complex and diverse community of microorganisms, known as the gut microbiome. In a healthy gut, microbial communities maintain a homeostatic metabolism and reside within the host in a state of immune tolerance. Abnormal shifts in the gut microbiome, however, have been implicated in the pathogenesis of age-related chronic diseases, including obesity, cardiovascular diseases and neurodegenerative diseases. The gut microbiome is emerging as a key factor in the aging process. In this review, we describe studies of humans and model organisms that suggest a direct causal role of the gut microbiome on host aging. Additionally, we also discuss sex-dimorphism in the gut microbiome and its possible roles in age-related sex-dimorphic phenotypes. We also provide an overview of widely used microbiome analysis methods and tools which could be used to explore the impact of microbiome remodeling on aging.
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Affiliation(s)
- Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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4
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Kim M, Benayoun BA. The microbiome: An emerging key player in aging and longevity. TRANSLATIONAL MEDICINE OF AGING 2020. [DOI: 10.1016/j.tma.2020.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Wang Y, Zheng F, Liu S, Luo H. Research Progress in Fecal Microbiota Transplantation as Treatment for Irritable Bowel Syndrome. Gastroenterol Res Pract 2019; 2019:9759138. [PMID: 31885549 PMCID: PMC6914991 DOI: 10.1155/2019/9759138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/10/2019] [Accepted: 11/07/2019] [Indexed: 12/15/2022] Open
Abstract
Irritable bowel syndrome is a functional disorder characterized by abdominal pain or discomfort associated with altered bowel habits. Due to the uncertainty of the pathogenesis of IBS and the diversity of its clinical manifestations, IBS cannot be completely cured. Increasing evidence suggests the key role of altered intestinal microbiota in the pathogenesis of IBS. Therefore, attention is being shifted to adjusting the changes in intestinal microbiota to control IBS symptoms. Fecal microbiota transplantation (FMT), antibiotics, probiotics, and synbiotics are currently often employed as treatment for IBS. And FMT is the most significant therapeutic efficacy with the least number of side effects. FMT provides a creative way to restore the abnormal gut microbiome in patients with IBS. But although current clinical studies confirm the effectiveness of FMT in the treatment of IBS, they are short-term studies of small samples, and there is still a lack of large-scale long-term studies. In this paper, we review the intestinal microbiota changes of IBS, the common methods of treating IBS with intestinal microbes, and the research status of FMT for the treatment of IBS. Finally, we put forward some opinions on the future research direction of FMT treatment of IBS.
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Affiliation(s)
- Yao Wang
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, China
| | - Fengling Zheng
- The Journal Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, China
| | - Shan Liu
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, China
| | - Huanhuan Luo
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510006, China
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Li J, Zhan S, Liu X, Lin Q, Jiang J, Li X. Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae. Front Microbiol 2018; 9:1823. [PMID: 30214431 PMCID: PMC6125396 DOI: 10.3389/fmicb.2018.01823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Gastrointestinal microbiota may shape the adaptation of their hosts to different habitats and lifestyles, thereby driving their evolutionary diversification. It remains unknown if gastrointestinal microbiota diverge in congruence with the phylogenetic relationships of their hosts. To evaluate the phylosymbiotic relationships, here we analyzed the compositions of fecal microbiota of seven Cervinae species raised in the Chengdu Zoo. All sampled animals were kept in the same environmental condition and fed identical fodder for years. Results showed that Firmicutes and Bacteroidetes were dominant in their fecal microbiota. Even though some bacteria (e.g., Ruminococcaceae) were found to be common in the feces of all investigated species, some genera (e.g., Sharpea and Succinivibrio) were only observed in animals with particular digestive systems. As for the intraspecies variations of microbial communities, only a few operational taxonomic units (OTUs) were shared among replicates of the same host species although they accounted for most of the total abundance. Correlation was observed between the fecal microbiota divergence and host phylogeny, but they were not congruent completely. This may shed new light on the coevolution of host species and their microbiota.
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Affiliation(s)
- Jiaying Li
- Key Laboratory of Environmental and Applied Microbiology - Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Xuanzhen Liu
- Chengdu Zoo, Chengdu Institute of Wildlife, Chengdu, China
| | - Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology - Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangzhen Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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Song KH, Jung HK, Kim HJ, Koo HS, Kwon YH, Shin HD, Lim HC, Shin JE, Kim SE, Cho DH, Kim JH, Kim HJ. Clinical Practice Guidelines for Irritable Bowel Syndrome in Korea, 2017 Revised Edition. J Neurogastroenterol Motil 2018; 24:197-215. [PMID: 29605976 PMCID: PMC5885719 DOI: 10.5056/jnm17145] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/11/2018] [Accepted: 02/27/2018] [Indexed: 12/12/2022] Open
Abstract
In 2011, the Korean Society of Neurogastroenterology and Motility (KSNM) published clinical practice guidelines on the management of irritable bowel syndrome (IBS) based on a systematic review of the literature. The KSNM planned to update the clinical practice guidelines to support primary physicians, reduce the socioeconomic burden of IBS, and reflect advances in the pathophysiology and management of IBS. The present revised version of the guidelines is in continuity with the previous version and targets adults diagnosed with, or suspected to have, IBS. A librarian created a literature search query, and a systematic review was conducted to identify candidate guidelines. Feasible documents were verified based on predetermined inclusion and exclusion criteria. The candidate seed guidelines were fully evaluated by the Guidelines Development Committee using the Appraisal of Guidelines for Research and Evaluation II quality assessment tool. After selecting 7 seed guidelines, the committee prepared evidence summaries to generate data exaction tables. These summaries comprised the 4 main themes of this version of the guidelines: colonoscopy; a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols; probiotics; and rifaximin. To adopt the core recommendations of the guidelines, the Delphi technique (ie, a panel of experts on IBS) was used. To enhance dissemination of the clinical practice guidelines, a Korean version will be made available, and a food calendar for patients with IBS is produced.
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Affiliation(s)
- Kyung Ho Song
- Department of Internal Medicine, Konyang University College of Medicine, Daejeon,
Korea
- Konyang University Myunggok Medical Research Institute Daejeon,
Korea
| | - Hye-Kyung Jung
- Department of Internal Medicine, Ewha Womans University School of Medicine, Seoul,
Korea
- Correspondence: Hye-Kyung Jung, MD, PhD Department of Internal Medicine, Ewha Womans University Medical Center, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul 07985, Korea, Tel: +82-2-2650-2874, Fax: +82-2-2655-2874, E-mail:
| | - Hyun Jin Kim
- Department of Internal Medicine, Gyeongsang National University, College of Medicine, Jinju,
Korea
| | - Hoon Sup Koo
- Department of Internal Medicine, Konyang University College of Medicine, Daejeon,
Korea
| | - Yong Hwan Kwon
- Department of Internal Medicine, Kyungpook National University, School of Medicine, Daegu,
Korea
| | - Hyun Duk Shin
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan,
Korea
| | - Hyun Chul Lim
- Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin,
Korea
| | - Jeong Eun Shin
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan,
Korea
| | - Sung Eun Kim
- Department of Internal Medicine, Kosin University College of Medicine, Busan,
Korea
| | - Dae Hyeon Cho
- Department of Internal Medicine, Sungkyunkwan University School of Medicine, Changwon,
Korea
| | - Jeong Hwan Kim
- Department of Internal Medicine, Konkuk University School of Medicine, Seoul,
Korea
| | - Hyun Jung Kim
- Department of Preventive Medicine, Korea University College of Medicine, Seoul,
Korea
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Handley N, Eide J, Taylor R, Wuertz B, Gaffney P, Ondrey F. PPARγ targeted oral cancer treatment and additional utility of genomics analytic techniques. Laryngoscope 2017; 127:E124-E131. [PMID: 27896820 PMCID: PMC5360511 DOI: 10.1002/lary.26423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/26/2016] [Accepted: 10/18/2016] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Peroxisome proliferator-activated receptor γ (PPARγ) agonists have been shown to have anti-proliferative, anti-angiogenic, and proapoptotic effects, leading to interest in their use as cancer therapeutics. Pioglitazone, a U.S. Food and Drug Administration-approved type II diabetes medication and PPARγ agonist, may have a role in adjuvant head-and-neck squamous cell carcinoma treatment or prevention. Therefore, the purpose of this study was: 1) to treat oral cavity cancer cells with the PPARγ activator, pioglitazone, to analyze gene expression changes; and 2) to compare those changes with our preexisting genomic data for development of hypothesis-driven additional basic and clinical studies. STUDY DESIGN Prospective in vitro. METHODS We utilized microarray technology, as well as OCPlus (Bioconductor open source software) and Ingenuity Pathway Analysis (Qiagen, Redwood City, CA), to analyze differential gene expression in tumor and pioglitazone-treated tumor cells on a genome-wide level to demonstrate the feasibility of such an approach and determine appropriate sample size for future investigations. RESULTS We found that approximately 35 samples are required to adequately power future studies. We next discovered that pioglitazone significantly affects Inducible T-Cell Costimulator (iCOS)-Ligand for the T-cell-specific cell surface receptor ICOS (iCOSL) and type II diabetes mellitus pathways as a putative anti-cancer mechanism. CONCLUSION Genome-wide analysis is possible for the exploration of differential pathway modulation and rapid hypothesis generation. Both inflammation and type II diabetes pathways were significantly altered and therefore might provide unique hypothesis-driven pharmacodynamic parameters for future in vitro or in vivo studies utilizing thiazolidinediones. These techniques could be applied to microarray or other high throughput data from a variety of hypothesis-generating research scenarios in otolaryngology (e.g., middle ear proteomics, sinus microbiome studies). LEVEL OF EVIDENCE NA. Laryngoscope, 127:E124-E131, 2017.
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Affiliation(s)
- Nathan Handley
- Molecular Oncology Program, Department of Otolaryngology, University of Minnesota, Minneapolis, MN
| | - Jacob Eide
- Molecular Oncology Program, Department of Otolaryngology, University of Minnesota, Minneapolis, MN
| | | | - Beverly Wuertz
- Molecular Oncology Program, Department of Otolaryngology, University of Minnesota, Minneapolis, MN
| | | | - Frank Ondrey
- Molecular Oncology Program, Department of Otolaryngology, University of Minnesota, Minneapolis, MN
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Fourie NH, Wang D, Abey SK, Creekmore AL, Hong S, Martin CG, Wiley JW, Henderson WA. Structural and functional alterations in the colonic microbiome of the rat in a model of stress induced irritable bowel syndrome. Gut Microbes 2017; 8:33-45. [PMID: 28059627 PMCID: PMC5341915 DOI: 10.1080/19490976.2016.1273999] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 11/29/2016] [Accepted: 12/13/2016] [Indexed: 02/03/2023] Open
Abstract
Stress is known to perturb the microbiome and exacerbate irritable bowel syndrome (IBS) associated symptoms. Characterizing structural and functional changes in the microbiome is necessary to understand how alterations affect the biomolecular environment of the gut in IBS. Repeated water avoidance (WA) stress was used to induce IBS-like symptoms in rats. The colon-mucosa associated microbiome was characterized in 13 stressed and control animals by 16S sequencing. In silico analysis of the functional domains of microbial communities was done by inferring metagenomic profiles from 16S data. Microbial communities and functional profiles were compared between conditions. WA animals exhibited higher α-diversity and moderate divergence in community structure (β-diversity) compared with controls. Specific clades and taxa were consistently and significantly modified in the WA animals. The WA microbiome was particularly enriched in Proteobacteria and depleted in several beneficial taxa. A decreased capacity in metabolic domains, including energy- and lipid-metabolism, and an increased capacity for fatty acid and sulfur metabolism was inferred for the WA microbiome. The stressed condition favored the proliferation of a greater diversity of microbes that appear to be functionally similar, resulting in a functionally poorer microbiome with implications for epithelial health. Taxa, with known beneficial effects, were found to be depleted, which supports their relevance as therapeutic agents to restore microbial health. Microbial sulfur metabolism may form a key component of visceral nerve sensitization pathways and is therefore of interest as a target metabolic domain in microbial ecological restoration.
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Affiliation(s)
- Nicolaas H Fourie
- a National Institutes of Health, Division of Intramural Research, NINR, DHHS , Bethesda , MD , USA
| | - Dan Wang
- a National Institutes of Health, Division of Intramural Research, NINR, DHHS , Bethesda , MD , USA
| | - Sarah K Abey
- a National Institutes of Health, Division of Intramural Research, NINR, DHHS , Bethesda , MD , USA
| | - Amy L Creekmore
- b University of Michigan Medical School , Department of Internal Medicine - Gastroenterology , Ann Arbor , MI , USA
| | - Shuangsong Hong
- b University of Michigan Medical School , Department of Internal Medicine - Gastroenterology , Ann Arbor , MI , USA
| | - Christiana G Martin
- a National Institutes of Health, Division of Intramural Research, NINR, DHHS , Bethesda , MD , USA
| | - John W Wiley
- b University of Michigan Medical School , Department of Internal Medicine - Gastroenterology , Ann Arbor , MI , USA
| | - Wendy A Henderson
- a National Institutes of Health, Division of Intramural Research, NINR, DHHS , Bethesda , MD , USA
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10
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Betrapally NS, Gillevet PM, Bajaj JS. Gut microbiome and liver disease. Transl Res 2017; 179:49-59. [PMID: 27477080 PMCID: PMC5164947 DOI: 10.1016/j.trsl.2016.07.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/09/2016] [Accepted: 07/06/2016] [Indexed: 02/07/2023]
Abstract
Gut microbiota changes are important in determining the occurrence and progression of chronic liver disease related to alcohol, nonalcoholic fatty liver disease, and cirrhosis. Specifically, the systemic inflammation, endotoxemia, and the vasodilation that leads to complications such as spontaneous bacterial peritonitis and hepatic encephalopathy could be related to the gut milieu. Given the poor prognosis of these events, their prevention and early management are essential. Microbiota may be an essential component of the gut milieu that can impact these clinical events, and the study of their composition and function in a culture-independent manner could help understand the prognosis. Recent human and animal studies have shown that the relative abundance and the functional changes of microbiota in the stool, colonic mucosa, and saliva have varying consequences on the presence and prognosis of chronic liver disease and cirrhosis. The impact of therapies on the microbiota is slowly being understood and will likely lead to a more targeted approach to gut microbiota modification in chronic liver disease and cirrhosis.
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Affiliation(s)
| | | | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Va.
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Deshmukh RA, Joshi K, Bhand S, Roy U. Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview. Microbiologyopen 2016; 5:901-922. [PMID: 27397728 PMCID: PMC5221461 DOI: 10.1002/mbo3.383] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/20/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022] Open
Abstract
Waterborne diseases have emerged as global health problems and their rapid and sensitive detection in environmental water samples is of great importance. Bacterial identification and enumeration in water samples is significant as it helps to maintain safe drinking water for public consumption. Culture‐based methods are laborious, time‐consuming, and yield false‐positive results, whereas viable but nonculturable (VBNCs) microorganisms cannot be recovered. Hence, numerous methods have been developed for rapid detection and quantification of waterborne pathogenic bacteria in water. These rapid methods can be classified into nucleic acid‐based, immunology‐based, and biosensor‐based detection methods. This review summarizes the principle and current state of rapid methods for the monitoring and detection of waterborne bacterial pathogens. Rapid methods outlined are polymerase chain reaction (PCR), digital droplet PCR, real‐time PCR, multiplex PCR, DNA microarray, Next‐generation sequencing (pyrosequencing, Illumina technology and genomics), and fluorescence in situ hybridization that are categorized as nucleic acid‐based methods. Enzyme‐linked immunosorbent assay (ELISA) and immunofluorescence are classified into immunology‐based methods. Optical, electrochemical, and mass‐based biosensors are grouped into biosensor‐based methods. Overall, these methods are sensitive, specific, time‐effective, and important in prevention and diagnosis of waterborne bacterial diseases.
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Affiliation(s)
- Rehan A Deshmukh
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Kopal Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Sunil Bhand
- Biosensor Lab, Department of Chemistry, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Utpal Roy
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
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Effects of Rifaximin on Transit, Permeability, Fecal Microbiome, and Organic Acid Excretion in Irritable Bowel Syndrome. Clin Transl Gastroenterol 2016; 7:e173. [PMID: 27228404 PMCID: PMC4893683 DOI: 10.1038/ctg.2016.32] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/19/2016] [Indexed: 12/19/2022] Open
Abstract
Objectives: Rifaximin relieves irritable bowel syndrome (IBS) symptoms, bloating, abdominal pain, and loose or watery stools. Our objective was to investigate digestive functions in rifaximin-treated IBS patients. Methods: In a randomized, double-blind, placebo-controlled, parallel-group study, we compared the effects of rifaximin, 550 mg t.i.d., and placebo for 14 days in nonconstipated IBS and no evidence of small intestinal bacterial overgrowth (SIBO). All subjects completed baseline and on-treatment evaluation of colonic transit by scintigraphy, mucosal permeability by lactulose–mannitol excretion, and fecal microbiome, bile acids, and short chain fatty acids measured on random stool sample. Overall comparison of primary response measures between treatment groups was assessed using intention-to-treat analysis of covariance (ANCOVA, with baseline value as covariate). Results: There were no significant effects of treatment on bowel symptoms, small bowel or colonic permeability, or colonic transit at 24 h. Rifaximin was associated with acceleration of ascending colon emptying (14.9±2.6 h placebo; 6.9±0.9 h rifaximin; P=0.033) and overall colonic transit at 48 h (geometric center 4.0±0.3 h placebo; 4.7±0.2 h rifaximin; P=0.046); however, rifaximin did not significantly alter total fecal bile acids per g of stool or proportion of individual bile acids or acetate, propionate, or butyrate in stool. Microbiome studies showed strong associations within subjects, modest associations with time across subjects, and a small but significant association of microbial richness with treatment arm (rifaximin vs. treatment). Conclusions: In nonconstipated IBS without documented SIBO, rifaximin treatment is associated with acceleration of colonic transit and changes in microbial richness; the mechanism for reported symptomatic benefit requires further investigation.
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Li J, Zhu W, Liu W, Wu Y, Wu B. Rifaximin for Irritable Bowel Syndrome: A Meta-Analysis of Randomized Placebo-Controlled Trials. Medicine (Baltimore) 2016; 95:e2534. [PMID: 26825893 PMCID: PMC5291563 DOI: 10.1097/md.0000000000002534] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The current treatments for irritable bowel syndrome (IBS) are suboptimal. The findings of previous studies of rifaximin treatment for IBS may have differed due to variations in study design. Our study aimed to determine the therapeutic and adverse effects of rifaximin treatment for IBS based on a meta-analysis of published randomized controlled trials (RCTs). We searched the MEDLINE, EMBASE, EBSCO, Springer, Ovid, and Cochrane Library databases for RCTs investigating the effects of rifaximin on IBS. Data from each selected RCT was evaluated individually based on an intention-to-treat analysis, and a meta-analysis was performed in which the odds ratios (ORs) and 95% confidence intervals (CIs) of clinical outcomes and adverse events were calculated using fixed-effects models. Four eligible studies were identified. Overall relief of IBS symptoms in the rifaximin groups was greater than that in the placebo groups at the ends of both the treatment and follow-up periods (OR = 1.19; 95% CI: 1.08-1.32 and OR = 1.36; 95% CI: 1.18-1.58, respectively, P < 0.05 for both). Significant relief of abdominal distention was observed at the follow-up endpoint (OR = 1.69; 95% Cl: 1.27-2.23; P < 0.05), but not at the treatment endpoint (OR = 1.19; 95% CI: 0.96-1.49; P > 0.05). Abdominal pain (OR = 1.01; 95% CI: 0.98-1.03; P > 0.05), nausea (OR = 1.00; 95% CI: 0.98-1.02; P > 0.05), vomiting (OR: 0.99; 95% CI: 0.98-1.01; P > 0.05), and headache (OR = 1.01; 95% CI: 0.98-1.03; P > 0.05) did not differ significantly between the rifaximin and placebo groups. In the RCTs selected, our meta-analysis showed that the efficacy of rifaximin for the resolution of overall IBS symptoms was greater than that of the placebos, and that rifaximin was well-tolerated. The course of relief from abdominal distention in IBS patients treated with rifaximin may be delayed in some patients, compared with that of overall IBS symptom relief.
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Affiliation(s)
- Jun Li
- From the Department of Gastroenterology, Chinese PLA General Hospital, Fuxing Road (JL, WL, YW, BW); and Department of Oncology, Chinese 309th Hospital of PLA, Hei Shan Hu Road, Beijing, China (WZ)
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Ramírez-Castillo FY, Loera-Muro A, Jacques M, Garneau P, Avelar-González FJ, Harel J, Guerrero-Barrera AL. Waterborne pathogens: detection methods and challenges. Pathogens 2015; 4:307-34. [PMID: 26011827 PMCID: PMC4493476 DOI: 10.3390/pathogens4020307] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/08/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022] Open
Abstract
Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.
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Affiliation(s)
- Flor Yazmín Ramírez-Castillo
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Abraham Loera-Muro
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Mario Jacques
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Philippe Garneau
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Francisco Javier Avelar-González
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Josée Harel
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Alma Lilián Guerrero-Barrera
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
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Lees H, Swann J, Poucher SM, Nicholson JK, Holmes E, Wilson ID, Marchesi JR. Age and microenvironment outweigh genetic influence on the Zucker rat microbiome. PLoS One 2014; 9:e100916. [PMID: 25232735 PMCID: PMC4169429 DOI: 10.1371/journal.pone.0100916] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/01/2014] [Indexed: 12/31/2022] Open
Abstract
Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?
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Affiliation(s)
- Hannah Lees
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jonathan Swann
- Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading, United Kingdom
| | - Simon M. Poucher
- Cardiovascular and Gastro-Intestinal Disorders Innovative Medicines, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Jeremy K. Nicholson
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Elaine Holmes
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ian D. Wilson
- Section of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Julian R. Marchesi
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Centre for Digestive and Gut Health, Imperial College London, London, United Kingdom
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Choi JJ, Eum SY, Rampersaud E, Daunert S, Abreu MT, Toborek M. Exercise attenuates PCB-induced changes in the mouse gut microbiome. ENVIRONMENTAL HEALTH PERSPECTIVES 2013; 121:725-30. [PMID: 23632211 PMCID: PMC3672930 DOI: 10.1289/ehp.1306534] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/23/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND The gut microbiome, a dynamic bacterial community that interacts with the host, is integral to human health because it regulates energy metabolism and immune functions. The gut microbiome may also play a role in risks from environmental toxicants. OBJECTIVES We investigated the effects of polychlorinated biphenyls (PCBs) and exercise on the composition and structure of the gut microbiome in mice. METHODS After mice exercised voluntarily for 5 weeks, they were treated by oral gavage with a mixture of environmentally relevant PCB congeners (PCB153, PCB138, and PCB180; total PCB dose, 150 µmol/kg) for 2 days. We then assessed the microbiome by determination of 16S rRNA using microarray analysis. RESULTS Oral exposure to PCBs significantly altered the abundance of the gut microbiome in mice primarily by decreasing the levels of Proteobacteria. The activity level of the mice correlated with a substantial shift in abundance, biodiversity, and composition of the microbiome. Importantly, exercise attenuated PCB-induced changes in the gut microbiome. CONCLUSIONS Our results show that oral exposure to PCBs can induce substantial changes in the gut microbiome, which may then influence their systemic toxicity. These changes can be attenuated by behavioral factors, such as voluntary exercise.
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Affiliation(s)
- Jeong June Choi
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 33136, USA
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The intestinal microbiota in the rat model: major breakthroughs from new technologies. Anim Health Res Rev 2013; 13:54-63. [PMID: 22853927 DOI: 10.1017/s1466252312000072] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The mammalian intestine harbors a large and diverse community of micro-organisms, known as the intestinal microbiota. Recent developments in molecular profiling methods, mainly based on microbial 16S ribosomal RNA gene sequencing, have provided unprecedented insights into the make-up and diversity of intestinal microbial communities. Using these culture-independent analyses, gut microbiota of several mammals including laboratory rodents, have been revisited. The laboratory rat is one of the major species bred and kept for scientific research. Although this animal is bred in confined environments and subjected to procedures for satisfying health requirements that hamper natural colonization, some major features of mammalian gut microbiota are conserved. However, the gut microbiota varies according to the breeding conditions of the rats and this could impact reproducibility of the experimental models. Determining the non-pathogenic microbial community might be relevant in standards of quality control of laboratory animals. Molecular profiling techniques could be applied to document this information.
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Abstract
The human body is colonized by a vast array of microbes, which form communities of bacteria, viruses and microbial eukaryotes that are specific to each anatomical environment. Every community must be studied as a whole because many organisms have never been cultured independently, and this poses formidable challenges. The advent of next-generation DNA sequencing has allowed more sophisticated analysis and sampling of these complex systems by culture-independent methods. These methods are revealing differences in community structure between anatomical sites, between individuals, and between healthy and diseased states, and are transforming our view of human biology.
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Affiliation(s)
- George M Weinstock
- The Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
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Ishaq SL, Wright ADG. Insight into the bacterial gut microbiome of the North American moose (Alces alces). BMC Microbiol 2012; 12:212. [PMID: 22992344 PMCID: PMC3585231 DOI: 10.1186/1471-2180-12-212] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 09/17/2012] [Indexed: 02/07/2023] Open
Abstract
Background The work presented here provides the first intensive insight into the bacterial populations in the digestive tract of the North American moose (Alces alces). Eight free-range moose on natural pasture were sampled, producing eight rumen samples and six colon samples. Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose. Results A total of 789 unique OTUs were used for analysis, which passed the fluorescence and the positive fraction thresholds. There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families. Overall, there were 164 OTUs that were found in 100% of the samples. The Firmicutes were the most dominant bacteria phylum in both the rumen and the colon. Microarray data available at ArrayExpress, accession number E-MEXP-3721. Conclusions Using PhyloTrac and UniFrac computer software, samples clustered into two distinct groups: rumen and colon, confirming that the rumen and colon are distinct environments. There was an apparent correlation of age to cluster, which will be validated by a larger sample size in future studies, but there were no detectable trends based upon gender.
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Affiliation(s)
- Suzanne L Ishaq
- Department of Animal Science, College of Agriculture and Life Sciences, University of Vermont, 203 Terrill Building, 570 Main Street, Burlington, VT 05405, USA.
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Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F, Qi J. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. Nucleic Acids Res 2012; 41:e3. [PMID: 22941634 PMCID: PMC3592448 DOI: 10.1093/nar/gks828] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time.
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Affiliation(s)
- Jiemeng Liu
- State Key Laboratory of Genetic Engineering, State Key Laboratory of Surface Physics, The T-Life Research Center, School of Life Sciences, Fudan University, School of Life Sciences, Shanghai Jiaotong University, Shanghai 200433, People's Republic of China
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Gillanders LJ, Elborn JS, Gilpin DF, Schneiders T, Tunney MM. The airway microbiome in cystic fibrosis: challenges for therapy. ACTA ACUST UNITED AC 2011. [DOI: 10.2217/thy.11.81] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Holmes S, Alekseyenko A, Timme A, Nelson T, Pasricha PJ, Spormann A. Visualization and statistical comparisons of microbial communities using R packages on Phylochip data. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2011:142-53. [PMID: 21121042 PMCID: PMC3347925 DOI: 10.1142/9789814335058_0016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This article explains the statistical and computational methodology used to analyze species abundances collected using the LNBL Phylochip in a study of Irritable Bowel Syndrome (IBS) in rats. Some tools already available for the analysis of ordinary microarray data are useful in this type of statistical analysis. For instance in correcting for multiple testing we use Family Wise Error rate control and step-down tests (available in the multtest package). Once the most significant species are chosen we use the hypergeometric tests familiar for testing GO categories to test specific phyla and families. We provide examples of normalization, multivariate projections, batch effect detection and integration of phylogenetic covariation, as well as tree equalization and robustification methods.
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Affiliation(s)
- Susan Holmes
- Statistics Department, Stanford University, Stanford, CA 94305, USA.
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