1
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Spencer PS, Palmer VS, Kisby GE, Lagrange E, Horowitz BZ, Valdes Angues R, Reis J, Vernoux JP, Raoul C, Camu W. Early-onset, conjugal, twin-discordant, and clusters of sporadic ALS: Pathway to discovery of etiology via lifetime exposome research. Front Neurosci 2023; 17:1005096. [PMID: 36860617 PMCID: PMC9969898 DOI: 10.3389/fnins.2023.1005096] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/09/2023] [Indexed: 02/17/2023] Open
Abstract
The identity and role of environmental factors in the etiology of sporadic amyotrophic lateral sclerosis (sALS) is poorly understood outside of three former high-incidence foci of Western Pacific ALS and a hotspot of sALS in the French Alps. In both instances, there is a strong association with exposure to DNA-damaging (genotoxic) chemicals years or decades prior to clinical onset of motor neuron disease. In light of this recent understanding, we discuss published geographic clusters of ALS, conjugal cases, single-affected twins, and young-onset cases in relation to their demographic, geographic and environmental associations but also whether, in theory, there was the possibility of exposure to genotoxic chemicals of natural or synthetic origin. Special opportunities to test for such exposures in sALS exist in southeast France, northwest Italy, Finland, the U.S. East North Central States, and in the U.S. Air Force and Space Force. Given the degree and timing of exposure to an environmental trigger of ALS may be related to the age at which the disease is expressed, research should focus on the lifetime exposome (from conception to clinical onset) of young sALS cases. Multidisciplinary research of this type may lead to the identification of ALS causation, mechanism, and primary prevention, as well as to early detection of impending ALS and pre-clinical treatment to slow development of this fatal neurological disease.
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Affiliation(s)
- Peter S. Spencer
- Department of Neurology, School of Medicine, Oregon Health and Science University, Portland, OR, United States,Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR, United States,*Correspondence: Peter S. Spencer,
| | - Valerie S. Palmer
- Department of Neurology, School of Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Glen E. Kisby
- College of Osteopathic Medicine of the Pacific Northwest, Western University of Health Sciences, Lebanon, OR, United States
| | - Emmeline Lagrange
- Department of Neurology, Reference Center of Neuromuscular Disease and ALS Consultations, Grenoble University Hospital, Grenoble, France
| | - B. Zane Horowitz
- Department of Emergency Medicine, Oregon-Alaska Poison Center, Oregon Health and Science University, Portland, OR, United States
| | - Raquel Valdes Angues
- Department of Neurology, School of Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Jacques Reis
- University of Strasbourg, Faculté de Médecine, Strasbourg, France
| | - Jean-Paul Vernoux
- Normandie Université, UNICAEN, Unité de Recherche Aliments Bioprocédés Toxicologie Environnements, Caen, France
| | - Cédric Raoul
- INM, University of Montpellier, INSERM, Montpellier, France
| | - William Camu
- ALS Reference Center, Montpellier University Hospital and University of Montpellier, INSERM, Montpellier, France
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2
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Ionica E, Gaina G, Tica M, Chifiriuc MC, Gradisteanu-Pircalabioru G. Contribution of Epithelial and Gut Microbiome Inflammatory Biomarkers to the Improvement of Colorectal Cancer Patients’ Stratification. Front Oncol 2022; 11:811486. [PMID: 35198435 PMCID: PMC8859258 DOI: 10.3389/fonc.2021.811486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022] Open
Abstract
In order to ensure that primary endpoints of clinical studies are attained, the patients’ stratification is an important aspect. Selection criteria include age, gender, and also specific biomarkers, such as inflammation scores. These criteria are not sufficient to achieve a straightforward selection, however, in case of multifactorial diseases, with unknown or partially identified mechanisms, occasionally including host factors, and the microbiome. In these cases, the efficacy of interventions is difficult to predict, and as a result, the selection of subjects is often random. Colorectal cancer (CRC) is a highly heterogeneous disease, with variable clinical features, outcomes, and response to therapy; the CRC onset and progress involves multiple sequential steps with accumulation of genetic alterations, namely, mutations, gene amplification, and epigenetic changes. The gut microbes, either eubiotic or dysbiotic, could influence the CRC evolution through a complex and versatile crosstalk with the intestinal and immune cells, permanently changing the tumor microenvironment. There have been significant advances in the development of personalized approaches for CRC screening, treatment, and potential prevention. Advances in molecular techniques bring new criteria for patients’ stratification—mutational analysis at the time of diagnosis to guide treatment, for example. Gut microbiome has emerged as the main trigger of gut mucosal homeostasis. This may impact cancer susceptibility through maintenance of the epithelial/mucus barrier and production of protective metabolites, such as short-chain fatty acids (SCFAs) via interactions with the hosts’ diet and metabolism. Microbiome dysbiosis leads to the enrichment of cancer-promoting bacterial populations, loss of protective populations or maintaining an inflammatory chronic state, all of which contribute to the development and progression of CRC. Meanwhile, variations in patient responses to anti-cancer immuno- and chemotherapies were also linked to inter-individual differences in intestine microbiomes. The authors aim to highlight the contribution of epithelial and gut microbiome inflammatory biomarkers in the improvement of CRC patients’ stratification towards a personalized approach of early diagnosis and treatment.
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Affiliation(s)
- Elena Ionica
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- *Correspondence: Elena Ionica,
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Miology, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Mihaela Tica
- Bucharest Emergency University Hospital, Bucharest, Romania
| | - Mariana-Carmen Chifiriuc
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Biological Science Division, Romanian Academy of Sciences, Bucharest, Romania
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3
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Sędzikowska A, Szablewski L. Human Gut Microbiota in Health and Selected Cancers. Int J Mol Sci 2021; 22:13440. [PMID: 34948234 PMCID: PMC8708499 DOI: 10.3390/ijms222413440] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 12/24/2022] Open
Abstract
The majority of the epithelial surfaces of our body, and the digestive tract, respiratory and urogenital systems, are colonized by a vast number of bacteria, archaea, fungi, protozoans, and viruses. These microbiota, particularly those of the intestines, play an important, beneficial role in digestion, metabolism, and the synthesis of vitamins. Their metabolites stimulate cytokine production by the human host, which are used against potential pathogens. The composition of the microbiota is influenced by several internal and external factors, including diet, age, disease, and lifestyle. Such changes, called dysbiosis, may be involved in the development of various conditions, such as metabolic diseases, including metabolic syndrome, type 2 diabetes mellitus, Hashimoto's thyroidis and Graves' disease; they can also play a role in nervous system disturbances, such as multiple sclerosis, Alzheimer's disease, Parkinson's disease, and depression. An association has also been found between gut microbiota dysbiosis and cancer. Our health is closely associated with the state of our microbiota, and their homeostasis. The aim of this review is to describe the associations between human gut microbiota and cancer, and examine the potential role of gut microbiota in anticancer therapy.
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Affiliation(s)
| | - Leszek Szablewski
- Chair and Department of General Biology and Parasitology, Medical University of Warsaw, ul. Chalubinskiego 5, 02-004 Warsaw, Poland;
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4
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Chen Q, He Z, Zhuo Y, Li S, Yang W, Hu L, Zhong H. Rubidium chloride modulated the fecal microbiota community in mice. BMC Microbiol 2021; 21:46. [PMID: 33588762 PMCID: PMC7885239 DOI: 10.1186/s12866-021-02095-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/19/2021] [Indexed: 12/24/2022] Open
Abstract
Background The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated for their characteristics and bacterial microbiome changes. Results The 16S ribosomal RNA gene sequencing of fecal microbiota showed that RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio, but significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. With regarding to the archaea, we only observed two less richness archaea Sulfolobus and Acidiplasma at the genus level. Conclusions Changes of fecal microbes may in part contribute to the anticancer or anti-depressant effects of RbCl. These findings further validate that the microbiome could be a target for therapeutic intervention. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02095-4.
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Affiliation(s)
- Qian Chen
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Zhiguo He
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yuting Zhuo
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Shuzhen Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Wenjing Yang
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Liang Hu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Hui Zhong
- School of Life Sciences, Central South University, Changsha, 410013, China.
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5
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Liu Y, Li Z, Wu Y, Jing X, Li L, Fang X. Intestinal Bacteria Encapsulated by Biomaterials Enhance Immunotherapy. Front Immunol 2021; 11:620170. [PMID: 33643302 PMCID: PMC7902919 DOI: 10.3389/fimmu.2020.620170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
The human intestine contains thousands of bacterial species essential for optimal health. Aside from their pathogenic effects, these bacteria have been associated with the efficacy of various treatments of diseases. Due to their impact on many human diseases, intestinal bacteria are receiving increasing research attention, and recent studies on intestinal bacteria and their effects on treatments has yielded valuable results. Particularly, intestinal bacteria can affect responses to numerous forms of immunotherapy, especially cancer therapy. With the development of precision medicine, understanding the factors that influence intestinal bacteria and how they can be regulated to enhance immunotherapy effects will improve the application prospects of intestinal bacteria therapy. Further, biomaterials employed for the convenient and efficient delivery of intestinal bacteria to the body have also become a research hotspot. In this review, we discuss the recent findings on the regulatory role of intestinal bacteria in immunotherapy, focusing on immune cells they regulate. We also summarize biomaterials used for their delivery.
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Affiliation(s)
- Yilun Liu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhongmin Li
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yuanyu Wu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xiabin Jing
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Lin Li
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xuedong Fang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
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6
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Shojaee S, Sharma A, Gottel N, Sanchez T, Gilbert JA, Rahman NM. Microbiome profile associated with malignant pleural effusion. PLoS One 2020; 15:e0232181. [PMID: 32384089 PMCID: PMC7209204 DOI: 10.1371/journal.pone.0232181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/08/2020] [Indexed: 11/18/2022] Open
Abstract
Introduction There is ongoing research into the development of novel molecular markers that may complement fluid cytology malignant pleural effusion (MPE) diagnosis. In this exploratory pilot study, we hypothesized that there are distinct differences in the pleural fluid microbiome profile of malignant and non-malignant pleural diseases. Method From a prospectively enrolled pleural fluid biorepository, samples of MPE were included. Non-MPE effusion were included as comparators. 16S rRNA gene V4 region amplicon sequencing was performed. Exact Sequence Variants (ESVs) were used for diversity analyses. The Shannon and Richness indices of alpha diversity and UniFrac beta diversity measures were tested for significance using permutational multivariate analysis of variance. Analyses of Composition of Microbiome was used to identify differentially abundant bacterial ESVs between the groups controlled for multiple hypothesis testing. Results 38 patients with MPE and 9 with non-MPE were included. A subgroup of patients with metastatic adenocarcinoma histology were identified among MPE group (adenocarcinoma of lung origin (LA-MPE) = 11, breast origin (BA-MPE) = 11). MPE presented with significantly greater alpha diversity compared to non-MPE group. Within the MPE group, BA-MPE was more diverse compared to LA-MPE group. In multivariable analysis, ESVs belonging to family S24-7 and genera Allobaculum, Stenotrophomonas, and Epulopiscium were significantly enriched in the malignant group compared to the non-malignant group. Conclusion Our results are the first to demonstrate a microbiome signature according to MPE and non-MPE. The role of microbiome in pleural effusion pathogenesis needs further exploration.
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Affiliation(s)
- Samira Shojaee
- Division of Pulmonary and Critical Care Medicine, Virginia Commonwealth University Medical Center, Richmond, VA, United States of America
- * E-mail:
| | - Anukriti Sharma
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, United States of America
| | - Neil Gottel
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, United States of America
- Scripps Institution of Oceanography, UCSD, San Diego, CA, United States of America
| | - Trinidad Sanchez
- Division of Pulmonary and Critical Care Medicine, Virginia Commonwealth University Medical Center, Richmond, VA, United States of America
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, United States of America
- Scripps Institution of Oceanography, UCSD, San Diego, CA, United States of America
| | - Najib M. Rahman
- Oxford Respiratory Trials Unit, Oxford Centre for Respiratory Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom
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7
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Alterations of the Predominant Fecal Microbiota and Disruption of the Gut Mucosal Barrier in Patients with Early-Stage Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2948282. [PMID: 32280686 PMCID: PMC7114766 DOI: 10.1155/2020/2948282] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/18/2020] [Accepted: 03/09/2020] [Indexed: 12/16/2022]
Abstract
Growing evidence indicated that the gut microbiota was the intrinsic and essential component of the cancer microenvironment, which played vital roles in the development and progression of colorectal cancer (CRC). In our present study, we investigated the alterations of fecal abundant microbiota with real-time quantitative PCR and the changes of indicators of gut mucosal barrier from 53 early-stage CRC patients and 45 matched healthy controls. We found that the traditional beneficial bacteria such as Lactobacillus and Bifidobacterium decreased significantly and the carcinogenic bacteria such as Enterobacteriaceae and Fusobacterium nucleatum were significantly increased in CRC patients. We also found gut mucosal barrier dysfunction in CRC patients with increased levels of endotoxin (LPS), D-lactate, and diamine oxidase (DAO). With Pearson's correlation analysis, D-lactate, LPS, and DAO were correlated negatively with Lactobacillus and Bifidobacterium and positively with Enterobacteriaceae and F. nucleatum. Our present study found dysbiosis of the fecal microbiota and dysfunction of the gut mucosal barrier in patients with early-stage CRC, which implicated that fecal abundant bacteria and gut mucosal barrier indicators could be used as targets to monitor the development and progression of CRC in a noninvasive and dynamic manner.
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8
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Xu S, Yin W, Zhang Y, Lv Q, Yang Y, He J. Foes or Friends? Bacteria Enriched in the Tumor Microenvironment of Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12020372. [PMID: 32041122 PMCID: PMC7072156 DOI: 10.3390/cancers12020372] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the second most commonly diagnosed cancer and the third cause of cancer death in the world, while intestinal microbiota is a community of microbes living in human intestine that can potentially impact human health in many ways. Accumulating evidence suggests that intestinal microbiota, especially that from the intestinal bacteria, play a key role in the CRC development; therefore, identification of bacteria involved in CRC development can provide new targets for the CRC diagnosis, prevention, and treatment. Over the past decade, there have been considerable advances in applying 16S rDNA sequencing data to verify associated intestinal bacteria in CRC patients; however, due to variations of individual and environment factors, these results seem to be inconsistent. In this review, we scrutinized the previous 16S rDNA sequencing data of intestinal bacteria from CRC patients, and identified twelve genera that are specifically enriched in the tumor microenvironment. We have focused on their relationship with the CRC development, and shown that some bacteria could promote CRC development, acting as foes, while others could inhibit CRC development, serving as friends, for human health. Finally, we highlighted their potential applications for the CRC diagnosis, prevention, and treatment.
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9
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Settanni CR, Quaranta G, Bibbò S, Gasbarrini A, Cammarota G, Ianiro G. Oral supplementation with lactobacilli to prevent colorectal cancer in preclinical models. MINERVA GASTROENTERO 2019; 66:48-69. [PMID: 31760735 DOI: 10.23736/s1121-421x.19.02631-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is still a major threat for public health, as it is the third most common cancer in men and the second in women and it ranks second among tumors in terms of mortality. Evidence from the last decades emphasizes the complex role of gut microbial composition in CRC development. Historically, it is believed that dairy products, a source of lactobacilli and other lactic acid bacteria, are beneficial for human health and help in preventing CRC. We searched online literature for trials evaluating the preventive role of lactobacilli in CRC animal models. Most of selected studied assessed a relevant role of lactobacilli in preventing CRC and precursor lesions. Mechanisms through which this effect was achieved are supposed to regard immunomodulation, regulation of apoptosis, gut microbial modulation, genes expression, reduction of oxidative stress and others. Lactobacilli oral supplementation is reported to be effective in preventing CRC in animal models, even if the underlying mechanisms of action are still not fully understood.
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Affiliation(s)
- Carlo R Settanni
- Digestive Disease Center, Agostino Gemelli University Polyclinic, IRCCS and Foundation, Sacred Heart Catholic University, Rome, Italy
| | - Gianluca Quaranta
- Institute of Microbiology, Agostino Gemelli University Polyclinic, IRCCS and Foundation, Sacred Heart Catholic University, Rome, Italy
| | - Stefano Bibbò
- Digestive Disease Center, Agostino Gemelli University Polyclinic, IRCCS and Foundation, Sacred Heart Catholic University, Rome, Italy
| | - Antonio Gasbarrini
- Digestive Disease Center, Agostino Gemelli University Polyclinic, IRCCS and Foundation, Sacred Heart Catholic University, Rome, Italy
| | - Giovanni Cammarota
- Digestive Disease Center, Agostino Gemelli University Polyclinic, IRCCS and Foundation, Sacred Heart Catholic University, Rome, Italy
| | - Gianluca Ianiro
- Digestive Disease Center, Agostino Gemelli University Polyclinic, IRCCS and Foundation, Sacred Heart Catholic University, Rome, Italy -
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10
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Piazzi G, Prossomariti A, Baldassarre M, Montagna C, Vitaglione P, Fogliano V, Biagi E, Candela M, Brigidi P, Balbi T, Munarini A, Belluzzi A, Pariali M, Bazzoli F, Ricciardiello L. A Mediterranean Diet Mix Has Chemopreventive Effects in a Murine Model of Colorectal Cancer Modulating Apoptosis and the Gut Microbiota. Front Oncol 2019; 9:140. [PMID: 30915275 PMCID: PMC6423077 DOI: 10.3389/fonc.2019.00140] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/18/2019] [Indexed: 12/24/2022] Open
Abstract
Objectives: Unhealthy dietary patterns have been associated with colorectal cancer (CRC) onset while Mediterranean Diet (MD) has been proposed for CRC prevention. This study evaluated the effect of a Mediterranean Diet Mix (MD-MIX) on colonic tumors development in A/J mice fed a low-fat (LFD) or a high-fat western diet (HFWD), and injected with the procarcinogen azoxymethane (AOM). Materials and Methods: Forty A/J male mice were randomly assigned into four feeding arms (10 mice/arm; LFD, LFD-MD-MIX, HFWD, HFWD-MD-MIX) to be treated with AOM. Ten mice were exposed to the diets alone (Healthy LFD and Healthy HFWD) to be used as control. Tumor incidence and multiplicity were evaluated at sacrifice. Mucosal fatty acid content and urinary phenolic compounds were assayed by mass spectrometry. Apoptosis was evaluated by TUNEL assay and gene expression markers. Cell proliferation was evaluated by Ki67 immunohistochemistry. Microbiota composition was assessed at different time points by 16S RNA sequencing. Results: A tumor incidence of 100% was obtained in AOM-treated mice. The MD-MIX supplementation was able to reduce the number of colonic lesions in both LFD and HFWD-fed mice and to induce apoptosis, in particular in the LFD-MD-MIX arm. Moreover, a preventive effect on low-grade dysplasia and macroscopical lesions (>1 mm) development was found in HFWD-fed mice together with a regulation of the AOM-driven intestinal dysbiosis. Conclusions: MD-MIX was able to counteract CRC development in mice under different dietary backgrounds through the regulation of apoptosis and gut microbiota.
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Affiliation(s)
- Giulia Piazzi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Anna Prossomariti
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Maurizio Baldassarre
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Claudio Montagna
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Paola Vitaglione
- Department of Agricultural Sciences, University of Naples, Portici, Italy
| | - Vincenzo Fogliano
- Food Quality and Design Group, Wageningen University, Wageningen, Netherlands
| | - Elena Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Tiziana Balbi
- Pathology Unit, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Alessandra Munarini
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Andrea Belluzzi
- Gastroenterology Unit, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Milena Pariali
- Center for Applied Biomedical Research (CRBA), S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Franco Bazzoli
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Luigi Ricciardiello
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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11
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Novel strains of Bacteroides fragilis and Bacteroides ovatus alleviate the LPS-induced inflammation in mice. Appl Microbiol Biotechnol 2019; 103:2353-2365. [PMID: 30666361 DOI: 10.1007/s00253-019-09617-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 02/08/2023]
Abstract
Lipopolysaccharide (LPS) can promote the expression of pro-inflammatory cytokines, damage the tight junction of epithelial walls, and thereby lead to chronic low-grade intestinal inflammatory disorders. Evidences of many beneficial functions from Bacteroides strains suggest their intervention capabilities in LPS-induced inflammation. In the present study, both healthy and LPS-treated mice were consistently treated with Bacteroides strains for 5 days. The intestinal microbiota alteration, epithelial permeability, cytokine expression, and autoimmune and innate immune responses were analyzed. B. fragilis HCK-B3 and B. ovatus ELH-B2 from our laboratory collection were demonstrated to assist intestinal equilibrium by maintaining the diversity of gut microbiota and relieve LPS-induced inflammation by either modulating cytokine production or restoring the Treg/Th-17 balance. Our research indicated that the Bacteroides strains with capabilities of alleviating inflammation have the potential as therapeutics to prevent intestinal inflammatory disorders and provided scientific supports for discovering next-generation probiotics.
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12
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Lazar V, Ditu LM, Pircalabioru GG, Gheorghe I, Curutiu C, Holban AM, Picu A, Petcu L, Chifiriuc MC. Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Front Immunol 2018; 9:1830. [PMID: 30158926 PMCID: PMC6104162 DOI: 10.3389/fimmu.2018.01830] [Citation(s) in RCA: 297] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/24/2018] [Indexed: 12/12/2022] Open
Abstract
The microbiota consists of a dynamic multispecies community of bacteria, fungi, archaea, and protozoans, bringing to the host organism a dowry of cells and genes more numerous than its own. Among the different non-sterile cavities, the human gut harbors the most complex microbiota, with a strong impact on host homeostasis and immunostasis, being thus essential for maintaining the health condition. In this review, we outline the roles of gut microbiota in immunity, starting with the background information supporting the further presentation of the implications of gut microbiota dysbiosis in host susceptibility to infections, hypersensitivity reactions, autoimmunity, chronic inflammation, and cancer. The role of diet and antibiotics in the occurrence of dysbiosis and its pathological consequences, as well as the potential of probiotics to restore eubiosis is also discussed.
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Affiliation(s)
- Veronica Lazar
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Lia-Mara Ditu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Gratiela Gradisteanu Pircalabioru
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Irina Gheorghe
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Carmen Curutiu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Alina Maria Holban
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
| | - Ariana Picu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- National Institute for Diabetes, Nutrition and Metabolic Diseases Prof. Dr. N. Paulescu, Bucharest, Romania
| | - Laura Petcu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- National Institute for Diabetes, Nutrition and Metabolic Diseases Prof. Dr. N. Paulescu, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, Bucharest, Romania
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Bamola VD, Ghosh A, Kapardar RK, Lal B, Cheema S, Sarma P, Chaudhry R. Gut microbial diversity in health and disease: experience of healthy Indian subjects, and colon carcinoma and inflammatory bowel disease patients. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017; 28:1322447. [PMID: 28588430 PMCID: PMC5444350 DOI: 10.1080/16512235.2017.1322447] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/17/2017] [Indexed: 02/08/2023]
Abstract
Background: The intestinal microbiota, through complex interactions with the gut mucosa, play a key role in the pathogenesis of colon carcinoma and inflammatory bowel disease (IBD). The disease condition and dietary habits both influence gut microbial diversity. Objective: The aim of this study was to assess the gut microbial profile of healthy subjects and patients with colon carcinoma and IBD. Healthy subjects included 'Indian vegetarians/lactovegetarians', who eat plant produce, milk and milk products, and 'Indian non-vegetarians', who eat plant produce, milk and milk products, certain meats and fish, and the eggs of certain birds and fish. 'Indian vegetarians' are different from 'vegans', who do not eat any foods derived wholly or partly from animals, including milk products. Design: Stool samples were collected from healthy Indian vegetarians/lactovegetarians and non-vegetarians, and colon cancer and IBD patients. Clonal libraries of 16S ribosomal DNA (rDNA) of bacteria were created from each sample. Clones were sequenced from one representative sample of each group. Approximately 500 white colonies were picked at random from each sample and 100 colonies were sequenced after amplified rDNA restriction analysis. Results: The dominant phylum from the healthy vegetarian was Firmicutes (34%), followed by Bacteroidetes (15%). The balance was reversed in the healthy non-vegetarian (Bacteroidetes 84%, Firmicutes 4%; ratio 21:1). The colon cancer and IBD patients had higher percentages of Bacteroidetes (55% in both) than Firmicutes (26% and 12%, respectively) but lower Bacteroidetes:Firmicutes ratios (3.8:1 and 2.4:1, respectively) than the healthy non-vegetarian. Bacterial phyla of Verrucomicrobiota and Actinobacteria were detected in 23% and 5% of IBD and colon patients, respectively. Conclusions: Ribosomal Database Project profiling of gut flora in this study population showed remarkable differences, with unique diversity attributed to different diets and disease conditions.
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Affiliation(s)
- V. Deepak Bamola
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Arnab Ghosh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Raj Kishor Kapardar
- Microbial Biotechnology Division, The Energy and Resources Institute, New Delhi, India
| | - Banwari Lal
- Microbial Biotechnology Division, The Energy and Resources Institute, New Delhi, India
| | - Simrita Cheema
- Microbial Biotechnology Division, The Energy and Resources Institute, New Delhi, India
| | - Priyangshu Sarma
- Microbial Biotechnology Division, The Energy and Resources Institute, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model. Sci Rep 2016; 6:31027. [PMID: 27503127 PMCID: PMC4977522 DOI: 10.1038/srep31027] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023] Open
Abstract
Gut microbiota dysbiosis are associated with a wide range of human diseases, including inflammatory bowel diseases. The physiopathology of these diseases has multifactorial aetiology in which environmental factors, particularly pollution could play a crucial role. Among the different pollutants listed, Polycyclic Aromatic Hydrocarbons (PAHs) are subject to increased monitoring due to their wide distribution and high toxicity on Humans. Here, we used 16S rRNA gene sequencing to investigate the impact of benzo[a]pyrene (BaP, most toxic PAH) oral exposure on the faecal and intestinal mucosa-associated bacteria in C57BL/6 mice. Intestinal inflammation was also evaluated by histological observations. BaP oral exposure significantly altered the composition and the abundance of the gut microbiota and led to moderate inflammation in ileal and colonic mucosa. More severe lesions were observed in ileal segment. Shifts in gut microbiota associated with moderate inflammatory signs in intestinal mucosa would suggest the establishment of a pro-inflammatory intestinal environment following BaP oral exposure. Therefore, under conditions of genetic susceptibility and in association with other environmental factors, exposure to this pollutant could trigger and/or accelerate the development of inflammatory pathologies.
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15
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Yu H, Meng H, Zhou F, Ni X, Shen S, Das UN. Urinary microbiota in patients with prostate cancer and benign prostatic hyperplasia. Arch Med Sci 2015; 11:385-94. [PMID: 25995756 PMCID: PMC4424255 DOI: 10.5114/aoms.2015.50970] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/02/2014] [Accepted: 06/12/2014] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Inflammation is associated with promotion of the initiation of various malignancies, partly due to bacterial infection-induced microenvironmental changes. However, the exact association between microbiota in urine, seminal fluid and the expressed prostatic secretions and benign prostatic hypertrophy and prostate cancer is not clear. MATERIAL AND METHODS In the present study, we investigated the type of microbiota in the expressed prostatic secretions (EPS) of patients with prostate cancer and benign prostatic hyperplasia (BPH) by the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method using universal bacterial primers. In order to understand the possible association between various bacteria and prostate cancer, quantitative real-time PCR assay was performed to quantify the amount of strains of bacteria in urine, EPS and seminal fluid. RESULTS The prostate cancer group had a significantly increased number of Bacteroidetes bacteria, Alphaproteobacteria, Firmicutes bacteria, Lachnospiraceae, Propionicimonas, Sphingomonas, and Ochrobactrum, and a decrease in Eubacterium and Defluviicoccus compared to the BPH group. The number of Escherichia coli in the prostate cancer group was significantly decreased in urine and increased in the EPS and seminal fluid, while the number of Enterococcus was significantly increased in the seminal fluid with little change in urine and EPS. CONCLUSIONS Based on these results, we suggest that there are significant changes in the microbial population in EPS, urine and seminal fluid of subjects with prostate cancer and BPH, indicating a possible role for these bacteria in these two conditions.
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Affiliation(s)
- Haining Yu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Hongzhou Meng
- Department of Urology, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Feng Zhou
- Department of Urology, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xiaofeng Ni
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Shengrong Shen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
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16
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Abstract
The trillions of bacteria that naturally reside in the human gut collectively constitute the complex system known the gut microbiome, a vital player for the host's homeostasis and health. However, there is mounting evidence that dysbiosis, a state of pathological imbalance in the gut microbiome is present in many disease states. In this review, we present recent insights concerning the gut microbiome's contribution to the development of colorectal adenomas and the subsequent progression to colorectal cancer (CRC). In the United States alone, CRC is the second leading cause of cancer deaths. As a result, there is a high interest in identifying risk factors for adenomas, which are intermediate precursors to CRC. Recent research on CRC and the microbiome suggest that modulation of the gut bacterial composition and structure may be useful in preventing adenomas and CRC. We highlight the known risk factors for colorectal adenomas and the potential mechanisms by which microbial dysbiosis may contribute to the etiology of CRC. We also underscore novel findings from recent studies on the gut microbiota and colorectal adenomas along with current knowledge gaps. Understanding the microbiome may provide promising new directions towards novel diagnostic tools, biomarkers, and therapeutic interventions for CRC.
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17
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Gao Z, Guo B, Gao R, Zhu Q, Qin H. Microbiota disbiosis is associated with colorectal cancer. Front Microbiol 2015; 6:20. [PMID: 25699023 PMCID: PMC4313696 DOI: 10.3389/fmicb.2015.00020] [Citation(s) in RCA: 342] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 01/07/2015] [Indexed: 12/12/2022] Open
Abstract
The dysbiosis of the human intestinal microbiota is linked to sporadic colorectal carcinoma (CRC). The present study was designed to investigate the gut microbiota distribution features in CRC patients. We performed pyrosequencing based analysis of the 16S rRNA gene V3 region to investigate microbiota of the cancerous tissue and adjacent non-cancerous normal tissue in proximal and distal CRC samples. The results revealed that the microbial structures of the CRC patients and healthy individuals differed significantly. Firmicutes and Fusobacteria were over-represented whereas Proteobacteria was under-represented in CRC patients. In addition, Lactococcus and Fusobacterium exhibited a relatively higher abundance while Pseudomonas and Escherichia-Shigella was reduced in cancerous tissues compared to adjacent non-cancerous tissues. Meanwhile, the overall microbial structures of proximal and distal colon cancerous tissues were similar; but certain potential pro-oncogenic pathogens were different. These results suggested that the mucosa-associated microbiota is dynamically associated with CRC, which may provide evidences for microbiota-associated diagnostic, prognostic, preventive, and therapeutic strategies for CRC.
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Affiliation(s)
- Zhiguang Gao
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai, China
| | - Bomin Guo
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai, China
| | - Renyuan Gao
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai, China
| | - Qingchao Zhu
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai, China
| | - Huanlong Qin
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai, China
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18
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Zhu Q, Jin Z, Wu W, Gao R, Guo B, Gao Z, Yang Y, Qin H. Analysis of the intestinal lumen microbiota in an animal model of colorectal cancer. PLoS One 2014; 9:e90849. [PMID: 24603888 PMCID: PMC3946251 DOI: 10.1371/journal.pone.0090849] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/30/2014] [Indexed: 12/25/2022] Open
Abstract
Recent reports have suggested that multiple factors such as host genetics, environment and diet can promote the progression of healthy mucosa towards sporadic colorectal carcinoma. Accumulating evidence has additionally associated intestinal bacteria with disease initiation and progression. In order to examine and analyze the composition of gut microbiota in the absence of confounding influences, we have established an animal model of 1, 2-dimethylhydrazine (DMH)-induced colon cancer. Using this model, we have performed pyrosequencing of the V3 region of the 16S rRNA genes in this study to determine the diversity and breadth of the intestinal microbial species. Our findings indicate that the microbial composition of the intestinal lumen differs significantly between control and tumor groups. The abundance of Firmicutes was elevated whereas the abundance of Bacteroidetes and Spirochetes was reduced in the lumen of CRC rats. Fusobacteria was not detected in any of the healthy rats and there was no significant difference in observed Proteobacteria species when comparing the bacterial communities between our two groups. Interestingly, the abundance of Proteobacteria was higher in CRC rats. At the genus level, Bacteroides exhibited a relatively higher abundance in CRC rats compared to controls (14.92% vs. 9.22%, p<0.001). Meanwhile, Prevotella (55.22% vs. 26.19%), Lactobacillus (3.71% vs. 2.32%) and Treponema (3.04% vs. 2.43%), were found to be significantly more abundant in healthy rats than CRC rats (p<0.001, respectively). We also demonstrate a significant reduction of butyrate-producing bacteria such as Roseburia and Eubacterium in the gut microbiota of CRC rats. Furthermore, a significant increase in Desulfovibrio, Erysipelotrichaceae and Fusobacterium was also observed in the tumor group. A decrease in probiotic species such as Ruminococcus and Lactobacillus was likewise observed in the tumor group. Collectively, we can conclude that a significant difference in intestinal bacterial flora exists between healthy rats and CRC rats.
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Affiliation(s)
- Qingchao Zhu
- Department of Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Zhiming Jin
- Department of Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Wen Wu
- Department of Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Renyuan Gao
- Department of Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Bomin Guo
- Department of Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Zhiguang Gao
- Department of Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Yongzhi Yang
- Department of Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Huanlong Qin
- Department of Surgery, The Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
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Lindström C, Xu J, Oste R, Holst O, Molin G. Oral administration of live exopolysaccharide-producing Pediococcus parvulus, but not purified exopolysaccharide, suppressed Enterobacteriaceae without affecting bacterial diversity in ceca of mice. Appl Environ Microbiol 2013; 79:5030-7. [PMID: 23770909 PMCID: PMC3754715 DOI: 10.1128/aem.01456-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/09/2013] [Indexed: 01/19/2023] Open
Abstract
Growing evidence indicates that the gut microbiota could have an important role in the development of diet- and lifestyle-induced diseases. It has been shown that modulation of the gut microbiota by means of probiotics and prebiotics could improve host health. An oat-based product fermented by the exopolysaccharide (EPS)-producing organism Pediococcus parvulus 2.6 has been reported to have a bifidogenic effect. To find out whether the effect could be attributed to the EPS or the bacterium, mice were fed a diet supplemented with 2% purified EPS or 10(8) CFU/g of live P. parvulus 2.6 for 6 weeks. Both supplementations altered the gut microbiota composition but in different directions. Purified EPS not only significantly lowered the microbial diversity (P < 0.001) but decreased the bifidobacterial population (P = 0.01). In contrast, the live EPS-producing bacterium P. parvulus 2.6 antagonized Enterobacteriaceae without disturbing the homeostasis of the cecal microbiota.
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Affiliation(s)
- Cecilia Lindström
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden.
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Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity. Appl Environ Microbiol 2013; 79:5962-9. [PMID: 23872556 DOI: 10.1128/aem.01282-13] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Ever since Carl Woese introduced the use of 16S rRNA genes for determining the phylogenetic relationships of prokaryotes, this method has been regarded as the "gold standard" in both microbial phylogeny and ecology studies. However, intragenomic heterogeneity within 16S rRNA genes has been reported in many investigations and is believed to bias the estimation of prokaryotic diversity. In the current study, 2,013 completely sequenced genomes of bacteria and archaea were analyzed and intragenomic heterogeneity was found in 952 genomes (585 species), with 87.5% of the divergence detected being below the 1% level. In particular, some extremophiles (thermophiles and halophiles) were found to harbor highly divergent 16S rRNA genes. Overestimation caused by 16S rRNA gene intragenomic heterogeneity was evaluated at different levels using the full-length and partial 16S rRNA genes usually chosen as targets for pyrosequencing. The result indicates that, at the unique level, full-length 16S rRNA genes can produce an overestimation of as much as 123.7%, while at the 3% level, an overestimation of 12.9% for the V6 region may be introduced. Further analysis showed that intragenomic heterogeneity tends to concentrate in specific positions, with the V1 and V6 regions suffering the most intragenomic heterogeneity and the V4 and V5 regions suffering the least intragenomic heterogeneity in bacteria. This is the most up-to-date overview of the diversity of 16S rRNA genes within prokaryotic genomes. It not only provides general guidance on how much overestimation can be introduced when applying 16S rRNA gene-based methods, due to its intragenomic heterogeneity, but also recommends that, for bacteria, this overestimation be minimized using primers targeting the V4 and V5 regions.
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21
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Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One 2012; 7:e39743. [PMID: 22761885 PMCID: PMC3386193 DOI: 10.1371/journal.pone.0039743] [Citation(s) in RCA: 668] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 05/25/2012] [Indexed: 12/12/2022] Open
Abstract
Recent reports have suggested the involvement of gut microbiota in the progression of colorectal cancer (CRC). We utilized pyrosequencing based analysis of 16S rRNA genes to determine the overall structure of microbiota in patients with colorectal cancer and healthy controls; we investigated microbiota of the intestinal lumen, the cancerous tissue and matched noncancerous normal tissue. Moreover, we investigated the mucosa-adherent microbial composition using rectal swab samples because the structure of the tissue-adherent bacterial community is potentially altered following bowel cleansing. Our findings indicated that the microbial structure of the intestinal lumen and cancerous tissue differed significantly. Phylotypes that enhance energy harvest from diets or perform metabolic exchange with the host were more abundant in the lumen. There were more abundant Firmicutes and less abundant Bacteroidetes and Proteobacteria in lumen. The overall microbial structures of cancerous tissue and noncancerous tissue were similar; howerer the tumor microbiota exhibited lower diversity. The structures of the intestinal lumen microbiota and mucosa-adherent microbiota were different in CRC patients compared to matched microbiota in healthy individuals. Lactobacillales was enriched in cancerous tissue, whereas Faecalibacterium was reduced. In the mucosa-adherent microbiota, Bifidobacterium, Faecalibacterium, and Blautia were reduced in CRC patients, whereas Fusobacterium, Porphyromonas, Peptostreptococcus, and Mogibacterium were enriched. In the lumen, predominant phylotypes related to metabolic disorders or metabolic exchange with the host, Erysipelotrichaceae, Prevotellaceae, and Coriobacteriaceae were increased in cancer patients. Coupled with previous reports, these results suggest that the intestinal microbiota is associated with CRC risk and that intestinal lumen microflora potentially influence CRC risk via cometabolism or metabolic exchange with the host. However, mucosa-associated microbiota potentially affects CRC risk primarily through direct interaction with the host.
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Affiliation(s)
- Weiguang Chen
- State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Fanlong Liu
- Department of Anus and Intestine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zongxin Ling
- State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojuan Tong
- State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Charlie Xiang
- State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- * E-mail:
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Characterisation of the bacterial community in expressed prostatic secretions from patients with chronic prostatitis/chronic pelvic pain syndrome and infertile men: a preliminary investigation. Asian J Androl 2012; 14:566-73. [PMID: 22635162 DOI: 10.1038/aja.2012.30] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The expressed prostatic secretions (EPSs) of men with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), infertile men and normal men were subjected to microbiological study. EPSs were collected from the subjects, which included 26 normal men, 11 infertile patients and 51 CP/CPPS patients. DNA was extracted from each specimen, and the V3 regions of the 16S rRNA genes were amplified using universal bacterial primers. The results showed that the EPS 16S rRNA gene-positive rate in the CP/CPPS and infertile patients was much higher than in the normal men, but without any difference among the three patient groups. The denaturing gradient gel electrophoresis (DGGE) method was used to characterize the EPS bacterial community structure of the prostate fluid from patients with CP/CPPS or infertility issues. Principal component analysis (PCA) and partial least squares (PLS) analyses of PCR-DGGE profiles revealed that the EPS bacterial community structure differed among the three groups. Three bands were identified as the key factors responsible for the discrepancy between CP/CPPS patients and infertile patients (P<0.05). Two bands were identified as priority factors in the discrepancy of category IIIA and category IIIB prostatitis patients (P<0.05). According to this research, the ecological balance of the prostate and low urethra tract, when considered as a microenvironment, might play an important role in the maintenance of a healthy male reproductive tract.
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Dostal A, Chassard C, Hilty FM, Zimmermann MB, Jaeggi T, Rossi S, Lacroix C. Iron depletion and repletion with ferrous sulfate or electrolytic iron modifies the composition and metabolic activity of the gut microbiota in rats. J Nutr 2012; 142:271-7. [PMID: 22190022 PMCID: PMC3260059 DOI: 10.3945/jn.111.148643] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Iron (Fe) deficiency anemia is a global health concern and Fe fortification and supplementation are common corrective strategies. Fe is essential not only for the human host but also for nearly all gut bacteria. We studied the impact of Fe deficiency and Fe repletion on the gut microbiota in rats. Weanling rats were fed an Fe-deficient diet for 24 d and then repleted for 13 d with FeSO₄ (n = 15) or electrolytic Fe (n = 14) at 10 and 20 mg Fe · kg diet⁻¹. In addition, one group of rats (n = 8) received the Fe-deficient diet and one group (n = 3) received a Fe-sufficient control diet for all 37 d. Fecal samples were collected at baseline and after the depletion and repletion periods, and colonic tissues were examined histologically. Microbial metabolite composition in cecal water was measured and fecal samples were analyzed for microbial composition with temporal temperature gradient gel electrophoresis and qPCR. Compared to Fe-sufficient rats, Fe-deficient rats had significantly lower concentrations of cecal butyrate (-87%) and propionate (-72%) and the abundance of dominant species was strongly modified, including greater numbers of lactobacilli and Enterobacteriaceae and a large significant decrease of the Roseburia spp./E. rectale group, a major butyrate producer. Repletion with 20 mg FeSO₄ · kg diet⁻¹ significantly increased cecal butyrate concentrations and partially restored bacterial populations compared to Fe-deficient rats at endpoint. The effects on the gut microbiota were stronger in rats repleted with FeSO₄ than in rats repleted with electrolytic Fe, suggesting ferrous Fe may be more available for utilization by the gut microbiota than elemental Fe. Repletion with FeSO₄ significantly increased neutrophilic infiltration of the colonic mucosa compared to Fe-deficient rats. In conclusion, Fe depletion and repletion strongly affect the composition and metabolic activity of rat gut microbiota.
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Affiliation(s)
| | | | | | - Michael B. Zimmermann
- Institute of Food, Nutrition and Health, Zurich, Switzerland,Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - Tanja Jaeggi
- Institute of Food, Nutrition and Health, Zurich, Switzerland
| | - Samuela Rossi
- Institute of Food, Nutrition and Health, Zurich, Switzerland
| | - Christophe Lacroix
- Institute of Food, Nutrition and Health, Zurich, Switzerland,To whom correspondence should be addressed. E-mail:
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Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X, Jia W, Cai S, Zhao L. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME JOURNAL 2011; 6:320-9. [PMID: 21850056 DOI: 10.1038/ismej.2011.109] [Citation(s) in RCA: 854] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite a long-suspected role in the development of human colorectal cancer (CRC), the composition of gut microbiota in CRC patients has not been adequately described. In this study, fecal bacterial diversity in CRC patients (n=46) and healthy volunteers (n=56) were profiled by 454 pyrosequencing of the V3 region of the 16S ribosomal RNA gene. Both principal component analysis and UniFrac analysis showed structural segregation between the two populations. Forty-eight operational taxonomic units (OTUs) were identified by redundancy analysis as key variables significantly associated with the structural difference. One OTU closely related to Bacteroides fragilis was enriched in the gut microbiota of CRC patients, whereas three OTUs related to Bacteroides vulgatus and Bacteroides uniformis were enriched in that of healthy volunteers. A total of 11 OTUs belonging to the genera Enterococcus, Escherichia/Shigella, Klebsiella, Streptococcus and Peptostreptococcus were significantly more abundant in the gut microbiota of CRC patients, and 5 OTUs belonging to the genus Roseburia and other butyrate-producing bacteria of the family Lachnospiraceae were less abundant. Real-time quantitative PCR further validated the significant reduction of butyrate-producing bacteria in the gut microbiota of CRC patients by measuring the copy numbers of butyryl-coenzyme A CoA transferase genes (Mann-Whitney test, P<0.01). Reduction of butyrate producers and increase of opportunistic pathogens may constitute a major structural imbalance of gut microbiota in CRC patients.
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Affiliation(s)
- Tingting Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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