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Roy R, Singh SK. The Microbiome Modulates the Immune System to Influence Cancer Therapy. Cancers (Basel) 2024; 16:779. [PMID: 38398170 PMCID: PMC10886470 DOI: 10.3390/cancers16040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The gut microbiota composition can affect the tumor microenvironment and its interaction with the immune system, thereby having implications for treatment predictions. This article reviews the studies available to better understand how the gut microbiome helps the immune system fight cancer. To describe this fact, different mechanisms and approaches utilizing probiotics to improve advancements in cancer treatment will be discussed. Moreover, not only calorie intake but also the variety and quality of diet can influence cancer patients' immunotherapy treatment because dietary patterns can impair immunological activities either by stimulating or suppressing innate and adaptive immunity. Therefore, it is interesting and critical to understand gut microbiome composition as a biomarker to predict cancer immunotherapy outcomes and responses. Here, more emphasis will be given to the recent development in immunotherapies utilizing microbiota to improve cancer therapies, which is beneficial for cancer patients.
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Affiliation(s)
- Ruchi Roy
- UICentre for Drug Discovery, The University of Illinois, Chicago, IL 60612, USA
| | - Sunil Kumar Singh
- Department of Surgery, Division of Surgical Oncology, The University of Illinois at Chicago, Chicago, IL 60612, USA
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2
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Williams AJ, Paramsothy R, Wu N, Ghaly S, Leach S, Paramsothy S, Corte C, O'Brien C, Burke C, Wark G, Samocha-Bonet D, Lambert K, Ahlenstiel G, Wasinger V, Dutt S, Pavli P, Grimm M, Lemberg D, Connor S, Leong R, Hold G. Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study. BMJ Open 2021; 11:e042493. [PMID: 33593778 PMCID: PMC7888320 DOI: 10.1136/bmjopen-2020-042493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
INTRODUCTION Crohn's disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia's first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota. METHODS The AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants; 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal samples are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be sampled whenever a colonoscopy is performed. Dietary intake, general health and psychological state will be assessed using validated self-report questionnaires. Samples will undergo metagenomic, transcriptomic, proteomic, metabolomic and culturomic analyses. Omics data will be integrated with clinical data to identify predictive biomarkers of response to therapy, disease behaviour and environmental factors in patients with IBD. ETHICS AND DISSEMINATION Ethical approval for this study has been obtained from the South Eastern Sydney Local Health District Research Ethics Committee (HREC 2019/ETH11443). Findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals. TRIAL REGISTRATION NUMBER ACTRN12619000911190.
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Affiliation(s)
- Astrid-Jane Williams
- Department of Gastroenterology, Liverpool Hospital, Liverpool, New South Wales, Australia
- Ingham Institute, Liverpool, New South Wales, Australia
| | - Ramesh Paramsothy
- Department of Gastroenterology & Hepatology, Blacktown Hospital, Blacktown, New South Wales, Australia
| | - Nan Wu
- St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Simon Ghaly
- Gastroenterology, St Vincent's Hospital Sydney, Darlinghurst, New South Wales, Australia
| | - Steven Leach
- Westfield Research Laboratories, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Sudarshan Paramsothy
- Macquarie University Faculty of Medicine and Health Sciences, Sydney, New South Wales, Australia
- Concord Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Crispin Corte
- AW Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Claire O'Brien
- Faculty of Science and Technology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Catherine Burke
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Gabrielle Wark
- Gastroenterology, St Vincent's Hospital Sydney, Darlinghurst, New South Wales, Australia
| | - Dorit Samocha-Bonet
- Diabetes Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Kelly Lambert
- Centre for Health Research Illawarra Shoalhaven Population, University of Wollongong Faculty of Business, Wollongong, New South Wales, Australia
- Illawarra Shoalhaven Local Health District, Wollongong, New South Wales, Australia
| | - Golo Ahlenstiel
- Blacktown & Mount Druitt Hospital, Blacktown, New South Wales, Australia
| | - Valerie Wasinger
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, New South Wales, Australia
| | - Shoma Dutt
- Department of Gastroenterology, The Sydney Children's Hospitals Network Randwick and Westmead, Westmead, New South Wales, Australia
| | - Paul Pavli
- Gastroenterology Unit, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Michael Grimm
- St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Lemberg
- Department of Gastroenterology, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia
| | - Susan Connor
- Department of Gastroenterology, Liverpool Hospital, Liverpool, New South Wales, Australia
- South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Rupert Leong
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Georgina Hold
- Microbiome Research Centre, University of New South Wales, Sydney, New South Wales, Australia
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Laskar F, Das Purkayastha S, Sen A, Bhattacharya MK, Misra BB. Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems. J Basic Microbiol 2017; 58:101-119. [PMID: 29083035 DOI: 10.1002/jobm.201700341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/15/2022]
Abstract
About half of the global methane (CH4 ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.
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Affiliation(s)
- Folguni Laskar
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Aniruddha Sen
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Biswapriya B Misra
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, Texas, USA
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4
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Liu J, Williams B, Frank D, Dillon SM, Wilson CC, Landay AL. Inside Out: HIV, the Gut Microbiome, and the Mucosal Immune System. THE JOURNAL OF IMMUNOLOGY 2017; 198:605-614. [PMID: 28069756 DOI: 10.4049/jimmunol.1601355] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022]
Abstract
The components of the human gut microbiome have been found to influence a broad array of pathologic conditions ranging from heart disease to diabetes and even to cancer. HIV infection upsets the delicate balance in the normal host-microbe interaction both through alterations in the taxonomic composition of gut microbial communities as well as through disruption of the normal host response mechanisms. In this article we review the current methods of gut microbiome analysis and the resulting data regarding how HIV infection might change the balance of commensal bacteria in the gut. Additionally, we cover the various effects gut microbes have on host immune homeostasis and the preliminary but intriguing data on how HIV disrupts those mechanisms. Finally, we briefly describe some of the important biomolecules produced by gut microbiota and the role that they may play in maintaining host immune homeostasis with and without HIV infection.
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Affiliation(s)
- Jay Liu
- Division of Infectious Disease, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045
| | - Brett Williams
- Division of Infectious Disease, Department of Medicine, Rush Medical College, Chicago, IL 60612; and
| | - Daniel Frank
- Division of Infectious Disease, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045
| | - Stephanie M Dillon
- Division of Infectious Disease, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045
| | - Cara C Wilson
- Division of Infectious Disease, Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045
| | - Alan L Landay
- Department of Immunology and Microbiology, Rush Medical College, Chicago, IL 60612
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5
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Chen T, Shi Y, Wang X, Wang X, Meng F, Yang S, Yang J, Xin H. High‑throughput sequencing analyses of oral microbial diversity in healthy people and patients with dental caries and periodontal disease. Mol Med Rep 2017; 16:127-132. [PMID: 28534987 PMCID: PMC5482155 DOI: 10.3892/mmr.2017.6593] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 03/07/2017] [Indexed: 01/20/2023] Open
Abstract
Recurrence of oral diseases caused by antibiotics has brought about an urgent requirement to explore the oral microbial diversity in the human oral cavity. In the present study, the high-throughput sequencing method was adopted to compare the microbial diversity of healthy people and oral patients and sequence analysis was performed by UPARSE software package. The Venn results indicated that a mean of 315 operational taxonomic units (OTUs) was obtained, and 73, 64, 53, 19 and 18 common OTUs belonging to Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria, respectively, were identified in healthy people. Moreover, the reduction of Firmicutes and the increase of Proteobacteria in the children group, and the increase of Firmicutes and the reduction of Proteobacteria in the youth and adult groups, indicated that the age bracket and oral disease had largely influenced the tooth development and microbial development in the oral cavity. In addition, the traditional ‘pathogenic bacteria’ of Firmicutes, Proteobacteria and Bacteroidetes (accounted for >95% of the total sequencing number in each group) indicated that the ‘harmful’ bacteria may exert beneficial effects on oral health. Therefore, the data will provide certain clues for curing some oral diseases by the strategy of adjusting the disturbed microbial compositions in oral disease to healthy level.
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Affiliation(s)
- Tingtao Chen
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Yan Shi
- Department of Conservative Dentistry and Endodontics, Stomatological Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xiaolei Wang
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Xin Wang
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Fanjing Meng
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Shaoguo Yang
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Jian Yang
- Department of Conservative Dentistry and Endodontics, Stomatological Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Hongbo Xin
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
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Deane KD, Demoruelle MK, Kelmenson LB, Kuhn KA, Norris JM, Holers VM. Genetic and environmental risk factors for rheumatoid arthritis. Best Pract Res Clin Rheumatol 2017; 31:3-18. [PMID: 29221595 PMCID: PMC5726551 DOI: 10.1016/j.berh.2017.08.003] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/12/2017] [Accepted: 07/17/2017] [Indexed: 01/13/2023]
Abstract
Multiple genetic and environmental factors have been associated with an increased risk for rheumatoid arthritis (RA). Of these, the strongest associations have been seen with female sex, a family history of RA, the genetic factor the "shared epitope," and exposure to tobacco smoke. There is also renewed interest in mucosal inflammation and microbial factors as contributors to the development of RA. However, the identification of a "preclinical" period of RA that can be defined as local or systemic autoimmunity as measured by autoantibodies and other biomarkers prior to the development of clinically apparent synovitis suggests that the risk factors for RA are acting long prior to first clinical evidence of IA. As such, a major challenge to the field will be to investigate the full spectrum of the development of RA, from initiation and propagation of autoimmunity during preclinical RA and transition to clinically apparent synovitis and classifiable RA, to determine which genetic and environmental factors are important at each stage of disease development. Understanding the exact role and timing of action of risk factors for RA is especially important given the advent of prevention trials in RA, and the hope that a full understanding of genetic and environmental factors in RA could lead to effective preventive interventions.
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Affiliation(s)
- Kevin D Deane
- Division of Rheumatology, University of Colorado Denver School of Medicine, USA.
| | | | - Lindsay B Kelmenson
- Division of Rheumatology, University of Colorado Denver School of Medicine, USA
| | - Kristine A Kuhn
- Division of Rheumatology, University of Colorado Denver School of Medicine, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado Denver School of Medicine, USA
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7
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Abstract
An expanding body of evidence supports a role for gut microbes in the etiology of cancer. Previously, the focus was on identifying individual bacterial species that directly initiate or promote gastrointestinal malignancies; however, the capacity of gut microbes to influence systemic inflammation and other downstream pathways suggests that the gut microbial community may also affect risk of cancer in tissues outside of the gastrointestinal tract. Functional contributions of the gut microbiota that may influence cancer susceptibility in the broad sense include (1) harvesting otherwise inaccessible nutrients and/or sources of energy from the diet (i.e., fermentation of dietary fibers and resistant starch); (2) metabolism of xenobiotics, both potentially beneficial or detrimental (i.e., dietary constituents, drugs, carcinogens, etc.); (3) renewal of gut epithelial cells and maintenance of mucosal integrity; and (4) affecting immune system development and activity. Understanding the complex and dynamic interplay between the gut microbiome, host immune system, and dietary exposures may help elucidate mechanisms for carcinogenesis and guide future cancer prevention and treatment strategies.
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Affiliation(s)
- Meredith A J Hullar
- Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, M4-B402, PO Box 19024, Seattle, WA, 98109, USA
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8
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Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD. Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLoS One 2010; 5:e14116. [PMID: 21124791 PMCID: PMC2991352 DOI: 10.1371/journal.pone.0014116] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 11/02/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The microbiome of the male urogenital tract is poorly described but it has been suggested that bacterial colonization of the male urethra might impact risk of sexually transmitted infection (STI). Previous cultivation-dependent studies showed that a variety of non-pathogenic bacteria colonize the urethra but did not thoroughly characterize these microbiomes or establish links between the compositions of urethral microbiomes and STI. METHODOLOGY/FINDINGS Here, we used 16S rRNA PCR and sequencing to identify bacteria in urine specimens collected from men who lacked symptoms of urethral inflammation but who differed in status for STI. All of the urine samples contained multiple bacterial genera and many contained taxa that colonize the human vagina. Uncultivated bacteria associated with female genital tract pathology were abundant in specimens from men who had STI. CONCLUSIONS Urine microbiomes from men with STI were dominated by fastidious, anaerobic and uncultivated bacteria. The same taxa were rare in STI negative individuals. Our findings suggest that the composition of male urine microbiomes is related to STI.
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Affiliation(s)
- David E Nelson
- Department of Biology, Indiana University, Bloomington, Indiana, USA.
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9
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Frank DN, Wysocki A, Specht-Glick DD, Rooney A, Feldman RA, St Amand AL, Pace NR, Trent JD. Microbial diversity in chronic open wounds. Wound Repair Regen 2009; 17:163-72. [PMID: 19320883 DOI: 10.1111/j.1524-475x.2009.00472.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chronic wounds expose the dermal matrix and underlying tissue to a diversity of microbes from the body and surrounding environment. We determined the microbial diversity of 19 chronic wounds using both molecular methods (sequence analysis of rRNA genes) and routine clinical culturing methods using swab samples. We identified 93 phylotypes in 2,653 rRNA clone sequences and found that compared with other environments, the microbial diversity of chronic wounds is relatively well characterized, i.e., 95% of sequences have > or =97% identity with known human commensals. In total, 75% of sequences belonged to four well-known wound-associated phylotypes: Staphylococcus (25%), Corynebacterium (20%), Clostridiales (18%), and Pseudomonas (12%). Approximately 0.5% of sequences (seven phylotypes) belonged to potentially new species. Individual wound samples contained four to 22 phylotypes, but in all wounds only a few (one to three) phylotypes were dominant. In more than half the wound specimens, polymerase chain reaction and culturing methods gave different diversity and dominance information about the microbes present. This exploratory study suggests that combining molecular and culturing methods provides a more complete characterization of the microbial diversity of chronic wounds, and can thereby expand our understanding of how microbiology impacts chronic wound pathology and healing.
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Affiliation(s)
- Daniel N Frank
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, USA
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10
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Abstract
PURPOSE OF REVIEW Advances in DNA sequence-based technologies now permit genetic analysis of complex microbial populations without the need for prior cultivation. This review summarizes the molecular methods of culture-independent microbiology ('metagenomics') and their recent application to studies of the human gastrointestinal tract in both health and disease. RECENT FINDINGS Culture-independent metagenomic surveys reveal unprecedented microbial biodiversity in the human intestine. Upwards of 40,000 bacterial species are estimated to comprise the collective gastrointestinal microbiome, most of which have not been characterized by culture. Diverse conditions such as antibiotic-associated diarrhea, Crohn's disease, ulcerative colitis, obesity, and pouchitis have been correlated with large-scale imbalances in gastrointestinal microbiota, or 'dysbiosis'. These findings demonstrate the importance of commensal microorganisms in maintaining gastrointestinal health. SUMMARY Through technological and conceptual innovations in metagenomics, the complex microbial habitat of the human gastrointestinal tract is now amenable to detailed ecological analysis. Large-scale shifts in gut commensal populations, rather than occurrence of particular microorganisms, are associated with several gastroenterological conditions; redress of these imbalances may ameliorate the conditions.
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11
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Sepehri S, Kotlowski R, Bernstein CN, Krause DO. Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm Bowel Dis 2007; 13:675-83. [PMID: 17262808 DOI: 10.1002/ibd.20101] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition without any known cause or cure. An imbalance in normal gut biota has been identified as an important factor in the inflammatory process. METHODS Fifty-eight biopsies from Crohn's disease (CD, n = 10), ulcerative colitis (UC, n = 15), and healthy controls (n = 16) were taken from a population-based case-control study. Automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphisms (T-RFLP) were used as molecular tools to investigate the intestinal microbiota in these biopsies. RESULTS ARISA and T-RFLP data did not allow a high level of clustering based on disease designation. However, if clustering was done based on the inflammation criteria, the majority of biopsies grouped either into inflamed or noninflamed groups. We conducted statistical analyses using incidence-based species richness and diversity as well as the similarity measures. These indices suggested that the noninflamed tissues form an intermediate population between controls and inflamed tissue for both CD and UC. Of particular interest was that species richness increased from control to noninflamed tissue, and then declined in fully inflamed tissue. CONCLUSIONS We hypothesize that there is a recruitment phase in which potentially pathogenic bacteria colonize tissue, and once the inflammation sets in, a decline in diversity occurs that may be a byproduct of the inflammatory process. Furthermore, we suspect that a better knowledge of the microbial species in the noninflamed tissue, thus before inflammation sets in, holds the clues to the microbial pathogenesis of IBD.
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Affiliation(s)
- Shadi Sepehri
- Department of Medical Microbiology and Infectious Diseases, Winnipeg, Manitoba, Canada
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12
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Dalby AB, Frank DN, St Amand AL, Bendele AM, Pace NR. Culture-independent analysis of indomethacin-induced alterations in the rat gastrointestinal microbiota. Appl Environ Microbiol 2006; 72:6707-15. [PMID: 17021222 PMCID: PMC1610281 DOI: 10.1128/aem.00378-06] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed for a variety of inflammatory conditions; however, the benefits of this class of drugs are accompanied by deleterious side effects, most commonly gastric irritation and ulceration. NSAID-induced ulceration is thought to be exacerbated by intestinal microbiota, but previous studies have not identified specific microbes that contribute to these adverse effects. In this study, we conducted a culture-independent analysis of approximately 1,400 bacterial small-subunit rRNA genes associated with the small intestines and mesenteric lymph nodes of rats treated with the NSAID indomethacin. This is the first molecular analysis of the microbiota of the rat small intestine. A comparison of clone libraries and species-specific quantitative PCR results from rats treated with indomethacin and untreated rats revealed that organisms closely related to Enterococcus faecalis were heavily enriched in the small intestine and mesenteric lymph nodes of the treated rats. These data suggest that treatment of NSAID-induced ulceration may be facilitated by addressing the microbiological imbalances.
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Affiliation(s)
- Andrew B Dalby
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
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13
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Green GL, Brostoff J, Hudspith B, Michael M, Mylonaki M, Rayment N, Staines N, Sanderson J, Rampton DS, Bruce KD. Molecular characterization of the bacteria adherent to human colorectal mucosa. J Appl Microbiol 2006; 100:460-9. [PMID: 16478485 DOI: 10.1111/j.1365-2672.2005.02783.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS To study large intestinal mucosal bacterial communities by Denaturing Gradient Gel Electrophoresis (DGGE) profiling and sequencing of 16S rRNA gene polymerase chain reaction (PCR) products amplified from DNA extracted from colorectal biopsies taken from healthy individuals. The specific aims were to determine how similar the mucosa-associated bacterial communities are within and between individuals and also to characterize the phylogenetic origin of isolated DGGE bands. METHODS AND RESULTS Human colorectal biopsies were taken at routine colonoscopy from 33 patients with normal looking mucosa. The DNA was extracted directly from single biopsies and the bacterial 16S rDNA PCR amplified. The PCR products were profiled using DGGE to generate a fingerprint of the dominant members of the bacterial community associated with the biopsy. The reproducibility of this method was high (>98%). Washed and unwashed biopsies gave similar DGGE banding patterns (Median Similarity Coefficient - MSC 96%, InterQuartile Range - IQR 3.0%, n = 5). Adjacent biopsies sampled from the same patient using different forceps gave similar DGGE profiles (MSC 94%, n = 2). Two colorectal biopsies sampled at locations 2-5 cm apart, from each of 18 patients, resulted in very similar profiles (MSC 100%, IQR 2.8%). Biopsies sampled from different locations within the large intestine of the same patient also gave similar DGGE profiles (MSC 98% IQR 3.3%n = 6). Although all patients (n = 33) gave different DGGE profiles, some similarity (c. 34%) was observed between profiles obtained from 15 patients arbitrarily selected. 35 DGGE bands were excised and sequenced. Many were found to be most closely related to uncultured bacterial sequence entries in the Genbank database. Others belonged to typical gut bacterial genera including Bacteroides, Ruminococcus, Faecalibacterium and Clostridium. CONCLUSIONS Bacterial communities adherent to colorectal mucosa within a normal patient show little variation; in contrast, mucosal bacterial communities sampled from different patients with normal colorectal mucosa show a high degree of variation. SIGNIFICANCE AND IMPACT OF THE STUDY This research demonstrates that DGGE profiling of 16S rRNA gene PCR products amplified from DNA extracted directly from mucosal samples offers fresh insight into the bacterial communities that are adherent to colorectal mucosa. These findings are important with respect to further studies on the gastrointestinal tract in health and disease.
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Affiliation(s)
- G L Green
- Life Sciences, King's College London, London, UK
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14
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Louis P, Duncan SH, McCrae SI, Millar J, Jackson MS, Flint HJ. Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J Bacteriol 2004; 186:2099-106. [PMID: 15028695 PMCID: PMC374397 DOI: 10.1128/jb.186.7.2099-2106.2004] [Citation(s) in RCA: 317] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-coenzyme A (CoA):acetate CoA-transferase. Degenerate PCR and enzymatic assays were used to assess the presence of butyrate kinase among 38 anaerobic butyrate-producing bacterial isolates from human feces that represent three different clostridial clusters (IV, XIVa, and XVI). Only four strains were found to possess detectable butyrate kinase activity. These were also the only strains to give PCR products (verifiable by sequencing) with degenerate primer pairs designed within the butyrate kinase gene or between the linked butyrate kinase/phosphotransbutyrylase genes. Further analysis of the butyrate kinase/phosphotransbutyrylase genes of one isolate, L2-50, revealed similar organization to that described previously from different groups of clostridia, along with differences in flanking sequences and phylogenetic relationships. Butyryl-CoA:acetate CoA-transferase activity was detected in all 38 strains examined, suggesting that it, rather than butyrate kinase, provides the dominant route for butyrate formation in the human colonic ecosystem that contains a constantly high concentration of acetate.
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Affiliation(s)
- Petra Louis
- Division of Gut Microbiology and Immunology, Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, UK.
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Finegold SM, Lawson PA, Vaisanen ML, Molitoris DR, Song Y, Liu C, Collins MD. Anaerofustis stercorihominis gen. nov., sp. nov., from human feces. Anaerobe 2004; 10:41-5. [PMID: 16701499 DOI: 10.1016/j.anaerobe.2003.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Revised: 10/20/2003] [Accepted: 10/23/2003] [Indexed: 10/26/2022]
Abstract
Phenotypic and phylogenetic studies were performed on an unidentified Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped bacterium isolated from human feces. The organism was catalase-negative, resistant to 20% bile, produced acetic and butyric acids as end products of glucose metabolism, and possessed a G+C content of approximately 70 mol%. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was a member of the Clostridium sub-phylum of the Gram-positive bacteria, and formed a loose association with rRNA cluster XV. Sequence divergence values of 12% or greater were observed between the unidentified bacterium and all other recognized species within this and related rRNA clusters. Treeing analysis showed the unknown anaerobe formed a deep line branching near to the base of rRNA cluster XV and phylogenetically represents a hitherto unknown taxon, distinct from Acetobacterium, Eubacterium sensu stricto, Pseudoramibacter and other related organisms. Based on both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from feces be classified in a new genus Anaerofustis, as Anaerofustis stercorihominis sp. nov. The type strain of Anaerofustis stercorihominis is ATCC BAA-858(T)=CCUG 47767(T).
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Affiliation(s)
- Sydney M Finegold
- Infectious Diseases Section (111F), VA Medical Center, 11301 Wilshire Boulervard, West Los Angeles, CA, USA.
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Frank DN, Spiegelman GB, Davis W, Wagner E, Lyons E, Pace NR. Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. J Clin Microbiol 2003; 41:295-303. [PMID: 12517864 PMCID: PMC149572 DOI: 10.1128/jcm.41.1.295-303.2003] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular-phylogenetic sequence analyses have provided a new perspective on microbial communities by allowing the detection and identification of constituent microorganisms in the absence of cultivation. In this study we used broad-specificity amplification of ribosomal DNA (rDNA) genes to survey organisms present in the human outer ear canal. Samples were obtained from 24 individuals, including members of three extended families, in order to survey the resident microbiota and to examine microbial population structures in individuals related by familial or household associations. To examine the stability of the microbial populations, one individual was sampled four times and another twice over a 14-month period. We found that a distinct set of microbial types was present in the majority of the subjects sampled. The two most prevalent rDNA sequence types that were identified in multiple individuals corresponded closely to those of Alloiococcus otitis and Corynebacterium otitidis, commonly thought to be associated exclusively with infections of the middle ear. Our results suggest, therefore, that the outer ear canal may serve as a reservoir for normally commensal microbes that can contribute to pathogenesis upon introduction into the middle ear. Alternatively, culture analyses of diseases of the middle ear may have been confounded by these contaminating commensal organisms.
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Affiliation(s)
- Daniel N Frank
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA
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Wu Q, Watts JEM, Sowers KR, May HD. Identification of a bacterium that specifically catalyzes the reductive dechlorination of polychlorinated biphenyls with doubly flanked chlorines. Appl Environ Microbiol 2002; 68:807-12. [PMID: 11823222 PMCID: PMC126686 DOI: 10.1128/aem.68.2.807-812.2002] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A microorganism whose growth is linked to the dechlorination of polychlorinated biphenyls (PCBs) with doubly flanked chlorines was identified. Identification was made by reductive analysis of community 16S ribosomal DNA (rDNA) sequences from a culture enriched in the presence of 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB), which was dechlorinated at the para position. Denaturing gradient gel electrophoresis (DGGE) analysis of total 16S rDNA extracted from the culture led to identification of three operational taxonomic units (OTUs 1, 2, and 3). OTU 1 was always detected when 2,3,4,5-CB or other congeners with doubly flanked chlorines were present and dechlorinated. Only OTUs 2 and 3 were detected in the absence of PCBs and when other PCBs (i.e., PCBs lacking doubly flanked chlorines) were not dechlorinated. Partial sequences of OTUs 2 and 3 exhibited 98.2% similarity to the sequence of "Desulfovibrio caledoniensis" (accession no. DCU53465). A sulfate-reducing vibrio isolated from the culture generated OTUs 2 and 3. This organism could not dechlorinate 2,3,4,5-CB. From these results we concluded that OTU 1 represents the dechlorinating bacterium growing in a coculture with a Desulfovibrio sp. The 16S rDNA sequence of OTU 1 is most similar to the 16S rDNA sequence of bacterium o-17 (89% similarity), an ortho-PCB-dechlorinating bacterium. The PCB dechlorinator, designated bacterium DF-1, reductively dechlorinates congeners with doubly flanked chlorines when it is supplied with formate or H(2)-CO(2) (80:20).
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Affiliation(s)
- Qingzhong Wu
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Ave., Charleston, SC 29425-2230, USA
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