Abstract:
:The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influence on health and disease due to its interaction with the human immune system. Its overall composition and microbial ecology have been implicated in many autoimmune diseases, and it represents a particularly important area for translational research as a new target for diagnostics and therapeutics in complex inflammatory conditions. Determining the biomolecular mechanisms by which altered microbial communities contribute to human disease will be an important outcome of current functional studies of the human microbiome. In this review, we discuss functional profiling of the human microbiome using metagenomic and metatranscriptomic approaches, focusing on the implications for inflammatory conditions such as inflammatory bowel disease and rheumatoid arthritis. Common themes in gut microbial ecology have emerged among these diverse diseases, but they have not yet been linked to targetable mechanisms such as microbial gene and genome composition, pathway and transcript activity, and metabolism. Combining these microbial activities with host gene, transcript and metabolic information will be necessary to understand how and why these complex interacting systems are altered in disease-associated inflammation.
journal_name
Genome Medjournal_title
Genome medicineauthors
Börnigen D,Morgan XC,Franzosa EA,Ren B,Xavier RJ,Garrett WS,Huttenhower Cdoi
10.1186/gm469subject
Has Abstractpub_date
2013-07-31 00:00:00pages
65issue
7issn
1756-994Xpii
gm469journal_volume
5pub_type
杂志文章,评审相关文献
Genome Medicine文献大全abstract::With exome sequencing becoming a tool for mutation detection in routine diagnostics there is an increasing need for platform-independent methods of quality control. We present a genotype-weighted metric that allows comparison of all the variant calls of an exome to a high-quality reference dataset of an ethnically mat...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm473
更新日期:2013-07-31 00:00:00
abstract:BACKGROUND:Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin caused by either the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultraviolet-induced damage to the tumor genome from excessive sunlight exposure. An increasing number of deep s...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-020-00727-4
更新日期:2020-03-18 00:00:00
abstract::Stem cell banks are increasingly seen as an essential resource of biological materials for both basic and translational research. Stem cell banks support transnational access to quality-controlled and ethically sourced stem cell lines from different origins and of varying grades. According to the Organisation for Econ...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm194
更新日期:2010-10-05 00:00:00
abstract:BACKGROUND:Myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML) are characterised by abnormal epigenetic repression and differentiation of bone marrow haematopoietic stem cells (HSCs). Drugs that reverse epigenetic repression, such as 5-azacytidine (5-AZA), induce haematological improvement in half of trea...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-019-0707-x
更新日期:2019-12-23 00:00:00
abstract::Rett syndrome is a profound neurological disorder caused by mutations in the MECP2 gene, but preclinical research has indicated that it is potentially treatable. Progress towards this goal depends on the development of increasingly relevant model systems and on our improving knowledge of MeCP2 function in the brain. ...
journal_title:Genome medicine
pub_type: 信件,评审
doi:10.1186/s13073-017-0411-7
更新日期:2017-02-17 00:00:00
abstract:BACKGROUND:Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A, C, W and Y) are available as plain-polysaccharide and protein-polysaccharide conjugate vaccines. Here we apply contemporary...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-017-0400-x
更新日期:2017-01-30 00:00:00
abstract:BACKGROUND:For circadian medicine to influence health, such as when to take a drug or undergo a procedure, a biomarker of molecular clock phase is required--one that is easily measured and generalizable across a broad population. It is not clear that any circadian biomarker yet satisfies these criteria. METHODS:We ana...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-020-00768-9
更新日期:2020-08-21 00:00:00
abstract:BACKGROUND:Phenotypic changes during cancer progression are associated with alterations in gene expression, which can be exploited to build molecular signatures for tumor stage identification and prognosis. However, it is not yet known whether the relative abundance of transcript isoforms may be informative for clinica...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-016-0339-3
更新日期:2016-08-17 00:00:00
abstract:BACKGROUND:Establishing the cancer type and site of origin is important in determining the most appropriate course of treatment for cancer patients. Patients with cancer of unknown primary, where the site of origin cannot be established from an examination of the metastatic cancer cells, typically have poor survival. H...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-017-0493-2
更新日期:2017-11-28 00:00:00
abstract::During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online "immuno-analytics" resource that combines epitope, sequence, protein and SARS-CoV-2 mutation analysis. SARS-CoV-2 spike and nucleocapsid prote...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-020-00822-6
更新日期:2021-01-07 00:00:00
abstract::This is an Erratum to Genome Medicine 2013, 5:89, highlighting an error in Table 1 of the original article. Please see related article: http://genomemedicine.com/content/5/9/89.[This corrects the article DOI: 10.1186/gm492.]. ...
journal_title:Genome medicine
pub_type: 已发布勘误
doi:10.1186/s13073-015-0163-1
更新日期:2015-05-07 00:00:00
abstract::Prenatal diagnosis of fetal aneuploidies and chromosomal anomalies is likely to undergo a profound change in the near future. On the one hand this is mediated by new technical developments, such as chromosomal microarrays, which allow a much more precise delineation of minute sub-microscopic chromosomal aberrancies th...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm171
更新日期:2010-08-05 00:00:00
abstract:BACKGROUND:Tuberous sclerosis complex (TSC) is a genetic disease characterized by benign tumor growths in multiple organs and neurological symptoms induced by mTOR hyperfunction. Because the molecular pathology is highly complex and the etiology poorly understood, we employed a defined human neuronal model with a singl...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-016-0347-3
更新日期:2016-09-21 00:00:00
abstract:BACKGROUND:Molecular diagnostics can resolve locus heterogeneity underlying clinical phenotypes that may otherwise be co-assigned as a specific syndrome based on shared clinical features, and can associate phenotypically diverse diseases to a single locus through allelic affinity. Here we describe an apparently novel s...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm415
更新日期:2013-02-05 00:00:00
abstract::Primary biliary cirrhosis (PBC) is an autoimmune hepatobiliary disease characterized by immune-mediated injury of small and medium-sized bile ducts, eventually leading to liver cirrhosis. Several studies have addressed PBC immunopathology, and the data support an immune activation leading to autoantibodies and autorea...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm126
更新日期:2010-01-26 00:00:00
abstract::A genetic contribution to infectious disease in human populations has long been suspected and is now supported by more than 50 years of epidemiological evidence showing, for example, infection rates to be much higher than disease rates. In successful family studies of high-penetrance effects, single gene mutations hav...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm19
更新日期:2009-02-10 00:00:00
abstract:BACKGROUND:While clinical factors such as age, grade, stage, and histological subtype provide physicians with information about patient prognosis, genomic data can further improve these predictions. Previous studies have shown that germline variants in known cancer driver genes are predictive of patient outcome, but no...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-020-0718-7
更新日期:2020-02-17 00:00:00
abstract:BACKGROUND:The human gut microbiome is associated with the development of colon cancer, and recent studies have found changes in the microbiome in cancer patients compared to healthy controls. Studying the microbial communities in the tumor microenvironment may shed light on the role of host-bacteria interactions in co...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-015-0177-8
更新日期:2015-06-24 00:00:00
abstract:BACKGROUND:Cigarette smoking is well-known to associate with accelerated skin aging as well as cardiovascular disease and lung cancer, in large part due to oxidative stress. Because metabolites are downstream of genetic variation, as well as transcriptional changes and post-translational modifications of proteins, they...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm313
更新日期:2012-02-23 00:00:00
abstract:BACKGROUND:Alzheimer's disease affects ~13% of people in the United States 65 years and older, making it the most common neurodegenerative disorder. Recent work has identified roles for environmental, genetic, and epigenetic factors in Alzheimer's disease risk. METHODS:We performed a genome-wide screen of DNA methylat...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-015-0258-8
更新日期:2016-01-19 00:00:00
abstract::There are still many open questions in data-analytic research pertaining to biomarker development in the era of personalized/precision medicine and big data. Among them is the question of what constitutes best practice for the extraction of prioritized lists of candidate biomarkers from smaller studies that are 'hypot...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm507
更新日期:2013-11-29 00:00:00
abstract::The zebrafish model is rapidly gaining prominence in the study of development, hematopoiesis, and disease. The zebrafish provides distinct advantages over other vertebrate models during early embryonic development by producing transparent, externally fertilized embryos. Embryonic zebrafish are easily visualized and ma...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm299
更新日期:2011-12-29 00:00:00
abstract:BACKGROUND:Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and to vancomycin has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be confer...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-020-00825-3
更新日期:2021-01-20 00:00:00
abstract:BACKGROUND:As public health interventions drive parasite populations to elimination, genetic epidemiology models that incorporate population genomics can be powerful tools for evaluating the effectiveness of continued intervention. However, current genetic epidemiology models may not accurately simulate the population ...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-017-0398-0
更新日期:2017-01-24 00:00:00
abstract::Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic barriers, and exposure to nosocomial (hospital-acquired) pathogens. Consequently, cancer-related infections are u...
journal_title:Genome medicine
pub_type: 杂志文章,评审
doi:10.1186/s13073-016-0306-z
更新日期:2016-04-18 00:00:00
abstract:BACKGROUND:Evidence for genetic contribution to complex diseases is described by recurrence risks to relatives of diseased individuals. Genome-wide association studies allow a description of the genetics of the same diseases in terms of risk loci, their effects and allele frequencies. To reconcile the two descriptions ...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm131
更新日期:2010-02-02 00:00:00
abstract:BACKGROUND:Young age at portoenterostomy has been linked to improved outcome in biliary atresia, but pre-existing biological factors may influence the rate of disease progression. In this study, we aimed to determine whether molecular profiling of the liver identifies stages of disease at diagnosis. METHODS:We examine...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm154
更新日期:2010-05-13 00:00:00
abstract::A report on the Keystone Symposium 'Complex Traits: Genomics and Computational approaches', Breckenridge, Colorado, USA, 20-25 February 2012. ...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm328
更新日期:2012-03-30 00:00:00
abstract:BACKGROUND:Autism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. The neonatal epigenome has the potential to reflect past interactions between genetic and environmental factors during early development and influence future health outcomes. METHODS:We ...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/s13073-020-00785-8
更新日期:2020-10-14 00:00:00
abstract::Genome-wide association analyses on large patient cohorts are generating large sets of candidate disease genes. This is coupled with the availability of ever-increasing genomic databases and a rapidly expanding repository of biomedical literature. Computational approaches to disease-gene association attempt to harness...
journal_title:Genome medicine
pub_type: 杂志文章
doi:10.1186/gm77
更新日期:2009-08-07 00:00:00