Abstract：
:Studying the microbial composition of internal organs and their associations with disease remains challenging due to the difficulty of acquiring clinical biopsies. We designed a statistical model to analyze the prevalence of species across sample types from The Cancer Genome Atlas (TCGA), revealing that species equiprevalent across sample types are predominantly contaminants, bearing unique signatures from each TCGA-designated sequencing center. Removing such species mitigated batch effects and isolated the tissue-resident microbiome, which was validated by original matched TCGA samples. Gene copies and nucleotide variants can further distinguish mixed-evidence species. We, thus, present The Cancer Microbiome Atlas (TCMA), a collection of curated, decontaminated microbial compositions of oropharyngeal, esophageal, gastrointestinal, and colorectal tissues. This led to the discovery of prognostic species and blood signatures of mucosal barrier injuries and enabled systematic matched microbe-host multi-omic analyses, which will help guide future studies of the microbiome's role in human health and disease.
journal_name
Cell Host Microbejournal_title
Cell host & microbeauthors
Dohlman AB,Arguijo Mendoza D,Ding S,Gao M,Dressman H,Iliev ID,Lipkin SM,Shen Xdoi
10.1016/j.chom.2020.12.001subject
Has Abstractpub_date
2020-12-21 00:00:00eissn
1931-3128issn
1934-6069pii
S1931-3128(20)30663-6pub_type
杂志文章abstract：:The complex microbial community residing within the intestine plays important roles in host defense. However, the impact of enteric infection and inflammation on this resident community has not been fully explored. In this issue of Cell Host & Microbe, Lupp and coworkers reveal that the composition of the intestinal m...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2007.07.006
更新日期：2007-08-16 00:00:00
abstract：:Typhoidal and non-typhoidal Salmonelleae (NTS) cause typhoid fever and gastroenteritis, respectively, in humans. Salmonella typhoid toxin contributes to typhoid disease progression and chronic infection, but little is known about the role of its NTS ortholog. We found that typhoid toxin and its NTS ortholog induce dif...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2020.04.005
更新日期：2020-06-10 00:00:00
abstract：:Colitis results from breakdown of homeostasis between intestinal microbiota and the mucosal immune system, with both environmental and genetic influencing factors. Flagellin receptor TLR5-deficient mice (T5KO) display elevated intestinal proinflammatory gene expression and colitis with incomplete penetrance, providing...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2012.07.004
更新日期：2012-08-16 00:00:00
abstract：:Vibrio cholerae is the causative agent of the diarrheal disease cholera. Although many V. cholerae virulence factors have been studied, the role of interbacterial interactions within the host gut and their influence on colonization are poorly understood. Here, we utilized the conjugative properties of a Vibrio-specifi...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2017.12.006
更新日期：2018-02-14 00:00:00
abstract：:The intestinal immune system has to strike a delicate balance between initiating inflammatory responses against invading bacterial pathogens and avoiding their induction against microbiota colonizing the lumen. Adequate inflammatory responses against bacterial invasion result in the lumenal secretion of antimicrobial ...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2010.06.003
更新日期：2010-07-22 00:00:00
abstract：:Clostridium difficile infection (CDI) is the number one hospital-acquired infection in the United States. CDI is more common and severe in inflammatory bowel disease patients. Here, we studied the mechanism by which prior colitis exacerbates CDI. Mice were given dextran sulfate sodium (DSS) colitis, recovered for 2 we...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2019.03.003
更新日期：2019-05-08 00:00:00
abstract：:Neutrophil swarming is defined by large numbers of cells simultaneously and rapidly migrating to a site of injury or infection. In this issue of Cell Host & Microbe, Lee et al. (2018) demonstrate that intravascular swarming of neutrophils occurs in response to Candida albicans infection and causes vascular occlusion a...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2017.12.011
更新日期：2018-01-10 00:00:00
abstract：:Local infection in the Drosophila larval intestine elicits a systemic immune reaction in fat bodies. In this issue, Wu and colleagues (2012) show that this is a reactive oxygen species-dependent communication. ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2012.04.003
更新日期：2012-04-19 00:00:00
abstract：:The ecological dynamics underlying the coexistence between antagonistic populations of bacteria and their viruses, bacteriophages (phages), in the mammalian gut microbiota remain poorly understood. We challenged a murine synthetic bacterial community with phages to study the factors allowing phages-bacteria coexistenc...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2020.06.002
更新日期：2020-09-09 00:00:00
abstract：:Bone marrow transplantation (BMT) offers curative potential for patients with high-risk hematologic malignancies, but the post-transplantation period is characterized by profound immunodeficiency. Recent studies indicate that the intestinal microbiota not only regulates mucosal immunity, but can also contribute to sys...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2018.03.002
更新日期：2018-04-11 00:00:00
abstract：:Eradication of pathogens from the bloodstream is critical to prevent disseminated infections and sepsis. Kupffer cells in the liver form an intravascular firewall that captures and clears pathogens from the blood. Here, we show that the catching and killing of circulating pathogens by Kupffer cells in vivo are promote...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2020.07.014
更新日期：2020-11-11 00:00:00
abstract：:The Salmonella enterica effector SteD depletes mature MHC class II (mMHCII) molecules from the surface of infected antigen-presenting cells through ubiquitination of the cytoplasmic tail of the mMHCII β chain. Here, through a genome-wide mutant screen of human antigen-presenting cells, we show that the NEDD4 family HE...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2020.04.024
更新日期：2020-07-08 00:00:00
abstract：:The switch from culture-based enumeration to deep sequencing has enabled microbial community composition to be profiled en masse. In a new article, Maurice et al. (2013) report the use of fluorescence-activated cell sorting (FACS) to perform a high-throughput analysis of gut microbiota community function. ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2013.01.011
更新日期：2013-02-13 00:00:00
abstract：:Overcoming the cellular type I interferon (IFN) host defense response is critical for a virus to ensure successful infection. Investigating the effects of human adenovirus (HAdV) infection on global cellular histone posttranslational modification (hPTM), we discovered that virus infection-induced activation of IFN sig...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2012.05.005
更新日期：2012-06-14 00:00:00
abstract：:Influenza A virus (IAV) infection is initiated by the attachment of the viral glycoprotein hemagglutinin (HA) to sialic acid on the host cell surface. However, the sialic acid-containing receptor crucial for IAV infection has remained unidentified. Here, we show that HA binds to the voltage-dependent Ca2+ channel Cav1...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2018.04.015
更新日期：2018-06-13 00:00:00
abstract：:In this issue of Cell Host & Microbe, Thanabalasuriar et al. (2019) show how neutrophils and biofilm-forming bacteria respond reciprocally, resulting in the formation of a barricade comprised of neutrophil extracellular traps. Disrupting this exchange and the resulting barrier can be detrimental unless balanced in fav...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2019.03.014
更新日期：2019-04-10 00:00:00
abstract：:Successful viruses must overcome the body's immune defenses. In this issue of Cell Host & Microbe, Goffinet et al. (2009) provide evidence that the host protein CD317, the target of the HIV Vpu protein, is part of an ancient innate immune response directed against budding viruses. ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2009.02.002
更新日期：2009-03-19 00:00:00
abstract：:Innate immune responses are characterized by precise gene expression whereby gene subsets are temporally induced to limit infection, although the mechanisms involved are incompletely understood. We show that antiviral immunity in Drosophila requires the transcriptional pausing pathway, including negative elongation fa...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2012.08.011
更新日期：2012-10-18 00:00:00
abstract：:The plant immune signaling network needs to be robust against attack from fast-evolving pathogens and tunable to optimize immune responses. We investigated the basis of robustness and tunability in the signaling network controlling pattern-triggered immunity (PTI) in Arabidopsis. A dynamic network model containing fou...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2013.12.002
更新日期：2014-01-15 00:00:00
abstract：:Enveloped viruses escape infected cells by budding through limiting membranes. In the decade since the discovery that HIV recruits cellular ESCRT (endosomal sorting complexes required for transport) machinery to facilitate viral budding, this pathway has emerged as the major escape route for enveloped viruses. In cell...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2013.08.012
更新日期：2013-09-11 00:00:00
abstract：:Many enveloped viruses hijack the cellular ESCRT machinery to catalyze their escape from host cells. One paper in a recent issue of Cell by Kostelansky et al. and another in this issue of Cell Host & Microbe by Morita et al. shed new light on the structure and function of ESCRT-I. Both papers focus on a fourth ESCRT-I...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2007.06.006
更新日期：2007-07-12 00:00:00
abstract：:Much of the mutualistic relationship between humans and their resident intestinal Bacteroides species is founded on glycans. The host provides plant polysaccharides and host-derived glycans and, in return, receives beneficial end products of bacterial fermentation. Glycans from the bacteria themselves are required for...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2009.05.010
更新日期：2009-06-18 00:00:00
abstract：:For proliferation, the malaria parasite Plasmodium falciparum needs to modify the infected host cell extensively. To achieve this, the parasite exports proteins containing a Plasmodium export element (PEXEL) into the host cell. Phosphatidylinositol-3-phosphate binding and cleavage of the PEXEL are thought to mediate p...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2012.09.010
更新日期：2012-11-15 00:00:00
abstract：:A family of apicomplexa-specific proteins containing AP2 DNA-binding domains (ApiAP2s) was identified in malaria parasites. This family includes sequence-specific transcription factors that are key regulators of development. However, functions for the majority of ApiAP2 genes remain unknown. Here, a systematic knockou...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2016.12.003
更新日期：2017-01-11 00:00:00
abstract：:RNA interference (RNAi) is an established antiviral defense mechanism in plants and invertebrates. Whether RNAi serves a similar function in mammalian cells remains unresolved. We find that in some cell types, mammalian RNAi activity is reduced shortly after viral infection via poly-ADP-ribosylation of the RNA-induced...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2013.09.002
更新日期：2013-10-16 00:00:00
abstract：:Cure of rodent malaria with the biocide triclosan highlighted the enzyme FabI as an antimalarial drug target. In this issue of Cell Host & Microbe, Yu et al. (2008) show that FabI is not the principle target of triclosan yet plays an important role specifically in malaria liver stage development. ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2008.11.006
更新日期：2008-12-11 00:00:00
abstract：:Periodontitis is a common disease that is characterized by resorption of the alveolar bone and mediated by commensal bacteria that trigger host immune responses and bone destruction through unidentified mechanisms. We report that Nod1, an innate intracellular host receptor for bacterial peptidoglycan-related molecules...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2013.04.005
更新日期：2013-05-15 00:00:00
abstract：:Kaposi's sarcoma-associated herpesvirus (KSHV) is linked to human malignancies. The majority of tumor cells harbor latent virus, and a small percentage undergo spontaneous lytic replication. Both latency and lytic replication are important for viral pathogenesis and spread, but the cellular players involved in the swi...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2012.12.005
更新日期：2013-02-13 00:00:00
abstract：:Invasion of epithelial cells by Shigella is a critical step in the pathogenesis of bacillary dysentery. In this issue of Cell Host & Microbe, Bergounioux et al. (2012) uncover a complex interplay of proinvasion, prosurvival, and prodeath signals centered on the activation of calpain protease by the Shigella VirA prote...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2012.02.004
更新日期：2012-03-15 00:00:00
abstract：:In addition to classically defined immune mechanisms, cell-intrinsic processes can restrict virus infection and have shaped virus evolution. The details of this virus-host interaction are still emerging. Following a genome-wide siRNA screen for host factors affecting replication of Semliki Forest virus (SFV), a positi...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2014.08.007
更新日期：2014-09-10 00:00:00
