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：:Although Drosophila systemic immunity is extensively studied, little is known about the fly's intestine-specific responses to bacterial infection. Global gene expression analysis of Drosophila intestinal tissue to oral infection with the Gram-negative bacterium Erwinia carotovora revealed that immune responses in the ...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2009.01.003
更新日期：2009-02-19 00:00:00
abstract：:The replication vacuole of Legionella pneumophila makes contact with host mitochondria. In this issue of Cell Host & Microbe, Escoll et al. (2017) dissect the mechanisms of this interaction, the effect of the T4SS effector MitF on mitochondrial function, and the resultant metabolic reprogramming of infected cells to b...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2017.08.014
更新日期：2017-09-13 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
abstract：:Mutations in the autophagy gene EPG5 are linked to the multisystem human disease Vici syndrome, which is characterized in part by pulmonary abnormalities, including recurrent infections. We found that Epg5-deficient mice exhibited elevated baseline innate immune cellular and cytokine-based lung inflammation and were r...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2015.12.011
更新日期：2016-01-13 00:00:00
abstract：:Rabies virus (RABV), the etiological agent for the lethal disease of rabies, is a deadly zoonotic pathogen. The RABV glycoprotein (RABV-G) is a key factor mediating virus entry and the major target of neutralizing antibodies. Here, we report the crystal structures of RABV-G solved in the free form at ∼pH-8.0 and in th...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2019.12.012
更新日期：2020-03-11 00:00:00
abstract：:Intracellular pathogens like Shigella flexneri enter host cells by phagocytosis. Once inside, the pathogen breaks the vacuolar membrane for cytosolic access. The fate and function of the vacuolar membrane remnants are not clear. Examining Shigella-infected nonmyeloid cells, we observed that proteins associated with va...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2009.07.005
更新日期：2009-08-20 00:00:00
abstract：:Disruption of homeostasis between the host immune system and the intestinal microbiota leads to inflammatory bowel disease (IBD). Whether IBD is instigated by individual species or disruptions of entire microbial communities remains controversial. We characterized the fecal microbial communities in the recently descri...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2010.08.004
更新日期：2010-09-16 00:00:00
abstract：:Lujo virus (LUJV) is an arenavirus that emerged in 2008 associated with a cluster of human cases of severe hemorrhagic fever. In this issue of Cell Host & Microbe, Raaben et al. (2017) identify neuropilin (NRP)-2 as cell surface receptor and the tetraspannin protein CD63 as intracellular entry factor for LUJV. ...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2017.10.014
更新日期：2017-11-08 00:00:00
abstract：:The difficulty in detecting rare infected cells immediately after mucosal HIV transmission has hindered our understanding of the initial cells targeted by the virus. Working with the macaque simian immunodeficiency virus (SIV) vaginal challenge model, we developed methodology to identify discrete foci of SIV (mac239) ...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2016.03.005
更新日期：2016-04-13 00:00:00
abstract：:Perturbation of the gut microbiota is associated with inflammatory bowel disease, obesity, and even cancer. In this issue of Cell Host & Microbe, Gogokhia et al. 2019 sought to kill cancer-causing bacteria with bacteriophages. However, the bacteriophages themselves directly stimulated an immune response, which worsene...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2019.01.020
更新日期：2019-02-13 00:00:00
abstract：:According to a classical view of bacterial-host interactions at intestinal surfaces, the commensal microbiota establishes tolerance, and invasive pathogens cause stereotypic inflammation. The reality is more complex, marked by a "ménage à trois" situation encompassing three emerging concepts: (1) pathogens take advant...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2008.05.010
更新日期：2008-06-12 00:00:00
abstract：:Monoclonal antibodies derived from blood plasma cells of acute HIV-1-infected individuals are predominantly targeted to the HIV Env gp41 and cross-reactive with commensal bacteria. To understand this phenomenon, we examined anti-HIV responses in ileum B cells using recombinant antibody technology and probed their rela...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2014.07.003
更新日期：2014-08-13 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：:Newborns are colonized with an intestinal microbiota shortly after birth, but the factors governing the retention and abundance of specific microbial lineages are unknown. Nursing infants consume human milk oligosaccharides (HMOs) that pass undigested to the distal gut, where they may be digested by microbes. We deter...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2011.10.007
更新日期：2011-11-17 00:00:00
abstract：:Commensal bacteria are known to provide colonization resistance in the gut. But exactly which ones provide this function? In a recent paper in Science, Kim et al. (2017) revealed that Clostridia added to mouse infant gut microbiota are sufficient to limit colonization of pathogenic Enterobacteriaceae. ...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2017.06.002
更新日期：2017-06-14 00:00:00
abstract：:Blockade of immune checkpoint molecules, a group of molecules normally involved in maintaining self-tolerance and limiting T cell responses, has emerged as a breakthrough in cancer therapy. Two recent studies published in Science show that, in mice, gut commensal microbes promote antitumor immunity and may determine t...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2015.11.014
更新日期：2015-12-09 00:00:00
abstract：:Vaccines are needed to combat the global rise in fungal diseases. In this issue of Cell Host & Microbe, Wüthrich et al. (2015) identify calnexin as a target of antigen-specific CD4 T cell responses against multiple fungal pathogens. This study illustrates that a conserved epitope triggers convergent cell-mediated immu...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2015.03.012
更新日期：2015-04-08 00:00:00
abstract：:Microbial CRISPR-Cas acts as a defense, but also as a gatekeeper controlling the flow of new genes into microbial genomes. In a recent Cell paper, Jiang et al. (2016) uncover the functional importance of transcription-dependent RNA targeting in type III-A CRISPR-Cas antiviral defense and provide insight into the co-ev...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章
doi：10.1016/j.chom.2016.01.015
更新日期：2016-02-10 00:00:00
abstract：:Parasites undergo complex life cycles that comprise a wide variety of cellular differentiation events in different host compartments and transmission across multiple hosts. As parasites depend on host resources, it is not surprising they have developed efficient mechanisms to sense alterations and adapt to the availab...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2018.05.018
更新日期：2018-06-13 00:00:00
abstract：:Leishmaniasis is a chronic infection in which intracellular parasites avoid destruction by the immune system. Using intravital imaging, Filipe-Santos et al. (2009) demonstrate that some parasitized dendritic cells receive much less attention than others during their choreographed dance with T cells, suggesting that th...
journal_title：Cell host & microbe
pub_type： 评论,杂志文章,评审
doi：10.1016/j.chom.2009.07.002
更新日期：2009-07-23 00:00:00
abstract：:Cerebral malaria is a complication of Plasmodium falciparum infection characterized by sudden coma, death, or neurodisability. Studies using a mouse model of experimental cerebral malaria (ECM) have indicated that blood-brain barrier disruption and CD8 T cell recruitment contribute to disease, but the spatiotemporal m...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2014.04.008
更新日期：2014-05-14 00:00:00
abstract：:Live attenuated vaccines remain the safest, most cost-effective intervention against viral infections. Because live vaccine strains are generated empirically and the basis for attenuation is usually ill defined, many important viruses lack an efficient live vaccine. Here, we present a general strategy for the rational...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2008.08.003
更新日期：2008-09-11 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：:Recent studies have revealed remarkable species specificity of the Toll-like receptors (TLRs) TLR11 and TLR12 and the immunity-related GTPase (IRG) proteins that are essential elements for detection and immune control of Toxoplasma gondii in mice, but not in humans. The biological and evolutionary implications of thes...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2014.01.004
更新日期：2014-02-12 00:00:00
abstract：:To maintain tissue homeostasis and avoid disease, epithelial cells damaged by pathogens need to be readily replenished, and this is mainly achieved by the activation of stem cells. In this Short Review, we discuss recent developments in the exciting field of host epithelia-pathogen interaction in Drosophila as well as...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2009.10.001
更新日期：2009-10-22 00:00:00
abstract：:Neutralizing antibodies (NAbs) are traditionally thought to inhibit virus infection by preventing virion entry into target cells. In addition, antibodies can engage Fc receptors (FcRs) on immune cells to activate antiviral responses. We describe a mechanism by which NAbs inhibit chikungunya virus (CHIKV), the most com...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2018.07.018
更新日期：2018-09-12 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：:Intracellular pathogens manipulate host organelles to support replication within cells. For Legionella pneumophila, the bacterium translocates proteins that establish an endoplasmic reticulum (ER)-associated replication compartment. We show here that the bacterial Sde proteins target host reticulon 4 (Rtn4) to control...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2016.12.007
更新日期：2017-02-08 00:00:00
abstract：:The role of gut microbes in health and disease has often been surmised from stool, which is easily sampled and rich in microbial diversity, density, and abundance. Microbial analyses of stool have been accepted as measures to determine the relationship of gut microbiomes with host health and disease, based on the beli...
journal_title：Cell host & microbe
pub_type： 杂志文章,评审
doi：10.1016/j.chom.2019.08.011
更新日期：2019-09-11 00:00:00
abstract：:Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever, a life-threatening human disease. The lack of animal models due to S. Typhi's strict human host specificity has hindered its study and vaccine development. We find that immunodeficient Rag2(-/-) γc(-/-) mice engrafted with human fetal liver hematopoiet...
journal_title：Cell host & microbe
pub_type： 杂志文章
doi：10.1016/j.chom.2010.09.003
更新日期：2010-10-21 00:00:00
