The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants.


: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.


Cell Host Microbe


Cell host & microbe


Dohlman AB,Arguijo Mendoza D,Ding S,Gao M,Dressman H,Iliev ID,Lipkin SM,Shen X




Has Abstract


2020-12-21 00:00:00








  • Drosophila intestinal response to bacterial infection: activation of host defense and stem cell proliferation.

    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


    authors: Buchon N,Broderick NA,Poidevin M,Pradervand S,Lemaitre B

    更新日期:2009-02-19 00:00:00

  • Fragment and Conquer.

    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


    authors: Kozjak-Pavlovic V,Chowdhury SR,Rudel T

    更新日期:2017-09-13 00:00:00

  • The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication.

    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


    authors: Balistreri G,Horvath P,Schweingruber C,Zünd D,McInerney G,Merits A,Mühlemann O,Azzalin C,Helenius A

    更新日期:2014-09-10 00:00:00

  • Homeostatic Control of Innate Lung Inflammation by Vici Syndrome Gene Epg5 and Additional Autophagy Genes Promotes Influenza Pathogenesis.

    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


    authors: Lu Q,Yokoyama CC,Williams JW,Baldridge MT,Jin X,DesRochers B,Bricker T,Wilen CB,Bagaitkar J,Loginicheva E,Sergushichev A,Kreamalmeyer D,Keller BC,Zhao Y,Kambal A,Green DR,Martinez J,Dinauer MC,Holtzman MJ,Crouch EC

    更新日期:2016-01-13 00:00:00

  • Structural Analysis of Rabies Virus Glycoprotein Reveals pH-Dependent Conformational Changes and Interactions with a Neutralizing Antibody.

    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


    authors: Yang F,Lin S,Ye F,Yang J,Qi J,Chen Z,Lin X,Wang J,Yue D,Cheng Y,Chen Z,Chen H,You Y,Zhang Z,Yang Y,Yang M,Sun H,Li Y,Cao Y,Yang S,Wei Y,Gao GF,Lu G

    更新日期:2020-03-11 00:00:00

  • Shigella phagocytic vacuolar membrane remnants participate in the cellular response to pathogen invasion and are regulated by autophagy.

    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


    authors: Dupont N,Lacas-Gervais S,Bertout J,Paz I,Freche B,Van Nhieu GT,van der Goot FG,Sansonetti PJ,Lafont F

    更新日期:2009-08-20 00:00:00

  • Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis.

    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


    authors: Garrett WS,Gallini CA,Yatsunenko T,Michaud M,DuBois A,Delaney ML,Punit S,Karlsson M,Bry L,Glickman JN,Gordon JI,Onderdonk AB,Glimcher LH

    更新日期:2010-09-16 00:00:00

  • Breaking the Barrier: Host Cell Invasion by Lujo Virus.

    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


    authors: Kunz S,de la Torre JC

    更新日期:2017-11-08 00:00:00

  • Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques.

    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


    authors: Stieh DJ,Matias E,Xu H,Fought AJ,Blanchard JL,Marx PA,Veazey RS,Hope TJ

    更新日期:2016-04-13 00:00:00

  • The Innate Sense of Bacteriophages.

    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


    authors: Bollyky PL,Secor PR

    更新日期:2019-02-13 00:00:00

  • Commensals, bacterial pathogens and intestinal inflammation: an intriguing ménage à trois.

    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


    authors: Pédron T,Sansonetti P

    更新日期:2008-06-12 00:00:00

  • HIV-1 envelope gp41 antibodies can originate from terminal ileum B cells that share cross-reactivity with commensal bacteria.

    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


    authors: Trama AM,Moody MA,Alam SM,Jaeger FH,Lockwood B,Parks R,Lloyd KE,Stolarchuk C,Scearce R,Foulger A,Marshall DJ,Whitesides JF,Jeffries TL Jr,Wiehe K,Morris L,Lambson B,Soderberg K,Hwang KK,Tomaras GD,Vandergrift N,Ja

    更新日期:2014-08-13 00:00:00

  • Dyeing to learn more about the gut microbiota.

    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


    authors: Donia MS,Fischbach MA

    更新日期:2013-02-13 00:00:00

  • Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways.

    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


    authors: Marcobal A,Barboza M,Sonnenburg ED,Pudlo N,Martens EC,Desai P,Lebrilla CB,Weimer BC,Mills DA,German JB,Sonnenburg JL

    更新日期:2011-11-17 00:00:00

  • Protectors of the Neonatal Gut: Clostridia Send Pathogens Packing.

    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


    authors: Behnsen J

    更新日期:2017-06-14 00:00:00

  • Beating Cancer with a Gut Feeling.

    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


    authors: Gorjifard S,Goldszmid RS

    更新日期:2015-12-09 00:00:00

  • Calnexin bridges the gap toward a pan-fungal vaccine.

    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


    authors: Rivera A,Hohl TM

    更新日期:2015-04-08 00:00:00

  • CRISPR-Cas Gatekeeper: Slow on the Uptake but Gets the Job Done.

    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


    authors: Whitaker RJ,Vanderpool CK

    更新日期:2016-02-10 00:00:00

  • Parasite Sensing of Host Nutrients and Environmental Cues.

    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


    authors: Zuzarte-Luís V,Mota MM

    更新日期:2018-06-13 00:00:00

  • Finding Leishmania: a deadly game of hide-and-seek.

    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


    authors: Scott P

    更新日期:2009-07-23 00:00:00

  • Olfactory plays a key role in spatiotemporal pathogenesis of cerebral malaria.

    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


    authors: Zhao H,Aoshi T,Kawai S,Mori Y,Konishi A,Ozkan M,Fujita Y,Haseda Y,Shimizu M,Kohyama M,Kobiyama K,Eto K,Nabekura J,Horii T,Ishino T,Yuda M,Hemmi H,Kaisho T,Akira S,Kinoshita M,Tohyama K,Yoshioka Y,Ishii KJ,Co

    更新日期:2014-05-14 00:00:00

  • Harnessing endogenous miRNAs to control virus tissue tropism as a strategy for developing attenuated virus vaccines.

    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


    authors: Barnes D,Kunitomi M,Vignuzzi M,Saksela K,Andino R

    更新日期:2008-09-11 00:00:00

  • Tracking Vibrio cholerae Cell-Cell Interactions during Infection Reveals Bacterial Population Dynamics within Intestinal Microenvironments.

    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


    authors: Fu Y,Ho BT,Mekalanos JJ

    更新日期:2018-02-14 00:00:00

  • Innate resistance against Toxoplasma gondii: an evolutionary tale of mice, cats, and men.

    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


    authors: Gazzinelli RT,Mendonça-Neto R,Lilue J,Howard J,Sher A

    更新日期:2014-02-12 00:00:00

  • Homeostasis in infected epithelia: stem cells take the lead.

    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


    authors: Pitsouli C,Apidianakis Y,Perrimon N

    更新日期:2009-10-22 00:00:00

  • Neutralizing Antibodies Inhibit Chikungunya Virus Budding at the Plasma Membrane.

    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


    authors: Jin J,Galaz-Montoya JG,Sherman MB,Sun SY,Goldsmith CS,O'Toole ET,Ackerman L,Carlson LA,Weaver SC,Chiu W,Simmons G

    更新日期:2018-09-12 00:00:00

  • Mechanisms underlying robustness and tunability in a plant immune signaling network.

    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


    authors: Kim Y,Tsuda K,Igarashi D,Hillmer RA,Sakakibara H,Myers CL,Katagiri F

    更新日期:2014-01-15 00:00:00

  • A Single Legionella Effector Catalyzes a Multistep Ubiquitination Pathway to Rearrange Tubular Endoplasmic Reticulum for Replication.

    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


    authors: Kotewicz KM,Ramabhadran V,Sjoblom N,Vogel JP,Haenssler E,Zhang M,Behringer J,Scheck RA,Isberg RR

    更新日期:2017-02-08 00:00:00

  • Regional Diversity of the Gastrointestinal Microbiome.

    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


    authors: Martinez-Guryn K,Leone V,Chang EB

    更新日期:2019-09-11 00:00:00

  • A mouse model for the human pathogen Salmonella typhi.

    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


    authors: Song J,Willinger T,Rongvaux A,Eynon EE,Stevens S,Manz MG,Flavell RA,Galán JE

    更新日期:2010-10-21 00:00:00