A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes.

Abstract:

UNLABELLED:As diet is considered the major regulator of the gut ecosystem, the overall objective of this work was to demonstrate that a detailed knowledge of the phytochemical composition of food could add to our understanding of observed changes in functionality and activity of the gut microbiota. We used metatranscriptomic data from a human dietary intervention study to develop a network that consists of >400 compounds present in the administered plant-based diet linked to 609 microbial targets in the gut. Approximately 20% of the targeted bacterial proteins showed significant changes in their gene expression levels, while functional and topology analyses revealed that proteins in metabolic networks with high centrality are the most "vulnerable" targets. This global view and the mechanistic understanding of the associations between microbial gene expression and dietary molecules could be regarded as a promising methodological approach for targeting specific bacterial proteins that impact human health. IMPORTANCE:It is a general belief that microbiome-derived drugs and therapies will come to the market in coming years, either in the form of molecules that mimic a beneficial interaction between bacteria and host or molecules that disturb a harmful interaction or proteins that can modify the microbiome or bacterial species to change the balance of "good" and "bad" bacteria in the gut microbiome. However, among the numerous factors, what has proven the most influential for modulating the microbial composition of the gut is diet. In line with this, we demonstrate here that a systematic analysis of the interactions between the small molecules present in our diet and the gut bacterial proteome holds great potential for designing dietary interventions to improve human health.

journal_name

mBio

journal_title

mBio

authors

Ni Y,Li J,Panagiotou G

doi

10.1128/mBio.01263-15

subject

Has Abstract

pub_date

2015-10-27 00:00:00

pages

e01263-15

issue

6

issn

2150-7511

pii

mBio.01263-15

journal_volume

6

pub_type

杂志文章

相关文献

mBio文献大全
  • Simultaneous Binding of Multiple EF-Tu Copies to Translating Ribosomes in Live Escherichia coli.

    abstract::In bacteria, elongation factor Tu is a translational cofactor that forms ternary complexes with aminoacyl-tRNA (aa-tRNA) and GTP. Binding of a ternary complex to one of four flexible L7/L12 units on the ribosome tethers a charged tRNA in close proximity to the ribosomal A site. Two sequential tests for a match between...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02143-17

    authors: Mustafi M,Weisshaar JC

    更新日期:2018-01-16 00:00:00

  • The membrane-proximal region (MPR) of herpes simplex virus gB regulates association of the fusion loops with lipid membranes.

    abstract::Glycoprotein B (gB), gD, and gH/gL constitute the fusion machinery of herpes simplex virus (HSV). Prior studies indicated that fusion occurs in a stepwise fashion whereby the gD/receptor complex activates the entire process, while gH/gL regulates the fusion reaction carried out by gB. Trimeric gB is a class III fusion...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00429-12

    authors: Shelly SS,Cairns TM,Whitbeck JC,Lou H,Krummenacher C,Cohen GH,Eisenberg RJ

    更新日期:2012-11-20 00:00:00

  • Topological Analysis of the Type 3 Secretion System Translocon Pore Protein IpaC following Its Native Delivery to the Plasma Membrane during Infection.

    abstract::Many Gram-negative bacterial pathogens require a type 3 secretion system (T3SS) to deliver effector proteins into eukaryotic cells. Contact of the tip complex of the T3SS with a target eukaryotic cell initiates secretion of the two bacterial proteins that assemble into the translocon pore in the plasma membrane. The t...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00877-19

    authors: Russo BC,Duncan JK,Goldberg MB

    更新日期:2019-05-28 00:00:00

  • Identification of a New Lipoprotein Export Signal in Gram-Negative Bacteria.

    abstract::Bacteria of the phylum Bacteroidetes, including commensal organisms and opportunistic pathogens, harbor abundant surface-exposed multiprotein membrane complexes (Sus-like systems) involved in carbohydrate acquisition. These complexes have been mostly linked to commensalism, and in some instances, they have also been s...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01232-16

    authors: Lauber F,Cornelis GR,Renzi F

    更新日期:2016-10-25 00:00:00

  • Stapled Peptides Based on Human Angiotensin-Converting Enzyme 2 (ACE2) Potently Inhibit SARS-CoV-2 Infection In Vitro.

    abstract::SARS-CoV-2 uses human angiotensin-converting enzyme 2 (ACE2) as the primary receptor to enter host cells and initiate the infection. The critical binding region of ACE2 is an ∼30-amino-acid (aa)-long helix. Here, we report the design of four stapled peptides based on the ACE2 helix, which is expected to bind to SARS-C...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02451-20

    authors: Curreli F,Victor SMB,Ahmed S,Drelich A,Tong X,Tseng CK,Hillyer CD,Debnath AK

    更新日期:2020-12-11 00:00:00

  • The Yeast PCNA Unloader Elg1 RFC-Like Complex Plays a Role in Eliciting the DNA Damage Checkpoint.

    abstract::The PCNA (proliferating cell nuclear antigen) ring plays central roles during DNA replication and repair. The yeast Elg1 RFC-like complex (RLC) is the principal unloader of chromatin-bound PCNA and thus plays a central role in maintaining genome stability. Here we identify a role for Elg1 in the unloading of PCNA duri...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01159-19

    authors: Sau S,Liefshitz B,Kupiec M

    更新日期:2019-06-11 00:00:00

  • Cryptococcus gattii in the Age of Whole-Genome Sequencing.

    abstract::Cryptococcus gattii, the sister species of Cryptococcus neoformans, is an emerging pathogen which gained importance in connection with the ongoing cryptococcosis outbreak on Vancouver Island. Many molecular studies have divided this species into for major lineages: VGI, VGII, VGIII, and VGIV. This commentary summarize...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01761-15

    authors: Meyer W

    更新日期:2015-11-17 00:00:00

  • Range Expansion and the Origin of USA300 North American Epidemic Methicillin-Resistant Staphylococcus aureus.

    abstract::The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from th...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02016-17

    authors: Challagundla L,Luo X,Tickler IA,Didelot X,Coleman DC,Shore AC,Coombs GW,Sordelli DO,Brown EL,Skov R,Larsen AR,Reyes J,Robledo IE,Vazquez GJ,Rivera R,Fey PD,Stevenson K,Wang SH,Kreiswirth BN,Mediavilla JR,Arias CA

    更新日期:2018-01-02 00:00:00

  • Elegant Science.

    abstract::Elegance is a prized quality in science that is associated with simplicity and explanatory power. This essay considers the qualities that make a scientific model, experiment, method, or theory "elegant," with a focus on the life sciences. We propose a definition of elegance that includes clarity, cleverness, correctne...

    journal_title:mBio

    pub_type: 社论

    doi:10.1128/mBio.00043-18

    authors: Casadevall A,Fang FC

    更新日期:2018-02-20 00:00:00

  • Bacteriophage Distributions and Temporal Variability in the Ocean's Interior.

    abstract::Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacifi...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01903-17

    authors: Luo E,Aylward FO,Mende DR,DeLong EF

    更新日期:2017-11-28 00:00:00

  • In Vivo Biotinylation of the Toxoplasma Parasitophorous Vacuole Reveals Novel Dense Granule Proteins Important for Parasite Growth and Pathogenesis.

    abstract:UNLABELLED:Toxoplasma gondii is an obligate intracellular parasite that invades host cells and replicates within a unique parasitophorous vacuole. To maintain this intracellular niche, the parasite secretes an array of dense granule proteins (GRAs) into the nascent parasitophorous vacuole. These GRAs are believed to pl...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00808-16

    authors: Nadipuram SM,Kim EW,Vashisht AA,Lin AH,Bell HN,Coppens I,Wohlschlegel JA,Bradley PJ

    更新日期:2016-08-02 00:00:00

  • Identification of Novel Alleles Conferring Superior Production of Rose Flavor Phenylethyl Acetate Using Polygenic Analysis in Yeast.

    abstract::Flavor compound metabolism is one of the last areas in metabolism where multiple genes encoding biosynthetic enzymes are still unknown. A major challenge is the involvement of side activities of enzymes having their main function in other areas of metabolism. We have applied pooled-segregant whole-genome sequence anal...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01173-17

    authors: Trindade de Carvalho B,Holt S,Souffriau B,Lopes Brandão R,Foulquié-Moreno MR,Thevelein JM

    更新日期:2017-11-07 00:00:00

  • Functional Differences between E. coli and ESKAPE Pathogen GroES/GroEL.

    abstract::As the GroES/GroEL chaperonin system is the only bacterial chaperone that is essential under all conditions, we have been interested in the development of GroES/GroEL inhibitors as potential antibiotics. Using Escherichia coli GroES/GroEL as a surrogate, we have discovered several classes of GroES/GroEL inhibitors tha...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02167-20

    authors: Sivinski J,Ambrose AJ,Panfilenko I,Zerio CJ,Machulis JM,Mollasalehi N,Kaneko LK,Stevens M,Ray AM,Park Y,Wu C,Hoang QQ,Johnson SM,Chapman E

    更新日期:2021-01-12 00:00:00

  • SsaV Interacts with SsaL to Control the Translocon-to-Effector Switch in the Salmonella SPI-2 Type Three Secretion System.

    abstract::Nonflagellar type III secretion systems (nf T3SSs) form a cell surface needle-like structure and an associated translocon that deliver bacterial effector proteins into eukaryotic host cells. This involves a tightly regulated hierarchy of protein secretion. A switch involving SctP and SctU stops secretion of the needle...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01149-18

    authors: Yu XJ,Grabe GJ,Liu M,Mota LJ,Holden DW

    更新日期:2018-10-02 00:00:00

  • Designing the Next Generation of Vaccines: Relevance for Future Pandemics.

    abstract::The development of vaccines is one of the greatest medical interventions in the history of global infectious diseases and has contributed to the annual saving of at least 2 to 3 million lives worldwide. However, many diseases are not preventable through currently available vaccines, and the potential of modulating the...

    journal_title:mBio

    pub_type: 杂志文章,评审

    doi:10.1128/mBio.02616-20

    authors: Domínguez-Andrés J,van Crevel R,Divangahi M,Netea MG

    更新日期:2020-12-22 00:00:00

  • Nuclear Factor Y (NF-Y) Modulates Encystation in Entamoeba via Stage-Specific Expression of the NF-YB and NF-YC Subunits.

    abstract::Nuclear factor Y (NF-Y) is a heterotrimeric transcription factor composed of three subunits, namely, NF-YA, NF-YB, and NF-YC, which are conserved throughout evolution. In higher eukaryotes, NF-Y plays important roles in several cellular processes (development, cell cycle regulation, apoptosis, and response to growth, ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00737-19

    authors: Manna D,Singh U

    更新日期:2019-06-18 00:00:00

  • A Single-Cell Approach to the Elusive Latent Human Cytomegalovirus Transcriptome.

    abstract::Herpesvirus latency has been difficult to understand molecularly due to low levels of viral genomes and gene expression. In the case of the betaherpesvirus human cytomegalovirus (HCMV), this is further complicated by the heterogeneity inherent to hematopoietic subpopulations harboring genomes and, as a consequence, th...

    journal_title:mBio

    pub_type: 评论,杂志文章

    doi:10.1128/mBio.01001-18

    authors: Goodrum F,McWeeney S

    更新日期:2018-06-12 00:00:00

  • Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues.

    abstract::EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal antiserum raised against the putative receptor binding domain (RBD) o...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02772-20

    authors: McCarthy KR,Timpona JL,Jenni S,Bloyet LM,Brusic V,Johnson WE,Whelan SPJ,Robinson-McCarthy LR

    更新日期:2020-11-17 00:00:00

  • A Salmonella virulence factor activates the NOD1/NOD2 signaling pathway.

    abstract::The invasion-associated type III secretion system (T3SS-1) of Salmonella enterica serotype Typhimurium (S. Typhimurium) activates the transcription factor NF-κB in tissue culture cells and induces inflammatory responses in animal models through unknown mechanisms. Here we show that bacterial delivery or ectopic expres...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00266-11

    authors: Keestra AM,Winter MG,Klein-Douwel D,Xavier MN,Winter SE,Kim A,Tsolis RM,Bäumler AJ

    更新日期:2011-12-20 00:00:00

  • Intercellular diffusion of a fluorescent sucrose analog via the septal junctions in a filamentous cyanobacterium.

    abstract:UNLABELLED:Many filamentous cyanobacteria produce specialized nitrogen-fixing cells called heterocysts, which are located at semiregular intervals along the filament with about 10 to 20 photosynthetic vegetative cells in between. Nitrogen fixation in these complex multicellular bacteria depends on metabolite exchange b...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02109-14

    authors: Nürnberg DJ,Mariscal V,Bornikoel J,Nieves-Morión M,Krauß N,Herrero A,Maldener I,Flores E,Mullineaux CW

    更新日期:2015-03-17 00:00:00

  • Cap0037, a Novel Global Regulator of Clostridium acetobutylicum Metabolism.

    abstract::An operon comprising two genes, CA_P0037 and CA_P0036, that encode proteins of unknown function that were previously shown to be highly expressed in acidogenic cells and repressed in solventogenic and alcohologenic cells is located on the pSOL1 megaplasmid of Clostridium acetobutylicum upstream of adhE2 A CA_P0037::in...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01218-16

    authors: Nguyen NP,Linder S,Flitsch SK,Schiel-Bengelsdorf B,Dürre P,Soucaille P

    更新日期:2016-10-04 00:00:00

  • The CpxQ sRNA Negatively Regulates Skp To Prevent Mistargeting of β-Barrel Outer Membrane Proteins into the Cytoplasmic Membrane.

    abstract:UNLABELLED:The promoter most strongly induced upon activation of the Cpx two-component envelope stress response is the cpxP promoter. The 3' untranscribed region (UTR) of the cpxP transcript is shown to produce a small RNA (sRNA), CpxQ. We investigated the role of CpxQ in combating envelope stress. Remarkably, the two ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00312-16

    authors: Grabowicz M,Koren D,Silhavy TJ

    更新日期:2016-04-05 00:00:00

  • Biosynthesis of Conjugate Vaccines Using an O-Linked Glycosylation System.

    abstract:UNLABELLED:Conjugate vaccines are known to be one of the most effective and safest types of vaccines against bacterial pathogens. Previously, vaccine biosynthesis has been performed by using N-linked glycosylation systems. However, the structural specificity of these systems for sugar substrates has hindered their appl...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00443-16

    authors: Pan C,Sun P,Liu B,Liang H,Peng Z,Dong Y,Wang D,Liu X,Wang B,Zeng M,Wu J,Zhu L,Wang H

    更新日期:2016-04-26 00:00:00

  • Cuts Both Ways: Proteases Modulate Virulence of Enterohemorrhagic Escherichia coli.

    abstract::Enterohemorrhagic Escherichia coli (EHEC) is a major cause of foodborne gastrointestinal illness. EHEC uses a specialized type III secretion system (T3SS) to form attaching and effacing lesions in the colonic epithelium and outcompete commensal gut microbiota to cause disease. A recent report in mBio (E. A. Cameron, M...

    journal_title:mBio

    pub_type: 评论,杂志文章

    doi:10.1128/mBio.00115-19

    authors: Palmer LD,Skaar EP

    更新日期:2019-02-26 00:00:00

  • Laccase Affects the Rate of Cryptococcus neoformans Nonlytic Exocytosis from Macrophages.

    abstract::Nonlytic exocytosis is a process in which previously ingested microbes are expelled from host phagocytes with the concomitant survival of both cell types. This process has been observed in the interaction of Cryptococcus spp. and other fungal cells with phagocytes as distant as mammalian, bird, and fish macrophages an...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02085-20

    authors: Frazão SO,Sousa HR,Silva LGD,Folha JDS,Gorgonha KCM,Oliveira GP Jr,Felipe MSS,Silva-Pereira I,Casadevall A,Nicola AM,Albuquerque P

    更新日期:2020-09-08 00:00:00

  • Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island.

    abstract::Exudative cutaneous ulcers (CU) in yaws-endemic areas are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD), but one-third of CU cases are idiopathic (IU). Using mass drug administration (MDA) of azithromycin, a yaws eradication campaign on Lihir Island in Papua New Guinea reduced bu...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.03162-20

    authors: Griesenauer B,González-Beiras C,Fortney KR,Lin H,Gao X,Godornes C,Nelson DE,Katz BP,Lukehart SA,Mitjà O,Dong Q,Spinola SM

    更新日期:2021-01-12 00:00:00

  • Cytokeratin 8 is an epithelial cell receptor for Pet, a cytotoxic serine protease autotransporter of Enterobacteriaceae.

    abstract:UNLABELLED:The group of proteins known as serine protease autotransporters of Enterobacteriaceae (SPATE) is a growing family of serine proteases secreted to the external milieu by the type V secretion system. Pet toxin and some other SPATE belong to the class 1 cytotoxic SPATE, which have comparable protease strength o...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00838-13

    authors: Nava-Acosta R,Navarro-Garcia F

    更新日期:2013-12-10 00:00:00

  • The Antituberculosis Drug Ethambutol Selectively Blocks Apical Growth in CMN Group Bacteria.

    abstract::Members of the genus Mycobacterium are the most prevalent cause of infectious diseases. Mycobacteria have a complex cell envelope containing a peptidoglycan layer and an additional arabinogalactan polymer to which a mycolic acid bilayer is linked; this complex, multilayered cell wall composition (mAGP) is conserved am...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02213-16

    authors: Schubert K,Sieger B,Meyer F,Giacomelli G,Böhm K,Rieblinger A,Lindenthal L,Sachs N,Wanner G,Bramkamp M

    更新日期:2017-02-07 00:00:00

  • Pilus adhesin RrgA interacts with complement receptor 3, thereby affecting macrophage function and systemic pneumococcal disease.

    abstract:UNLABELLED:Pneumococcal pili have been shown to influence pneumococcal colonization, disease development, and the inflammatory response in mice. The role of the pilus-associated RrgA adhesin in pneumococcal interactions with murine and human macrophages was investigated. Expression of pili with RrgA enhanced the uptake...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00535-12

    authors: Orrskog S,Rounioja S,Spadafina T,Gallotta M,Norman M,Hentrich K,Fälker S,Ygberg-Eriksson S,Hasenberg M,Johansson B,Uotila LM,Gahmberg CG,Barocchi M,Gunzer M,Normark S,Henriques-Normark B

    更新日期:2012-12-26 00:00:00

  • GRP78 and Integrins Play Different Roles in Host Cell Invasion during Mucormycosis.

    abstract::Mucormycosis, caused by Rhizopus species, is a life-threatening fungal infection that occurs in patients immunocompromised by diabetic ketoacidosis (DKA), cytotoxic chemotherapy, immunosuppressive therapy, hematologic malignancies, or severe trauma. Inhaled Rhizopus spores cause pulmonary infections in patients with h...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01087-20

    authors: Alqarihi A,Gebremariam T,Gu Y,Swidergall M,Alkhazraji S,Soliman SSM,Bruno VM,Edwards JE Jr,Filler SG,Uppuluri P,Ibrahim AS

    更新日期:2020-06-02 00:00:00