Species interactions differ in their genetic robustness.

Abstract:

:Conflict and cooperation between bacterial species drive the composition and function of microbial communities. Stability of these emergent properties will be influenced by the degree to which species' interactions are robust to genetic perturbations. We use genome-scale metabolic modeling to computationally analyze the impact of genetic changes when Escherichia coli and Salmonella enterica compete, or cooperate. We systematically knocked out in silico each reaction in the metabolic network of E. coli to construct all 2583 mutant stoichiometric models. Then, using a recently developed multi-scale computational framework, we simulated the growth of each mutant E. coli in the presence of S. enterica. The type of interaction between species was set by modulating the initial metabolites present in the environment. We found that the community was most robust to genetic perturbations when the organisms were cooperating. Species ratios were more stable in the cooperative community, and community biomass had equal variance in the two contexts. Additionally, the number of mutations that have a substantial effect is lower when the species cooperate than when they are competing. In contrast, when mutations were added to the S. enterica network the system was more robust when the bacteria were competing. These results highlight the utility of connecting metabolic mechanisms and studies of ecological stability. Cooperation and conflict alter the connection between genetic changes and properties that emerge at higher levels of biological organization.

journal_name

Front Microbiol

authors

Chubiz LM,Granger BR,Segrè D,Harcombe WR

doi

10.3389/fmicb.2015.00271

subject

Has Abstract

pub_date

2015-04-14 00:00:00

pages

271

issn

1664-302X

journal_volume

6

pub_type

杂志文章
  • A Novel Tightly Regulated Gene Expression System for the Human Intestinal Symbiont Bacteroides thetaiotaomicron.

    abstract::There is considerable interest in studying the function of Bacteroides species resident in the human gastrointestinal (GI)-tract and the contribution they make to host health. Reverse genetics and protein expression techniques, such as those developed for well-characterized Escherichia coli cannot be applied to Bacter...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01080

    authors: Horn N,Carvalho AL,Overweg K,Wegmann U,Carding SR,Stentz R

    更新日期:2016-07-13 00:00:00

  • Frontiers in Plant Breeding: Perspectives for the Selection of Vegetables Less Susceptible to Enteric Pathogens.

    abstract::Fresh vegetables including baby greens, microgreens, and sprouts can host human pathogens without exhibiting any visible signs of spoilage. It is clear that the vast majority of foodborne disease outbreaks associated with vegetable produce are not simply a result of an oversight by a producer, as it was shown that zoo...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2020.01087

    authors: Henriquez T,Lenzi A,Baldi A,Marvasi M

    更新日期:2020-05-28 00:00:00

  • LAB Bacteriocins Controlling the Food Isolated (Drug-Resistant) Staphylococci.

    abstract::Staphylococci are a group of microorganisms that can be often found in processed food and they might pose a risk for human health. In this study we have determined the content of staphylococci in 7 different fresh goat-milk cheeses. These bacteria were present in all of them, ranging from 103 to 106 CFU/g based on gro...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01143

    authors: Perales-Adán J,Rubiño S,Martínez-Bueno M,Valdivia E,Montalbán-López M,Cebrián R,Maqueda M

    更新日期:2018-06-12 00:00:00

  • From Farms to Markets: Gram-Negative Bacteria Resistant to Third-Generation Cephalosporins in Fruits and Vegetables in a Region of North Africa.

    abstract::The role of food in human exposure to antimicrobial-resistant bacteria is a growing food safety issue. The contribution of fruits and vegetables eaten raw to this exposure is still unclear. The evaluation of contamination levels of fruits, vegetables and the agricultural environment by third-generation cephalosporin (...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01569

    authors: Mesbah Zekar F,Granier SA,Marault M,Yaici L,Gassilloud B,Manceau C,Touati A,Millemann Y

    更新日期:2017-08-24 00:00:00

  • The Mitogen-Activated Protein Kinase CgMK1 Governs Appressorium Formation, Melanin Synthesis, and Plant Infection of Colletotrichum gloeosporioides.

    abstract::The fungus Colletotrichum gloeosporiodes infects plant hosts with a specialized cell called an appressorium, which is melanized and required for plant cell wall penetration. Here, we show that the mitogen-activated protein kinase CgMK1 governs appressorium formation and virulence in the poplar anthracnose fungus C. gl...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.02216

    authors: He P,Wang Y,Wang X,Zhang X,Tian C

    更新日期:2017-11-10 00:00:00

  • Prevalence and Antibiotic Resistance of Non-typhoidal Salmonella Isolated from Raw Chicken Carcasses of Commercial Broilers and Spent Hens in Tai'an, China.

    abstract::The present study was aimed to determine the prevalence and characteristics of Salmonella isolated from meat samples of commercial broilers (CB) and spent hens (SH). Between March and June 2016, 200 retail raw chicken carcasses (100 from CB and 100 from SH) were obtained from local supermarkets in Tai'an city of China...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.02106

    authors: Li S,Zhou Y,Miao Z

    更新日期:2017-10-31 00:00:00

  • RskA Is a Dual Function Activator-Inhibitor That Controls SigK Activity Across Distinct Bacterial Genera.

    abstract::It has been previously shown that RskA, the anti-Sigma factor K of Mycobacterium tuberculosis, inhibits SigK and that mutations in RskA promote high expression of the SigK regulon. The latter observation led us to hypothesize that RskA mutations lead to loss of the anti-Sigma factor function. In this report, we used n...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.558166

    authors: Veyrier FJ,Nieves C,Lefrancois LH,Trigui H,Vincent AT,Behr MA

    更新日期:2020-09-09 00:00:00

  • DivIVA Controls Progeny Morphology and Diverse ParA Proteins Regulate Cell Division or Gliding Motility in Bdellovibrio bacteriovorus.

    abstract::The predatory bacterium B. bacteriovorus grows and divides inside the periplasm of Gram-negative bacteria, forming a structure known as a bdelloplast. Cell division of predators inside the dead prey cell is not by binary fission but instead by synchronous division of a single elongated filamentous cell into odd or eve...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00542

    authors: Milner DS,Ray LJ,Saxon EB,Lambert C,Till R,Fenton AK,Sockett RE

    更新日期:2020-04-21 00:00:00

  • Functional Biology and Molecular Mechanisms of Host-Pathogen Interactions for Aflatoxin Contamination in Groundnut (Arachis hypogaea L.) and Maize (Zea mays L.).

    abstract::Aflatoxins are secondary metabolites produced by soilborne saprophytic fungus Aspergillus flavus and closely related species that infect several agricultural commodities including groundnut and maize. The consumption of contaminated commodities adversely affects the health of humans and livestock. Aflatoxin contaminat...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2020.00227

    authors: Soni P,Gangurde SS,Ortega-Beltran A,Kumar R,Parmar S,Sudini HK,Lei Y,Ni X,Huai D,Fountain JC,Njoroge S,Mahuku G,Radhakrishnan T,Zhuang W,Guo B,Liao B,Singam P,Pandey MK,Bandyopadhyay R,Varshney RK

    更新日期:2020-03-03 00:00:00

  • Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography.

    abstract::Seeds play key roles in the acquisition of plant pioneer microbiota, including the transmission of microbes from parent plants to offspring. However, the issues about seed microbial communities are mostly unknown, especially for their potential origins and the factors influencing the structure and composition. In this...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00995

    authors: Zhou X,Wang JT,Zhang ZF,Li W,Chen W,Cai L

    更新日期:2020-07-10 00:00:00

  • Sex Modulates Lactobacillus johnsonii N6.2 and Phytophenol Effectiveness in Reducing High Fat Diet Induced mTOR Activation in Sprague-Dawley Rats.

    abstract::Metabolic syndrome (MetS) is the underlying cause of some devastating diseases, including type 2 diabetes and cardiovascular disease. These diseases have been associated with over-activation of the mechanistic Target of Rapamycin (mTOR) pathway. This study utilizes a high fat diet (HFD) to induce MetS and to dissect t...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02649

    authors: Kling DN,DeBose-Scarlett EM,Teixeira LD,Gezan SA,Lorca GL,Gonzalez CF

    更新日期:2018-11-06 00:00:00

  • CRISPR-Cas Systems Features and the Gene-Reservoir Role of Coagulase-Negative Staphylococci.

    abstract::The claimed role of gene reservoir of coagulase-negative staphylococci (CoNS) could be contradicted by estimates that CRISPR/Cas systems are found in the genomes of 40-50% of bacteria, as these systems interfere with plasmid uptake in staphylococci. To further correlate this role with presence of CRISPR, we analyzed, ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01545

    authors: Rossi CC,Souza-Silva T,Araújo-Alves AV,Giambiagi-deMarval M

    更新日期:2017-08-15 00:00:00

  • Highly Sensitive Colorimetric Biosensor for Staphylococcal Enterotoxin B by a Label-Free Aptamer and Gold Nanoparticles.

    abstract::A simple, sensitive and selective colorimetric biosensor for the detection of Staphylococcal enterotoxin B (SEB) was developed using SEB-binding aptamer (SEB2) as recognition element and unmodified gold nanoparticles (AuNPs) as colorimetric probes. The assay is based on color change from red to purple due to conformat...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00179

    authors: Mondal B,Ramlal S,Lavu PS,N B,Kingston J

    更新日期:2018-02-13 00:00:00

  • Probiotic Lactobacillus rhamnosus GG Promotes Mouse Gut Microbiota Diversity and T Cell Differentiation.

    abstract::Lactic acid bacteria (LAB) are the primary genera of the intestinal flora and have many probiotic functions. In the present study, Lactobacillus rhamnosus GG (LGG) ATCC 53103 was used to treat BALB/c mice. After LGG intervention, both low and high LGG doses were shown to improve the observed OTU, Chao1, ACE, and Shann...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.607735

    authors: Shi CW,Cheng MY,Yang X,Lu YY,Yin HD,Zeng Y,Wang RY,Jiang YL,Yang WT,Wang JZ,Zhao DD,Huang HB,Ye LP,Cao X,Yang GL,Wang CF

    更新日期:2020-12-17 00:00:00

  • Degradation of Chrysene by Enriched Bacterial Consortium.

    abstract::Chrysene is a high molecular weight (HMW), polycyclic aromatic hydrocarbon (PAH) known for its recalcitrance and carcinogenic properties and sparsely soluble (0.003 mg/L) in aqueous medium. Due to these refractory properties, bioavailability of chrysene is very low and therefore is persistence in the environment escap...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01333

    authors: Vaidya S,Devpura N,Jain K,Madamwar D

    更新日期:2018-06-26 00:00:00

  • Functional Characterization of PknI-Rv2159c Interaction in Redox Homeostasis of Mycobacterium tuberculosis.

    abstract::Mycobacterium tuberculosis adapts to stress conditions by responding to the signals from its external environment. M. tuberculosis genome encodes 11 eukaryotic like serine/threonine protein kinases (STPK) and their importance in regulating the physiology and virulence of the bacteria are being explored. Previous study...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01654

    authors: Venkatesan A,Palaniyandi K,Sharma D,Bisht D,Narayanan S

    更新日期:2016-10-21 00:00:00

  • Phosphorus Deficiency Inhibits Cell Division But Not Growth in the Dinoflagellate Amphidinium carterae.

    abstract::Phosphorus (P) is an essential nutrient element for the growth of phytoplankton. How P deficiency affects population growth and the cell division cycle in dinoflagellates has only been studied in some species, and how it affects photosynthesis and cell growth remains poorly understood. In the present study, we investi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00826

    authors: Li M,Shi X,Guo C,Lin S

    更新日期:2016-06-01 00:00:00

  • Shedding Light on the Cell Biology of the Predatory Bacterium Bdellovibrio bacteriovorus.

    abstract::Bdellovibrio bacteriovorus is a predatory bacterium that feeds upon and proliferates inside other Gram-negative bacteria. Upon entry into the periplasmic space of the prey envelope, B. bacteriovorus initiates an exquisite developmental program in which it digests the host resources and grows as a filament, which event...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.03136

    authors: Laloux G

    更新日期:2020-01-21 00:00:00

  • 1H-NMR-Based Endometabolome Profiles of Burkholderia cenocepacia Clonal Variants Retrieved from a Cystic Fibrosis Patient during Chronic Infection.

    abstract::During cystic fibrosis (CF) chronic lung infections, bacteria of the Burkholderia cepacia complex (Bcc) are exposed for several years to a stressful and changing environment. These environmental challenges results in genetic changes of the initial infecting strain with the consequent diversification of genotypes and p...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.02024

    authors: Moreira AS,Lourenço AB,Sá-Correia I

    更新日期:2016-12-20 00:00:00

  • Characterization of the surfaceome of the metal-reducing bacterium Desulfotomaculum reducens.

    abstract::Desulfotomaculum reducens strain MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing Fe(III). Metal reduction in Gram-positive bacteria is poorly understood. Here, we investigated Fe(III) reduction with lactate, a non-fermentable substrate, as the electron donor. Lactate consumption is concomi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2014.00432

    authors: Dalla Vecchia E,Shao PP,Suvorova E,Chiappe D,Hamelin R,Bernier-Latmani R

    更新日期:2014-08-19 00:00:00

  • Occurrence of Hepatitis E Virus in Pigs and Pork Cuts and Organs at the Time of Slaughter, Spain, 2017.

    abstract::Zoonotic hepatitis E, mainly caused by hepatitis E virus (HEV) genotype (gt) 3, is a foodborne disease that has emerged in Europe in recent decades. The main animal reservoir for genotype 3 is domestic pigs. Pig liver and liver derivates are considered the major risk products, and studies focused on the presence of HE...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02990

    authors: García N,Hernández M,Gutierrez-Boada M,Valero A,Navarro A,Muñoz-Chimeno M,Fernández-Manzano A,Escobar FM,Martínez I,Bárcena C,González S,Avellón A,Eiros JM,Fongaro G,Domínguez L,Goyache J,Rodríguez-Lázaro D

    更新日期:2020-01-28 00:00:00

  • Actin and DNA Protect Histones from Degradation by Bacterial Proteases but Inhibit Their Antimicrobial Activity.

    abstract::Histones are small polycationic proteins located in the cell nucleus. Together, DNA and histones are integral constituents of the nucleosomes. Upon apoptosis, necrosis, and infection - induced cell death, histones are released from the cell. The extracellular histones have strong antimicrobial activity but are also cy...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01248

    authors: Sol A,Skvirsky Y,Blotnick E,Bachrach G,Muhlrad A

    更新日期:2016-08-09 00:00:00

  • The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria.

    abstract::Bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. Yet the water column, which has been studied largely by metagenomic approaches, is poor in such bacteria and their algal-polysaccharide-degrading enzymes. Even more surprisingly, the few published studie...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.01487

    authors: Martin M,Barbeyron T,Martin R,Portetelle D,Michel G,Vandenbol M

    更新日期:2015-12-24 00:00:00

  • Dissemination of Linezolid Resistance Through Sex Pheromone Plasmid Transfer in Enterococcus faecalis.

    abstract::Despite recent recognition of the ATP-binding cassette protein OptrA as an important mediator of linezolid resistance in Enterococcus faecalis worldwide, the mechanisms of optrA gene acquisition and transfer remain poorly understood. In this study, we performed comprehensive molecular and phenotypic profiling of 44 op...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01185

    authors: Zou J,Tang Z,Yan J,Liu H,Chen Y,Zhang D,Zhao J,Tang Y,Zhang J,Xia Y

    更新日期:2020-06-04 00:00:00

  • The in vitro Effect of Fibers With Different Degrees of Polymerization on Human Gut Bacteria.

    abstract::Human gut bacteria contribute significantly to human health and several studies have evaluated the effects of dietary fibers on human gut bacterial ecology. However, the relationship between different degrees of fiber polymerization and human gut bacteria is unknown. Here, we analyzed three fiber substrates with diffe...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00819

    authors: Chen M,Fan B,Liu S,Imam KMSU,Xie Y,Wen B,Xin F

    更新日期:2020-05-15 00:00:00

  • Diversity of Metabolically Active Bacteria in Water-Flooded High-Temperature Heavy Oil Reservoir.

    abstract::The goal of this work was to study the overall genomic diversity of microorganisms of the Dagang high-temperature oilfield (PRC) and to characterize the metabolically active fraction of these populations. At this water-flooded oilfield, the microbial community of formation water from the near-bottom zone of an injecti...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.00707

    authors: Nazina TN,Shestakova NM,Semenova EM,Korshunova AV,Kostrukova NK,Tourova TP,Min L,Feng Q,Poltaraus AB

    更新日期:2017-04-25 00:00:00

  • Comparative Transcriptomic and Metagenomic Analyses of Influenza Virus-Infected Nasal Epithelial Cells From Multiple Individuals Reveal Specific Nasal-Initiated Signatures.

    abstract::In vitro and in vivo research based on cell lines and animals are likely to be insufficient in elucidating authentic biological and physiological phenomena mimicking human systems, especially for generating pre-clinical data on targets and biomarkers. There is an obvious need for a model that can further bridge the ga...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02685

    authors: Tan KS,Yan Y,Koh WLH,Li L,Choi H,Tran T,Sugrue R,Wang Y,Chow VT

    更新日期:2018-11-14 00:00:00

  • Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level.

    abstract::Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly comp...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00063

    authors: Schmid M,Muri J,Melidis D,Varadarajan AR,Somerville V,Wicki A,Moser A,Bourqui M,Wenzel C,Eugster-Meier E,Frey JE,Irmler S,Ahrens CH

    更新日期:2018-01-30 00:00:00

  • FPR2: A Novel Promising Target for the Treatment of Influenza.

    abstract::The Formyl-peptide receptor-2 (FPR2) is a seven transmembrane G protein-coupled receptor, which plays an important role in sensing of bacteria and modulation of immune responses. FPR2 is also used by viruses for their own profit. Annexin A1, one of the multiple ligands of FPR2, is incorporated in the budding virus mem...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2017.01719

    authors: Alessi MC,Cenac N,Si-Tahar M,Riteau B

    更新日期:2017-09-05 00:00:00

  • The Characterization of Two-Component System PmrA/PmrB in Cronobacter sakazakii.

    abstract::Cronobacter sakazakii is an opportunistic Gram-negative pathogen that could cause meningitis and necrotizing enterocolitis. Several Gram-negative bacteria use the PmrA/PmrB system to sense and adapt to environmental change by resistance to cationic antimicrobial peptides of host immune systems. The PmrA/PmrB two-compo...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00903

    authors: Hua J,Jia X,Zhang L,Li Y

    更新日期:2020-06-17 00:00:00