RESUMO
In ecological terms, the microbiome is defined as the microbiota and its environment, a definition that encompasses the human host. The size, species composition, and biogeography of microbial communities is shaped by host interactions, and, in turn, the microbiota influences many aspects of human health. Here we discuss the concept of microbiota-nourishing immunity, a host-microbe chimera composed of the microbiota and host factors that shape the microbial ecosystem, which functions in conferring colonization resistance against pathogens. We propose that dysbiosis is a biomarker of a weakening in microbiota-nourishing immunity and that homeostasis can be defined as a state of immune competence. Microbiota-nourishing immunity thus provides a conceptual framework to further examine the mechanisms that preserve a healthy microbiome and the drivers and consequences of dysbiosis.
Assuntos
Disbiose/imunologia , Interações Hospedeiro-Patógeno , Microbiota/imunologia , Animais , Autoantígenos/imunologia , Homeostase , Humanos , Imunidade , Imunocompetência , Tolerância a Antígenos PrópriosRESUMO
From the moment of birth, the newborn gastrointestinal tract is infiltrated by various bacteria originating from both maternal and environmental sources. These colonizing bacteria form a complex microbiota community that undergoes continuous changes until adulthood and plays an important role in infant health. The maturation of the infant gut microbiota is driven by many factors and follows a distinct patterned trajectory, with specific bacterial taxa establish in the intestine in accordance with developmental milestones as the infant grows. In this review, we highlight how elements such as diet and host physiology select for specific microbial functions and shape the composition of the bacterial community in the large intestine.
RESUMO
Enteropathogenic Escherichia coli (EPEC), a common cause of infant diarrhea, is associated with high risk of mortality in developing countries. The primary niche of infecting EPEC is the apical surface of intestinal epithelial cells. EPEC employs a type three secretion system (TTSS) to inject the host cells with dozens of effector proteins, which facilitate attachment to these cells and successful colonization. Here we show that EPEC elicit strong NF-κB activation in infected host cells. Furthermore, the data indicate that active, pore-forming TTSS per se is necessary and sufficient for this NF-κB activation, regardless of any specific effector or protein translocation. Importantly, upon infection with wild type EPEC this NF-κB activation is antagonized by anti-NF-κB effectors, including NleB, NleC and NleE. Accordingly, this NF-κB activation is evident only in cells infected with EPEC mutants deleted of nleB, nleC, and nleE. The TTSS-dependent NF-κB activation involves a unique pathway, which is independent of TLRs and Nod1/2 and converges with other pathways at the level of TAK1 activation. Taken together, our results imply that epithelial cells have the capacity to sense the EPEC TTSS and activate NF-κB in response. Notably, EPEC antagonizes this capacity by delivering anti-NF-κB effectors into the infected cells.
Assuntos
Escherichia coli Enteropatogênica/metabolismo , Células Epiteliais/microbiologia , Infecções por Escherichia coli/metabolismo , Infecções por Escherichia coli/microbiologia , Proteínas de Escherichia coli/metabolismo , NF-kappa B/metabolismo , Sistemas de Secreção Tipo III/metabolismo , Escherichia coli Enteropatogênica/genética , Células Epiteliais/metabolismo , Infecções por Escherichia coli/genética , Proteínas de Escherichia coli/genética , Interações Hospedeiro-Patógeno , Humanos , NF-kappa B/genética , Transdução de Sinais , Sistemas de Secreção Tipo III/genéticaRESUMO
Intestinal inflammation caused by Salmonella enterica serovar Typhimurium increases the availability of electron acceptors that fuel a respiratory growth of the pathogen in the intestinal lumen. Here we show that one of the carbon sources driving this respiratory expansion in the mouse model is 1,2-propanediol, a microbial fermentation product. 1,2-propanediol utilization required intestinal inflammation induced by virulence factors of the pathogen. S. Typhimurium used both aerobic and anaerobic respiration to consume 1,2-propanediol and expand in the murine large intestine. 1,2-propanediol-utilization did not confer a benefit in germ-free mice, but the pdu genes conferred a fitness advantage upon S. Typhimurium in mice mono-associated with Bacteroides fragilis or Bacteroides thetaiotaomicron. Collectively, our data suggest that intestinal inflammation enables S. Typhimurium to sidestep nutritional competition by respiring a microbiota-derived fermentation product.
Assuntos
Colite/microbiologia , Interações Hospedeiro-Patógeno/fisiologia , Propilenoglicol/metabolismo , Salmonelose Animal/metabolismo , Salmonella typhimurium/patogenicidade , Animais , Respiração Celular/fisiologia , Modelos Animais de Doenças , Camundongos , Camundongos Endogâmicos C57BL , Reação em Cadeia da Polimerase , Salmonella typhimurium/crescimento & desenvolvimento , Fatores de Virulência/metabolismoRESUMO
Enteropathogenic Escherichia coli (EPEC) represents a major causative agent of infant diarrhea associated with significant morbidity and mortality in developing countries. Although studied extensively in vitro, the investigation of the host-pathogen interaction in vivo has been hampered by the lack of a suitable small animal model. Using RT-PCR and global transcriptome analysis, high throughput 16S rDNA sequencing as well as immunofluorescence and electron microscopy, we characterize the EPEC-host interaction following oral challenge of newborn mice. Spontaneous colonization of the small intestine and colon of neonate mice that lasted until weaning was observed. Intimate attachment to the epithelial plasma membrane and microcolony formation were visualized only in the presence of a functional bundle forming pili (BFP) and type III secretion system (T3SS). Similarly, a T3SS-dependent EPEC-induced innate immune response, mediated via MyD88, TLR5 and TLR9 led to the induction of a distinct set of genes in infected intestinal epithelial cells. Infection-induced alterations of the microbiota composition remained restricted to the postnatal period. Although EPEC colonized the adult intestine in the absence of a competing microbiota, no microcolonies were observed at the small intestinal epithelium. Here, we introduce the first suitable mouse infection model and describe an age-dependent, virulence factor-dependent attachment of EPEC to enterocytes in vivo.
Assuntos
Modelos Animais de Doenças , Escherichia coli Enteropatogênica/patogenicidade , Infecções por Escherichia coli/microbiologia , Interações Hospedeiro-Patógeno/fisiologia , Animais , Animais Recém-Nascidos , Suscetibilidade a Doenças/microbiologia , Escherichia coli Enteropatogênica/metabolismo , Infecções por Escherichia coli/metabolismo , Fímbrias Bacterianas/ultraestrutura , Imunofluorescência , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Microscopia Eletrônica , Análise de Sequência com Séries de Oligonucleotídeos , Sistemas de Secreção Tipo III/metabolismo , Fatores de Virulência/metabolismoRESUMO
Enteropathogenic Escherichia coli (EPEC) is a major cause of food poisoning, leading to significant morbidity and mortality. EPEC virulence is dependent on a type III secretion system (T3SS), a molecular syringe employed by EPEC to inject effector proteins into host cells. The injected effector proteins subvert host cellular functions to the benefit of the infecting bacteria. The T3SS and related genes reside in several operons clustered in the locus of enterocyte effacement (LEE). We carried out simultaneous analysis of the expression dynamics of all the LEE promoters and the rate of maturation of the T3SS. The results showed that expression of the LEE1 operon is activated immediately upon shifting the culture to inducing conditions, while expression of other LEE promoters is activated only â¼70 min postinduction. Parallel analysis showed that the T3SS becomes functional around 100 min postinduction. The T3SS core proteins EscS, EscT, EscU, and EscR are predicted to be involved in the first step of T3SS assembly and are therefore included among the LEE1 genes. However, interfering with the temporal regulation of EscS, EscT, EscU, and EscR expression has only a marginal effect on the rate of the T3SS assembly. This study provides a comprehensive description of the transcription dynamics of all the LEE genes and correlates it to that of T3SS biogenesis.
Assuntos
Escherichia coli Enteropatogênica/genética , Proteínas de Escherichia coli/genética , Regulação Bacteriana da Expressão Gênica , Regiões Promotoras Genéticas/genética , Escherichia coli Enteropatogênica/metabolismo , Proteínas de Escherichia coli/metabolismo , Proteínas de Fluorescência Verde , Células HeLa , Humanos , Óperon/genética , Fosfoproteínas/genética , Proteínas Recombinantes de Fusão , Deleção de Sequência , Fatores de TempoRESUMO
Common nutrients in our diet often affect our health through unexpected mechanisms. In a recent issue of Nature, Scott et al. show gut microbes convert dietary tryptophan into metabolites activating intestinal dopamine receptors, which can block attachment of bacterial pathogens to host cells.
Assuntos
Dopamina , Microbioma Gastrointestinal , Microbioma Gastrointestinal/fisiologia , Dopamina/metabolismo , Humanos , Receptores Dopaminérgicos/metabolismo , Animais , Triptofano/metabolismo , Trato Gastrointestinal/microbiologia , Trato Gastrointestinal/metabolismo , Bactérias/metabolismo , Interações Hospedeiro-Patógeno , Aderência BacterianaRESUMO
We present the genomic sequences of 10 spore-forming bacteria from the Bacillaceae family isolated from fecal samples of mice residing in the Tisch Family Biblical Zoo, Jerusalem. These isolates suggest Bacillus bacteria are a native component of rodent gut flora, facilitating further research into gut colonization and microbiome diversity.
RESUMO
Bacterial species respond differently to consecutive antibiotic exposures with potential consequences on the host microbiome. In this issue of Cell Host & Microbe, Münch et al. investigate the effects of intermittent antibiotic treatments on specific bacteria using a consortium of microbes comprising a functional intestinal microbiota in germ-free mice.
Assuntos
Microbioma Gastrointestinal , Microbiota , Animais , Camundongos , Antibacterianos/farmacologia , Microbioma Gastrointestinal/fisiologia , BactériasRESUMO
Changes in the microbiota composition are associated with many human diseases, but factors that govern strain abundance remain poorly defined. We show that a commensal Escherichia coli strain and a pathogenic Salmonella enterica serovar Typhimurium isolate both utilize nitrate for intestinal growth, but each accesses this resource in a distinct biogeographical niche. Commensal E. coli utilizes epithelial-derived nitrate, whereas nitrate in the niche occupied by S. Typhimurium is derived from phagocytic infiltrates. Surprisingly, avirulent S. Typhimurium was shown to be unable to utilize epithelial-derived nitrate because its chemotaxis receptors McpB and McpC exclude the pathogen from the niche occupied by E. coli. In contrast, E. coli invades the niche constructed by S. Typhimurium virulence factors and confers colonization resistance by competing for nitrate. Thus, nutrient niches are not defined solely by critical resources, but they can be further subdivided biogeographically within the host into distinct microhabitats, thereby generating new niche opportunities for distinct bacterial species.
Assuntos
Microbioma Gastrointestinal , Salmonella typhimurium , Escherichia coli , Humanos , Nitratos , NutrientesRESUMO
Several major bacterial pathogens use the type III secretion system (TTSS) to deliver virulence factors into host cells. Bacterial Rho GTPase activating proteins (RhoGAPs) comprise a remarkable family of type III secreted toxins that modulate cytoskeletal dynamics and manipulate cellular signaling pathways. We show that the RhoGAP activity of Salmonella SptP and Pseudomonas ExoS toxins is resistant to variations in the concentration of NaCl or MgCl(2), unlike the known salt dependant nature of the activity of some eukaryotic GAPs such as p190, RanGAP and p120GAP. Furthermore, SptP-GAP and ExoS-GAP display full activity after treatment at 80°C or with 6 m urea, which suggests that these protein domains are capable of spontaneous folding into an active state following denaturing such as what might occur upon transit through the TTSS needle. We determined the catalytic activity of bacterial GAPs for Rac1, CDC42 and RhoA GTPases and found that ExoS, in addition to Yersinia YopE and Aeromonas AexT toxins, display higher catalytic efficiencies for Rac1 and CDC42 than the known eukaryotic GAPs, making them the most catalytically efficient RhoGAPs known. This study expands our knowledge of the mechanism of action of GAPs and of the ways bacteria mimic host activities and promote catalysis of eukaryotic signaling proteins.
Assuntos
Biocatálise , Proteínas Ativadoras de GTPase/química , Proteínas Ativadoras de GTPase/metabolismo , Pseudomonas/enzimologia , Salmonella/enzimologia , Proteínas rho de Ligação ao GTP/metabolismo , Humanos , Cloreto de Magnésio/farmacologia , Desnaturação Proteica/efeitos dos fármacos , Cloreto de Sódio/farmacologia , Especificidade por SubstratoRESUMO
A Western-style, high-fat diet promotes cardiovascular disease, in part because it is rich in choline, which is converted to trimethylamine (TMA) by the gut microbiota. However, whether diet-induced changes in intestinal physiology can alter the metabolic capacity of the microbiota remains unknown. Using a mouse model of diet-induced obesity, we show that chronic exposure to a high-fat diet escalates Escherichia coli choline catabolism by altering intestinal epithelial physiology. A high-fat diet impaired the bioenergetics of mitochondria in the colonic epithelium to increase the luminal bioavailability of oxygen and nitrate, thereby intensifying respiration-dependent choline catabolism of E. coli In turn, E. coli choline catabolism increased levels of circulating trimethlamine N-oxide, which is a potentially harmful metabolite generated by gut microbiota.
Assuntos
Colo/fisiologia , Dieta Hiperlipídica , Escherichia coli/metabolismo , Mucosa Intestinal/fisiologia , Metilaminas/metabolismo , Animais , Hipóxia Celular , Colina/administração & dosagem , Colina/metabolismo , Colo/citologia , Metabolismo Energético , Células Epiteliais/fisiologia , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Fezes/microbiologia , Microbioma Gastrointestinal , Inflamação , Mucosa Intestinal/metabolismo , Masculino , Metilaminas/sangue , Camundongos , Camundongos Endogâmicos C57BL , Mitocôndrias/metabolismo , Nitratos/metabolismo , Obesidade , Consumo de OxigênioRESUMO
The colonic microbiota exhibits cross-sectional heterogeneity, but the mechanisms that govern its spatial organization remain incompletely understood. Here we used Citrobacter rodentium, a pathogen that colonizes the colonic surface, to identify microbial traits that license growth and survival in this spatial niche. Previous work showed that during colonic crypt hyperplasia, type III secretion system (T3SS)-mediated intimate epithelial attachment provides C. rodentium with oxygen for aerobic respiration. However, we find that prior to the development of colonic crypt hyperplasia, T3SS-mediated intimate attachment is not required for aerobic respiration but for hydrogen peroxide (H2O2) respiration using cytochrome c peroxidase (Ccp). The epithelial NADPH oxidase NOX1 is the primary source of luminal H2O2 early after C. rodentium infection and is required for Ccp-dependent growth. Our results suggest that NOX1-derived H2O2 is a resource that governs bacterial growth and survival in close proximity to the mucosal surface during gut homeostasis.
Assuntos
Citrobacter rodentium/crescimento & desenvolvimento , Citrobacter rodentium/metabolismo , Citocromo-c Peroxidase/fisiologia , Peróxido de Hidrogênio/metabolismo , NADPH Oxidase 1/fisiologia , Anaerobiose , Animais , Colo/microbiologia , DNA Bacteriano , Fezes/microbiologia , Feminino , Vida Livre de Germes , Homeostase , Interações Hospedeiro-Patógeno , Mucosa Intestinal/microbiologia , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , RNA Ribossômico 16S , Organismos Livres de Patógenos Específicos , Sistemas de Secreção Tipo III/fisiologiaRESUMO
Bacterial GTPase-activating proteins (GAPs) subvert their host's eukaryotic Rho GTPases to their own advantage. Studies of bacterial GAPs extend our understanding of the action of eukaryotic GAPs, provide new tools for studies of cytoskeletal dynamics and offer new targets for anti-bacterial drugs.
Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Proteínas Ativadoras de GTPase/química , Proteínas Ativadoras de GTPase/metabolismo , Sequência de Aminoácidos , Arginina/química , Arginina/genética , Arginina/metabolismo , Proteínas de Bactérias/genética , Catálise , Células Eucarióticas/metabolismo , Proteínas Ativadoras de GTPase/genética , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Molecular , Dobramento de Proteína , Alinhamento de Sequência , Homologia de Sequência de AminoácidosRESUMO
Klebsiella pneumoniae, Escherichia coli, and other members of the Enterobacteriaceae family are common human pathogens that have acquired broad antibiotic resistance, rendering infection by some strains virtually untreatable. Enterobacteriaceae are intestinal residents, but generally represent <1% of the adult colonic microbiota. Antibiotic-mediated destruction of the microbiota enables Enterobacteriaceae to expand to high densities in the colon, markedly increasing the risk of bloodstream invasion, sepsis, and death. Here, we demonstrate that an antibiotic-naive microbiota suppresses growth of antibiotic-resistant clinical isolates of Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis by acidifying the proximal colon and triggering short chain fatty acid (SCFA)-mediated intracellular acidification. High concentrations of SCFAs and the acidic environment counter the competitive edge that O2 and NO3 respiration confer upon Enterobacteriaceae during expansion. Reestablishment of a microbiota that produces SCFAs enhances clearance of Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis from the intestinal lumen and represents a potential therapeutic approach to enhance clearance of antibiotic-resistant pathogens.
Assuntos
Colo/metabolismo , Farmacorresistência Bacteriana , Infecções por Enterobacteriaceae/metabolismo , Enterobacteriaceae/crescimento & desenvolvimento , Microbioma Gastrointestinal , Animais , Colo/microbiologia , Colo/patologia , Infecções por Enterobacteriaceae/microbiologia , Infecções por Enterobacteriaceae/patologia , Ácidos Graxos/metabolismo , Feminino , Humanos , Concentração de Íons de Hidrogênio , Masculino , CamundongosRESUMO
Lack of reproducibility is a prominent problem in biomedical research. An important source of variation in animal experiments is the microbiome, but little is known about specific changes in the microbiota composition that cause phenotypic differences. Here, we show that genetically similar laboratory mice obtained from four different commercial vendors exhibited marked phenotypic variation in their susceptibility to Salmonella infection. Faecal microbiota transplant into germ-free mice replicated donor susceptibility, revealing that variability was due to changes in the gut microbiota composition. Co-housing of mice only partially transferred protection against Salmonella infection, suggesting that minority species within the gut microbiota might confer this trait. Consistent with this idea, we identified endogenous Enterobacteriaceae, a low-abundance taxon, as a keystone species responsible for variation in the susceptibility to Salmonella infection. Protection conferred by endogenous Enterobacteriaceae could be modelled by inoculating mice with probiotic Escherichia coli, which conferred resistance by using its aerobic metabolism to compete with Salmonella for resources. We conclude that a mechanistic understanding of phenotypic variation can accelerate development of strategies for enhancing the reproducibility of animal experiments.
Assuntos
Enterobacteriaceae/fisiologia , Microbioma Gastrointestinal , Interações Microbianas/fisiologia , Salmonelose Animal/microbiologia , Experimentação Animal , Animais , Biomarcadores , Vias Biossintéticas , Modelos Animais de Doenças , Enterobacteriaceae/classificação , Escherichia coli/fisiologia , Transplante de Microbiota Fecal , Microbioma Gastrointestinal/genética , Vida Livre de Germes , Camundongos , Camundongos Endogâmicos C57BL , Fenótipo , Probióticos , Reprodutibilidade dos Testes , SalmonellaRESUMO
Neonates are highly susceptible to infection with enteric pathogens, but the underlying mechanisms are not resolved. We show that neonatal chick colonization with Salmonella enterica serovar Enteritidis requires a virulence-factor-dependent increase in epithelial oxygenation, which drives pathogen expansion by aerobic respiration. Co-infection experiments with an Escherichia coli strain carrying an oxygen-sensitive reporter suggest that S. Enteritidis competes with commensal Enterobacteriaceae for oxygen. A combination of Enterobacteriaceae and spore-forming bacteria, but not colonization with either community alone, confers colonization resistance against S. Enteritidis in neonatal chicks, phenocopying germ-free mice associated with adult chicken microbiota. Combining spore-forming bacteria with a probiotic E. coli isolate protects germ-free mice from pathogen colonization, but the protection is lost when the ability to respire oxygen under micro-aerophilic conditions is genetically ablated in E. coli. These results suggest that commensal Enterobacteriaceae contribute to colonization resistance by competing with S. Enteritidis for oxygen, a resource critical for pathogen expansion.
Assuntos
Enterobacteriaceae/crescimento & desenvolvimento , Enterobacteriaceae/fisiologia , Oxigênio/metabolismo , Salmonella/crescimento & desenvolvimento , Simbiose , Animais , Animais Recém-Nascidos , Ceco/microbiologia , Ceco/patologia , Galinhas , Coinfecção , Enterobacteriaceae/genética , Escherichia coli , Feminino , Microbioma Gastrointestinal , Masculino , Camundongos , Probióticos , Salmonella/genética , Salmonella/patogenicidade , Salmonelose Animal , Salmonella enteritidis/crescimento & desenvolvimento , Salmonella enteritidis/patogenicidade , Esporos Bacterianos/crescimento & desenvolvimento , Fatores de VirulênciaRESUMO
An imbalance in the colonic microbiota might underlie many human diseases, but the mechanisms that maintain homeostasis remain elusive. Recent insights suggest that colonocyte metabolism functions as a control switch, mediating a shift between homeostatic and dysbiotic communities. During homeostasis, colonocyte metabolism is directed toward oxidative phosphorylation, resulting in high epithelial oxygen consumption. The consequent epithelial hypoxia helps to maintain a microbial community dominated by obligate anaerobic bacteria, which provide benefit by converting fiber into fermentation products absorbed by the host. Conditions that alter the metabolism of the colonic epithelium increase epithelial oxygenation, thereby driving an expansion of facultative anaerobic bacteria, a hallmark of dysbiosis in the colon. Enteric pathogens subvert colonocyte metabolism to escape niche protection conferred by the gut microbiota. The reverse strategy, a metabolic reprogramming to restore colonocyte hypoxia, represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.
Assuntos
Colo/citologia , Colo/microbiologia , Microbioma Gastrointestinal , Mucosa Intestinal/metabolismo , Polaridade Celular , Colite Ulcerativa/metabolismo , Colite Ulcerativa/microbiologia , Disbiose/metabolismo , Disbiose/microbiologia , Interações Hospedeiro-Patógeno , Humanos , Consumo de OxigênioRESUMO
A balanced gut microbiota is important for health, but the mechanisms maintaining homeostasis are incompletely understood. Anaerobiosis of the healthy colon drives the composition of the gut microbiota towards a dominance of obligate anaerobes, while dysbiosis is often associated with a sustained increase in the abundance of facultative anaerobic Proteobacteria, indicative of a disruption in anaerobiosis. The colonic epithelium is hypoxic, but intestinal inflammation or antibiotic treatment increases epithelial oxygenation in the colon, thereby disrupting anaerobiosis to drive a dysbiotic expansion of facultative anaerobic Proteobacteria through aerobic respiration. These observations suggest a dysbiotic expansion of Proteobacteria is a potential diagnostic microbial signature of epithelial dysfunction, a hypothesis that could spawn novel preventative or therapeutic strategies for a broad spectrum of human diseases.