Biochemical mechanisms of pathogen restriction by intestinal bacteria.pdf

Biochemical mechanisms of pathogen restriction by intestinal bacteriaKavita J.Rangan1 and Howard C.Hang1,*1Laboratory of Chemical Biology and Microbial PathogenesisAbstractThe intestine is a highly complex ecosystem where many bacterial species interact with each other and host cells to influence animal physiology and susceptibility to pathogens.Genomic methods have provided a broad framework for understanding how alterations in microbial communities are associated with host physiology and infection,but the biochemical mechanisms of specific intestinal bacterial species are only emerging.In this review,we focus on recent studies that have characterized the biochemical mechanisms by which intestinal bacteria interact with other bacteria and host pathways to restrict pathogen infection.Understanding the biochemical mechanisms of intestinal microbiota function should provide new opportunities for therapeutic development towards a variety of infectious diseases.Emerging mechanisms and applications of microbiota-mediated pathogen resistanceThe intestinal microbiota(see Glossary)is central to host metabolism and immunity 1,2.As a result,the microbiome as a whole broadly impacts host physiology and response to intestinal and systemic diseases.The composition of the intestinal microbiome is dynamic and is influenced by environmental factors including host diet and exposure to drugs,infection,and probiotics,as well as by genetic factors.Advances in our understanding of specific bacterial genes and molecules have revealed a diversity of inter-bacterial interactions and immuno-modulatory roles for intestinal bacteria that influence pathogen fitness and host response to infection 3.This review will focus on recent studies of specific intestinal bacterial species,their metabolites and potential biochemical mechanisms(see Table 1 for examples presented in this review).Beyond infection,the intestinal microbiome widely influences host physiology,with specific bacterial factors contributing to diseases including obesity,cardiovascular disease,and diverse neurological disorders.These topics have been recently reviewed elsewhere 4,5 and will not be discussed in this review.A molecular understanding of intestinal microbiota-host interactions is of great medical and ecological importance.Insight into microbiota function can help us design targeted therapeutics against a variety of diseases and advance personalized medicine.While the clinical potential of probiotic and other microbiota-based therapies against infectious disease*Correspondence to:hhangrockefeller.edu.HHS Public AccessAuthor manuscriptTrends Biochem Sci.Author manuscript;available in PMC 2018 July 10.Published in final edited form as:Trends Biochem Sci.2017 November;42(11):887898.doi:10.1016/j.tibs.2017.08.005.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptis now being explored,available treatments are still coarse.For example,fecal transplantation has recently emerged as an investigational new drug for recurrent Clostridium difficile infection6,7.Transitioning to more targeted therapeutics,however,requires a better understanding of the specific mechanisms of individual bacterial species.Beyond the clinical potential,characterizing the intestinal microbiome gives us a generalizable framework for evaluating the ecology of other complex host-microbe interactions,which are ubiquitous on earth.Inter-bacterial interactionsThe intestinal microbiome is shaped by metabolic competition and communication.Inter-bacterial interactions within this community can affect the fitness of key species as well as overall community structure.In this section,we will discuss recently described mechanisms by which intestinal bacteria directly restrict enteric pathogens(Figure 1A).Inhibition of pathogen growth can occur through resource competition as well as through direct bactericidal mechanisms.Alternatively,pathogen infection can be attenuated by modulating specific virulence mechanisms.Metabolic competitionAlthough microbial community structure at the taxonomic/species level varies greatly across healthy individuals,functional metabolic capacity at the metagenomic level is largely stable 8.This highlights how metabolic competition and interdependence builds microbial community structure.Within this framework,host genetics and behavior can alter the intestinal environment and shift microbial composition.Niche competition not only defines microbial community structure,but also serves as a barrier for both enteric pathogens and pathobionts.Metabolic competition over resources including diverse carbon sources,trace metals,and vitamins such as B12 9,shapes the microbiota and likely contributes to colonization resistance.Due to metabolic similarity,competition is often greater between related species than unrelated species.Enterobacteriaceae is a large family of Gram-negative bacteria that includes commensal species as well as several intestinal pathogens including:Salmonella,Shigella,Yersinia,Citrobacter,and Enteropathogenic Escherichia coli.Indeed,metabolic competition between members of the Enterobacteriaceae has been described in vivo.For example,competition over monosaccharide use can restrict colonization by Citrobacter rodentium in wild-type mice 10.Colonization of mice with commensal E.coli provides greater competition-mediated growth restriction of C.rodentium than colonization with Bacteroides species,which are able to utilize a more diverse profile of mono-and polysaccharides.However,in an experimentally skewed intestinal environment with monosaccharides as the sole carbon source,colonization of mice with Bacteroides thetaiotaomicron can also provide colonization resistance towards C.rodentium.Competition over iron is another well-characterized example of inter-species competition in the intestine.Because iron is an essential and limiting nutrient,many intestinal bacteria produce iron-chelating siderophores to increase iron uptake.Host-secreted antimicrobial proteins,such as lipocalin-2,restrict bacterial growth by binding and inactivating diverse Rangan and HangPage 2Trends Biochem Sci.Author manuscript;available in PMC 2018 July 10.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptbacterial siderophores.Salmonella enterica can evade lipocalin-2-mediated growth inhibition by producing modified siderophores that cannot be bound by lipocalin-2 11,12,improving pathogen fitness 13.In this context,probiotic E.coli Nissle 1917,which expresses four iron uptake systems that are resistant to lipocalin-2,competitively reduces Salmonella colonization and subsequent inflammation 14.Many pathogens generate a distinct niche as a strategy to avoid competition with intestinal bacteria and gain access to nutrients.In a simplistic sense,adhesion to the surface of intestinal epithelial cells,or invasion into host cells,could be viewed as a means to evade competing intestinal bacteria.Intestinal pathogens may also have evolved unique nutrient utilization pathways compared to their commensal counterparts.For example,pathogenic strains of E.coli can consume a unique set of intestinal sugars as compared to commensal strains of E.coli 15.Alternatively,pathogen-induced inflammation can disrupt the microbiome,releasing unique metabolites to give pathogens a growth advantage.For example,Salmonella-induced intestinal inflammation leads to the generation of tetrathionate by host epithelial cells.Tetrathionate respiration by Salmonella confers a growth advantage over other intestinal bacteria that rely on fermentation 16.In the inflamed intestine,ethanolamine utilization by both Salmonella 17 and pathogenic E.coli 18 can also enhance their colonization 19.Inflammation-induced dysbiosis can also lead to the outgrowth of specific non-pathogenic species.For example,nitrate released in the inflamed intestine is used in anaerobic respiration by commensal E.coli strains 20.Whether proliferation of nitrate-utilizing E.coli species contributes to other pathogenesis mechanisms,however,is unclear.Antibiotic-induced dysbiosis can also alter nutrient availability to allow the outgrowth of pathogens and pathobionts.For example,antibiotic treatment can alter microbial composition to promote the proliferation of vancomycin-resistant Enterococci 21 as well as C.difficile 22,23.In the case of C.difficile infection,antibiotic treatment results in increases in both succinate 23 and sialic acid 22,which are utilized by C.difficile to enhance intestinal colonization.Direct bacterial warfareBeyond metabolic competition,intestinal bacteria can limit the growth of other bacterial species through the production of antibacterial compounds and inhibitory metabolites as well as through contact-dependent killing.Recent studies have highlighted how microbiota-produced antimicrobials can inhibit intestinal colonization by specific enteric pathogens and pathobionts.For example,bacteriocins are diverse secreted antibacterial peptides that target and lyse related bacterial species 24,25.In the intestine,colonization by bacteriocin-producing Enterococcus faecalis reduces the numbers of indigenous E.faecalis,as well as infection by vancomycin-resistant E.faecalis 26.Microcins produced under iron starvation conditions by probiotic E.coli Nissle 1917 reduce intestinal colonization by other commensal E.coli,as well as Salmonella 25.The large scale bioinformatic and biochemical mining of the microbiome for other antibacterial molecules has highlighted the potential of microbiota-based antimicrobial compounds as therapeutic leads for new antibiotics 27.Beyond specific antimicrobial compounds,other bacterial metabolites may Rangan and HangPage 3Trends Biochem Sci.Author manuscript;available in PMC 2018 July 10.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor Manuscriptalso directly inhibit pathogen growth.For example,Clostridium scindens inhibits C.difficile growth and pathogenesis in mice 28.This in vivo protection is correlated with the capacity to generate secondary bile acids,which can inhibit C.difficile growth in vitro.In addition to releasing antibacterial compounds into the extracellular space,many Gram-negative bacterial species can directly antagonize neighboring cells by injection of effector proteins using the type-VI secretion system(T6SS).T6SSs are encoded by commensals and pathogens alike,and T6SS-mediated competition is likely prevalent in the intestine.For example,T6SSs are widely encoded amongst the Bacteroidales 29,an order that includes abundant intestinal commensals,and T6SS-encoding Bacteroides can target sensitive Bacteroides species,presumably to limit competition 3032.Intestinal pathogens such as S.Typhimurum 33 and Vibrio cholerae also encode T6SSs,which may target intestinal bacteria and enhance pathogen colonization.Ex vivo,V.cholerae uses its T6SS to deliver antimicrobial effectors to intestinal bacteria,such as E.coli and Salmonella 34,and self-immunity to this secretion system is required for robust intestinal colonization,suggesting that V.cholera employs its T6SS in vivo 35.Interference with pathogen virulenceIn addition to restricting pathogen colonization and proliferation,intestinal bacteria can also directly affect pathogen virulence mechanisms.Virulence gene expression involves integrating a diversity of environmental cues,some of which can be modified by intestinal bacteria.For example,in response to a local increase in oxygen close to the intestinal epithelial surface,Shigella flexneri increases the secretion of effector proteins involved in host cell invasion 36.This raises the possibility that intestinal bacteria adhered to the mucosa could potentially inhibit Shigella invasion by consuming local oxygen.Intestinal bacteria may also alter the pool of available host-derived nutrients to affect pathogen virulence.For example,fucosidases expressed by Bacteroides thetaiotaomicron can release fucose from mucins.Fucose is sensed by Enterohemorrhagic E.coli through the FusK/R two-component system,and high fucose leads to a decrease in the expression of virulence genes required for the formation of attaching and effacing lesions 37.Although B.thetaiotaomicron has not been shown to directly affect EHEC virulence,fusK EHEC exhibit a growth defect in vivo,suggesting that the regulation of virulence through fucose sensing may be relevant to intestinal infection.Bacterial fermentation in the intestine results in the production of diverse short-chain fatty acids.Short-chain fatty acids not only modulate host immunity but have also been shown to directly modulate virulence gene expression of various pathogens ex vivo.For example,short-chain fatty acids can differentially regulate the expression of Salmonella virulence genes involved in host cell invasion in a chain-length dependent manner.Specifically,acetate enhances the expression of genes involved in invasion 38,while propionate 39 and butyrate 40 are inhibitory.Other molecules prevalent in the intestinal environment,such as bile acids,have also been shown to modulate virulence gene expression of enteric pathogens in vitro 4143,but the direct biochemical mechanisms of these metabolites on pathogen virulence is not clear.Rangan and HangPage 4Trends Biochem Sci.Author manuscript;available in PMC 2018 July 10.Author ManuscriptAuthor ManuscriptAuthor ManuscriptAuthor ManuscriptBeyond metabolite regulation of virulence mechanisms,quorum sensing is a widespread form of bacterial“communication”that regulates diverse processes,including pathogen virulence.In quorum sensing,bacteria use secreted small molecules to regulate gene expression in a density-dependent manner.Bacteria can integrate intra-species and inter-species quorum sensing signals to optimize gene expression based on local environment.In the intestine,the extent of quorum sensing-mediated communication is unclear;but intestinal delivery of the inter-species quorum sensing molecule autoinducer-2(AI-2)alters microbiota composition after antibiotic treatment,suggesting that intestinal bacteria can broadly respond to quorum sensing pathways in vivo 44.Pathogen sensing of another inter-species quorum sensing molecule class,N-acyl homoserine lactones(AHLs),has been proposed as a possible mechanism by which intestinal bacteria could modulate virulence.Both EHEC and Salmonella encode the transcription factor SdiA,which is required for AHL recognition,but lack the machinery to synthesize AHLs 45,46.In the case of EHEC,AHLs repress the expression of virulence genes involved in the formation of AE lesions,but enhance the expression of acid-resistance genes 47.Consistent with this,SdiA is required for EHEC colonization of the cow rumen,but has no effect on intestinal colonization.Curiously,AHLs are largely absent in the intestine 48,49,making the relevance of AHL-mediated quorum sensing in the intestine unclear.Host epithelial cells may also engage bacterial quorum sensing pathways to