Molecular microbiology in antibacterial research

The special issue of Journal of Microbiology contains six reviews dealing with cutting edge research achievements in the fields of molecular microbiology focusing on antibacterial research. In a more specific sense, this special issue helps outline the progress of 21^st-century basic molecular microbiology that can encompass related disciplines regarding a variety of interactions involving bacteria during bacterial pathogenesis and their control: sociomicrobiology (interaction between bacteria), immunology (interaction between bacteria and their hosts), and bacteriophage (phage) virology (interaction between bacteria and their parasites). Recent advancements have rapidly been made in our understanding of the real situation regarding polymicrobial interactions during bacterial infection and in non-mammalian host infection models to uncover the molecular mechanisms of host-bacteria interactions, which will complement our growing knowledge about immune responses toward bacterial and environmental elicitors. Moreover, much attention has recently been paid to phages and phage products as potential antibacterial therapeutics in the era of antibiotic resistance. Below, I summarize the individual contributions in these distinct categories.     

Lactoferrin binds CpG-containing oligonucleotides and inhibits their immunostimulatory effects on human B cells

Unmethylated CpG dinucleotide motifs in bacterial DNA, as well as oligodeoxynucleotides (ODN) containing these motifs, are potent stimuli for many host immunological responses. These CpG motifs may enhance host responses to bacterial infection and are being examined as immune activators for therapeutic applications in cancer, allergy/asthma, and infectious diseases. However, little attention has been given to processes that down-modulate this response. The iron-binding protein lactoferrin is present at mucosal surfaces and at sites of infection. Since lactoferrin is known to bind DNA, we tested the hypothesis that lactoferrin will bind CpG-containing ODN and modulate their biological activity. Physiological concentrations of lactoferrin (regardless of iron content) rapidly bound CpG ODN. The related iron-binding protein transferrin lacked this capacity. ODN binding by lactoferrin did not require the presence of CpG motifs and was calcium independent. The process was inhibited by high salt, and the highly cationic N-terminal sequence of lactoferrin (lactoferricin B) was equivalent to lactoferrin in its ODN-binding ability, suggesting that ODN binding by lactoferrin occurs via charge-charge interaction. Heparin and bacterial LPS, known to bind to the lactoferricin component of lactoferrin, also inhibited ODN binding. Lactoferrin and lactoferricin B, but not transferrin, inhibited CpG ODN stimulation of CD86 expression in the human Ramos B cell line and decreased cellular uptake of ODN, a process required for CpG bioactivity. Lactoferrin binding of CpG-containing ODN may serve to modulate and terminate host response to these potent immunostimulatory molecules at mucosal surfaces and sites of bacterial infection.     

Polymicrobial infections involving clinically relevant Gram‐negative bacteria and fungi

Interactions between fungi and bacteria and their relevance to human health and disease have recently attracted increased attention in biomedical fields. Emerging evidence shows that bacteria and fungi can have synergistic or antagonistic interactions, each with important implications for human colonization and disease. It is now appreciated that some of these interactions may be strategic and helps promote the survival of one or both microorganisms within the host. This review will shed light on clinically relevant interactions between fungi and Gram‐negative bacteria. Mechanism of interaction, host immune responses, and preventive measures will also be reviewed.     

Host binding proteins and bacterial adhesion: ecology and binding model

Defining the involvement of specific recognition and (or) adhesion molecules in the precise association formed between cells of an organism during development or between bacteria and specific host tissues has become a focus of extensive research. The possibility that the same molecules responsible for cellular adhesion in the host may also play a major role in determining host-bacterial interactions is now becoming more evident. The following review looks at the interaction of a group of host binding proteins, including lectins, fibronectin, and laminin, with respect to their specific association with bacteria. This information is dealt with both from the perspective of the ecology of the host and its autochthonous and pathogenic bacterial populations, as well as in terms of the difficulties in defining the nature of ligand associations even in the more simplified bacterial-host interaction.     

Bovine lactoferrin interacts with cable pili of Burkholderia cenocepacia

In this study we evaluated the ability of lactoferrin, the most abundant antimicrobial protein in airway secretions, to bind the surface structures of a Burkholderia strain cystic fibrosis-isolated. Burkholderia cenocepacia is a gram-negative bacterium involved as respiratory pathogen in cystic fibrosis patient infections. This bacterium possesses filamentous structures, named cable pili that have been proposed as virulence factors because of their ability to bind to respiratory epithelia and mucin. Previously, we demonstrated that bovine lactoferrin was able to influence the efficiency of invasion of different iron-regulated morphological forms of B. cenocepacia. Bovine lactoferrin showed to efficiently inhibit invasion of alveolar epithelial cells by free-living bacteria or iron-induced aggregates or biofilm. Results of the present study demonstrate that bovine lactoferrin is also able to specifically bind to B. cenocepacia cells and show that cable pili are involved in this interaction. The attachment of bovine lactoferrin to pili led to a reduced binding of bacterial cells to mucin. Since cable pili are implicated in mediating the bacterial interactions with mucin and epithelial cells, lactoferrin binding to these structures could play an important role in neutralizing bacterial infection in cystic fibrosis patients.     

MicroMeeting: Who's talking to whom? Epithelial–bacterial pathogen interactions

Our perception that host-bacterial interactions lead to disease comes from rare, unsuccessful interactions resulting in the development of detectable symptoms. In contrast, the majority of host-bacterial interactions go unnoticed as the host and bacteria perceive each other to be no threat. In July 2004, a focused international symposium on epithelial-bacterial pathogen interactions was held in Newcastle upon Tyne (UK). The symposium concentrated on recent advances in our understanding of bacterial interactions at respiratory and gastrointestinal mucosal epithelial layers. For the host these epithelial tissues represent a first line of defence against invading bacterial pathogens. Through the discovery that the innate immune system plays a pivotal role during host-bacterial interactions, it has become clear that epithelia are being utilized by the host to monitor or communicate with both pathogenic and commensal bacteria. Interest in understanding the bacterial perspective of these interactions has lead researchers to realize that the bacteria utilize the same factors associated with disease to establish successful long-term interactions. Here we discuss several common themes and concepts that emerged from recent studies that have allowed physiologists and microbiologists to interact at a common interface similar to their counterparts -- epithelia and bacterial pathogens. These studies highlight the need for further multidisciplinary studies into how the host differentiates between pathogenic and commensal bacteria.     

Bacterial Endocytic Systems in Plants and Animals: Ca2+ as a Common Theme?

Intracellular interactions between bacteria and host cells are widespread in nature. In this review, the similarity between the infection processes of bacteria in plant and animal cells will be addressed. As paradigms, we selected the symbiosis between rhizobia and leguminous plants, and the survival of intracellular pathogenic bacteria in animal cells. The rhizobial symbiosis with leguminous plants is a model system for the study of plant-bacterium interactions. Through this interaction, the bacteria are released in a vacuole-like structure, called the symbiosome. The molecular processes, which lead to a functional symbiosome, are far from known. However, membrane fusion processes, and therefore also Ca²⁺, are crucial to establish this highly specialized organelle-like structure. A homologous system is the infection by certain bacterial pathogens of animal cells. These bacteria enter their host via phagocytosis and avoid the fusion with lysosomes, resulting in a membrane-bound vacuole in which the pathogens survive. The origin and maturation of this phagosome depends on Ca²⁺-signaling processes in the host cell and on proteins that regulate membrane fusion processes, such as SNAREs, Rab proteins, synaptotagmins and calmodulin. The aim of this review is to compare the endosymbiosis in leguminous plants with the surviving pathogens in animal host cells with a focus on Ca²⁺-signaling and membrane fusion-related processes. For both systems, the interaction starts with a bacterial entry of the host cell. It will be demonstrated that in both cases Ca²⁺ is a crucial second messenger. However, more emphasis will be put on the comparison of the later stages of infection, i.e., the formation of specialized bacteria-containing vacuoles. From structural, functional, and proteomic data, it is clear that phagosomes and symbiosomes are more related to each other than originally assumed. Proteins such as V-ATPases, calreticulin, phosphatidylinositol-3-kinase, Rab proteins, and SNAREs are present in both the phagosome and the symbiosome membrane, indicating that common cellular processes are used for building these intracellular organelles.     

RNA profiling in host-pathogen interactions

The development of novel anti-bacterial treatment strategies will be aided by an increased understanding of the interactions that take place between bacteria and host cells during infection. Global expression profiling using microarray technologies can help to describe and define the mechanisms required by bacterial pathogens to cause disease and the host responses required to defeat bacterial infection.     

Host tissues as microhabitats for Wolbachia and quantitative insights into the bacterial community in terrestrial isopods

Animal–bacterial symbioses are highly dynamic in terms of multipartite interactions, both between the host and its symbionts as well as between the different bacteria constituting the symbiotic community. These interactions will be reflected by the titres of the individual bacterial taxa, for example via host regulation of bacterial loads or competition for resources between symbionts. Moreover, different host tissues represent heterogeneous microhabitats for bacteria, meaning that host‐associated bacteria might establish tissue‐specific bacterial communities. Wolbachia are widespread endosymbiotic bacteria, infecting a large number of arthropods and filarial nematodes. However, relatively little is known regarding direct interactions between Wolbachia and other bacteria. This study represents the first quantitative investigation of tissue‐specific Wolbachia–microbiota interactions in the terrestrial isopod Armadillidium vulgare. To this end, we obtained a more complete picture of the Wolbachia distribution patterns across all major host tissues, integrating all three feminizing Wolbachia strains (wVulM, wVulC, wVulP) identified to date in this host. Interestingly, the different Wolbachia strains exhibited strain‐specific tissue distribution patterns, with wVulM reaching lower titres in most tissues. These patterns were consistent across different host genetic backgrounds and might reflect different co‐evolutionary histories between the Wolbachia strains and A. vulgare. Moreover, Wolbachia‐infected females carried higher total bacterial loads in several, but not all, tissues, irrespective of the Wolbachia strain. Taken together, this quantitative approach indicates that Wolbachia is part of a potentially more diverse bacterial community, as exemplified by the presence of highly abundant bacterial taxa in the midgut caeca of several A. vulgare populations.     

An interaction between host and microbe genotypes determines colonization success of a key bumble bee gut microbiota member

There has been a proliferation of studies demonstrating an organism's health is influenced by its microbiota. However, factors influencing beneficial microbe colonization and the evolution of these relationships remain understudied relative to host–pathogen interactions. Vertically transmitted beneficial microbes are predicted to show high levels of specificity in colonization, including genotype matching, which may transpire through coevolution. We investigate how host and bacterial genotypes influence colonization of a core coevolved microbiota member in bumble bees. The hindgut colonizing Snodgrassella alvi confers direct benefits, but, as an early colonizer, also facilitates the further development of a healthy microbiota. Due to predominantly vertical transmission promoting tight evolution between colonization factors of bacteria and host lineages, we predict that genotype‐by‐genotype interactions will determine successful colonization. Germ‐free adult bees from seven bumble bee colonies (host genotypic units) were inoculated with one of six genetically distinct strains of S. alvi. Subsequent colonization within host and microbe genotypes combinations ranged from 0 to 100%, and an interaction between host and microbe genotypes determined colonization success. This novel finding of a genotype‐by‐genotype interaction determining colonization in an animal host‐beneficial microbe system has implications for the ecological and evolutionary dynamics of host and microbe, including associated host‐fitness benefits.     

Porphyromonas gingivalis fimbriae binds to neoglycoproteins: evidence for a lectin-like interaction

Porphyromonas gingivalis is a likely major pathogen in adult periodontitis. Fimbriae in particular have been suggested as playing an important role in facilitating the initial interaction between the bacteria and the host and triggers host responses. Murakami et al. [Biochem. Biophys. Res. Commun. 192 (1993) 826] have shown that fimbriae of P. gingivalis strongly induced TNF-alpha gene expression in macrophages and expression of TNF-alpha was inhibited by N-acetyl-D-galactosamine, but not inhibited by other sugars. Studies by Sojar et al. [FEBS Lett. 422 (1998) 205] suggested that the oligosaccharide moiety of lactoferrin is involved in the interaction of P. gingivalis fimbriae and human lactoferrin. In the present study, purified fimbriae from P. gingivalis and neoglycoproteins were used to assess lectin-like interaction of fimbriae. In dot blot and overlay assays, iodinated purified P. gingivalis fimbriae as well as biotinylated purified P. gingivalis fimbriae bound strongly to albumin-fucosylamide (albumin-1-amido-1-deoxy-L-fucose) and by lesser extent to albumin-N-acetyl-D-galactosamine (albumin-p-aminophenyl-N-acetyl-beta-D-galactosaminide). However, fimbriae failed to bind carbohydrate free bovine serum albumin, which was used in preparation of the neoglycoproteins. These results suggests that P. gingivalis fimbriae bind to glycoconjugates through lectin-like interaction with carbohydrate. This protein-carbohydrate interactions may be important for triggering events in these cells, which mediate the host response of this pathogen.     

Microbial biofilms in nature: unlocking their potential for agricultural applications

Soil environments are dynamic and the plant rhizosphere harbours a phenomenal diversity of micro-organisms which exchange signals and beneficial nutrients. Bipartite beneficial or symbiotic interactions with host roots, such as mycorrhizae and various bacteria, are relatively well characterized. In addition, a tripartite interaction also exists between plant roots, arbuscular mycorrhizal fungi (AMF) and associated bacteria. Bacterial biofilms exist as a sheet of bacterial cells in association with AMF structures, embedded within a self-produced exopolysaccharide matrix. Such biofilms may play important functional roles within these tripartite interactions. However, the details about such interactions in the rhizosphere and their relevant functional relationships have not been elucidated. This review explores the current understanding of naturally occurring microbial biofilms, and their interaction with biotic surfaces, especially AMF. The possible roles played by bacterial biofilms and the potential for their application for a more productive and sustainable agriculture is discussed in this review.     

荧光标记珊瑚组织来源细菌及其与虫黄藻相互作用的显微观察

【背景】研究珊瑚-细菌、虫黄藻-细菌的相互作用是解析珊瑚健康机理的关键。对珊瑚共附生细菌进行稳定荧光标记有助于原位观察细菌与虫黄藻或珊瑚的相互作用。当前,对于野生型珊瑚共附生细菌遗传操作体系的研究有限,限制了对细菌与珊瑚、虫黄藻原位互作模式的揭示。【目的】建立一种适合专性海洋细菌的遗传操作体系,利用其对珊瑚组织来源细菌进行绿色荧光蛋白标记,用于研究标记菌株与虫黄藻的相互作用。【方法】通过电穿孔的方式将构建好的广宿主重组质粒转入供体菌(Escherichia coli WM3064),然后将供体菌与添加海水才可以生长的受体菌SCSIO 12696 (港口球菌科,Porticoccaceae;分离自鹿角杯形珊瑚组织)按供、受体菌细胞数比分别为4:1、2:1、1:1比例混合,在25℃和30℃下于改良LB培养基上接合转移。显微观察标记细菌与虫黄藻相互作用。【结果】改良的LB培养基适用于需海水才可生长的专性海洋细菌的接合转移实验。接合转移的效率与供、受体菌的比例及温度有关。确定优化的接合转移条件为:供、受体菌的比例为1:1,温度为30℃。利用建立的接合转移体系,构建了增强型绿色荧光蛋白标记菌株S...     

Interaction of lactoferrin and transferrins with the outer membrane of Bordetella pertussis

Bordetella pertussis was able to grow in vitro under conditions where the only iron present was bound to the iron-binding proteins ovotransferrin, transferrin or lactoferrin. Under these conditions the bacteria produced neither hydroxamate nor phenolate-catecholate siderophores to assist in the procurement of iron. Examination of B. pertussis outer-membrane preparations by SDS-PAGE and immunoblotting showed that the iron-binding protein ovotransferrin was bound directly to the bacterial surface. Assays of the binding of radiolabelled transferrin by the bacteria showed that the association was a specific process and that there was turnover of the bound proteins. Competitive binding assays indicated that lactoferrin could be bound in the same way. It is suggested that B. pertussis obtains iron directly from host iron-binding proteins during infection.     

Porins OmpC and PhoE of Escherichia coli as specific cell-surface targets of human lactoferrin. Binding characteristics and biological effects.

The binding of lactoferrin, an iron-binding glycoprotein found in secretions and leukocytes, to the outer membrane of Gram-negative bacteria is a prerequisite to exert its bactericidal activity. It was proposed that porins, in addition to lipopolysaccharides, are responsible for this binding. We studied the interactions of human lactoferrin with the three major porins of Escherichia coli OmpC, OmpF, and PhoE. Binding experiments were performed on both purified porins and porin-deficient E. coli K12 isogenic mutants. We determined that lactoferrin binds to the purified native OmpC or PhoE trimer with molar ratios of 1.9 +/- 0.4 and 1.8 +/- 0.3 and Kd values of 39 +/- 18 and 103 +/- 15 nM, respectively, but not to OmpF. Furthermore, preferential binding of lactoferrin was observed on strains that express either OmpC or PhoE. It was also demonstrated that residues 1-5, 28-34, and 39-42 of lactoferrin interact with porins. Based on sequence comparisons, the involvement of lactoferrin amino acid residues and porin loops in the interactions is discussed. The relationships between binding and antibacterial activity of the protein were studied using E. coli mutants and planar lipid bilayers. Electrophysiological studies revealed that lactoferrin can act as a blocking agent for OmpC but not for PhoE or OmpF. However, a total inhibition of the growth was only observed for the PhoE-expressing strain (minimal inhibitory concentration of lactoferrin was 2.4 mg/ml). These data support the proposal that the antibacterial activity of lactoferrin may depend, at least in part, on its ability to bind to porins, thus modifying the stability and/or the permeability of the bacterial outer membrane.     

A centralized resource for bacterial–fungal interactions research

Research on bacterial-fungal interactions (BFIs) has revealed that fungi and bacteria frequently interact with one another within diverse ecosystems and microbiomes. Assessing the current state of knowledge within the field of BFI research, particularly with respect to what interactions between bacteria and fungi have been previously described, is very challenging and time consuming. This is largely due to a lack of any centralized resource, with reports of BFIs being spread across publications in numerous journals using non-standardized text to describe the relationships. To address this issue, we have developed the BFI Research Portal, a publicly accessible database of previously reported interactions between bacterial and fungal taxa to serve as a centralized resource for the field. Users can query bacterial or fungal taxa to see what members from the other kingdom have been observed as interaction partners. Search results are accompanied by interactive and intuitive visual outputs, and the database is a dynamic resource that will be updated as new BFIs are reported.     

Bovine lactoferrin and lactoferricin derived from milk: production and applications.

Bovine lactoferrin is produced on an industrial scale from cheese whey or skim milk. The safety of purified lactoferrin has been confirmed from the results of a reverse mutation test using bacteria, a 13-week oral repeated-dose toxicity study in rats, and clinical studies. In order to apply active lactoferrin to various products, a process for its pasteurization was developed. Subsequently, lactoferrin has been used in a wide variety of products since it was first added to infant formula in 1986. A pepsin hydrolysate of lactoferrin is also used in infant formula. This hydrolysate contains a potent antimicrobial peptide named lactoferricin that is derived from the lactoferrin molecule by pepsin digestion. Semilarge-scale purification of lactoferricin can be performed by hydrophobic interaction chromatography. Lactoferricin also exhibits several biological actions and appears to be the functional domain of lactoferrin. Recent studies have demonstrated that oral administration of lactoferrin or lactoferricin exerts a host-protective effect in various animals and in humans. The results of these studies strongly suggest that the effects of oral lactoferrin are mediated by modulation of the immune system. Further elucidation of the clinical efficacy and mechanism of action of lactoferrin will increase the value of lactoferrin-containing products.     

Antibody‐mediated crosslinking of gut bacteria hinders the spread of antibiotic resistance

The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a multiscale model of the interaction between antibiotic use and resistance spread in a host population, focusing on an important aspect of within‐host immunity. Antibodies secreted in the gut enchain bacteria upon division, yielding clonal clusters of bacteria. We demonstrate that immunity‐driven bacteria clustering can hinder the spread of a novel resistant bacterial strain in a host population. We quantify this effect both in the case where resistance preexists and in the case where acquiring a new resistance mutation is necessary for the bacteria to spread. We further show that the reduction of spread by clustering can be countered when immune hosts are silent carriers, and are less likely to get treated, and/or have more contacts. We demonstrate the robustness of our findings to including stochastic within‐host bacterial growth, a fitness cost of resistance, and its compensation. Our results highlight the importance of interactions between immunity and the spread of antibiotic resistance, and argue in the favor of vaccine‐based strategies to combat antibiotic resistance.     

Environmentally controlled bacterial vesicle‐mediated export

Over the past two decades, researchers studying both microbial and host cell communities have gained an appreciation for the ability of bacteria to produce, regulate, and functionally utilize outer membrane vesicles (OMVs) as a means to survive and interact with their cellular and acellular environments. Common ground has emerged, as it appears that vesicle production is an environmentally controlled and specific secretion process; however, it has been challenging to discover the principles that govern fundamentals of vesicle‐mediated transport. Namely, there does not appear to be a single mechanism modulating OMV export, nor universal “markers” for OMV cargo incorporation, nor particular host cell responses common to treatment with all OMVs. Given the diversity of species studied, their differences in envelope architecture and composition, the diversity of environmentally regulated bacterial processes, and the variety of interactions between bacteria and their abiotic and biotic environments, this is hardly surprising. Nevertheless, the ability of bacteria to control exported material in the context of a packaged insoluble particle, a vesicle, is emerging as a significant contribution to bacterial viability, biofilm communities, and bacterial‐host interactions. In this review, we focus on detailing important, recent findings regarding the content and functional differences in bacterially secreted vesicles that are influenced by growth conditions.