Evolutionary and ecological forces that shape the bacterial communities of the human gut

Since microbes were first described in the mid-1600s, we have come to appreciate that they live all around and within us with both beneficial and detrimental effects on nearly every aspect of our lives. The human gastrointestinal tract is inhabited by a dynamic community of trillions of bacteria that constantly interact with each other and their human host. The acquisition of these bacteria is not stochastic but determined by circumstance (environment), host rules (genetics, immune state, mucus, etc), and dynamic self-selection among microbes to form stable, resilient communities that are in balance with the host. In this review, we will discuss how these factors lead to formation of the gut bacterial community and influence its interactions with the host. We will also address how gut bacteria contribute to disease and how they could potentially be targeted to prevent and treat a variety of human ailments.     

CCL3L1 and CCR5 influence cell-mediated immunity and affect HIV-AIDS pathogenesis via viral entry-independent mechanisms

Although host defense against human immunodeficiency virus 1 (HIV-1) relies mainly on cell-mediated immunity (CMI), the determinants of CMI in humans are poorly understood. Here we demonstrate that variations in the genes encoding the chemokine CCL3L1 and HIV coreceptor CCR5 influence CMI in both healthy and HIV-infected individuals. CCL3L1-CCR5 genotypes associated with altered CMI in healthy subjects were similar to those that influence the risk of HIV transmission, viral burden and disease progression. However, CCL3L1-CCR5 genotypes also modify HIV clinical course independently of their effects on viral load and CMI. These results identify CCL3L1 and CCR5 as major determinants of CMI and demonstrate that these host factors influence HIV pathogenesis through their effects on both CMI and other viral entry-independent mechanisms.     

Is Lyme disease always poly microbial? – The jigsaw hypothesis

Lyme disease is considered to be caused by Borrelia species of bacteria but slowly evidence is accumulating which suggests that Lyme disease is a far more complex condition than Borreliosis alone. This hypothesis suggests that it may be more appropriate to regard Lyme disease as a tick borne disease complex. Over recent years numerous different microbes have been found in ticks which are known to be zoonotic and can coinfect the human host. The hypothesis suggests that multiple coinfections are invariably present in the clinical syndromes associated with Lyme disease and it is suggested that these act synergistically in complex ways. It may be that patterns of coinfection and host factors are the main determinants of the variable clinical features of Lyme disease rather than Borrelia types. An analogy with a jigsaw puzzle is presented with pieces representing Borreliae, coinfections and host factors. It is suggested that many pieces of the puzzle are missing and our knowledge of how the pieces fit together is rudimentary. It is hoped that the hypothesis will help our understanding of this complex, enigmatic condition.     

Bacterial outer membrane vesicles in disease and preventive medicine

Gram-negative bacteria have the ability to produce outer membrane-derived vesicles (OMVs) that are released into the extracellular milieu. Even though this intriguing phenomenon is well-known since many years, various aspects of bacterial OMVs are not fully described and are still in the process of being characterized in detail. One major reason for this is that depending on the bacterial species and its respective ecological niche, OMVs exhibit an enormous functional diversity. Research of the past years has clearly shown that OMVs of many pathogenic bacteria contribute to the virulence potential by enriching virulence factors and delivering them over long distances, superseding direct bacterial contact with their host. The subsequent interaction of OMVs with the host can occur at different levels regarding the type of immune response or the target cell type and may lead to different outcomes ranging from non-immunogenic activation or a pro-inflammatory response to cytotoxicity. In contrast to being virulence factors, OMVs are used for vaccination purposes in the combat against bacterial pathogens, and recent research thus is focused on to indirectly aim these versatile bacterial weapons against themselves.     

Effects of bacterial N-acyl homoserine lactones on human Jurkat T lymphocytes-OdDHL induces apoptosis via the mitochondrial pathway

Diverse Gram-negative bacteria communicate with each other by using diffusible N-acyl-homoserine lactone (AHL) signaling molecules to coordinate gene expression with cell population density. This mechanism termed ‘quorum sensing’ is involved in the regulation of physiological functions as well as multiple virulence determinants. It becomes more and more evident, that bacteria communicate not only with each other but also with their host. Up to now, little is known about this interkingdom communication. The AHL quorum sensing molecule N-3-(oxododecanoyl)-l-homoserine lactone (OdDHL) from Pseudomonas aeruginosa has been shown to influence the immune system of the host. The role and potential influence of other AHL molecules from other bacteria have so far not been determined. In this paper, we investigated the role of 7 different AHLs on apoptosis of human Jurkat T lymphocytes. We found, that among all homoserine lactones tested, only OdDHL rapidly induced apoptosis which was accompanied by the breakdown of the mitochondrial transmembrane potential (ΔΨ_m). Since overexpression of anti-apoptotic Bcl-2 completely abrogated the apoptotic effect, we presume that OdDHL induces apoptosis by activation of the intrinsic mitochondrial apoptosis pathway. The reason that bacteria induce apoptosis is largely unknown. We suspect that through apoptosis an anti-inflammatory response is triggered.     

Host,pathogen and treatment-related prognostic factors in rickettsioses

Diseases caused by rickettsiae, which are vector-borne bacteria, vary widely from mild and self-limiting, to severe and life-threatening. Factors influencing this diversity of outcome are related to the host, to the infectious agent and to the treatment used to treat the infection. A literature search was conducted on PubMed using the phrases “factors-related severity, outcome, host, pathogen, Rickettsia conorii, R. rickettsii, R. africae, R. felis, R. prowazekii, R. typhi, genomics”. Among host factors, old age and the male gender have been associated with poor outcome in rickettsioses. Co-morbidities, ethnical factors and the genetic background of the host also seem to influence the outcome of rickettsial diseases. Moreover, although the degree of the host response is beneficial, it could also partly explain the severity observed in some patients. Among pathogen-related factors, traditional concepts of factors of virulence had been challenged and genomic reductive evolution with loss of regulatory genes is the main hypothesis to explain virulence observed in some species, such as Rickettsia prowazekii, the agent of epidemic typhus. R. prowazekii is the more pathogenic rickettsiae and harbours the smaller genome size (1.1 Mb) compared to less or non-virulent species, and is not intracellularly motile, a factor considered as a virulence factor for other intracellular bacteria. The antibiotic regimen used to treat rickettsioses also has an influence on prognosis. Usual concepts of severity and virulence in rickettsioses are challenging and are frequently paradoxical. In this mini-review, we will describe factors currently thought to influence the outcome of the main rickettsioses responsible for illness in humans.     

Nocardia osteomyelitis in a pachymeningitis patient: an example of a difficult case to treat with antimicrobial agents

Antimicrobial agents played a miraculous role in the treatment of bacterial infections until resistant bacteria became widespread. Besides antimicrobial-resistant bacteria, many factors can influence the cure of infection. Nocardia infection may be a good example which is difficult to cure with antimicrobial agents alone. A 66-year-old man developed soft tissue infection of the right buttock and thigh. He was given prednisolone and azathioprine for pachymeningitis 3 months prior to admission. Despite surgical and antimicrobial treatment (sulfamethoxazole-trimethoprim), the infection spread to the femur and osteomyelitis developed. The case showed that treatment of bacterial infection is not always as successful as was once thought because recent isolates of bacteria are more often resistant to various antimicrobial agents, intracellular parasites are difficult to eliminate even with the active drug in vitro, and infections in some sites such as bone are refractory to treatment especially when the patient is in a compromised state. In conclusion, for the treatment of infections, clinicians need to rely on laboratory tests more than before and have to consider the influence of various host factors.     

Immunomodulation by Commensal and Probiotic Bacteria

Over the past decade there has been an increasing awareness of the role played by commensal bacteria in modulating mucosal immune responses and as a consequence there is now great interest in the therapeutic potential of probiotics and other bacteria based strategies for a range of immune disorders. Here we review current understanding of the mechanisms underlying the immunomodulatory actions of commensal and probiotic bacteria and probiotic organisms. We discuss prominent cell types involved in transducing signals from these bacteria, including epithelial cells, dendritic cells and T regulatory cells. We also draw attention to emerging data indicating interplay between the gut microbiota, enteric neurons and the immune system. There is a focus on the specific aspects of bacteria-host interactions that may influence the ability of a specific organism to confer potentially beneficial changes in immune responses. It is clear that there is still much to learn regarding the determinants of the diverse immune responses elicited by different bacterial strains by building on our current knowledge in these areas it may be possible to design clinically effective, bacteria based strategies to maintain and promote health.     

Authors, editors, policy makers, and the impact factor

Some aspects of the "impact factor", a quantitative measure of journals' influence on journals in scientific fields, were discussed in the preceding issue of the Croatian Medical Journal by Dr Eugene Garfield, one of its devisers. This factor can be of interest to authors, journal editors, and policy makers, but they should keep in mind the complexity of the determinants of impact factors while using them in coming to their particular kinds of decisions. A clearer picture of the influence a journal may have in its own scientific field rather than among all scientific journals could come from a variant of the impact factor, "the scope-adjusted impact factor". The calculation of this variant impact factor is described. A table presents some sample data from this calculation and shows how the relative positions of some major journals shift when they are ranked by this factor rather than the unadjusted impact factor. The possible value of this variant factor may merit further testing.     

Defense of zebrafish embryos against Streptococcus pneumoniae infection is dependent on the phagocytic activity of leukocytes

Severe community acquired pneumonia caused by Streptococcus pneumoniae is the most common cause of death from infection in developing countries. Serotype specific conjugate vaccines have decreased the incidence of invasive infections, but at the same time, disease due to non-vaccine serotypes have increased. New insights into host immune mechanisms against pneumococcus may provide better treatment and prevention strategies. Zebrafish is an attractive vertebrate model for studying host immune responses and infection biology. Here we show that an intravenous challenge with pneumococcus infects zebrafish embryos leading to death in a dose dependent manner. Survival rates correlate with the bacterial burden in the embryos. The production of proinflammatory cytokines is induced in zebrafish after pneumococcal exposure. Importantly, morpholino treated embryos lacking either myeloid cells or the ability to phagocytose bacteria have lowered survival rates compared to wild type embryos after pneumococcal challenge. These data suggest that the survival of zebrafish embryos upon intravenous infection with S. pneumoniae is dependent on the clearance of the bacteria by phagocytosing cells. Additionally, we demonstrate that mutant pneumococci lacking known virulence factors are attenuated in the zebrafish model. Our data demonstrate that zebrafish embryos can be used for study innate immune responses as well as virulence determinants in pneumococcal infections.     

From insects to human hosts: Identification of major genomic differences between entomopathogenic strains of Photorhabdus and the emerging human pathogen Photorhabdus asymbiotica

Pathogenic bacteria of the genus Photorhabdus are naturally found in symbiotic association with soil entomopathogenic nematodes, and are of increasing economic interest in view of their potential for the development of novel biopesticides. This bipartite natural system is currently used for the biological control of crop pests in several countries. However, an increasing number of Photorhabdus strains have recently been isolated from human clinical specimens in both the United States and Australia, associated with locally invasive soft tissue infections and disseminated bacteraemia. In view of their growing use in biological control, which increases the potential rate of exposure of humans to these pathogens, we decided to undertake a comparative study of the genomic differences between insect and human pathogenic strains of Photorhabdus, in an attempt to understand the genetic mechanisms involved in the apparent change of host specificity, presumably responsible for their recently acquired capacity to infect humans. The data presented here demonstrates that major genomic differences exist between strains of Photorhabdus exhibiting virulence against insects or humans. Several individual genes, coding for virulence factors, were isolated and shown to be specific to the Photorhabdus asymbiotica human pathogens. One of these genes, sopB, encoding a host cell invasion factor translocated via the type III secretion system, has been cloned and the comparison of its genomic context in different pathogens strongly indicates that horizontal gene transfer is implicated in the acquisition of these virulence factors specific to the human pathogens. The precise role of this and other virulence factors identified here in the pathogenicity of P. asymbiotica towards humans is currently under investigation.     

The effects of the microbiota on the host immune system

Abstract

The human gastrointestinal track harbors hundreds of species of commensal organisms, collectively known as microbiota. The composition of the intestinal microbiota is changeable by various factors, such as host genotype, diet, antibiotics, pathogen infections, among others. Changes in these factors can cause microbiome disruption known as dysbiosis, leading to the outgrowth of potential pathogenic bacteria or decrease in the number of beneficial bacteria. Dysbiosis has been implicated in numerous inflammatory and autoimmune diseases. This review is focused on host–microbiota interactions, specifically on influence of bacterial-derived signals on immune cell function and the mechanisms by which these signals modulate the development and progression of inflammatory and autoimmune diseases.     

Strategies toward vaccines against Burkholderia mallei and Burkholderia pseudomallei

Burkholderia mallei and Burkholderia pseudomallei are Gram-negative, rod-shaped bacteria, and are the causative agents of the diseases glanders and melioidosis, respectively. These bacteria have been recognized as important pathogens for over 100 years, yet a relative dearth of available information exists regarding their virulence determinants and immunopathology. Infection with either of these bacteria presents with nonspecific symptoms and can be either acute or chronic, impeding rapid diagnosis. The lack of a vaccine for either bacterium also makes them potential candidates for bioweaponization. Together with their high rate of infectivity via aerosols and resistance to many common antibiotics, both bacteria have been classified as category B priority pathogens by the US NIH and US CDC, which has spurred a dramatic increase in interest in these microorganisms. Attempts have been made to develop vaccines for these infections, which would not only benefit military personnel, a group most likely to be targeted in an intentional release, but also individuals who may come in contact with glanders-infected animals or live in areas where melioidosis is endemic. This review highlights some recent attempts of vaccine development for these infections and the strategies used to improve the efficacy of vaccine approaches.     

Bacterial pyrogenic exotoxins as superantigens.

The recent discovery of the mode of interaction between a group of microbial proteins known as superantigens and the immune system has opened a wide area of investigation into the possible role of these molecules in human diseases. Superantigens produced by certain viruses and bacteria, including Mycoplasma species, are either secreted or membrane-bound proteins. A unique feature of these proteins is that they can interact simultaneously with distinct receptors on different types of cells, resulting in enhanced cell-cell interaction and triggering a series of biochemical reactions that can lead to excessive cell proliferation and the release of inflammatory cytokines. However, although superantigens share many features, they can have very different biological effects that are potentiated by host genetic and environmental factors. This review focuses on a group of secreted pyrogenic toxins that belong to the superantigen family and highlights some of their structural-functional features and their roles in diseases such as toxic shock and autoimmunity. Deciphering the biological activities of the various superantigens and understanding their role in the pathogenesis of microbial infections and their sequelae will enable us to devise means by which we can intervene with their activity and/or manipulate them to our advantage.     

Host and bacterial determinants of initial severity and outcome of Escherichia coli sepsis

A 1-year prospective cohort study of all episodes of Escherichia coli bacteraemia in two French university hospitals was conducted to assess simultaneously the influence of host and bacterial determinants on the initial severity and outcome of E. coli sepsis. Clinical data (community-acquired/nosocomial infection, immune status, underlying disease, primary source of infection, severity sepsis scoring and outcome), phylogenetic groups (A, B1, D and B2), nine virulence factors (VFs) (papC, papGII, papGIII, sfa/foc, hlyC, cnf1, iucC, fyuA and iroN) and the antibiotic susceptibility of isolates were investigated. All VFs except iucC were significantly more prevalent (p <0.05) among the B2 group isolates. The non-B2 isolates were more frequently resistant to antibiotics than were B2 isolates (p <0.05). There were significantly more B2 isolates from immunocompetent than from immunocompromised patients (p <0.05). No bacterial or host determinants influenced the initial severity of sepsis. Multivariate analysis revealed that the presence of papGIII, septic shock at baseline and a non-urinary tract origin of sepsis were associated independently with a fatal outcome (p 0.04, <0.0001 and 0.04, respectively). A factorial analysis of correspondence allowed two populations of isolates to be distinguished: those belonging to the B2 group were associated more frequently with susceptibility to antibiotics, community-acquired infection, a urinary tract origin and immunocompetent hosts; those belonging to the A, B1 or D groups were associated more frequently with resistance to antibiotics, a nosocomial origin, a non-urinary tract source and immunocompromised hosts. Although no influence of host or bacterial determinants on the initial severity of sepsis was detected, bacterial and host determinants both influenced the outcome of E. coli sepsis significantly.     

Dependence between cognitive impairment and metabolic syndrome applied to a Brazilian elderly dataset

Globally, the proportion of elderly individuals in the population has increased substantially in the last few decades. However, the risk factors that should be managed in advance to ensure a natural process of mental decline due to aging remain unknown. In this study, a dataset consisting of a Brazilian elderly sample was modelled using a Bayesian Network (BN) approach to uncover connections between cognitive performance measures and potential influence factors. Regarding its structure (a Directed Acyclic Graph), it was investigated the probabilistic dependence mechanism between two variables of medical interest: the suspected risk factor known as Metabolic Syndrome (MetS) and the indicator of mental decline referred to as Cognitive Impairment (CI). In this investigation, the concept known in the context of a BN as D-separation has been employed. Results of the conducted study revealed that the dependence between MetS and Cognitive Variables (CI and its direct determinants) in fact exists and depends on both Body Mass Index (BMI) and age.     

Genome-Wide Transposon Mutagenesis Indicates that Mycobacterium marinum Customizes Its Virulence Mechanisms for Survival and Replication in Different Hosts

The interaction of environmental bacteria with unicellular eukaryotes is generally considered a major driving force for the evolution of intracellular pathogens, allowing them to survive and replicate in phagocytic cells of vertebrate hosts. To test this hypothesis on a genome-wide level, we determined for the intracellular pathogen Mycobacterium marinum whether it uses conserved strategies to exploit host cells from both protozoan and vertebrate origin. Using transposon-directed insertion site sequencing (TraDIS), we determined differences in genetic requirements for survival and replication in phagocytic cells of organisms from different kingdoms. In line with the general hypothesis, we identified a number of general virulence mechanisms, including the type VII protein secretion system ESX-1, biosynthesis of polyketide lipids, and utilization of sterols. However, we were also able to show that M. marinum contains an even larger set of host-specific virulence determinants, including proteins involved in the modification of surface glycolipids and, surprisingly, the auxiliary proteins of the ESX-1 system. Several of these factors were in fact counterproductive in other hosts. Therefore, M. marinum contains different sets of virulence factors that are tailored for specific hosts. Our data imply that although amoebae could function as a training ground for intracellular pathogens, they do not fully prepare pathogens for crossing species barriers.     

The intricate connection between diet,microbiota, and cancer: A jigsaw puzzle

The microbial community has a decisive role in determining our health and disease susceptibility. Presumably, this is closely associated with the complex community network of bacteria, fungi, archaea and viruses that reside our guts. This dynamic ecosystem exists in a symbiotic relationship with its host and plays a fundamental role in the hosts’ physiological functions. The microbial community is highly personalized and therefore exhibits a high degree of inter-individual variability, which is dependent on host specifics such as genetic background, physiology and lifestyle. Although the gut microbiota is shaped early on during birth, there are several factors that affect the composition of microbiota during childhood and adulthood. Among them diet appears to be a consistent and prominent one. The metabolic activity of bacteria affects food digestion, absorption, energy production, and immunity. Thus, definition of the microbiota composition and functional profiles in response to a particular diet may lead to critical information on the direct and indirect role/use of the bacterial community during health and disease. In this review, I discuss gut microbiota and its potential link to cancer with specific emphasis on metabolism and diet.