Is the gut microbiome key to modulating vaccine efficacy?

Abstract

A symbiotic relationship with gut microbes is critical for the normal function of human health. Vaccination, however, tips the symbiotic balance slightly in favor of human health. Recent work has shown that gut bacterial residents can have great (positive) influence over vaccine-induced immunity. With an arsenal of modern high-throughput technologies in the hands of microbiologists and immunologists, it is now easier and more cost-effective than ever to characterize and measure the microbiome of vaccinees. Such data will lead to an understanding of how and to what extent gut microbes can impact vaccine efficacy.

Keywords:

• dysbiosis
• immunity
• microbiome
• systems vaccinology
• vaccine efficacy
• vaccines

Human health is undeniably dependent on the vast number of commensal microorganisms that inhabit the gut. Yet we have only recently begun to understand the mechanisms by which these microbes impact host immunity against infection and disease. Among millions of genes in tens of trillions of genomes (i.e., the gut microbiome), there is a large potential number of microbe-associated molecular patterns (MAMPs [1]) that can fine tune both innate and adaptive immunity.

Vaccines are tremendously successful in protection against a broad range of diseases; however, what determines vaccine efficacy (at the individual level) is largely unknown. Decades of vaccine research have shown that several factors may affect vaccine efficacy, including genetic background, prior exposure to antigen via natural infection or vaccination and nutritional status. A growing body of evidence now suggests that gut microbiota may also play an important role in determining vaccine efficacy. Studies have demonstrated that immunogenicity of oral vaccines against cholera [2,3], rotavirus [4] and polio [5] is lower in populations from regions with poor sanitation who have a higher occurrence of fecal-oral bacterial exposure. While this observation may be confounded by factors such as socioeconomic status, genetics or malnutrition, the prevailing hypothesis is that exposure to harmful microbes could alter the composition of bacteria in the gut [6], and the composition of the gut may influence vaccine immunogenicity.

Most vaccines contain a complex mixture of functional components designed to interact with host receptor molecules and induce specific immune responses. These components are either the antigens themselves or the adjuvants in which they are formulated to stimulate innate immune receptors. The yellow fever YF-17D vaccine, for instance, is based on a live attenuated virus containing a single RNA strain and no more than eight polypeptides. These antigens as well as the immune-stimulant sequences that are part of the vaccine interact with host target molecules and pattern recognition receptors, such as toll-like receptors (TLRs) and nucleotide-binding oligomerization domain-like receptors, triggering specific signaling cascades that stimulate antigen-specific immune cells from a non-responsive to a highly stimulated state. Many commensal microorganisms, present in the gut of vaccinees, also have components which can be detected by the same innate immune receptors [7]. Thus, it is likely that gut microbiota can provide a constant source of natural adjuvants for certain vaccines.

Why has it taken scientists so long to learn more about this mechanism? The answer is largely due to limited availability of tools and technologies required to obtain a detailed level of the microbiota and the human immune system itself. Major advances in high-throughput technology and immunological assays now allow us to investigate the complex interplay between the host immune system and the microbiota. However, interaction of commensal gut microbiota with the host cannot be characterized simply by determining microorganism abundance, relative percentages of larger or narrower microorganism families or microbial gene expression within the host. The challenge lies in first identifying the MAMPs sensed by host immune cells, as well as determining which vaccines are influenced by microbiota and which arm of vaccine-induced immunity do they stimulate. More importantly, there is a need for holistic approaches (e.g., systems biology) to unravel the complex gene networks and signaling pathways triggered by the interactions between vaccine- and/or microbiota-derived components with host immune cells.

In response to these challenges, systems vaccinology [8] has emerged as a multidisciplinary field that combines modern high-throughput technologies, computational modeling and conventional immunology to provide a holistic view of the molecular mechanisms of vaccine-induced immunity. Systems vaccinology may be able to help determine the overall interaction pathways between commensal microorganisms and their host, thus allowing a better prediction of vaccine immunogenicity and efficacy. This approach has been successfully applied to study a broad range of vaccines, including yellow-fever [9], influenza [10], meningococcal and malaria vaccines. In addition, we have successfully demonstrated the application of systems approaches in identifying early innate signatures that accurately predict the adaptive CD8+ T cell and antibody responses to YF-17D vaccination [9] and seasonal trivalent inactivated influenza vaccine (TIV) [10].

An essential feature of systems vaccinology relies on its capacity to generate new insights and data-driven hypotheses. One example of insight arose from our attempts to identify genes whose expression in the blood of TIV vaccinees at early time points (less than 7 days after vaccination) correlated with TIV immunogenicity [10]. We found that the expression of the TLR5 gene at day 3 post-TIV vaccination was directly correlated with the antibody response 28 days later [10]. TLR5 recognizes flagellin, the main structural protein of bacterial flagella. Since TIV did not stimulate directly TLR5 and since the human gut can harbor many flagellated bacteria [11], our findings suggested that commensals could help boost TIV immunogenicity. The hypothesis that flagellin from gut microbes may act as a natural adjuvant of TIV vaccine was then tested in mice. Initially, Oh et al. [12] showed that antibody responses of TLR5-deficient mice immunized with TIV were significantly reduced in comparison to responses in wild-type mice, demonstrating that TIV-induced antibody responses were dependent on TLR5 expression. To test whether commensal bacteria was the source of TLR5 ligands, we also analyzed the TIV-induced antibody responses of mice treated with antibiotics and germ-free mice [12]. Again, antibody responses were significantly lower when compared to untreated mice or conventionally housed pathogen-free mice. We then assessed the microbiome of mice following antibiotic treatment and found that a major bacterial phyla, Firmicutes, was significantly reduced upon treatment, and also that different classes of bacteria can impact antibody responses after TIV immunization [12]. Interestingly, antibiotic treatment did not reduce the magnitude of antibody responses in mice following immunization with either Tdap vaccine (an adjuvanted vaccine against tetanus-diphtheria-pertussis) or YF-17D [12]. These results suggest that the immunogenicity of certain types of vaccines (particularly those containing adjuvants or those that activate multiple TLRs) is influenced to a lesser extent by the presence of microbiota. More importantly, for inactivated non-adjuvanted parenteral vaccines such as TIV and poliovirus vaccine inactivated (IPOL^®) (polio vaccine), gut microbiota can play a crucial role in boosting vaccine-induced immune responses [12].

Controlled experiments in humans were performed by several groups to attempt to evaluate the possible role of gut resident bacteria on the immunogenicity and efficacy of vaccines (reviewed in [13]). Different approaches tested the potential adjuvant effect of probiotics (i.e., beneficial microorganisms) or prebiotics (non-digestible carbohydrates that nourish probiotics) during vaccination. In most settings, volunteers first received either placebo or probiotics (e.g., Lactobacillus spp. and Bifidobacterium spp.) during weeks to months prior to vaccination. Immune responses post-vaccination were then determined and compared. Overall, these ‘gain-of-function’ experiments showed inconsistent results [13]. While probiotics led to augmented antibody responses against some vaccines tested (influenza, cholera and polio), they had modest or no effect on the remaining vaccines tested (Tdap, tetanus, Hib, PCV7 and MMRV), similar to our results in mice [12]. The effect of probiotic supplementation may also be influenced by different vaccine schedules, as shown with hepatitis B vaccination in infants [14]. Although the experimental conditions widely varied across studies, these differences indicate again that the impact of gut microbiota on vaccine immunogenicity is far from being universal.

Interesting discoveries and hypotheses lie ahead as this field evolves and more data are collected. Immunization experiments with probiotics-treated mice lacking different TLRs and other pattern recognition receptors must be performed to assess the molecular mechanisms underlying the adjuvant effects of probiotics. Additionally, ‘loss-of-(gut bacteria)-function’ human clinical studies, where subjects voluntarily take antibiotics prior to vaccination, are needed to rule out if gut commensals in homeostatic normal conditions is already sufficient to ‘boost’ vaccine-induced immune responses. Unfortunately, such experiments are precluded by strict human subject regulations. In future randomized controlled vaccine efficacy trials, rapid and sensitive high-throughput technologies may help determine gut microbial composition of large cohorts from different regions and environments. In addition to identification of key microbe-derived biomarkers of vaccine efficacy (metabolites, MAMPs, cytokines), this type of research may reveal that gut microbial composition is a stratum that needs to be properly represented. At an individual patient level, doctors will be able to recommend administration of pre- and pro-biotics prior vaccination or control antibiotic treatments to improve vaccine immunogenicity. Finally, it will become increasingly clear that microbiota from other host sites, such as airways mucosa, genital tract or skin [15,16], as well as MAMPs from viruses, fungi and protozoa organisms, can also play a significant role on vaccine-induced immunity.

Financial & competing interests disclosure

The authors are employees of the Brazilian government. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.