Linking genetic variation in human Toll-like receptor 5 genes to the gut microbiome's potential to cause inflammation

Abstract

Immunodeficiencies can lead to alterations of the gut microbiome that render it pathogenic and capable of transmitting disease to naïve hosts. Here, we review the role of Toll-like receptor (TLR) 5, the innate receptor for bacterial flagellin, in immune responses to the normal gut microbiota with a focus its role on adaptive immunity. Loss of TLR5 has profound effects on the microbiota that include greater temporal instability of major lineages and upregulation of flagellar motility genes that may be linked to the reduced levels of anti-flagellin antibodies in the TLR5(-/-) host. A variety of human TLR5 gene alleles exist that also associated with inflammatory conditions and may do so via effects on the gut microbiome and altered host-microbial crosstalk.

Keywords: Adaptive immunity; Allelic variation; Gut microbiome; Metagenomics; TLR5; Toll-like receptor 5.

Figure 1. Possible mechanisms for the production of anti-flagellin antibodies

A: Dendritic cells (DCs) present flagellin to T cells via MHCII. DCs in the lamina propria express TLR5, but whether this is necessary for antigen presentation is uncertain. (B) Flagellin-specific B cells endocytose flagellin and present it to flagellin-specific T cells that have received activation signals from a DC (A). The T cell provides the necessary cytokine and costimulation for B cells to produce flagellin-specific antibody. B cells express TLR5 in the lamina propria, but whether stimulation of TLR5 by flagellin is necessary for a normal anti-flagellin antibody response is uncertain. (C) B cells can directly present flagellin in MHCII to flagellin-specific T cells after endocytosing flagellin and receiving stimulation through TLR5. In this scenario, there is no requirement for DCs since the T cells can directly provide costimulation and cytokines to the B cells. In (D), flagellin-specific B cells can engage repeating units of flagellin through the B cell receptor and TLR5, which together provide all the stimulation that is needed for the B cell to produce anti-flagellin antibodies. This would occur independently of T cells. Whether this T-independent mechanism can result in production of anti-flagellin antibody is not known.

Figure 2. TLR5 deficiency alters the gut microbiome in multiple ways

Cartoon summary of alterations to the microbiome observed in TLR5-deficient mice (TLR5^−/−) compared to wild type (WT), based on real data observations. Panels A–C refer to hypothetical 16S rRNA gene sequence survey data. (A) Beta-diversity (between-sample) patterns for WT and TLR5^−/− gut microbiomes in a hypothetical principal coordinates analysis of unweighted UniFrac distances calculated for a set of TLR5^−/− and WT mouse gut microbiomes. Each symbols refers to a hypothetical microbiome characterized by sequencing thousands of 16S rRNA genes. When symbols cluster closely, the microbiomes for those samples are more similar. The pattern shown here is one of greater beta-diversity for TLR5^−/− mice compared to WT. Note that for certain individual TLR5^−/− mice, their microbiome composition may be quite similar to WT, but overall the TLR5^−/− are more different from one another than are the WT to one another. (B) Hypothetical alpha-diversity patterns (within-sample diversity) showing lower overall taxonomic richness for TLR5^−/− versus WT microbiomes. As sequencing effort increases, the number of new taxa discovered is lowest for the TLR5^−/− microbiome, indicating reduced species richness compared to the WT microbiome. (C) Hypothetical data showing greater volatility of proteobacterial populations over time in the TLR5^−/− host. Plotted are relative abundances of sequences classified as Proteobacteria over 7 weeks. Levels in the TLR5^−/− host are more variable over time. (D) Hypothetical data showing inverse patterns of anti-flagellin antibody levels in the gut versus protein flagellin for TLR5^−/− and WT hosts. (E) Hypothetical metagenomes and metatranscriptomes for three TLR5^−/− and three WT microbiomes. Metagenomes consist of randomly sampled genes from the composite genomes of the microbes in the microbiome; metatranscriptomes consist of randomly sampled gene transcripts (expressed genes) in the microbiome. Six gene categories are shown for both the metagenomes and the metatranscriptomes, and the relative levels of functional genes or their expression across the six microbiomes are shown using a color scale, where red indicates greater capacity (metagenomes) or greater upregulation (metatranscritpomes). The expression of flagellar motility genes is far greater in the TLR5−/− compared to the WT mouse, despite equivalent coding capacity (similar levels of these genes in the metagenome). The gene expression levels of the functional genes can be used to differentiate the host genotype of the six mice (as indicated by clustering in the right dendrogram) but the metagenome, which represents the functional gene capacity of the microbiomes, cannot distinguish the genotypes (left dendrogram).