IgA-deficient humans exhibit gut microbiota dysbiosis despite secretion of compensatory IgM

Abstract

Immunoglobulin A is the dominant antibody isotype found in mucosal secretions and enforces host-microbiota symbiosis in mice, yet selective IgA-deficiency (sIgAd) in humans is often described as asymptomatic. Here, we determined the effects of IgA deficiency on human gut microbiota composition and evaluated the possibility that mucosal secretion of IgM can compensate for a lack of secretory IgA. We used 16S rRNA gene sequencing and bacterial cell sorting to evaluate gut microbiota composition and taxa-specific antibody coating of the gut microbiota in 15 sIgAd subjects and matched controls. Despite the secretion of compensatory IgM into the gut lumen, sIgAd subjects displayed an altered gut microbiota composition as compared to healthy controls. These alterations were characterized by a trend towards decreased overall microbial diversity as well as significant shifts in the relative abundances of specific microbial taxa. While secretory IgA in healthy controls targeted a defined subset of the microbiota via high-level coating, compensatory IgM in sIgAd subjects showed less specificity than IgA and bound a broader subset of the microbiota. We conclude that IgA plays a critical and non-redundant role in controlling gut microbiota composition in humans and that secretory IgA has evolved to maintain a diverse and stable gut microbial community.

Figure 1

sIgAd subjects exhibit compensatory secretion of microbiota-targeted IgM. (a) Serum IgG and IgA levels for 15 sIgAd subjects. (b) Secretory IgA levels in the feces as measured by ELISA. (c) Secretory IgM levels in the feces as measured by ELISA. (d) Bacterial coating with IgA or IgM in the fecal microbiotas from fifteen healthy controls of sIgAd subjects. ***p < 0.001 via Mann-Whitney U test.

Figure 2

Humans with selective IgA deficiency harbor altered gut microbial communities. (a) Alpha diversity analyses of gut microbiota from sIgAd subjects and healthy controls (HC) as measured by observed species (OTUs), Chao1, Simpson and Shannon Diversity indices. (b) Principal Coordinate Analysis plots of unweighted and weighted UniFrac distances (c,d). Relative abundances of bacterial phyla (c) or species level taxa (d) exhibiting a significant difference between sIgAd and control subjects. *p < 0.01, **p < 0.001, ***p < 0.0001 by Mann-Whitney U test. ^#indicates FDR < 0.05 using the Benjamini and Hochberg method using R console.

Figure 3

Secretory IgA in healthy controls and compensatory secreted IgM in sIgAd subjects display distinct patterns of bacterial coating. (a) Alpha diversity analysis (observed OTUs, Chao1, Simpson and Shannon Diversity indices) of antibody coated and non-coated fecal bacteria from healthy controls and sIgAd subjects. (b) Principal Coordinate Analyses of unweighted and weighted Unifrac distances for antibody coated and non-coated bacteria from healthy controls and sIgAd subjects. (c) Cladogram of linear discriminant analysis effect size (LEfSe) comparisons of secretory antibody coated versus non-coated bacteria from healthy controls (coated with IgA or non-coated) or sIgAd subjects (coated with IgM or non-coated) with p < 0.01. (d,e) Relative abundances of taxa that were significantly different between IgA-coated and non-coated fractions from control subjects (d) or between IgM coated and non-coated fractions in sIgAd subjects (e). (f) Relative abundances of bacterial taxa in healthy controls and sIgAd subjects that were previously demonstrated to be significantly more abundant in the IgA-coated fraction than non-coated fraction in healthy controls (g) Bar chart depicting mean IgA or IgM coating index scores (ICI scores) of taxa with mean ICI scores >10 in either sIgAd subjects or healthy controls. *p < 0.05, **p < 0.01, ***p < 0.001 by Mann Whitney U test. ^#indicates FDR < 0.05 using the Benjamini and Hochberg method using R console. Bars indicate mean +/− SEM.

Figure 4

Alterations in gut microbiota composition in sIgAd subjects are durable across multiple timepoints. (a) Alpha diversity analyses of gut microbiota composition comparing initial and follow up stool samples from both healthy controls and sIgAd subjects as measured by observed OTU, Chao1, Simpson and Shannon Diversity Index. (b) Relative abundances of species level taxa from healthy controls and sIgAd subjects that had, in Fig. 2d, exhibited a significant difference between in relative abundance these two groups. (c) Bray-Curtis comparisons of initial and repeat samples from healthy control and IgA deficient subjects *p < 0.05, **p < 0.01, ***p < 0.001 by Mann Whitney U test.