The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota

Abstract

Gut commensal bacteria are known to have a significant role in regulating the innate and adaptive immune homeostasis. Alterations in the intestinal microbial composition have been associated with several disease states, including autoimmune and inflammatory conditions. However, it is not entirely clear how commensal gut microbiota modulate and contribute to the systemic immunity, and whether circulating elements of the host immune system could regulate the microbiome. Thus, we have studied the diversity and abundance of specific taxons in the gut microbiota of inbred GalT-KO mice during 7 months of animal life by metagenetic high-throughput sequencing (16S rRNA gene, variable regions V3–V5). The repertoire of glycan-specific natural antibodies, obtained by printed glycan array technology, was then associated with the microbial diversity for each animal by metagenome-wide association studies (MWAS). Our data show that the orders clostridiales (most abundant), bacteriodales, lactobacillales, and deferribacterales may be associated with the development of the final repertoire of natural anti-glycan antibodies in GalT-KO mice. The main changes in microbiota diversity (month-2 and month-3) were related to important changes in levels and repertoire of natural anti-glycan antibodies in these mice. Additionally, significant positive and negative associations were found between the gut microbiota and the pattern of specific anti-glycan antibodies. Regarding individual features, the gut microbiota and the corresponding repertoire of natural anti-glycan antibodies showed differences among the examined animals. We also found redundancy in different taxa associated with the development of specific anti-glycan antibodies. Differences in microbial diversity did not, therefore, necessarily influence the overall functional output of the gut microbiome of GalT-KO mice. In summary, the repertoire of natural anti-carbohydrate antibodies may be partially determined by the continuous antigenic stimulation produced by the gut bacterial population of each GalT-KO mouse. Small differences in gut microbiota diversity could determine different repertoire and levels of natural anti-glycan antibodies and consequently might induce different immune responses to pathogens or other potential threats.

Development of smart anti-glycan reagents using immunized lampreys

“…2a-d). Both mice contained circulating anti-glycan IgM antibodies in their serum prior to immunization, as has been observed previously 40,41 . The repertoire of these IgM antibodies for both animals analyzed were highly correlated (r = 0.88), and were against a variety of blood group and Lewis antigens to name a few ( Fig.…”

Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome

“…Our study fits with previous observations that indirectly suggested that gut microbiome was the main source of production of the Gal antigen (18) resulting in the rise of the anti-Gal within the first year of life. Interestingly, in α1,3GT-KO mice, modifications of gut microbiome followed during the first months of life were related to anti-Gal Ab levels (31). However, our estimation likely underestimates the actual proportion of the microbiota able to produce the Gal antigen as also suggested by the presence of anti-Gal antibodies in most of the adult individuals tested.…”

“…Instead, it performs exhaustive pairwise alignment on all sequences using dynamic programming without statistical approximations, and hence avoids the need for ensemble analysis that may be required when using other approximate tools that may have sensitivity/specificity tradeoffs in pursuing or calculating alignments. Especially for lower alignment identities, general-purpose techniques designed for speedy approximate alignment (read mappers, classifiers) are not applicable, as they use approximations that are reasonable for short-read mapping but not lower-identity alignment (under some metrics of precision/accuracy/sensitivity/recall) (29)(30)(31). Because we are looking for potentially divergent sequences, we selected BURST over high-speed metagenomic classifiers such as MEGAN, MEGAN-LR (31) or Kraken (29) despite the increased computational cost.…”

“…Especially for lower alignment identities, general-purpose techniques designed for speedy approximate alignment (read mappers, classifiers) are not applicable, as they use approximations that are reasonable for short-read mapping but not lower-identity alignment (under some metrics of precision/accuracy/sensitivity/recall) (29)(30)(31). Because we are looking for potentially divergent sequences, we selected BURST over high-speed metagenomic classifiers such as MEGAN, MEGAN-LR (31) or Kraken (29) despite the increased computational cost. Here, our reference database was the collection of α1,3GT gene sequences collected from the literature, ExPASy, KEGG, and UniProt as described above.…”

Unique repertoire of anti-carbohydrate antibodies in individual human serum

“…Pure polysaccharides are considered to be relatively weak antigens in mammals when used as immunogens alone or used independently of their expression on a microbe, as such free polysaccharides are often T cell-independent and generate a biased IgM response 6 – 8 . Some zwitterionic polysaccharides can directly induce T cell-dependent IgG anti-carbohydrate antibodies 9 , 10 , and ACAs to the gut microbiota have been identified 11 , 12 . Regardless of whether responses are T cell-independent or -dependent, the presence of a diverse array of IgG antibodies to carbohydrates has been observed in many preparations of IVIG, purified IgG products prepared from pooled human plasma and made available through many different commercial sources 13 .…”