Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema

Abstract

Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months. Microbial genomic DNA were extracted from stool samples and used for shotgun sequencing. Comparative metagenomic analysis showed that immune-regulatory TCAAGCTTGA motifs were significantly enriched in the six healthy controls (C) communities compared to the six eczema subjects (E), with many encoded by Bifidobacterium (38% of the total motifs in the C communities). Draft genomes of five Bifidobacterium species populations (B. longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum) were recovered from metagenomic datasets. The B. longum BFN-121-2 genome encoded more TCAAGCTTGA motifs (4.2 copies per one million genome sequence) than other Bifidobacterium genomes. Additionally, the communities in the stool of controls (C) were also significantly enriched in functions associated with tetrapyrrole biosynthesis compared to those of eczema (E). Our results show distinct immune-modulatory genomic properties of gut microbiota in infants associated with eczema and provide new insights into potential role of gut microbiota in affecting human immune homeostasis.

Fucosylated Human Milk Oligosaccharides and N-Glycans in the Milk of Chinese Mothers Regulate the Gut Microbiome of Their Breast-Fed Infants during Different Lactation Stages

“…pseudocatenulatum was a major feature in the early (days 6 and 42) gut microbiota of infants fed by secretor CMs. This species has been found to exert several beneficial effects on infants (62, 63). However, it is not the most common Bifidobacterium species found in the feces of breast-fed infants (64); B.…”

The role of gut microbiome in inflammatory skin disorders: a systematic review

“…We found sixteen articles that correlated atopic dermatitis (AD) and the gut microbiome. Even though ten reports stated there were non-significant differences in the bacterial families between healthy and AD, [23][24][25][26][27][28][29][30][31][32] four articles support significant low abundance diversity in AD gut microbiome (Table 2). [33][34][35][36] The subjects of all the papers ranged from infants, toddlers, and children.…”

The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling

“…The processing and analysis of the data acquired are crucial for an appropriate and true depiction of the gut microbiome's community and stability [120]. The bacterial DNA sequences, extracted from fecal samples, are used in differentiating the gene patterns of the gut microbiome [121,122] and can be interpreted and identified using bioinformatic software such as MOTHUR, Greengenes and QIIME 2 [120,[123][124][125][126][127]. OTUs are assigned to bacterial DNA sequences based on a value of 97% similarity or higher, with normalization to control for differences in sequencing depths (a given number of reads of a nucleotide in a sequence), diversity (species present and its relative abundance) and log transformations to standardize variances, such as dominant and rare bacterial species [128].…”