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.
Highlights
Eczema, a complex inflammatory disease, is one of the earliest manifestations of the allergic march
All healthy controls did not have eczema, asthma, rhinitis in the first two years and had negative skin prick tests (SPT) to cow’s milk, egg white, fish, soy protein, peanut, Dermatophagoides pteronyssinus and Blomia tropicalis when examined at the age of 12 and 24 months
By examining differential abundances of the six individual populations as well as the total Bifidobacterium genus, we showed that the level of the specific Bifidobacterium population (B. longum–BFN-121-2) could discriminate C communities from E communities
Summary
A complex inflammatory disease, is one of the earliest manifestations of the allergic march. Metagenomic characterization of gut microbiota with eczema. SRR1791585 (ID: 161), SRR1818227 (ID: 165), SRR1802723 (ID: 166), SRR1818235 (ID: 170), SRR1785909 (ID: 176), SRR1818231 (ID: 177), SRR1793410 (ID: 192), SRR1793359 (ID: 221) from the Miseq V2 sequencer, and SRR1763038, SRR1766383 (ID: 157), SRR1773183 (ID: 161), SRR1768458 (ID: 176), and SRR1776761 (ID: 221) from the Roche 454 FLX Titanium sequencer
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