Akkermansia muciniphila outer membrane protein Amuc_0904 promotes goblet cell differentiation

Akkermansia muciniphila is recognized as a promising probiotic that improves the symptoms of a variety of diseases. However, the role and mechanism of A. muciniphila in regulating intestinal homeostasis remain to be explored. Here, we discovered that A. muciniphila was dramatically increased during colitis recovery, and its colonization greatly increased goblet cells to protect the intestinal barrier in mice. Amuc_0904, a previously uncharacterized A. muciniphila outer membrane protein, was identified to induce goblet cell differentiation. Total RNA was extracted from HT-29 cells using TRIzol Reagent according the manufacturer’s instructions. The RNA quality was determined using a 2100 Bioanalyser (Agilent), and the RNA concentration was quantified using the ND-2000 (NanoDrop Technologies). RNAseq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA). Paired-end RNAseq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2×150 bp read length) according to the standard protocols by Majorbio Bio-Pharm Technology Co. Ltd. The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml). The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.