sMETASeq: Combined Profiling of Microbiota and Host Small RNAs

Abstract

Understanding microbial communities' roles in human health and disease requires methods that accurately characterize the microbial composition and their activity and effects within human biological samples. We present sMETASeq (small RNA Metagenomics by Sequencing), a novel method that uses sequencing of small RNAs to jointly measure host small RNA expression and create metagenomic profiles and detect small bacterial RNAs. We evaluated the performance of sMETA-Seq on a mock bacterial community and demonstrated its use on different human samples, including colon cancer, oral leukoplakia, cervix cancer, and a panel of human biofluids. In all datasets, the detected microbes reflected the biology of the different sample types.

sRNAflow: A Tool for the Analysis of Small RNA-Seq Data

“…Using a simulated dataset, we conducted a performance comparison of sRNAflow with several programs designed for small RNA analysis and traditionally used pipelines. These include sMETASeq [ 30 ], exceRpt [ 31 ], and sRNAtoolbox [ 29 ], which is well-known and encompasses analysis of microbiome and host small RNAs. Kraken2 is a taxonomic classification system using exact k-mer matches, widely used in the analysis of microbiomes.…”

“…The field of small RNA data analysis is rapidly advancing, with new tools for analysing specific subsets of data being published each year [ 25 , 26 , 27 , 28 , 29 , 30 , 31 ]. However, many of these tools demand computational or basic programming expertise from users.…”

Immunoglobulin E-virus phenotypes of infant bronchiolitis and risk of childhood asthma

“…All small RNA-seq samples had sufficient sequence depth (mean of 26,736,490 pair-end reads/sample) to obtain a high sequence coverage. From clean small RNA-seq reads, we estimated miRNA detection and abundance by sMETASeq ( 23 ). We mapped trimmed reads against human miRNA sequences from miRBase V22 ( 24 ).…”

Prospects for Leveraging the Microbiota as Medicine for Hypertension

“…9 A bidirectional interaction between the immune system and gut microbiota exists, whereby the gut microbiota can modulate the immune responses and vice versa. [73][74][75][76] Studies have also linked gut microbiota with elevated sympathetic drive, but precise mechanisms remain unknown. [77][78][79] SCFAs can directly regulate the activity of the sympathetic ganglia and modulate BP centrally by affecting the brain cardioregulatory regions.…”