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Genome Biology Papers on Aging, SMOOTH-seq, Akkermansia Bacterial Diversity

A University of Edinburgh-led team outlines more than 100 loci with ties to DNA methylation-based aging biomarkers. The researchers brought together SNP genotyping and DNA methylation profiles for more than 40,900 individuals with European, African American, or Hispanic ancestry between the ages of 27 and 79 from available datasets, narrowing in on 137 new or known loci linked to aging-related methylation markers or methylation variants contributing to previously reported "epigenetic clock" signatures. From there, they came up with a polygenic risk score that showed promise for predicting the presence of epigenetic markers of aging or aging-related traits in European participants. "Overall," the authors say, "this study highlights the shared genetic architecture between epigenetic aging, lifestyle factors (smoking, obesity), and parental longevity, which shows that [DNA methylation]-based biomarkers are valuable endophenotypes of biological aging."

Researchers at Peking University, Bioland Laboratory, and the Ministry of Education Key Laboratory of Cell Proliferation and Differentiation describe a third-generation sequencing approach focused on finding structural variants and other features in individual cells. The team's "single-molecule real-time sequencing of long fragments amplified through transposon insertion," or SMOOTH-seq, library preparation approach designed to bump up the number of DNA fragments that can be successfully sequenced from individual cells. For their proof-of-principle experiments, the authors used SMOOTH-seq to track down insertions, deletions, translocations, duplications, or extra-chromosomal circular DNA molecules in human cancer cell lines and in almost 100 individual tumor cells from an individual with colorectal cancer.

An international team led by investigators at Italy's University of Trento takes a genomic look at bacterial species in the Akkermansia genus, including an A. muciniphila species previously implicated in intestinal mucus physiology and other human gut functions. The investigators considered genome sequences for nearly 200 Akkermansia isolates and more than 2,200 metagenome-assembled genomes from metagenomic sequences on humans or other animals, classifying the Akkermansia strains into five genetically diverse candidate species containing a wide range of CRISPR-Cas loci linked to defense against described or putative bacteriophage representatives. "The five candidate species are prevalent in the human gut microbiome and are found in other mammals such as mice and non-human primates almost exclusively when living in man-made environments," they write, "suggesting that all Akkermansia candidate species are specifically adapted to the human gut."