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PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted this week.

An international team led by investigators at the Max Planck Institute for the Science of Human History explores the evolution of microbial communities in human mouths and in the mouths of related hominids. Using metagenomic sequencing, the researchers profiled oral microbiome membership and microbial genes in 124 ancient and modern dental biofilm samples, spanning humans from Late Pleistocene to present-day populations, as well as Neanderthals, chimps, gorillas, and New World howler monkeys. Their results suggest that a handful of core microbes have persisted in the oral microbiome across hominid evolution, though the oral microbial community relationships and community structure patterns did not necessarily track with host hominid relationships. "We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, including an apparent Homo-specific acquisition of starch digestion capability in oral streptococci, suggesting microbial co-adaptation with host diet," the authors conclude.

Investigators in Brazil and the US present findings from a comparative genomic analysis of the jararaca lancehead, Bothrops jararaca, focusing on snake toxin evolution. Starting with a new B. jararaca genome — assembled using multiple short-read, long-read, and hybrid assembly strategies and informed by tissue transcriptome and venom proteome data — the team retraced the ancestral forms of genes in a dozen toxin families. Together with sequences from other vertebrates, including venomous snakes and lizards, the B. jararaca genome highlighted toxin-related changes to gene families not previously involved in toxin production. "These results support a new perspective in venom evolution, in which gene duplications in most toxin families occurred after, rather than before, initial toxin recruitment from non-toxin genes, contributing to the evolutionary optimization of snake venoms," the authors report, noting that the findings "emphasize the importance of correctly identifying orthologous loci to accurately trace the genomic pathways that lead to the evolutionary origination of new traits."

A team from Taiwan and the US takes a look at transcription factor binding sites in humans and mice using chromatin immunoprecipitation sequencing (ChIP-seq) and a new computational pipeline specifically designed to analyze ChIP-seq data. Based on nearly 1,100 available human ChIP-seq profiles and more than 100 ChIP-seq experiments in mice, the researchers flagged 2,058 characteristic binding motifs for 354 human transcription factors, along with 163 binding motifs for transcription factors found in mice. From there, the authors analyzed the distribution of the transcription factor binding sites and interactions across the human genome, including regulatory regions coinciding with transcription start sites and binding motifs falling in enhancer regions and other intergenic sites.