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Common human skin bacteria could protect against cancer, say researchers View in LinkedIn

TWO UNIVERSES. “We could resolve the “species problem” (perhaps by dismissing it), appreciate the real differences in tempo and mode between prokaryote and “higher” eukaryote evolution, let unraveling of the complex histories of genes and genomes supersede the quest for one true “organismal phylogeny,” develop new models for diversification of prokaryotic niches and definitions of adaptedness, and, at the level of the gene, propose new scenarios for evolution of novel function.” https://lnkd.in/djKBnru View in LinkedIn

THE UNCULTURED MASSES. “In 2003, Schloss and Handelsman offered the term “metagenomics” to describe “the genomic analysis of uncultured microorganisms.” https://lnkd.in/ewnQ9Vg View in LinkedIn

OLD HAT. “Traditional models for prokaryotic evolution based on clonality and periodic selection are inadequate to describe the process of prokaryotic evolution at the species level and that treelike phylogenies are inadequate to represent the pattern of prokaryotic evolution at any level.” https://lnkd.in/djKBnru View in LinkedIn

AGGREGATE GENOMES. “In 1998, however, a new technology began to emerge that would transform our ability to study prokaryotes: Handelsman et al. coined the term “metagenome” to characterize the collective genomes of all microbes in a soil sample. They proposed to analyze this soil metagenome directly, without first having to culture the organisms in the soil.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

PRE-ISOLATION SPECIATION. “These models resemble sympatric speciation for genes, where ecological distinctiveness must arise before reproductive isolation.” https://lnkd.in/djKBnru View in LinkedIn

UNCHARACTERIZED LIFE. “Although non-eukaryotic microbes have long been known to be a ubiquitous and substantial component of the biosphere, the vast majority have been unculturable and thus completely resistant to study, rendering them effectively invisible. Until recently, a microscopic examination of any environment revealed a teeming, but largely mysterious prokaryotic world.” https://lnkd.in/ewnQ9Vg View in LinkedIn

HORIZONTAL ORTHOLOGS. “Most bacterial genome sequences reveal an abundance of paralogs which are often viewed as products of within-lineage duplication and divergence. However, many must be the result of the reuniting through horizontal gene transfer of orthologs that have diverged in separate lineages. Recognizing this encourages a rethinking of standard models of gene duplication and divergence.” https://lnkd.in/djKBnru View in LinkedIn

PARADIGM EVOLUTION. “When new discoveries challenge these fundamental concepts, the underlying data models must adapt or become obsolete. For example, the discovery that a gene could occur within another gene rendered obsolete any data model that was based on the fundamental assumption that genes are non-overlapping objects.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn

TWO DIFFERENT KINGDOMS. “The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology. The unveiling of biological dark matter is allowing us to see, for the first time, the diversity of the entire biosphere and, to paraphrase Darwin, is providing a new view of life. Advancing and understanding that view will require major revisions to some of the most fundamental concepts and theories in biology.” https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0180-8 View in LinkedIn