Machine Learning for GEnomics

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Healthy octocorals have a microbiome that is distinct from the surrounding environment, host genus-specific and defined by so-far uncultured groups of bacteria In contrast, the microbiome of necrotic coral tissue shows large shifts in its community structure compared to healthy tissue and is colonized by seawater bacteria. Functional analysis showed that healthy corals were enriched in microbial genes associated with antiviral defense, host symbiosis recognition, micronutrient acquisition and heat-stress response. This was the first study to apply primer-less, metagenomic sequencing to octocorals which allowed researchers to identify so-far uncultured, likely obligate symbionts as the core members of the octocoral microbiome. These results can be used to guide future studies into coral reef conservation and microbiome therapies for octocorals.

Metagenome-Assembled Genome Sequences of Three Uncultured Planktomarina sp. Strains from the Northeast Atlantic Ocean

We report three metagenome-assembled genomes (MAGs) of Planktomarina strains from coastal seawater (Portugal) to help illuminate the functions of understudied Rhodobacteraceae bacteria in marine environments. The MAGs encode proteins involved in aerobic anoxygenic photosynthesis and a versatile carbohydrate metabolism, strengthening the role of Planktomarina species in oceanic carbon cycling.

Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host-associated and free-living Aquimarina (Bacteroidetes, Flavobacteriaceae) species

Previously underestimated, complex secondary metabolism is revealed for the recently described bacterial genus Aquimarina, an emerging keystone taxon mediating carbon and nitrogen cycling and host-microbe interactions across multiple marine microniches.

Bioactive secondary metabolites from octocoral-associated microbes: new chances for blue growth

This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth.

Draft genome sequence of Sphingorhabdus sp. strain EL138, a metabolically versatile Alphaproteobacterium isolated from the gorgonian coral Eunicella labiata

Here, we report the draft genome sequence of Sphingorhabdus sp. strain EL138, an alphaproteobacterium that shows potential to degrade polycyclic aromatic compounds and to cope with various heavy metals and antibiotics. Moreover, the strain, isolated from the gorgonian coral Eunicella labiata, possesses several genes involved in the biosynthesis of polyphosphates, polyketides, and terpenoids.