André Soares

Phagocytosis without mitochondria is a lineage trait of planctomycetal bacteria of prey

The paper shows that some mitochondria-lacking planctomycetal bacteria can engulf prey, challenging mitochondria-first eukaryogenesis models.

Automated refinement of metagenomic bins and estimation of binning success using itBins

itBins refines metagenomic bins and estimates binning success using %GC content, coverage, and taxonomy, outperforming existing tools in speed and accuracy.

A roadmap for fair reuse of public microbiome data

The paper proposes a roadmap for fair reuse of public microbiome data by introducing a Data Reuse Information tag (DRI) to facilitate communication between data creators and consumers.

Uranium mining fuels evolution in deep groundwater microbiomes

This study shows that uranium mining alters deep groundwater microbiomes, causing genetic and functional changes through increased radiation and uranium exposure.

Complex compositional and cellular response of river sediment microbiomes to multiple anthropogenic stressors

This study shows river sediment microbiomes are highly sensitive to reduced flow velocity, leading to altered community compositions and stress responses that recover after two weeks.

A uniform stress response of stream microbiomes in the hyporheic zone across North America

The paper analyzes hyporheic zone microbiomes across North America to show conserved stress responses and distinct metabolic activity in sediments versus surface water.

Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing

This paper uses long-read sequencing to infer replication states of bacteria and viruses in enrichment cultures by detecting non-canonical base incorporation.

Recovery of gene haplotypes from a metagenome

This paper introduces a method to recover gene haplotypes from metagenomes and shows it accurately identifies mutation rate differences between core and accessory gene families in rumen microbiomes.

Deep Sequencing: Intra-Terrestrial Metagenomics Illustrates The Potential Of Off-Grid Nanopore DNA Sequencing

The paper demonstrates the use of portable nanopore sequencing to analyze subsurface sediment microbiota, identifying dominant bacterial and fungal taxa.

In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

This paper demonstrates that in-field nanopore sequencing of metagenomes and 16S rRNA gene amplicons accurately characterizes glacier microbiota, matching lab-based sequencing results.