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Global multi-host genomic epidemiology of Acinetobacter baumannii reveals transmission at one health interfaces

Nature Communications - Acinetobacter baumannii is an important bacterial pathogen, yet little is known about non-human sources. Here, in a One Health angle, the authors characterize a large set of...

rdcu.be

NASA PACE Blog - PACE is BATS for Ocean’s Carbon Story

NASA PACE (Plankton, Aerosol, Cloud, ocean Ecosytem) blog

pace.oceansciences.org

Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study

The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

merenlab.org

biorxiv.org

Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

nature.com

Converting Relative Amplicon Abundances to Absolute Abundances via Flow Cytometry: Metagenomic Validation and Application to Long Ocean Transects

Abstract. With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. Whil

academic.oup.com

Arbitrium phages can manipulate each other’s lysis/lysogeny decisions

Arbitrium phages belonging to different species and genera can influence each other’s infection dynamics by secreting chemically similar, non-cognate signal peptides. These findings indicate that arbitrium-based communication is not as specific as previously thought.

dlvr.it

Predator-prey dynamics of Vibrio cholerae on chitin suggest an alternative mode of biofilm formation in marine snow conditions

Abstract. Vibrio cholerae is a ubiquitous marine bacterium that solubilizes and consumes chitin in the marine water column. In both the marine environment

academic.oup.com

Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans - Nature Communications

Marine bacteria Vibrio are emerging pathogens worldwide, yet their global dispersal is poorly understood. Combining metagenomic and ocean drifter data, authors show Vibrio dispersal across oceans, con...

nature.com

River Microbiomes as Sentinels of National‐Scale Freshwater Ecosystems

River biofilms are complex microbial assemblages that underpin aquatic food webs and play a central role in biogeochemical cycling. By responding to environmental signals over space and time, biofilm...

onlinelibrary.wiley.com

Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics

Abstract. Diverse phage-bacteria communities coexist at high densities in environmental, agricultural, and human-associated microbiomes. Phage-bacteria coe

academic.oup.com

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

pnas.org

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

pnas.org

Species-specific prophage induction by ciprofloxacin in human gut metagenomes

Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut. Importance Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations. ### Competing Interest Statement The authors have declared no competing interest. NIH Common Fund, https://ror.org/001d55x84 Natural Sciences and Engineering Research Council

biorxiv.org

Water mass specific genes dominate the Southern Ocean microbiome - Nature Communications

Southern Ocean microbial communities are less well studied. Here, the authors generate a circumpolar-scale gene catalog from 218 metagenomics samples revealing broadscale uniqueness and water-mass–spe...

nature.com

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems

MicrobeAtlas (www.microbeatlas.org) is an integrated, reference-based resource for truly planet-wide microbiomics, analyzing hundreds of thousands of microbial lineages across diverse environments, co...

cell.com

Phage-microbe interactions may contribute to the population structure and dynamics of hydrothermal vent symbionts

Abstract. Deep-sea hydrothermal vent ecosystems are sustained by chemoautotrophic bacteria that symbiotically provide organic matter to their animal hosts

academic.oup.com

academic.oup.com

biorxiv.org

Matters Microbial #122: Jumbo Marine Viruses and Nanoscopic Warfare

YouTube video by MicrobeTV

youtu.be