Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods

The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...

nature.com

Mykrobe2

mykrobe2.readthedocs.io

Tree of Life Web Project

tolweb.org

GitHub - RhysWhite/nexcision: Precise region-based excision of coordinate-labelled rows from NEXUS matrices.

Precise region-based excision of coordinate-labelled rows from NEXUS matrices. - RhysWhite/nexcision

github.com

Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens

Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...

doi.org

Browse data – AllTheBacteria

allthebacteria.org

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...

biorxiv.org

Muppet Doctor Gives Thumbs Up

ALT: Muppet Doctor Gives Thumbs Up

static.klipy.com

Modelling the role of the microbiome in antimicrobial resistance across scales

Nature Microbiology, Published online: 22 June 2026; doi:10.1038/s41564-026-02390-8The microbiome plays a significant yet underexplored role in antimicrobial resistance by influencing ecological and evolutionary processes. This Perspective proposes a framework to integrate microbiome–AMR interactions into predictive models while highlighting key mechanisms and data gaps to improve resistance understanding and interventions.

go.nature.com

Cross-study metagenomics analysis reveals distinct microbial signatures of urinary tract infections

Background Urinary tract infections (UTIs) represent a major public health concern, increasingly complicated by rising antibiotic resistance, diminishing treatment efficacy, and increasing prevalence ...

biorxiv.org

A genome-resolved view of the wastewater RNA virome

Sequencing-based wastewater surveillance is emerging as an important tool in pathogen-agnostic threat detection, potentially enabling early identification before capture through clinical surveillance ...

medrxiv.org

Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes - BMC Microbiology

Background Single cell genomics has revolutionized microbial sequencing, but complete coverage of genomes in complex microbiomes is imperfect due to enormous variation in organismal abundance and amplification bias. Empirical methods that complement rapidly improving bioinformatic tools will improve characterization of microbiomes and facilitate better genome coverage for low abundance microbes. Methods We describe a new approach to sequencing individual species from microbiomes that combines antibody phage display against intact bacteria with fluorescence activated cell sorting (FACS). Single chain (scFv) antibodies are selected using phage display against a bacteria or microbial community, resulting in species-specific antibodies that can be used in FACS for relative quantification of an organism in a community, as well as enrichment or depletion prior to genome sequencing. Results We selected antibodies against Lactobacillus acidophilus and demonstrate a FACS-based approach for identification and enrichment of the organism from both laboratory-cultured and commercially derived bacterial mixtures. The ability to selectively enrich for L. acidophilus when it is present at a very low abundance (<0.2%) leads to complete (>99.8%) de novo genome coverage whereas the standard single-cell sequencing approach is incomplete (<68%). We show that specific antibodies can be selected against L. acidophilus when the monoculture is used as antigen as well as when a community of 10 closely related species is used demonstrating that in principal antibodies can be generated against individual organisms within microbial communities. Conclusions The approach presented here demonstrates that phage-selected antibodies against bacteria enable identification, enrichment of rare species, and depletion of abundant organisms making it tractable to virtually any microbe or microbial community. Combining antibody specificity with FACS provides a new approach for characterizing and manipulating microbial communities prior to genome sequencing.

doi.org

biorxiv.org

biorxiv.org

Taxonium

Interactive exploration of large phylogenetic trees

taxonium.org

biorxiv.org

Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology

Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.

nature.com

Assessing sequencing-based pathogen surveillance of a recreational swimming area in Oslo, Norway

Sequencing-based surveillance can enable rapid and sensitive detection of environmental pathogens. The Oslofjord inlet is relatively narrow and is exposed to substantial human activity, including occa...

microbiologyresearch.org

Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit

Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....

github.com

biorxiv.org

Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing

The growing resistance of Enterobacterales to last-resort antibiotics such as carbapenems puts a significant burden on healthcare systems, also due to plasmids driving a rapid spread of carbapenem res...

doi.org

Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages

Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...

microbiologyresearch.org

GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression

Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate

github.com

HLi Lab - Vacancies

Openings

hlilab.github.io