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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
..., Germany Corresponding author: christian.roedelsperger@tuebingen.mpg.deAbstractAll animals live in tight association with complex microbial communities, yet studying the effects of individual bacteria remains challenging. Bacterial feeding nematodes are powerful systems to study host-microbe interactions...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...Nora Zidane1, Carla Rodrigues1,2, Valérie Bouchez1,2, Martin Rethoret-Pasty1, Virginie Passet1,3, Sylvain Brisse1,2,3 and Chiara Crestani1 1Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France; 2Institut Pasteur, National Reference...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
..., playing crucial functional roles. Current methods for detecting bacterial DNA modifications via nanopore sequencing typically involve comparing raw current signals to a methylation-free control. In this study, we found that bacterial DNA modification induces errors in nanopore reads. And these errors...
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Method: Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors
- Mara Lohde,
- Gabriel E. Wagner,
- Johanna Dabernig-Heinz,
- Adrian Viehweger,
- Sascha D. Braun,
- Stefan Monecke,
- Celia Diezel,
- Claudia Stein,
- Mike Marquet,
- Ralf Ehricht,
- Mathias W. Pletz,
- and Christian Brandt
Genome Res. November 2024 34: 2039-2047; Published in Advance October 23, 2024, doi:10.1101/gr.278848.123
...and expansion of sequencing capacities in many laboratories and hospitals, predominantly using Illumina for short-read sequencing or Oxford Nanopore Technologies (ONT) for long-read sequencing (∼78% and 18%, respectively) (Brandt et al. 2021). Beyond viral pandemic tracking, bacterial pathogen outbreaks...
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Research: Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
- Morteza Roodgar,
- Benjamin H. Good,
- Nandita R. Garud,
- Stephen Martis,
- Mohan Avula,
- Wenyu Zhou,
- Samuel M. Lancaster,
- Hayan Lee,
- Afshin Babveyh,
- Sophia Nesamoney,
- Katherine S. Pollard,
- and Michael P. Snyder
Genome Res. August 2021 31: 1433-1446; Published in Advance July 22, 2021, doi:10.1101/gr.265058.120
...metas. Here, we took a different approach and developed new statistical methods that leverage longitudinal linked-read sequencing to detect and interpret fine-scale genetic changes that take place within the resident populations of individual bacterial species over time. This reference-based strategy...
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Resource: Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
- Peng Gao,
- Xiaotao Shen,
- Xinyue Zhang,
- Chao Jiang,
- Sai Zhang,
- Xin Zhou,
- Sophia Miryam Schüssler-Fiorenza Rose,
- and Michael Snyder
Genome Res. June 2022 32: 1199-1214; Published in Advance June 6, 2022, doi:10.1101/gr.276521.121
...and heterogeneity of individualized environmental exposures. Here, as a pilot case study, we integrated deep-profiled longitudinal personal exposome and internal multi-omics to systematically investigate how the exposome shapes a single individual's phenome. We annotated thousands of chemical and biological...
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Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
- Teemu Kallonen,
- Hayley J. Brodrick,
- Simon R. Harris,
- Jukka Corander,
- Nicholas M. Brown,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
...a decade, using nested systematic surveys of England and the Cambridge area. These were not selected based on ST or other bacterial characteristics. We investigated trends in population structure andmechanisms of antibiotic resistance and captured the introduction of ST131 and ST69, which enabled us...
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Method: Fast and flexible bacterial genomic epidemiology with PopPUNK
- John A. Lees,
- Simon R. Harris,
- Gerry Tonkin-Hill,
- Rebecca A. Gladstone,
- Stephanie W. Lo,
- Jeffrey N. Weiser,
- Jukka Corander,
- Stephen D. Bentley,
- and Nicholas J. Croucher
Genome Res. February 2019 29: 304-316; Published in Advance January 24, 2019, doi:10.1101/gr.241455.118
...London, London W2 1PG, United Kingdom Corresponding authors: john.lees@nyumc.org, n.croucher@imperial.ac.ukAbstractThe routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole- clustering and multilocus typing approaches do...
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Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
- Alexey Vorobev,
- Marion Dupouy,
- Quentin Carradec,
- Tom O. Delmont,
- Anita Annamalé,
- Patrick Wincker,
- and Eric Pelletier
Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
..., France Corresponding authors: voralexey@gmail.com, eric.pelletier@genoscope.cns.frAbstractLarge-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large...
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Method: Genome-reconstruction for eukaryotes from complex natural microbial communities
- Patrick T. West,
- Alexander J. Probst,
- Igor V. Grigoriev,
- Brian C. Thomas,
- and Jillian F. Banfield
Genome Res. April 2018 28: 569-580; Published in Advance March 1, 2018, doi:10.1101/gr.228429.117
...surveys or DNA “barcoding” are frequently used to identify eukaryotes in microbial communities and have demonstrated the breadth of eukaryotic diversity (Pawlowski et al. 2012). However, these approaches can only detect species and are unable to provide information about metabolism or lifestyle...

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