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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...transcriptomic diversity conferred by A-to-I RNA editing. We bridge the gut–brain axis with RNA editing, providing innovative perspectives on how the gut microbiome influences gene regulation in the nervous system. Methods Generation of GF and CV honeybees The honeybee bacterial colonization process followed...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology Abigail L. Lind1,2, Nathan A. McDonald2,3, Elias R. Gerrick4, Ami S. Bhatt5,6 and Katherine S. Pollard1,7,8 1Gladstone Institute for Data Science...
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Resource: Global compositional and functional states of the human gut microbiome in health and disease
- Sunjae Lee,
- Theo Portlock,
- Emmanuelle Le Chatelier,
- Fernando Garcia-Guevara,
- Frederick Clasen,
- Florian Plaza Oñate,
- Nicolas Pons,
- Neelu Begum,
- Azadeh Harzandi,
- Ceri Proffitt,
- Dorines Rosario,
- Stefania Vaga,
- Junseok Park,
- Kalle von Feilitzen,
- Fredric Johansson,
- Cheng Zhang,
- Lindsey A. Edwards,
- Vincent Lombard,
- Franck Gauthier,
- Claire J. Steves,
- David Gomez-Cabrero,
- Bernard Henrissat,
- Doheon Lee,
- Lars Engstrand,
- Debbie L. Shawcross,
- Gordon Proctor,
- Mathieu Almeida,
- Jens Nielsen,
- Adil Mardinoglu,
- David L. Moyes,
- Stanislav Dusko Ehrlich,
- Mathias Uhlen,
- and Saeed Shoaie
Genome Res. June 2024 34: 967-978; Published in Advance July 22, 2024, doi:10.1101/gr.278637.123
....shoaie@kcl.ac.ukAbstractThe human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of meta-assembled s, there have been few pan...
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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
...their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here, we characterize the gut microbiome of a single individual at high temporal and genetic resolution through a period of health, disease, antibiotic treatment, and recovery...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed s from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs...
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Research: Rapid evolution and strain turnover in the infant gut microbiome
- Daisy W. Chen and
- Nandita R. Garud
Genome Res. June 2022 32: 1124-1136; Published in Advance May 11, 2022, doi:10.1101/gr.276306.121
...of new traits. For example, genetic variants in the human gut microbiome are known to confer traits such as the ability to digest food (Hehemann et al. 2010; Kenny et al. 2020), metabolize drugs (Spanogiannopoulos et al. 2016), and evade antibiotics (Gumpert et al. 2017). Recent studies illustrate...
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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
...framework for future mechanistic studies in P. pacificus, and may also be conceptually transferred and reimplemented in other organisms in order to investigate the evolution of the host–microbe interactomes.The human gut microbiome exemplifies the intricate associations between organisms and bacteria...
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Research: Selective maternal seeding and environment shape the human gut microbiome
- Katri Korpela,
- Paul Costea,
- Luis Pedro Coelho,
- Stefanie Kandels-Lewis,
- Gonneke Willemsen,
- Dorret I. Boomsma,
- Nicola Segata,
- and Peer Bork
Genome Res. April 2018 28: 561-568; Published in Advance March 1, 2018, doi:10.1101/gr.233940.117
...of the infant gut microbiome and impact of antibiotic treatments on strain-level diversity and stability. Sci Transl Med 8: 343. ↵Zeller G, Tap J, Voigt A, Sunagawa S, Kultima J, Costea P, Amiot A, Böhm J, Brunetti F, Habermann N, et al. 2014. Potential of fecal microbiota for early-stage detection...
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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
..., Mellmann A. 2014. Bacterial whole- sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes. J Clin Microbiol 52: 2365–2370. doi:10.1128/JCM.00262-14 ↵Lerminiaux NA, Cameron ADS. 2019. Horizontal transfer of antibiotic...
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Research: Tissue-specific reprogramming of host tRNA transcriptome by the microbiome
- Jia Huang,
- Wenjun Chen,
- Fan Zhou,
- Zhichang Pang,
- Luoluo Wang,
- Tao Pan,
- and Xiaoyun Wang
Genome Res. June 2021 31: 947-957; Published in Advance April 15, 2021, doi:10.1101/gr.272153.120
..., Seveau S, Roy H, Ibba M. 2012. A pseudo-tRNA modulates antibiotic resistance in Bacillus cereus. PLoS One 7: e41248. doi:10.1371/journal.pone.0041248 ↵Sandhu KV, Sherwin E, Schellekens H, Stanton C, Dinan TG, Cryan JF. 2017. Feeding the microbiota-gut-brain axis: diet, microbiome, and neuropsychiatry...
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