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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- 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 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
.... This slight discrepancy may be attributed to variations in the gut microbial 373 composition among different CV bees. Although microbial colonization consistently 374 increased RNA editing levels at the Adar p.482 Ile>Met site and elevated global editing 375 activity, only a subset of editing sites remained...
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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
...and strongly associated with the eukaryotic hosts. Thus, their ecology is very different from environmental bacteria, and the extent to which our findings generalize to other environments is currently unclear. Future studies that leverage the ever-increasing global metagenomic sequences will be useful...
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Research: Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules
- Jonathon L. Baker,
- James T. Morton,
- Márcia Dinis,
- Ruth Alvarez,
- Nini C. Tran,
- Rob Knight,
- and Anna Edlund
Genome Res. January 2021 31: 64-74; Published in Advance November 25, 2020, doi:10.1101/gr.265645.120
...microbiome at an unprecedented resolution and contributed several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.Dental caries, the most prevalent chronic infectious disease globally, is caused by a dysbiotic oral microbiota that creates...
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Resource: Organ-level protein networks as a reference for the host effects of the microbiome
- Robert H. Mills,
- Jacob M. Wozniak,
- Alison Vrbanac,
- Anaamika Campeau,
- Benoit Chassaing,
- Andrew Gewirtz,
- Rob Knight,
- and David J. Gonzalez
Genome Res. February 2020 30: 276-286; Published in Advance January 28, 2020, doi:10.1101/gr.256875.119
...were constructed into protein–protein interaction networks for the brain, spleen, heart, small intestine, and colon, as well as a global network. While the brains and gastrointestinal tract of GF mice have been characterized in several studies, other organs such as the heart and spleen may...
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Research: Reshaping the gut microbiome with bacterial transplantation and antibiotic intake
- Chaysavanh Manichanh,
- Jens Reeder,
- Prudence Gibert,
- Encarna Varela,
- Marta Llopis,
- Maria Antolin,
- Roderic Guigo,
- Rob Knight,
- and Francisco Guarner
Genome Res. October 2010 20: 1411-1419; Published in Advance August 24, 2010, doi:10.1101/gr.107987.110
...of the Bacteroidetes phylum (Supplemental Fig. S4). Three months after drug discontinuation, these changes still persisted, leading to both a global diversity loss and a reshaping of the twomain bacterial phyla: The proportion of Firmicutes increased and of Bacteroidetes decreased (P < 0.01) in comparison...
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Perspective: The intersection of microbiome and host at the skin interface: genomic- and metagenomic-based insights
- Elizabeth A. Grice
Genome Res. October 2015 25: 1514-1520; doi:10.1101/gr.191320.115
...defense response. Proc Natl Acad Sci 107: 14799–14804. Holmfeldt K, Solonenko N, Shah M, Corrier K, Riemann L, Verberkmoes NC, Sullivan MB. 2013. Twelve previously unknown phage genera are ubiquitous in global oceans. Proc Natl Acad Sci 110: 12798–12803. TheHumanMicrobiome Project Consortium. 2012...
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Research: Country-specific antibiotic use practices impact the human gut resistome
- Kristoffer Forslund,
- Shinichi Sunagawa,
- Jens Roat Kultima,
- Daniel R. Mende,
- Manimozhiyan Arumugam,
- Athanasios Typas,
- and Peer Bork
Genome Res. July 2013 23: 1163-1169; Published in Advance April 8, 2013, doi:10.1101/gr.155465.113
...persistence over time of the already acquired individual resistomes can be overcome too. This outcome of our global, metagenomic-based approach, mapping variation within and between populations and covering a vast range of antibiotics, should provide a profound molecular basis for the ongoing debate...
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Resource: The NIH Human Microbiome Project
- The NIH HMP Working Group,
- Jane Peterson,
- Susan Garges,
- Maria Giovanni,
- Pamela McInnes,
- Lu Wang,
- Jeffery A. Schloss,
- Vivien Bonazzi,
- Jean E. McEwen,
- Kris A. Wetterstrand,
- Carolyn Deal,
- Carl C. Baker,
- Valentina Di Francesco,
- T. Kevin Howcroft,
- Robert W. Karp,
- R. Dwayne Lunsford,
- Christopher R. Wellington,
- Tsegahiwot Belachew,
- Michael Wright,
- Christina Giblin,
- Hagit David,
- Melody Mills,
- Rachelle Salomon,
- Christopher Mullins,
- Beena Akolkar,
- Lisa Begg,
- Cindy Davis,
- Lindsey Grandison,
- Michael Humble,
- Jag Khalsa,
- A. Roger Little,
- Hannah Peavy,
- Carol Pontzer,
- Matthew Portnoy,
- Michael H. Sayre,
- Pamela Starke-Reed,
- Samir Zakhari,
- Jennifer Read,
- Bracie Watson,
- and Mark Guyer
Genome Res. December 2009 19: 2317-2323; Published in Advance October 9, 2009, doi:10.1101/gr.096651.109
..., respect the data producers’ rights to publish a first global analysis of the data, credit the data producers in any publication, and confer with them regarding any use of the data in a publication prior to their first publication on the data. As earlier noted, human participants who provide samples...
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Research: The altered landscape of the human skin microbiome in patients with primary immunodeficiencies
- Julia Oh,
- Alexandra F. Freeman,
- NISC Comparative Sequencing Program,
- Morgan Park,
- Robert Sokolic,
- Fabio Candotti,
- Steven M. Holland,
- Julia A. Segre,
- and Heidi H. Kong
Genome Res. December 2013 23: 2103-2114; Published in Advance October 29, 2013, doi:10.1101/gr.159467.113
...Consortium 2012). These attributes differ significantly in disease states such as atopic dermatitis. Skin disease severity in atopic dermatitis patients was closely associated with marked shifts in the composition, diversity, and interpersonal and temporal variation of the resident microbial communities...
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Research: The human gut virome: Inter-individual variation and dynamic response to diet
- Samuel Minot,
- Rohini Sinha,
- Jun Chen,
- Hongzhe Li,
- Sue A. Keilbaugh,
- Gary D. Wu,
- James D. Lewis,
- and Frederic D. Bushman
Genome Res. October 2011 21: 1616-1625; Published in Advance August 31, 2011, doi:10.1101/gr.122705.111
...points to between-subject distances showed that betweensubject distances were significantly greater (Fig. 5B; P < 0.001, significance assessed by permutation of sample labels). Thus, each individual contained a unique virome that was globally stable over the 8-d time course. A previous study showed...

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