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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
...Dynamic A-to-I RNA editing in response to gut microbiome 1 in honey bees 2 3 Yuange Duan1 #, Min Huang1 #, Lin Ye1 #, Ling Ma1, Yashuai Wu1, Yating Du1, Jiyao Liu1, 4 Fan Song1, Li Tian1, Wanzhi Cai1, Hu Li1, Xin Zhou1, Shiqi Luo1 * 5 6 1. State Key Laboratory of Agricultural and Forestry...
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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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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
...249 healthy adults from the Human Microbiome Project (HMP) (The Human Microbiome Project Consortium 2012; Lloyd-Price et al. 2017) and 185 healthy adults from Qin et al. (2012; Table 1) to compare the evolutionary dynamics in adults versus infants. These data sets were chosen because...
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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
...author: wangxy@scnu.edu.cnAbstractTransfer RNAs (tRNAs) are essential for translation, and tRNA expression and modifications are regulated by many factors. However, the interplay between the microbiome and host tRNA profiles through host-microbiome interactions has not been explored. In this study, we...
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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: 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
..., respectively. The number of reads for each sample is listed in Supplemental Table S1. The raw sequencing data are available at the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under accession number PRJNA478018 with Sequence Read Archive (SRA) accession number SRP151559, as described...
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Research: Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
- Daniela S. Aliaga Goltsman,
- Christine L. Sun,
- Diana M. Proctor,
- Daniel B. DiGiulio,
- Anna Robaczewska,
- Brian C. Thomas,
- Gary M. Shaw,
- David K. Stevenson,
- Susan P. Holmes,
- Jillian F. Banfield,
- and David A. Relman
Genome Res. October 2018 28: 1467-1480; Published in Advance September 19, 2018, doi:10.1101/gr.236000.118
...associations between the vaginal microbiota and race/ethnicity (Hillier et al. 1995; Zhou et al. 2007; Ravel et al. 2011; The Human Microbiome Project Consortium 2012; Hyman et al. 2014) and, more recently, associations with premature birth (DiGiulio et al. 2015; Callahan et al. 2017; Kindinger et al. 2017...
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Insight/Outlook: Ethical, legal, and social considerations in conducting the Human Microbiome Project
- Amy L. McGuire,
- James Colgrove,
- Simon N. Whitney,
- Christina M. Diaz,
- Daniel Bustillos,
- and James Versalovic
Genome Res. December 2008 18: 1861-1864; Published in Advance October 29, 2008, doi:10.1101/gr.081653.108
...raised a host of ethical, legal, and social challenges. Scientists now undertaking research on the human microbiome—including those engaged in the National Institutes of Health’s (NIH) latest Roadmap initiative, the Human Microbiome Project (HMP)—confront a similarly uncharted ethical landscape. Not only...
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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
...for classification and diversity analysis to comprehensive all-encompassing packages that take the user from sequence quality control to graphical representation of the data, for example, QIIME (Caporaso et al. 2010) and mothur (Schloss et al. 2009). Another key impetus was the NIH Human Microbiome Project...
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Research: Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome
- Weibing Shi,
- Christina D. Moon,
- Sinead C. Leahy,
- Dongwan Kang,
- Jeff Froula,
- Sandra Kittelmann,
- Christina Fan,
- Samuel Deutsch,
- Dragana Gagic,
- Henning Seedorf,
- William J. Kelly,
- Renee Atua,
- Carrie Sang,
- Priya Soni,
- Dong Li,
- Cesar S. Pinares-Patiño,
- John C. McEwan,
- Peter H. Janssen,
- Feng Chen,
- Axel Visel,
- Zhong Wang,
- Graeme T. Attwood,
- and Edward M. Rubin
Genome Res. September 2014 24: 1517-1525; Published in Advance June 6, 2014, doi:10.1101/gr.168245.113
...Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome Weibing Shi 1 , 2 , Christina D. Moon 3 , Sinead C. Leahy 3 , Dongwan Kang 1 , 2 , Jeff Froula 1 , 2 , Sandra Kittelmann...

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