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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
...in CV and GF honeybees To investigate the effect of the gut microbiome on A-to-I RNA editing profile in A. mellifera, we fed the homogenates of nurse bee hindguts to the newly emerged GF bees to generate CV bees (Methods). Subsequently, we characterized the RNA editomes of CV and GF groups, each...
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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
...that different lineages of Blastocystis have varied ecological roles in the host gut.The vertebrate gut is host to a diverse ecosystem of bacteria, archaea, viruses, and microbial eukaryotes. This diverse microbial community has broad impacts on the physiology and development of the host. Gut microbes can...
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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
...microbial community before, during, and after antibiotic treatment.View larger version: In this window In a new window Figure 1. Read cloud sequencing of the gut microbiome of a single individual during disease, antibiotic treatment, and recovery. (A) Study design. Linked-read metagenomic sequencing...
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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
...chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host cytokines and chemokines were analyzed across 23 children with caries and 24 children with healthy dentition...
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Method: Microbial strain-level population structure and genetic diversity from metagenomes
- Duy Tin Truong,
- Adrian Tett,
- Edoardo Pasolli,
- Curtis Huttenhower,
- and Nicola Segata
Genome Res. April 2017 27: 626-638; Published in Advance February 6, 2017, doi:10.1101/gr.216242.116
...microbiome will require analysis of each community’s microbial strain population, ideally in high-throughput from culture-independent sequencing. Advances inmeta bioinformatics over the last decade have refined the resolution of microbial community taxonomic profiling from the phylum to the species...
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Method: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- Donovan H. Parks,
- Michael Imelfort,
- Connor T. Skennerton,
- Philip Hugenholtz,
- and Gene W. Tyson
Genome Res. July 2015 25: 1043-1055; Published in Advance May 14, 2015, doi:10.1101/gr.186072.114
...and demonstrate that s obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft s, we propose an objective measure of quality that can be used to select s suitable for specific gene- and -centric analyses of microbial communities. [Supplemental...
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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
...of microbial communities. However, techniques such as metagenomic and metatranscriptomic sequencing will become more widely employed, given the rich data sets gained from these techniques and their potential for functional insights. Herewe have identified challenges and opportunities for skin microbiome...
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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
...of their microbial community, host factors, and immunity. Genome-wide surveys of the microbes inhabiting the different microenvironments of the human body (e.g., gut, skin, oral) (The Human Microbiome Project Consortium 2012), model organisms (Chung et al. 2012), and geographic regions (Yatsunenko et al. 2012) have...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...expected per human (The 1000 Genomes Project Consortium 2015). Tools that detect SNVs and indels are broadly categorized into two major approaches: traditional statistical methods and machine learning-based techniques. An example of a statistical method is Longshot, which utilizes the Pair-Hidden Markov...

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