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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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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
..., operons, or plasmids (Tettelin et al. 2005). Although these genomic features can be accurately characterized in microbial isolates, they have been difficult to study using culture-independent approaches, despite thousands of human-associated metas being available. Translational applications of the human...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...the sequence correlations among these s, potentially introducing ambiguity and biases in metagenomic profiling. Here, we present PanTax, a pan graph-based taxonomic profiler that overcomes the shortcomings of sequence-based approaches, because pan graphs possess the capability to depict the full range...
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Method: Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
- Ilya B. Slizovskiy,
- Nathalie Bonin,
- Jonathan E. Bravo,
- Peter M. Ferm,
- Jacob Singer,
- Christina Boucher,
- and Noelle R. Noyes
Genome Res. November 2024 34: 2048-2060; Published in Advance November 5, 2024, doi:10.1101/gr.279226.124
..., and a mock human gut microbial community, allowing us to examine variables including genomic DNA input and probe set composition. Our findings demonstrated that TELSeq markedly improves the detection rates of ARGs and MGEs compared to traditional sequencing methods, underlining its potential for accurate AMR...
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Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
- Samuel T. Horsfield,
- Basil C.T. Fok,
- Yuhan Fu,
- Paul Turner,
- John A. Lees,
- and Nicholas J. Croucher
Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
..., ejecting the fragment (Payne et al. 2021). NAS increases target sequence yield by rejecting nontarget DNA, increasing the sensitivity for detecting of sequences of interest (Payne et al. 2021; Weilguny et al. 2023). This makes NAS well-suited for metagenomics, the culture-free DNA sequencing-based analysis...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...for enriching low-abundance microorganisms in diverse environmental samples, which could advance our understanding of the microbial diversity and ecological dynamics in complex ecosystems.ResultsH. mediterrane enrichment in a mock communityTo evaluate the performance of enriching low-abundance species with RU...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...-model for prediction. Inference. In the inference step, we take the tensor-like representation of the 100 bp window with potential sequencing errors and use that as an input to the encoder-only transformer model. The model predicts a sequence based on the read alignments. We then compare the predicted sequence...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...protocol and computational methods for assembly are available in the Supplemental Methods. Evaluation of properties (N50, contig count, etc.) was performed with QUAST v5.2.0 (Gurevich et al. 2013). Sequencing depth of the read sets was approximated by counting the total number of sequenced bases for each...
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Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
..., the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as -resolved metagenomics, can circumvent this limitation by obtaining meta...
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