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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
...areas of microbial evolution.Metagenomic sequencing preserves the majority of the genetic information and enables a strain-level analysis of microbial communities. This establishes significant advantages over amplicon sequencing and culture-based methods, because these two approaches, by design...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding...
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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
...and Banfield 2008; Sun et al. 2016) where spacers reflect exposures to phage and plasmids in a whole community metagenomic data set.The goal of this work was to survey the content and functional potential of microbial communities during gestation. We describe the vaginal, gut, and oral microbiomes from 10...
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Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
...Material, “Growth dynamics” (Supplemental Fig. S17), illustrates that this analysis represents yet another benefit of “complete metagenomics.”Phasing identified mutationsThe ability to call many mutations with controlled FDR in a contig is essential for phasing the strain-level haplotypes represented...
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Resource: Using populations of human and microbial genomes for organism detection in metagenomes
- Sasha K. Ames,
- Shea N. Gardner,
- Jose Manuel Marti,
- Tom R. Slezak,
- Maya B. Gokhale,
- and Jonathan E. Allen
Genome Res. July 2015 25: 1056-1067; Published in Advance April 29, 2015, doi:10.1101/gr.184879.114
...containing large amounts of human sequence, misidentification of these human reads can lead to costly and inaccurate downstream reporting of a sample’s microbial contents. New detailed genus, species, and strain-level taxonomic profiles, plasmid, and gene profiles for all HMP samples are made available along...
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Method: Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
- John Beaulaurier,
- Elaine Luo,
- John M. Eppley,
- Paul Den Uyl,
- Xiaoguang Dai,
- Andrew Burger,
- Daniel J. Turner,
- Matthew Pendelton,
- Sissel Juul,
- Eoghan Harrington,
- and Edward F. DeLong
Genome Res. March 2020 30: 437-446; Published in Advance February 19, 2020, doi:10.1101/gr.251686.119
...totaling <1.5 kb. We successfully preserved these strain-level differences in the polished s produced from the pipeline (Supplemental Fig. S2).The only two reference s that could not be recapitulated from the mock community were nearly identical to two of the polished s except for minor circular...
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Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
- Jens-Uwe Ulrich and
- Bernhard Y. Renard
Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
...al. 2015). Although Centrifuge was initially developed to analyze short-read metagenomic samples, MetaMaps specifically addresses the task of strain-level metagenomic assignment of long reads. We decided to use both tools and Kraken2 with default parameter configurations because this results...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
.... Highlighted haplotypes have >99% identity to the reference.Mussel-bacteria symbiont community with 11 estimated strainsAnsorge et al. (2019) investigated the strain-level diversity of an intracellular, sulfur-oxidizing bacterial symbiont community within deep-sea mussels. They sequenced one sample using...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
.... Nonetheless, bacteria offer several unique avenues for research into the process and mechanics of gene birth at a resolution not feasible in other organisms. Both their amenability to experimental evolutionary analysis and their strain-level variation in gene content foster investigations of how noncoding...
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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
...al. 2019). However, because these previous studies have included relatively few time points per host, or relatively shallow sampling of their microbiota, the population genetic processes that drive these strain-level dynamics remain poorly characterized. Understanding how the forces of mutation...
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