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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
..., two groups of Asgard archaea, using a combination of metagenomic, metatranscriptomic, and epigenetic approaches. Leveraging complete meta-assembled s and read-based population analyses, we track subtle strain variations of integrated MGEs over a soil depth profile. This approach allows us to establish...
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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
.... 2020; Mitchell et al. 2020). Strain tracking methods using single-nucleotide variants (SNVs) have revealed that mothers (Nayfach et al. 2016; Ferretti et al. 2018; Yassour et al. 2018; Mitchell et al. 2020), the family at large (Korpela et al. 2018; Hildebrand et al. 2021), and hospitals (Raveh...
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Research: Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling
- Yichen Hu,
- Amnon Amir,
- Xiaochang Huang,
- Yan Li,
- Shi Huang,
- Elaine Wolfe,
- Sophie Weiss,
- Rob Knight,
- and Zhenjiang Zech Xu
Genome Res. June 2022 32: 1112-1123; Published in Advance June 10, 2022, doi:10.1101/gr.276482.121
...-occurring patterns in saliva that are associated with the intricate biogeography of the oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to the salivary microbiome were dynamically affected by daily activities, reflecting the role of saliva in exchanging...
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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
...are profiled in each sample by reconstructing a sufficient subset of their s for variant calling, which provides a nucleotide-level consensus sequence for each strain. This is carried out by mapping metagenomic reads against species-specific marker sequences (up to 200 per species from a total set of ∼1...
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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
...sequencing reveals shifts in the genetic composition of 36 species in the same hostThe general pattern of persistence and recovery at the species level is shared by many other classes of antibiotics (Relman and Lipsitch 2018). However, the strain-level dynamics that give rise to this long-term stability...
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Research: Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates
- Matthew R. Olm,
- Christopher T. Brown,
- Brandon Brooks,
- Brian Firek,
- Robyn Baker,
- David Burstein,
- Karina Soenjoyo,
- Brian C. Thomas,
- Michael Morowitz,
- and Jillian F. Banfield
Genome Res. April 2017 27: 601-612; Published in Advance January 10, 2017, doi:10.1101/gr.213256.116
...differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature...
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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
...of Epidemiology and Biostatistics, University of California, San Francisco, California 94158, USA Corresponding author: katherine.pollard@gladstone.ucsf.eduAbstractMetagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across...
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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
...binned together in this MAG across multiple samples from the same person through metagenomic read recruitment. Organizing contigs based on their sequence composition and differential coverage patterns across three samples revealed two distinct clusters (Fig. 3), the smaller one of which contained 11...
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Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
- Hang Dai and
- Yongtao Guan
Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
..., and significant yet moderate correlations for the rest of the body habitats (Supplemental Table S4), revealing the necessity to study the contribution of unmapped reads in metagenomics studies. Lastly, we examined the beta-diversity of whole samples. Figure 6C shows that the clustering of whole samples is also...
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Method: Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
- Jeffrey S. McLean,
- Mary-Jane Lombardo,
- Michael G. Ziegler,
- Mark Novotny,
- Joyclyn Yee-Greenbaum,
- Jonathan H. Badger,
- Glenn Tesler,
- Sergey Nurk,
- Valery Lesin,
- Daniel Brami,
- Adam P. Hall,
- Anna Edlund,
- Lisa Z. Allen,
- Scott Durkin,
- Sharon Reed,
- Francesca Torriani,
- Kenneth H. Nealson,
- Pavel A. Pevzner,
- Robert Friedman,
- J. Craig Venter,
- and Roger S. Lasken
Genome Res. May 2013 23: 867-877; Published in Advance April 5, 2013, doi:10.1101/gr.150433.112
..., culturing will yield only a fraction of the species present, PCR of virulence or marker genes is mainly focused on a handful of known species, and shotgun metagenomics is limited in the ability to detect strain variations. In this study, we present a single-cell genome sequencing approach to address...
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