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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
...of these evolutionary changes occur in parallel across infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...findings by searching a third phage database (Shah et al. 2023), which is smaller but manually curated and was built from samples taken from infant guts. We observed similar patterns as for the larger databases, confirming that the proportion of SSOGs (and more generally, less conserved genes...
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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
...that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole- average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter...
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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
...that the subject's gut microbial community contained 66 bacterial species with median relative abundance >10−5, all but one of which exceeded 0.1% frequency in at least one time point (Fig. 1B; Methods). Consistent with previous studies (Danko et al. 2019), we found that the extensive taxonomic diversity...
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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
...) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity...
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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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Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
- Alexey Vorobev,
- Marion Dupouy,
- Quentin Carradec,
- Tom O. Delmont,
- Anita Annamalé,
- Patrick Wincker,
- and Eric Pelletier
Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
...been developed to shift the scientific paradigm from a gene-centric to an organism-centric view of environmental genomic and transcriptomic data. These methods use direct assemblies of metagenomic reads to generate contigs that encompass several genes. High recovery of bacterial and archaeal s has been...
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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
...the genetic variability of gut microbes, with Bacteroides species appearing remarkably consistent (0.45% median number of nucleotide variants between strains), whereas P. copri was among the most plastic gut colonizers. We thus characterize here the population genetics of previously inaccessible intestinal...
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Method: Genome-reconstruction for eukaryotes from complex natural microbial communities
- Patrick T. West,
- Alexander J. Probst,
- Igor V. Grigoriev,
- Brian C. Thomas,
- and Jillian F. Banfield
Genome Res. April 2018 28: 569-580; Published in Advance March 1, 2018, doi:10.1101/gr.228429.117
...environmental samples, many of which came from groundwater. In addition, we investigated previously published metas from infant fecal samples and a bioreactor community used to break down thiocyanate. Because the approach works regardless of a predetermined phylogenetic affiliation, it is now possible...
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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
...(Markowitz et al. 2014); Sludge bioreactor (Albertsen et al. 2013); Acid mine drainage (Tyson et al. 2004); Infant gut (Sharon et al. 2013); Acetate-amended aquifer (Wrighton et al. 2012); IMG (Markowitz et al. 2014). GEBA-RNB s were produced by the US Department of Energy Joint Genome Institute. a...
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