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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
...rates over the first month of life Figure 1. Compositional profile of microbial communities colonizing themouth, skin, and gut of two premature infants. Each colored box represents the percentage of nonhuman reads mapping to an assembled , and the stacked boxes for each sample show the fraction...
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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
...-based host– microbe research and future prospects for the field. The ecology of the human skin In 1954, Albert Kligman and Donald Pillsbury, two renowned dermatologists at the University of Pennsylvania who pioneered many of the seminal culture-based studies of the skin microbiota, stated, “a great deal more...
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Research: Genetic and environmental control of host-gut microbiota interactions
- Elin Org,
- Brian W. Parks,
- Jong Wha J. Joo,
- Benjamin Emert,
- William Schwartzman,
- Eun Yong Kang,
- Margarete Mehrabian,
- Calvin Pan,
- Rob Knight,
- Robert Gunsalus,
- Thomas A. Drake,
- Eleazar Eskin,
- and Aldons J. Lusis
Genome Res. October 2015 25: 1558-1569; Published in Advance August 10, 2015, doi:10.1101/gr.194118.115
...Corresponding author: jlusis@mednet.ucla.edu Abstract Genetics provides a potentially powerful approach to dissect host-gut microbiota interactions. Toward this end, we profiled gut microbiota using 16s rRNA gene sequencing in a panel of 110 diverse inbred strains of mice. This panel has previously...
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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
...Strain-level metagenomic profiling using pan graphs with PanTax Wenhai Zhang1,2,5, Yuansheng Liu3,5, Guangyi Li2,5, Jialu Xu2, Enlian Chen2, Alexander Schönhuth4 and Xiao Luo1,2 1Hunan Research Center of the Basic Discipline for Cell Signaling, Hunan University, Changsha, Hunan 410082, China; 2...
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Research: Meta-analyses of studies of the human microbiota
- Catherine A. Lozupone,
- Jesse Stombaugh,
- Antonio Gonzalez,
- Gail Ackermann,
- Doug Wendel,
- Yoshiki Vázquez-Baeza,
- Janet K. Jansson,
- Jeffrey I. Gordon,
- and Rob Knight
Genome Res. October 2013 23: 1704-1714; Published in Advance July 16, 2013, doi:10.1101/gr.151803.112
...a relatively stable adult-like configuration is established. Our results further show that the early gut microbiota more closely resembles other body sites, including the vagina and skin, than the fecal microbiota of Western adults. This is consistent with studies of the effects of delivery mode...
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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
...understanding of host–microbiome interactions, suggesting a bidirectional dialogue between skin commensals and the host organism. [Supplemental material is available for this article.] Although the relationships between microbiota, host, and disease are complex, investigators have long relied upon Koch...
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Method: Robust 16S rRNA classification based on a compressed LCA index
- Omar Ahmed,
- Christina Boucher,
- and Ben Langmead
Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
.... But the data structures that link pattern sequences to their clades of origin still do not scale well to large collections. Previous work proposed the document array profiles, which use words of space, where r is the number of maximal equal-letter runs in the Burrows–Wheeler transform, and d is the number...
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Research: Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants
- Juan Deng,
- Ya-Jing Liu,
- Wen-Tian Wei,
- Qi-Xuan Huang,
- Li-Ping Zhao,
- Ling-Yun Luo,
- Qi Zhu,
- Lin Zhang,
- Yuan Chen,
- Yan-Ling Ren,
- Shan-Gang Jia,
- Yu-Luan Lin,
- Ji Yang,
- Feng-Hua Lv,
- Hong-Ping Zhang,
- Feng-E Li,
- Li Li,
- and Meng-Hua Li
Genome Res. October 2023 33: 1690-1707; Published in Advance October 26, 2023, doi:10.1101/gr.278239.123
...of the rumen have not been constructed, nor have the interactions between the ruminal microbiota and epithelial cells of the host been explored.To this end, we performed integrated profiling of the single-cell transcriptomes of ruminal cells and metas of the rumen microbial community in sheep and goats over...
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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
...that eating activity markedly perturbed the salivary microbiota, with tongue-specific Campylobacter concisus and Oribacterium sinus and dental plaque-specific Lautropia mirabilis, Rothia aeria, and Neisseria oralis increased after every meal in a temporal order. The observation was reproducible in multiple...
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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
...on contributions of unmapped reads. Nubeam is also useful in analyzing 16S rRNA sequencing data, which is a more prevalent type of data set in metagenomics studies. In our analysis, Nubeam recapitulated the findings that natural microbiota in mouse gut are resilient under challenges, and Nubeam detected...
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