Author

S. M. Gibbons

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 8 Ecology· 2 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 10 Research Focus:cell type annotation· 8 Assay:metagenomics· 8 Approach:statistical model· 7 Approach:experimental assay· 5 Research Focus:differential expression· 4 Research Focus:clustering· 3 Research Focus:host-pathogen & immune response· 3

Frequent Co-Authors

C. Diener· 6 shared E. J. Alm· 4 shared M. Poyet· 3 shared N. S. Baliga· 3 shared J. J. Valenzuela· 2 shared J. Wilson· 2 shared M. Groussin· 2 shared R. J. Xavier· 2 shared

Activity by Year

2017-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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6 shared papersMicrobiology

C. Diener

Mutual co-authors in cluster

Author profile →

11 papers

Recent·Most cited

Disease-specific loss of microbial cross-feeding interactions in the human gut

V. Rossetto Marcelino, C. Welsh, C. Diener, E. L. Gulliver, E. L. Rutten, R. B. Young, E. M. Giles, S. M. Gibbons, C. Greening, S. C. Forster

The paper introduces a Metabolite Exchange Score to quantify microbial cross-feeding interactions in the gut and identifies disease-specific disruptions in these interactions.

Nature Communications · Oct 20, 2023Peer-reviewedMicrobiology

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease.

N. Quinn-Bohmann, J. A. Freixas-Coutin, J. Seo, R. Simmons, C. Diener, S. M. Gibbons

This study performs a meta-analysis of URT microbiome data to identify consistent taxonomic associations with health and disease across multiple respiratory conditions.

bioRxiv · Aug 10, 2023Microbiology

Island biogeography theory and the gut: why taller people tend to harbor more diverse gut microbiomes.

K. Ramos Sarmiento, A. Carr, C. Diener, K. J. Locey, S. M. Gibbons

The paper shows a positive association between human height and gut microbiome diversity, linking it to CDI risk and suggesting vegetable intake can mitigate this effect.

bioRxiv · Aug 8, 2023 · PreprintEcology

Origin of biogeographically distinct ecotypes during laboratory evolution

N. S. Baliga, J. J. Valenzuela, S. R. C. Immanuel, J. Wilson, S. Turkarslan, M. Ruiz, S. M. Gibbons, K. A. Hunt, M. Auer, M. Zemla, D. A. Stahl

This study shows how mutations in microbial species lead to resource partitioning and improved community productivity in a simulated subsurface environment.

bioRxiv · May 19, 2023Microbiology

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes.

J. J. Lim, C. Diener, J. Wilson, J. J. Valenzuela, N. S. Baliga, S. M. Gibbons

This paper estimates growth phases of gut bacterial populations in human stool metagenomes using a steady-state flow-through model, finding slower defecation correlates with more taxa in later growth phases.

bioRxiv · Apr 23, 2022Ecology

Weight loss response following lifestyle intervention associated with baseline gut metagenomic signature in humans

C. Diener, S. Qin, Y. Zhou, S. Patwardhan, L. Tang, J. Lovejoy, A. T. Magis, N. D. Price, L. Hood, S. M. Gibbons

The paper analyzes weight loss outcomes in response to a lifestyle intervention and identifies baseline gut metagenomic features associated with weight loss in humans.

bioRxiv · Jan 5, 2021Microbiology

Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome

M. Groussin, M. Poyet, A. Sistiaga, S. M. Kearney, K. Moniz, M. Noel, J. Hooker, S. M. Gibbons, L. Segurel, A. Froment, R. Said Mohamed, A. Fezeu, V. A. Juimo, C. Girard, L. T. T. Nguyen, , E. J. Alm

The paper shows that horizontal gene transfer in the human microbiome is more common within the same host and is linked to industrialization and lifestyle factors.

bioRxiv · Jan 28, 2020Microbiology

Negative plant-microbiome feedback limits productivity in aquaponics

J. A. Day, A. E. Otwell, C. Diener, K. E. Tams, B. M. Bebout, A. M. Detweiler, M. D. Lee, M. T. Scott, W. Ta, M. Ha, S. A. Carreon, K. Tong, A. A. Ali, S. M. Gibbons, N. S. Baliga

This study shows that transferring established microbiomes to aquaponic systems reduces lettuce growth due to pathogen enrichment, highlighting negative feedback mechanisms similar to soil ecology.

bioRxiv · Aug 28, 2019 · PreprintMicrobiology

Adaptive evolution within the gut microbiome of individual people

S. Zhao, T. D. Lieberman, M. Poyet, M. Groussin, S. M. Gibbons, R. J. Xavier, E. J. Alm

This study tracks genetic adaptation of B. fragilis in individual human gut microbiomes over time, revealing persistent evolutionary dynamics and niche differentiation within a single host.

bioRxiv · Mar 9, 2018Evolutionary Biology

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

S. M. Kearney, S. M. Gibbons, M. Poyet, T. Gurry, K. Bullock, J. Allegretti, C. Clish, E. J. Alm

The paper identifies variation in endospore and stress-resistant bacterial states across individuals and over time, showing their role in cross-host dissemination and response to dietary fatty acids.

bioRxiv · Feb 19, 2018Microbiology

Meta Analysis Of Microbiome Studies Identifies Shared And Disease-Specific Patterns

C. Duvallet, S. M. Gibbons, T. Gurry, R. A. Irizarry, E. J. Alm

The paper performs a meta-analysis of microbiome studies to identify shared and disease-specific patterns, finding common core microbes associated with multiple diseases.

bioRxiv · May 8, 2017Microbiology