EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Cantrell, Kalen; Fedarko, Marcus W.; Rahman, Gibraan; McDonald, Daniel; Yang, Yimeng; Zaw, Thant; González, Antonio; Estaki, Mehrbod; Haiminen, Niina; Beck, Kristen L.; Zhu, Qiyun; Sayyari, Erfan; Morton, James T.; Armstrong, George E.; Tripathi, Anupriya; Gauglitz, Julia M.; Marotz, Clarisse; Matteson, Nathaniel L.; Martino, Cameron; Sanders, Jon G.; Carrieri, Anna Paola; Song, Se Jin; Swafford, Austin D.; Dorrestein, Pieter C.; Andersen, Kristian G.; Parida, Laxmi; Kim, Ho Cheol; Vázquez-Baeza, Yoshiki; Knight, Rob

doi:10.1128/msystems.01216-20

Cited by 41 publications

(30 citation statements)

References 44 publications

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“…Trees were subsequently pruned in R using the package “phytools” ( Revell, 2012 ) to remove reference sequences. Trees and distributions of ASVs were plotted with EMPress ( Cantrell et al, 2021 ) as implemented in QIIME2.…”

Section: Methodsmentioning

confidence: 99%

Robustness of Mammalian Gut Microbiota to Humanization in Captivity

Trevelline

Moeller

2022

Front. Ecol. Evol.

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In mammals, the composition of the gut microbiota is associated with host phylogenetic history, and host-lineage specific microbiota have been shown, in some cases, to contribute to fitness-related traits of their hosts. However, in primates, captivity can disrupt the native microbiota through a process of humanization in which captive hosts acquire gut microbiota constituents found in humans. Despite the potential importance of this process for the health of captive hosts, the degree to which captivity humanizes the gut microbiota of other mammalian taxa has not been explored. Here, we analyzed hundreds of published gut microbiota profiles generated from wild and captive hosts spanning seven mammalian families to investigate the extent of humanization of the gut microbiota in captivity across the mammalian phylogeny. Comparisons of these hosts revealed compositional convergence between captive mammal and human gut microbiota in the majority of mammalian families examined. This convergence was driven by a diversity of microbial lineages, including members of the Archaea, Clostridium, and Bacteroides. However, the gut microbiota of two families—Giraffidae and Bovidae—were remarkably robust to humanization in captivity, showing no evidence of gut microbiota acquisition from humans relative to their wild confamiliars. These results demonstrate that humanization of the gut microbiota is widespread in captive mammals, but that certain mammalian lineages are resistant to colonization by human-associated gut bacteria.

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Section: Methodsmentioning

confidence: 99%

Robustness of Mammalian Gut Microbiota to Humanization in Captivity

Trevelline

Moeller

2022

Front. Ecol. Evol.

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“…Moreover, the potential microbiota phenotypes were predicted by BugBase pipeline ( 39 ). EMPress ( 40 ), forestplot , and ggplot2 ( 41 ) R packages were used for visualizations.…”

Section: Methodsmentioning

confidence: 99%

Axillary Microbiota Is Associated with Cognitive Impairment in Parkinson’s Disease Patients

et al. 2022

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“…A phylogeny of all ASVs was generated using SEPP insertion against the Greengenes 13.8 reference. The ASVs that were shared by urban wildlife and humans but not by non-urban wildlife were identified in R, and the phylogenetic distributions of these ASVs were plotted with empress (19).…”

Section: Phylogenetic Analyses Of Asvsmentioning

confidence: 99%

“…Three microbial genera-Clostridium sensu stricto 1, Blautia, and Bacteroides-included >5 ASVs that displayed this pattern. The phylogenetic distributions of these ASVs visualized with Empress (19) are presented in Figure 2-figure supplement 1.…”

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confidence: 99%

Humanization of wildlife gut microbiota in urban environments

Dillard

Chung

Gunderson

et al. 2022

Preprint

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Urbanization is rapidly altering Earth’s environments, demanding investigations of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans) and crested anole lizards (Anolis cristatellus) acquire gut microbiota constituents found in humans, including the gut bacterial lineages most significantly associated with urbanization in humans (e.g., Bacteroides). Comparisons of urban and rural wildlife and human populations revealed significant convergence of the gut microbiota among urban host populations. Remarkably, all microbial lineages found in humans that were overrepresented in urban wildlife relative to rural wildlife were also overrepresented in urban humans relative to rural humans. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities.

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Cited by 41 publications

References 44 publications

Robustness of Mammalian Gut Microbiota to Humanization in Captivity

Robustness of Mammalian Gut Microbiota to Humanization in Captivity

Axillary Microbiota Is Associated with Cognitive Impairment in Parkinson’s Disease Patients

Humanization of wildlife gut microbiota in urban environments

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