ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization

Yang, Chao; Mai, Jiahao; Cao, Xuan; Cominelli, Fabio; Zhang, Liangliang

doi:10.1093/bioinformatics/btad470

Cited by 53 publications

(20 citation statements)

References 30 publications

(33 reference statements)

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“… 107 Functional abundances were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) 108 and visualized using the R package ggpicrust2. 109 16S sequencing data were deposited in the NCBI BioProject: PRJNA900580.…”

Section: Methodsmentioning

confidence: 99%

Hyperbaric oxygen augments susceptibility to C. difficile infection by impairing gut microbiota ability to stimulate the HIF-1α-IL-22 axis in ILC3

Fachi,

Pral,

Assis

et al. 2024

Gut Microbes

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Hyperbaric oxygen (HBO) therapy is a well-established method for improving tissue oxygenation and is typically used for the treatment of various inflammatory conditions, including infectious diseases. However, its effect on the intestinal mucosa, a microenvironment known to be physiologically hypoxic, remains unclear. Here, we demonstrated that daily treatment with hyperbaric oxygen affects gut microbiome composition, worsening antibiotic-induced dysbiosis. Accordingly, HBO-treated mice were more susceptible to Clostridioides difficile infection (CDI), an enteric pathogen highly associated with antibiotic-induced colitis. These observations were closely linked with a decline in the level of microbiota-derived short-chain fatty acids (SCFAs). Butyrate, a SCFA produced primarily by anaerobic microbial species, mitigated HBO-induced susceptibility to CDI and increased epithelial barrier integrity by improving group 3 innate lymphoid cell (ILC3) responses. Mice displaying tissue-specific deletion of HIF-1 in RORγt-positive cells exhibited no protective effect of butyrate during CDI. In contrast, the reinforcement of HIF-1 signaling in RORγt-positive cells through the conditional deletion of VHL mitigated disease outcome, even after HBO therapy. Taken together, we conclude that HBO induces intestinal dysbiosis and impairs the production of SCFAs affecting the HIF-1α-IL-22 axis in ILC3 and worsening the response of mice to subsequent C. difficile infection.

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Section: Methodsmentioning

confidence: 99%

Hyperbaric oxygen augments susceptibility to C. difficile infection by impairing gut microbiota ability to stimulate the HIF-1α-IL-22 axis in ILC3

Fachi,

Pral,

Assis

et al. 2024

Gut Microbes

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show abstract

“…The functional genes were then mapped to their respective KO functions (KEGG level 4 classification unit) and the associated KEGG pathway (KEGG level 3 classification unit). We used the ggpicrust2 package (v1.7.2) for statistical analysis and visualization after obtaining the community functional abundance table (Yang et al., 2023).…”

Section: Methodsmentioning

confidence: 99%

Natural mating ability is associated with gut microbiota composition and function in captive male giant pandas

Yan,

Lei,

Zhao

et al. 2024

Ecology and Evolution

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The issue of poor sexual performance of some male giant pandas seriously impairs the growth and the genetic diversity of the captive population, yet there is still no clear understanding of the cause of the loss of this ability and its underlying mechanism. In this study, we analyzed the gut microbiota and its function in 72 fecal samples obtained from 20 captive male giant pandas, with an equal allocation between individuals capable and incapable of natural mating. Additionally, we investigated fecal hormone levels and behavioral differences between the two groups. A correlation analysis was then conducted among these factors to explore the influencing factors of their natural mating ability. The results showed significant differences in the composition of gut microbiota between the two groups of male pandas. The capable group had significantly higher abundance of Clostridium sensu stricto 1 (padjusted = .0021, GLMM), which was positively correlated with fatty acid degradation and two‐component system functions (Spearman, padjusted < .05). Additionally, the capable group showed higher gene abundance in gut microbiota function including purine and pyrimidine metabolism and galactose metabolism, as well as pathways related to biological processes such as ribosome and homologous recombination (DEseq2, padjusted < .05). We found no significant differences in fecal cortisol and testosterone levels between the two groups, and no difference was found in their behavior either. Our study provides a theoretical and practical basis for further studying the behavioral degradation mechanisms of giant pandas and other endangered mammal species.

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“…MetaCyc functional pathways and associated abundance were inferred from EC number abundances 96 . Differential abundance testing of functional pathways between tolerant and non-tolerant mice was analyzed and visualized using the R package ggpicrust2 (v1.7.3) 97 .…”

Section: Methodsmentioning

confidence: 99%

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic voluntary morphine

Sall,

Foxall,

Felth

et al. 2024

Preprint

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The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance which could be influenced by differences in microbiota, and yet no study has capitalized upon this natural variation to identify specific features linked to tolerance. We leveraged this natural variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar and predictive morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained differences in the development in tolerance. Mice that did not develop tolerance also maintained a higher abundance of taxa capable of producing the short-chain fatty acid (SCFA) butyrate, known to bolster intestinal barriers, suppress inflammation, and promote neuronal homeostasis. Furthermore, dietary butyrate supplementation significantly reduced the development of tolerance. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.

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ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization

Cited by 53 publications

References 30 publications

Hyperbaric oxygen augments susceptibility to C. difficile infection by impairing gut microbiota ability to stimulate the HIF-1α-IL-22 axis in ILC3

Hyperbaric oxygen augments susceptibility to C. difficile infection by impairing gut microbiota ability to stimulate the HIF-1α-IL-22 axis in ILC3

Natural mating ability is associated with gut microbiota composition and function in captive male giant pandas

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic voluntary morphine

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