ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram

Gao, Chunhui; Yu, Guangchuang; Cai, Peng

doi:10.3389/fgene.2021.706907

Cited by 169 publications

(115 citation statements)

References 9 publications

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“…The differentially abundant KEGG orthologues and pathways were evaluated with the ALDEx2 package (v1.22.0) 37 using default parameters. All data except for the LEfSe cladogram were visualized by ggplot2 (v3.3.3) 38 , pheatmap (v1.0.12) 39 , ggtern (v3.3.0) 40 , and ggVennDiagram (v0.3) 41 packages.…”

Section: Methodsmentioning

confidence: 99%

Analysis of colonic mucosa-associated microbiota using endoscopically collected lavage

Miyauchi

Taida

Kawasumi

et al. 2022

Sci Rep

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The bacterial composition of the gut lumen and mucosa is distinct and the mucosa-associated bacteria are thought to play a more critical role in interactions with the host immune system. However, limited studies of the gut mucosal microbiota in humans have been available due to methodological challenges. Here, we evaluated the potential use of colonic lavage samples for mucosal microbiota analysis in humans. Among the different types of colonic mucosal samples collected from healthy volunteers, the lavage samples contained a higher amount of bacterial DNA and were less contaminated with host DNA compared to mucosal brushing (brush) and biopsy. Although 16S gene amplicon sequencing showed that the bacterial composition of the lavage was intermediate between that of feces and biopsy, mucosal bacteria abundant in the biopsy were also enriched in lavage samples. Furthermore, differences in mucosal microbes between non-smokers and smokers were detectable in lavage samples. Our data emphasize that colonic lavage is suitable for analysis of the mucosal microbiota. Given its minimal invasiveness and high bacterial DNA content, the colonic lavage will promote research on the human mucosal microbiota, especially in gastrointestinal disorders.

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Section: Methodsmentioning

confidence: 99%

Analysis of colonic mucosa-associated microbiota using endoscopically collected lavage

Miyauchi

Taida

Kawasumi

et al. 2022

Sci Rep

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“…These ASVs represented only 4.3% of identified ASVs and 0.16% of the mean relative abundance of the dataset. Alpha and beta diversity measures (including UniFrac ( Lozupone & Knight, 2005 )) were calculated in R using phyloseq, and figures were plotted using ggplot2 ( Wickham, 2016 ) and ggVennDiagram ( Gao, Yu & Cai, 2021 ). Compositional analysis of the community was done using ANCOM-II in R (ANCOM v2.1 ( Kaul et al, 2017 ) in R v.4.0.3).…”

Section: Methodsmentioning

confidence: 99%

“…The analysis was performed at the rarefied genus level for the proximal colon and distal colon samples only. For the venn and euler diagrams, ASVs needed more than 2 reads assigned at a given site (between two replicates) to be considered detected, and were then plotted using ggVenDiagram ( Gao, Yu & Cai, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Microbial biogeography of the wombat gastrointestinal tract

Eisenhofer

D’Agnese

Taggart

et al. 2022

PeerJ

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Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region—the putative site of primary plant fermentation in wombats—are distinct from the distal colon, and that faecal samples may have limitations in capturing the diversity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account.

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“…We also compared them with a list of genes that are directly upregulated by VND7 and its homologs (Xu et al, 2014) to verify whether they were direct targets of VND7. Venn diagrams were established using the R package “ggVennDiagram” (Gao et al., 2021).…”

Section: Methodsmentioning

confidence: 99%

Plant secondary cell wall proteome analysis with an inducible system for xylem vessel cell differentiation

et al. 2021

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Plant cell walls are typically composed of polysaccharide polymers and cell wall proteins (CWPs). CWPs account for approximately 10% of the plant cell wall structure and perform a wide range of functions. Previous studies have identified approximately 1000 CWPs in the model plant Arabidopsis thaliana; however, the analyses mainly targeted primary cell walls, which are generated at cell division. In contrast, little is known about CWPs in secondary cell walls (SCWs), which are rigid and contain the phenolic polymer lignin. Here, we performed a cell wall proteome analysis to obtain novel insights into CWPs in SCWs. To this end, we tested multiple methods for cell wall extraction with cultured Arabidopsis cells carrying the VND7‐VP16‐GR system, with which cells can be transdifferentiated into xylem‐vessel‐like cells with lignified SCWs by dexamethasone treatment. We then subjected the protein samples to in‐gel trypsin digestion followed by LC‐MS/MS analysis. The different extraction methods resulted in the detection of different cell wall fraction proteins (CWFPs). In particular, centrifugation conditions had a strong impact on the extracted CWFP species, resulting in the increased number of identified CWFPs. We successfully identified 896 proteins as CWFPs in total, including proteases, expansins, purple phosphatase, well‐known lignin‐related enzymes (laccase and peroxidase), and 683 of 896 proteins were newly identified CWFPs. These results demonstrate the usefulness of our CWP analysis method. Further analyses of SCW‐related CWPs could be expected to produce information useful for understanding the roles of CWPs in plant cell functions.

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ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram

Cited by 169 publications

References 9 publications

Analysis of colonic mucosa-associated microbiota using endoscopically collected lavage

Analysis of colonic mucosa-associated microbiota using endoscopically collected lavage

Microbial biogeography of the wombat gastrointestinal tract

Plant secondary cell wall proteome analysis with an inducible system for xylem vessel cell differentiation

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