GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

Chen, Li; Reeve, James; Zhang, Lujun; Huang, Shengbing; Wang, Xuefeng; Chen, Jun

doi:10.7717/peerj.4600

Cited by 174 publications

(117 citation statements)

References 26 publications

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“…For alpha diversity measures, each sample was rarefied down to 15,000 sequences. For analyses other than alpha diversity, a normalization method for zero-inflated sequencing data (GMPR) was used (Chen et al, 2018). The function "estimate_richness" from the R package "phyloseq v1.22.3" (McMurdie and Holmes, 2013) was used to estimate Chao1 and Shannon alpha-diversity measures.…”

Section: Discussionmentioning

confidence: 99%

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar

et al. 2020

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Plant-associated microbial communities play a central role in the plant response to biotic and abiotic stimuli, improving plant fitness under challenging growing conditions. Many studies have focused on the characterization of changes in abundance and composition of root-associated microbial communities as a consequence of the plant response to abiotic factors such as altered soil nutrients and drought. However, changes in composition in response to abiotic factors are still poorly understood concerning the endophytic community associated to the phyllosphere, the above-ground plant tissues. In the present study, we applied high-throughput 16S rDNA gene sequencing of the phyllosphere endophytic bacterial communities colonizing wild Populus trichocarpa (black cottonwood) plants growing in native, nutrient-limited environments characterized by hot-dry (xeric) riparian zones (Yakima River, WA), riparian zones with mid hot-dry (Tieton and Teanaway Rivers, WA) and moist (mesic) climates (Snoqualmie, Skykomish and Skagit Rivers, WA). From sequencing data, 587 Amplicon Sequence Variants (ASV) were identified. Surprisingly, our data show that a core microbiome could be found in phyllosphere-associated endophytic communities in trees growing on opposite sides of the Cascades Mountain Range. Considering only taxa appearing in at least 90% of all samples within each climatic zone, the core microbiome was dominated only by two ASVs affiliated Pseudomonadaceae and two ASVs of the Enterobacteriaceae family. Alpha-diversity measures indicated that plants colonizing hot-dry environments showed a lower diversity than those from mid hot-dry and moist climates. Beta-diversity measures showed that bacterial composition was significantly different across sampling sites. Accordingly, we found that specific ASV affiliated to Pseudomonadaceae and Enterobacteriaceae were significantly more abundant in the phyllosphere endophytic community colonizing plants adapted to the xeric environment. In summary, this study highlights that sampling site is the major driver of variation and that only a few ASV showed a distribution that significantly correlated to climate variables.

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Section: Discussionmentioning

confidence: 99%

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar

et al. 2020

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“…The literature abounds in differential analysis methods dedicated to abundance data (Soneson and Delorenzi, 2013). Most of them differ in the normalization and preprocessing steps (Dillies et al, 2013;Chen et al, 2018). Count data coming from metagenomic studies are very similar to those found in RNA-Seq studies.…”

Section: Differential Abundances Studiesmentioning

confidence: 99%

Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control

et al. 2020

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We consider the problem of incorporating evolutionary information (e.g., taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierarchical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p-values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non-hierarchical, Benjamini-Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierarchical structure with profit but do not control the False Discovery Rate (FDR) a priori and remain inferior to a classical Benjamini-Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Intuition advocates that the use of hierarchical structures should increase the detection rate of differentially abundant taxa in microbiome studies. However, our results suggest that current hierarchical procedures are still inferior to standard methods and more effective procedures remain to be invented.

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“…iterations, to account for library size differences, while for beta-diversity analysis library size normalisation was done using GMPR (Chen et al, 2018). The ACE richness estimate (O'Hara, 2005) and Shannon's H diversity index were calculated using function EstimateR in the vegan package (Oksanen et al, 2018) and tested using ANOVA and Tukey HSD in the stats package.…”

Section: Sequence Processing and Analysis Of Bacterial Communities 30mentioning

confidence: 99%

The origin and role of biological rock crusts in rocky desert weathering

Wieler¹,

Gillor²,

Angel³

2018

Preprint

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<p><strong>Abstract.</strong> In drylands, microbes that colonise rock surfaces were linked to erosion because water scarcity excludes traditional weathering mechanisms. We studied the origin and role of rock biofilms in geomorphic processes of hard lime and dolomitic rocks that feature comparable weathering morphologies though originating from arid and hyperarid environments, respectively. We hypothesised that weathering patterns are fashioned by salt erosion and mediated by the rock biofilms that originate from the adjacent soil and dust. We used a combination of microbial and geological techniques to characterise rocks morphologies and the origin and diversity of their biofilm. Amplicon sequencing of the SSU rRNA gene suggested that bacterial diversity is low and dominated by Proteobacteria and Actinobacteria. These phyla formed laminar biofilms only on rock surfaces that were exposed to the atmosphere and burrowed up to 6&#8201;mm beneath the surface, protected by sedimentary deposits. Unexpectedly, the microbial composition of the biofilms differed between the two rock types and was also distinct from the communities identified in the adjacent soil and settled dust, showing a habitat-specific filtering effect. Moreover, the rock bacterial communities were shown to secrete extracellular polymeric substances that form an evaporation barrier, reducing water loss rates by 65&#8211;75&#8201;%. The reduced water transport rates through the rock also limit salt transport and its crystallisation in surface pores, which is thought to be the main force for weathering. Concomitantly, the biofilm layer stabilises the rock surface via coating and protects the weathered front. Our hypothesis contradicts common models, which typically consider biofilms as weathering-promoting agents. In contrast, we propose the microbial colonisation of mineral surfaces acts to mitigate geomorphic processes in hot, arid environments.</p>

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GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

Cited by 174 publications

References 26 publications

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar

Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control

The origin and role of biological rock crusts in rocky desert weathering

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