<i>microeco</i>: an R package for data mining in microbial community ecology

Liu, Chi; Cui, Yaoming; Li, Xiangzhen; Yao, Minjie

doi:10.1093/femsec/fiaa255

Cited by 721 publications

(400 citation statements)

References 26 publications

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“…We used LEfSe to calculate the differential abundance of microbial taxa between upstream (N = 14), downstream (N = 16), at the surface (N = 17) and at the bottom (N = 14) of hippo pools and calculated their effect size 69 . We then calculated the correlation of microbial taxa to the measured biogeochemistry using Pearson's correlation coefficient with a false discovery rate corrected p-value in the microeco R package 70 .…”

Section: Statistical Analysesmentioning

confidence: 99%

The meta-gut: community coalescence of animal gut and environmental microbiomes

Dutton

Subalusky

Sánchez

et al. 2021

Sci Rep

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All animals carry specialized microbiomes, and their gut microbiota are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and alter biogeochemical processes mediated by microbes. We demonstrate this dynamic in the hippopotamus (hippo) and the pools they inhabit. We used natural field gradients and experimental approaches to examine fecal and pool water microbial communities and aquatic biogeochemistry across a range of hippo inputs. Sequencing using 16S RNA methods revealed community coalescence between hippo gut microbiomes and the active microbial communities in hippo pools that received high inputs of hippo feces. The shared microbiome between the hippo gut and the waters into which they excrete constitutes a meta-gut system that could influence the biogeochemistry of recipient ecosystems and provide a reservoir of gut microbiomes that could influence other hosts. We propose that meta-gut dynamics may also occur where other animal species congregate in high densities, particularly in aquatic environments.

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Section: Statistical Analysesmentioning

confidence: 99%

The meta-gut: community coalescence of animal gut and environmental microbiomes

Dutton

Subalusky

Sánchez

et al. 2021

Sci Rep

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“…Data obtained on the occurrence of fungal species (both in fungal isolations and in ITS metabarcoding) and bacterial genera were used to calculate (1) the relative abundance of the most common fungal genera and bacterial phyla, (2) the numbers and proportions of shared and unique fungal species and bacterial genera, and to generate abundance heatmaps (using log10 transformed CFU or sequence data) for all fungal isolates, as well as the most common fungal species and bacterial genera identified from metabarcoding. Abundance was calculated, and heatmaps were constructed in R environment using the microeco [53] and pheatmap [54] packages, respectively. Ecological guilds of fungi detected in NGS analysis were determined according to the FUNGuild database using the FUNguilddedicated python script [55].…”

Section: Dna Extraction and The Metabarcoding Of Fungal Its And Bacterial 16s Ampliconsmentioning

confidence: 99%

Effect of Charcoal on the Properties, Enzyme Activities and Microbial Diversity of Temperate Pine Forest Soils

Lasota

Błońska

Babiak³

et al. 2021

Forests

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Relict charcoal hearths (RCHs) increases soil fertility in forest ecosystems. However, the effects of RCHs on the activity and abundance of soil microorganisms remain unknown. In this paper, we analysed the impact of relict charcoal production on the soil enzymatic activity and composition of soil bacterial and fungal communities in Scots pine forests of the Manowo Forest District in northern Poland. Moreover, we determined the effect of relict charcoal production on the soil properties. Our research was conducted by comparing the physical, chemical, enzymatic and microbiological properties of charcoal-enriched and charcoal-free soils. Significant differences in physical properties were found between these two soil types in terms of their structure and water holding capacity. As expected, horizons enriched with charcoal were characterised by a significantly higher organic carbon content (4.7% on average compared to 2.2% in control horizons), and also by a considerably higher content of available phosphorus (an average of 64.07 mg·kg−1 compared to 36.21 mg·kg−1 in the control). Similarly, RCH horizons displayed a higher pH and higher contents of Ca and Na cations. These results indicated that RCH soils provided more favourable conditions for the soil microbiome, as reflected by the higher enzymatic activity and diversity of the microorganisms. Moreover, bacterial and fungal communities in RCH soils were more diverse and had greater species/genera richness, especially in the case of fungi. Members of the genus Rhodoplanes dominated the bacterial community at both RCH and non-RCH sites, followed by Streptomyces, Burkholderia, Skermanella, Tsukamurella and Candidatus Solibacter. Both culture- and next generation sequencing (NGS)-based analyses showed that soil fungal communities were dominated by Ascomycota, with Penicillium as the most abundant genus. Our results showed that hearth soils may represent a significant C pool in the forest ecosystem. This study supports the strategy of safeguarding such charcoal-enriched soils as precious C reservoirs and ecologically important biodiversity hotspots. Moreover, the application of charcoal may effectively increase the microbial diversity of forest soils, especially during the reforestation or re-cultivation of disturbed habitats.

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“…Preprocessing included retaining taxa with 5 counts in a minimum of 5% of samples (using the core function in the microbiome package), agglomerating at each taxonomic rank and generating taxonomic abundance. Stacked bar plots (for individual samples and group means), iris plots and heatmaps of most abundant taxa were generated using the vegan, microeco and micoviz packages [ 27 , 28 , 29 ]. Derivations of alpha-diversity indices (Chao1, Shannon, Simpson and Fisher indices) at the genus level were done using vegan and microeco packages.…”

Section: Methodsmentioning

confidence: 99%

“…Associations of genus-level taxa abundance and circulating metabolic markers (glucose, insulin, HDL, LDL cholesterol, triglycerides, NEFA) and maternal early pregnancy BMI and fat mass (measured via BODPOD) were assessed using the microeco package [ 28 ]. Distance-based redundancy analysis (db-RDA) Bray–Cutis distances were used to summarize relationships between microbial taxa abundance and metabolic traits.…”

Section: Methodsmentioning

confidence: 99%

Associations between Maternal Diet, Body Composition and Gut Microbial Ecology in Pregnancy

et al. 2021

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Maternal body composition, gestational weight gain (GWG) and diet quality influence offspring obesity risk. While the gut microbiome is thought to play a crucial role, it is understudied in pregnancy. Using a longitudinal pregnancy cohort, maternal anthropometrics, body composition, fecal microbiome and dietary intake were assessed at 12, 24 and 36 weeks of gestation. Fecal samples (n = 101, 98 and 107, at each trimester, respectively) were utilized for microbiome analysis via 16S rRNA amplicon sequencing. Data analysis included alpha- and beta-diversity measures and assessment of compositional changes using MaAsLin2. Correlation analyses of serum metabolic and anthropometric markers were performed against bacterial abundance and predicted functional pathways. α-diversity was unaltered by pregnancy stage or maternal obesity status. Actinobacteria, Lachnospiraceae, Akkermansia, Bifidobacterium, Streptococcus and Anaerotuncus abundances were associated with gestation stage. Maternal obesity status was associated with increased abundance of Lachnospiraceae, Bilophila, Dialister and Roseburia. Maternal BMI, fat mass, triglyceride and insulin levels were positively associated with Bilophila. Correlations of bacterial abundance with diet intake showed that Ruminococcus and Paraprevotella were associated with total fat and unsaturated fatty acid intake, while Collinsella and Anaerostipes were associated with protein intake. While causal relationships remain unclear, collectively, these findings indicate pregnancy- and maternal obesity-dependent interactions between dietary factors and the maternal gut microbiome.

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microeco: an R package for data mining in microbial community ecology

Cited by 721 publications

References 26 publications

The meta-gut: community coalescence of animal gut and environmental microbiomes

The meta-gut: community coalescence of animal gut and environmental microbiomes

Effect of Charcoal on the Properties, Enzyme Activities and Microbial Diversity of Temperate Pine Forest Soils

Associations between Maternal Diet, Body Composition and Gut Microbial Ecology in Pregnancy

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