A practical guide to amplicon and metagenomic analysis of microbiome data

Protein & Cell, Journal Year: 2020, Volume and Issue: 12(5), P. 315 - 330

Published: May 11, 2020

Abstract Advances in high-throughput sequencing (HTS) have fostered rapid developments the field of microbiome research, and massive datasets are now being generated. However, diversity software tools complexity analysis pipelines make it difficult to access this field. Here, we systematically summarize advantages limitations methods. Then, recommend specific for amplicon metagenomic analyses, describe commonly-used databases, help researchers select appropriate tools. Furthermore, introduce statistical visualization methods suitable analysis, including alpha- beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, common styles informed choices. Finally, a step-by-step reproducible guide is introduced. We hope review will allow carry out data more effectively quickly order efficiently mine biological significance behind data.

Language: Английский

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Drought and host selection influence bacterial community dynamics in the grass root microbiome

The ISME Journal, Journal Year: 2017, Volume and Issue: 11(12), P. 2691 - 2704

Published: July 28, 2017

Abstract Root endophytes have been shown to important roles in determining host fitness under periods of drought stress, and yet the effect on broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles communities associated with drought-treated rhizosphere tissues 18 species plants varying degrees tolerance belonging Poaceae family, including crop plants. Through 16S rRNA gene profiling across two distinct watering regimes developmental time points, demonstrate that there is a strong correlation between distance microbiome dissimilarity within tissues, weakens by inducing conserved shifts composition. We identify significant enrichment wide variety Actinobacteria during roots all hosts, higher than it surrounding environments. Furthermore, show observed result an absolute increase Actinobacterial abundance previously hypothesized mechanisms for enrichments soils are unlikely fully account phenomena here plant root.

Language: Английский

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Host selection shapes crop microbiome assembly and network complexity

New Phytologist, Journal Year: 2020, Volume and Issue: 229(2), P. 1091 - 1104

Published: Aug. 27, 2020

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere bulk soil) multiple compartment niches (rhizoplane, root endosphere, phylloplane, leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate along soil-plant continuum is shaped predominantly by niche species rather than site or practice. From epiphytes endophytes, selection pressure sequentially increased diversity network complexity consequently reduced, with strongest effect endosphere. Source tracking indicates mainly derived gradually enriched filtered plant niches. Moreover, were dominated a few dominant taxa (c. 0.5% of phylotypes), bacilli identified as important biomarker for wheat barley Methylobacteriaceae maize. work provides comprehensive empirical evidence on selection, potential sources enrichment assembly, has implications future management manipulation sustainable agriculture.

Language: Английский

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Modulation of the Root Microbiome by Plant Molecules: The Basis for Targeted Disease Suppression and Plant Growth Promotion

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 10

Published: Jan. 24, 2020

Plants host a mesmerizing diversity of microbes inside and around their roots, known as the microbiome. The microbiome is composed mostly fungi, bacteria, oomycetes, archaea that can be either pathogenic or beneficial for plant health fitness. To grow healthy, plants need to surveil soil niches roots detection microbes, in parallel maximize services nutrients uptake growth promotion. employ palette mechanisms modulate including structural modifications, exudation secondary metabolites coordinated action different defence responses. Here, we review current understanding on composition activity root how molecules shape structure root-associated microbial communities. Examples are given interactions occur rhizosphere between soilborne fungi. We also present some well-established examples harnessing highlight fitness by selecting Understanding manipulate aid design next-generation inoculants targeted disease suppression enhanced growth.

Language: Английский

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The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Feb. 12, 2018

Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in plant niche-level microbiome, from rhizosphere soils to canopies, is imperative gain a better how both structural and functional processes microbiomes impact health overall holobiome. Using Populus trees as model ecosystem, we characterized archaeal/bacterial fungal microbiome across 30 different tissue-level niches replicated deltoides hybrid trichocarpa × individuals using 16S ITS2 rRNA gene analyses. Our analyses indicate that varied primarily broader habitat classes (leaves, stems, roots, soils) regardless genotype, except for communities leaf niches, which were greatly impacted by genotype. Differences between tree genotypes are evident elevated presence two potential pathogens, Marssonina brunnea Septoria sp., on P. may turn be contributing divergence composition. Archaeal/bacterial diversity increased leaves, stem, root, soil habitats, whereas was greatest stems soils. This study provides holistic structure bioenergy relevant host, one most complete any plant. As such, it constitutes detailed atlas or map further hypothesis testing significance individual microbial taxa specific habitats baseline comparisons other species.

Language: Английский

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Defining and quantifying the core microbiome: Challenges and prospects

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(51)

Published: Dec. 3, 2021

The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, core microbiome refers to any set of taxa, or genomic and functional attributes associated with those that are characteristic a host environment interest. Most commonly, microbiomes measured as taxa shared among two more samples from particular environment. Despite popularity this its growing use, there is little consensus about how should be quantified practice. Here, we present brief history concept use representative sample literature review different metrics commonly for quantifying core. Empirical analyses have wide range microbiome, including arbitrary occurrence abundance cutoff values, focal taxonomic level ranging phyla amplicon sequence variants. However, many these susceptible sampling other biases. Developing standardized accounts such biases necessary testing specific hypotheses ecological roles microbiomes.

Language: Английский

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Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly

BMC Microbiology, Journal Year: 2019, Volume and Issue: 19(1)

Published: Sept. 2, 2019

Plants have evolved intimate interactions with soil microbes for a range of beneficial functions including nutrient acquisition, pathogen resistance and stress tolerance. Further understanding this system is promising way to advance sustainable agriculture by exploiting the versatile benefits offered plant microbiome. The rhizosphere interface between soil, as first step defense root microbiome recruitment. It features specialized microbial community, intensive microbe-plant microbe-microbe interactions, complex signal communication. To decipher assembly soybean (Glycine max), we comprehensively characterized community using 16S rRNA gene sequencing evaluated structuring influence from both host genotype source.Comparison bulk revealed significantly different composition, metabolic capacity. Soil type cooperatively modulated predominantly shaping while slightly tuned recruitment process. undomesticated progenitor species, Glycine soja, had higher diversity in types tested comparison domesticated genotypes. Rhizobium, Novosphingobium, Phenylobacterium, Streptomyces, Nocardioides, etc. were robustly enriched irrespective tested. Co-occurrence network analysis dominant effects specific preferences key interactions. Functional prediction results demonstrated converged capacity among genotypes, pathways related xenobiotic degradation, plant-microbe transport being greatly rhizosphere.This comprehensive genotypes expands our microbe general provides foundational information legume crop cooperative modulating role emphasizes importance integrated consideration condition genetic variability future development application synthetic microbiomes. Additionally, detection tuning breeding programs integrate traits participating microbiota assembly.

Language: Английский

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Plant developmental stage drives the differentiation in ecological role of the maize microbiome

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Aug. 13, 2021

Abstract Background Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how development impacts the assembly, functions interactions crop microbiomes are poorly understood. Here we examined both bacterial fungal across soils, epiphytic endophytic niches leaf root, plastic fake plant (representing environment-originating microbes) at three developmental stages maize two contrasting sites, further explored potential function phylloplane based on metagenomics. Results Our results suggested that stage had a much stronger influence diversity, composition interkingdom networks in compartments than strongest effect phylloplane. Phylloplane were co-shaped by growth seasonal environmental factors, air (represented plants) as its important source. Further, found more strongly driven deterministic processes early similar pattern was for late stage. Moreover, taxa played role network yield prediction stage, while did so Metagenomic analyses indicated possessed higher functional diversity genes related to nutrient provision enriched N assimilation C degradation Coincidently, abundant beneficial like Actinobacteria, Burkholderiaceae Rhizobiaceae observed saprophytic fungi Conclusions suggest influences microbiome assembly functions, take differentiated ecological different development. This study provides empirical evidence exerting strong selection during These findings have implications future tools manipulate sustainable increase primary productivity.

Language: Английский

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Impact of root system architecture on rhizosphere and root microbiome

Rhizosphere, Journal Year: 2018, Volume and Issue: 6, P. 47 - 51

Published: March 6, 2018

Language: Английский

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Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions

Frontiers in Microbiology, Journal Year: 2019, Volume and Issue: 10

Published: June 20, 2019

Despite the widely observed predominance of Cand. Patescibacteria in subsurface communities, their input source and ecophysiology are poorly understood. Here we study mechanisms formation a groundwater microbiome subsequent differentiation Patescibacteria. In Hainich Critical Zone Exploratory, Germany, trace microorganisms from forested soils preferential recharge areas through fractured aquifers along 5.4 km hillslope well transect. were preferentially mobilized constituted 66% species-level OTUs shared between seepage shallow groundwater. These OTUs, mostly related to Kaiserbacteraceae, Nomurabacteraceae, unclassified UBA9983 at family level, represented relative abundance 71.4% community shallowest well, still 44.4% end Several subclass-level groups exhibited preferences for different conditions two aquifer assemblages investigated: Kaiserbacteraceae surprisingly showed positive correlations with oxygen concentrations, while Nomurabacteraceae negatively correlated. Co-occurrence network analysis revealed central role microbial communities pointed potential associations specific organisms, including abundant autotrophic taxa involved nitrogen, sulfur iron cycling. Strong among themselves further suggested that many within this phylum, distribution was mainly driven by commonly supporting fermentative life style without direct dependence on hosts. We propose import soil, hydrochemical conditions, availability organic resources hosts, determine success environments.

Language: Английский

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