Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Microbiology and Molecular Biology Reviews, Год журнала: 2017, Номер 81(4)

Опубликована: Окт. 12, 2017

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly microbial ecology. Although stochastic processes are believed to play nonnegligible roles shaping structure, their importance relative deterministic hotly debated. The of ecological stochasticity structure far less appreciated. Some main reasons for such heavy debates difficulty defining diverse methods used delineating stochasticity. Here, we provide critical review synthesis data from most recent studies on assembly We then describe both components embedded various processes, including selection, dispersal, diversification, drift. also different approaches inferring observational diversity patterns highlight experimental communities. In addition, research challenges, gaps, future directions research.

Язык: Английский

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Function and functional redundancy in microbial systems

Nature Ecology & Evolution, Год журнала: 2018, Номер 2(6), С. 936 - 943

Опубликована: Апрель 12, 2018

Язык: Английский

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Emergent simplicity in microbial community assembly

Science, Год журнала: 2018, Номер 361(6401), С. 469 - 474

Опубликована: Авг. 3, 2018

Interchanging species of similar function Under natural conditions, bacteria form mixed, interacting communities. Understanding how such communities assemble and stabilize is important in a range contexts, from biotechnological applications to what happens our guts. Goldford et al. sampled the microbial soil plants containing hundreds thousands sequence variants. The organisms were passaged after culture low concentrations single carbon sources cross-fed with each other's metabolites; then, resulting sequenced using 16S ribosomal RNA, outcomes modeled mathematically. mix that survived under steady conditions converged reproducibly reflect experimentally imposed rather than initially inoculated—although at coarse phylogenetic levels, taxonomic patterns persisted. Science , this issue p. 469

Язык: Английский

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

FEMS Microbiology Ecology, Год журнала: 2020, Номер 97(2)

Опубликована: Дек. 15, 2020

A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput technique, especially amplicon-sequencing-based data. After conducting initial bioinformatic analysis amplicon data, performing subsequent statistics and mining based on operational taxonomic unit assignment tables still complicated time-consuming. To address this problem, we present an integrated R package-'microeco' as pipeline for treating environmental This package was developed R6 class system combines a series commonly used advanced approaches research. The includes classes preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta differential test indicator taxon null model network functional analysis. Each designed to provide set that can be easily accessible users. Compared with other packages field, microeco fast, flexible modularized use provides powerful convenient tools researchers. installed from CRAN (The Comprehensive Archive Network) or github (https://github.com/ChiLiubio/microeco).

Язык: Английский

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NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

Nature Biotechnology, Год журнала: 2019, Номер 37(6), С. 676 - 684

Опубликована: Апрель 29, 2019

Язык: Английский

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DRAM for distilling microbial metabolism to automate the curation of microbiome function

Nucleic Acids Research, Год журнала: 2020, Номер 48(16), С. 8883 - 8900

Опубликована: Июль 22, 2020

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet specific reactions catalyzed by these biological engines are hard to decode due absence a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled Refined Annotation Metabolism), framework translate deluge microbiome-based genomic information into catalog microbial traits. To demonstrate applicability across diverse genomes, evaluated performance on defined, in silico soil community previously published human gut metagenomes. We show that accurately assigned contributions geochemical cycles automated partitioning carbohydrate metabolism at substrate levels. DRAM-v, mode DRAM, established rules identify virally-encoded auxiliary metabolic genes (AMGs), resulting categorization thousands putative AMGs from soils guts. Together DRAM-v provide critical profiling capabilities decipher mechanisms underpinning microbiome function.

Язык: Английский

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Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Фев. 26, 2018

The 16S ribosomal RNA gene is the most widely used marker in microbial ecology. Counts of sequence variants, often PCR amplicons, are to estimate proportions bacterial and archaeal taxa communities. Because different organisms contain copy numbers (GCNs), variant counts biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods based on sequenced genomes, order correct these biases. However, accuracy those predictions has not independently assessed. Here, we systematically evaluate predictability across clades, ∼ 6,800 public genomes several methods. Further, assess predicted by three published (PICRUSt, CopyRighter, PAPRICA) over a wide range 635 communities from varied environments. We find that regardless method tested, could only be accurately limited fraction taxa, namely closely moderately related representatives (≲15% divergence rRNA gene). Consistent this observation, all considered exhibit low predictive when evaluated against completely some cases explaining less than 10% variance. Substantial disagreement was also observed between (R2<0.5) majority tested nearest taxon index (NSTI) communities, i.e., average distance genome, strong predictor agreement GCN prediction non-animal-associated samples, but moderate animal-associated samples. recommend correcting microbiome surveys default, unless OTUs sufficiently or need true OTU warrants additional noise introduced, so community profiles remain interpretable comparable studies.

Язык: Английский

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A practical guide to amplicon and metagenomic analysis of microbiome data

Protein & Cell, Год журнала: 2020, Номер 12(5), С. 315 - 330

Опубликована: Май 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.

Язык: Английский

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Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

mSystems, Год журнала: 2017, Номер 2(1)

Опубликована: Янв. 4, 2017

Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa a myriad of factors. A drawback these is that the necessary library preparation bioinformatic analyses complicated continuously changing, which can be barrier for researchers new field. We present three essential components conducting microbiome experiment from start finish: first, simplified step-by-step custom protocol requires limited lab equipment, cost-effective, has been thoroughly tested utilized on various sample types; second, series scripts integrate commonly used tools available standalone installation or single downloadable virtual image; third, set workflows tutorials provide guidance education those This resource will foundations newly entering field much-needed best practices ensure quality research undertaken. All protocols, scripts, workflows, tutorials, images freely through Microbiome Helper website (https://github.com/mlangill/microbiome_helper/wiki). IMPORTANCE As continues grow, multitude learning how conduct proper experiments. outline here streamlined approach processing samples detailed construction standard operating procedures. allows rapid reliable analysis, allowing focus more their design results. Our bundled software Helper. evolve, updated with training materials.

Язык: Английский

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Rhizosphere bacteriome structure and functions

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Фев. 11, 2022

Abstract Microbial composition and functions in the rhizosphere—an important microbial hotspot—are among most fascinating yet elusive topics ecology. We used 557 pairs of published 16S rDNA amplicon sequences from bulk soils rhizosphere different ecosystems around world to generalize bacterial characteristics with respect community diversity, composition, functions. The selects microorganisms soil function as a seed bank, reducing diversity. is enriched Bacteroidetes, Proteobacteria, other copiotrophs. Highly modular but unstable networks (common for r -strategists) reflect interactions adaptations dynamic conditions. Dormancy strategies are dominated by toxin–antitoxin systems, while sporulation common soils. Functional predictions showed that genes involved organic compound conversion, nitrogen fixation, denitrification were strongly (11–182%), nitrification depleted.

Язык: Английский

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