How quantitative is metabarcoding: A meta‐analytical approach

Molecular Ecology, Год журнала: 2018, Номер 28(2), С. 420 - 430

Опубликована: Ноя. 8, 2018

Abstract Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the environmental DNA. However, after decade use these there is little consensus on extent to which proportions reads generated corresponds original species community. To quantify our current understanding, we conducted structured review meta‐analysis. The suggests that weak quantitative relationship may exist between biomass sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with large degree uncertainty. None tested moderators, sequencing platform type, number trial or source DNA, were able explain variance. Our understanding factors affecting performance metabarcoding still limited: additional research required before can be confidently utilized for applications. Until then, advocate inclusion mock communities when this facilitates direct assessment ability any given study.

Язык: Английский

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Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

Scientific Reports, Год журнала: 2019, Номер 9(1)

Опубликована: Авг. 20, 2019

Abstract As environmental DNA (eDNA) studies have grown in popularity for use ecological applications, it has become clear that their results differ significant ways from those of traditional, non-PCR-based surveys. In general, eDNA rely on amplicon sequencing may detect hundreds species present a sampled environment, but the resulting composition can be idiosyncratic, reflecting species’ true biomass abundances poorly or not at all. Here, we set simulations to develop mechanistic understanding processes leading kinds common mixed-template PCR-based (metabarcoding) studies. particular, focus effects PCR cycle number and primer amplification efficiency diversity metrics We then show proportional indices reads capture trends taxon with high accuracy, particularly where is (median correlation up 0.97). Our explain much observed behavior studies, lead recommendations best practices field.

Язык: Английский

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DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

Environmental DNA, Год журнала: 2019, Номер 1(3), С. 199 - 214

Опубликована: Авг. 8, 2019

Abstract Effective conservation of species and ecosystems requires the understanding important ecological traits, such as dietary habits, food webs, trophic niches. In diet studies, visual identification partially digested prey has been enhanced with recent more powerful accurate technique, DNA barcoding. Here, we summarize contribution this methodology to investigation both terrestrial aquatic taxa diet, compare level novelty uncovered through use technique regarding species' ecology. From a total 150 studies analyzed, focusing on than 250 vertebrate wild species, seven domesticated taxa, humans, suggest that barcoding led significant findings for ecosystems, where direct observations feeding events consequent niche are typically limited. Finally, introduce term (dDNA) describe environmental approaches extracted from gut, stomach, or fecal contents, aiming assess habits local biodiversity. Particularly, highlight complementarity (eDNA) dDNA new tool biodiversity assessments in remote areas, including most realm.

Язык: Английский

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Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

GigaScience, Год журнала: 2019, Номер 8(8)

Опубликована: Июль 30, 2019

Abstract Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well track the population levels established or endemic pests. Where these traps have low specificity and capture non-target species in excess target pests, need extensive specimen sorting identification creates a major diagnostic bottleneck. While recent development standardized molecular diagnostics has partly alleviated this requirement, single per reaction nature methods does not readily scale sheer number insects trapped programmes. Consequently, lists often restricted few high-priority allowing unanticipated avoid detection potentially establish populations. DNA metabarcoding recently emerged method conducting simultaneous, multi-species complex mixed communities may lend itself ideally rapid bulk trap samples. Moreover, high-throughput sequencing platforms could enable multiplexing hundreds diverse samples on flow cell, thereby providing means dramatically up terms both quantity that can be processed concurrently pest targeted. In review literature, we explore how tailored context highlight unique technical regulatory challenges must considered when implementing technologies into sensitive applications.

Язык: Английский

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Covariation of diet and gut microbiome in African megafauna

Proceedings of the National Academy of Sciences, Год журнала: 2019, Номер 116(47), С. 23588 - 23593

Опубликована: Ноя. 4, 2019

A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of nonhuman microbiomes have relied on relatively coarse dietary categorizations focused either individual wild populations or captive animals that are sheltered from environmental pressures, which may obscure effects variation microbiome composition diverse natural communities. We analyzed plant bacterial DNA fecal samples an assemblage 33 sympatric large-herbivore species (27 native, 6 domesticated) a semiarid East African savanna, enabled high-resolution assessment seasonal both diet composition. Phylogenetic relatedness strongly predicted (r = 0.91) was weakly but significantly correlated with 0.20). Dietary diversity did not predict across within any except kudu; however, species. found spectrum sensitivity at diet-microbiome nexus: Seasonal changes explained 25% Species' positions (and deviations from) this were obviously driven by body size, digestive strategy, composition; domesticated tended exhibit greater turnover than wildlife. Our results reveal marked differences influence degree covariation free-ranging megafauna, well canonical predictors nutritional ecology.

Язык: Английский

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The functional roles of mammals in ecosystems

Journal of Mammalogy, Год журнала: 2019, Номер 100(3), С. 942 - 964

Опубликована: Янв. 4, 2019

The diverse functional roles of over 6,000 species extant mammals that range in body size across eight orders magnitude, from blue whales (Balaenoptera musculus) to tiny Etruscan shrews (Suncus etruscus), contribute shaping Earth's ecosystems. Large mammalian herbivores (e.g., African elephants [Loxodonta africana], American bison [Bison bison], hippopotamuses [Hippopotamus amphibius]) and carnivores wolves [Canis lupus], pumas [Puma concolor], sea otters [Enhydra lutris]) often have significant effects on primary producers terrestrial, aquatic, marine systems through nutrient cycling, energy flow, the exertion bottom-up top-down processes. Small mammals, like bats, are important pollinators, dispersers fruits, consumers arthropods, others, especially rodents primates, predators seeds. Many these mammal-mediated processes occur simultaneously same ecosystem, community structure turn alter communities other vertebrates invertebrates. also ecosystem engineers elephants, beavers [Castor canadensis], porcupines [Erithezon dorsatum], prairie dogs [Cynomys spp.]) create, significantly modify, or destroy habitat, by doing so, they function increase habitat heterogeneity biodiversity. extensive influence ecosystems results services human well-being, such as pollination, insect pest control, bioturbation soils. rapid declines abundance many mammal populations associated extinction risk raise conservation concerns for mammals. To maintain diversity critical provide, scientists need mobilize concern their status strive more effective comprehensive action. We provide insights synthesis ecological role highlight key research questions future directions conservation.

Язык: Английский

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A guide to the application of Hill numbers to DNA‐based diversity analyses

Molecular Ecology Resources, Год журнала: 2019, Номер 19(4), С. 804 - 817

Опубликована: Апрель 4, 2019

Abstract With the advent of DNA sequencing‐based techniques, way we detect and measure biodiversity is undergoing a radical shift. There also an increasing awareness need to employ intuitively meaningful diversity measures based on unified statistical frameworks, so that different results can be easily interpreted compared. This article aimed serve as guide implementing assessment using general framework developed around Hill numbers into analysis systems characterized techniques (e.g., diet, microbiomes ecosystem biodiversity). Specifically, discuss (a) DNA‐based approaches for defining types upon which measured, (b) how weight importance each type, (c) differences between abundance‐based versus incidence‐based approaches, (d) implementation phylogenetic information measurement, (e) hierarchical partitioning, (f) dissimilarity overlap measurement (g) deal with zero‐inflated, insufficient biased data. All steps are reproduced real data provide step‐by‐step bash R scripts enable straightforward explained procedures.

Язык: Английский

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Promises and pitfalls of using high‐throughput sequencing for diet analysis

Molecular Ecology Resources, Год журнала: 2018, Номер 19(2), С. 327 - 348

Опубликована: Окт. 24, 2018

The application of high-throughput sequencing-based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits animals. Due the high resolution prey detection capacity they provide, both metabarcoding shotgun sequencing are increasingly used address ecological questions grounded in relationships. Despite their great promise this context, recent research unveiled how wealth biological (related study system) technical methodology) factors can distort signal taxonomic composition diversity. Here, we review these studies light assessment trophic interactions. We design account distortion factors, acknowledging limitations biases inherent diet analyses essential obtaining reliable results, thus drawing appropriate conclusions. Furthermore, suggest strategies minimize effect measures increase reproducibility, replicability comparability studies, options scale up analyses. In doing so, aim aid end-users designing by informing them about complexity analyses, encourage researchers create improve tools that will eventually drive field its maturity.

Язык: Английский

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Diversity and functional landscapes in the microbiota of animals in the wild

Science, Год журнала: 2021, Номер 372(6539)

Опубликована: Март 25, 2021

Animals in the wild are able to subsist on pathogen-infected and poisonous food show immunity various diseases. These may be due their microbiota, yet we have a poor understanding of animal microbial diversity function. We used metagenomics analyze gut microbiota more than 180 species wild, covering diverse classes, feeding behaviors, geographies, traits. Using de novo metagenome assembly, constructed functionally annotated database 5000 genomes, comprising 1209 bacterial which 75% unknown. The composition, diversity, functional content exhibit associations with taxonomy, diet, activity, social structure, life span. identify animals as largely untapped resource for discovery therapeutics biotechnology applications.

Язык: Английский

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Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 3270 - 3288

Опубликована: Авг. 11, 2020

With the growing anthropogenic pressure on marine ecosystems, need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding bulk samples is increasingly being implemented in ecosystem assessments and more cost-efficient less time-consuming than based morphology. However, before raw sequences are obtained from samples, a profound number methodological choices must be made. Here, we critically review recent methods used (including benthic, plankton diet samples) indicate how potential biases can introduced throughout sampling, preprocessing, extraction, marker primer selection, PCR amplification sequencing. From total 64 studies evaluated, our recommendations best practices include to (a) consider DESS as fixative instead ethanol, (b) use DNeasy PowerSoil kit any containing traces sediment, (c) not limit selection COI only, but preferably multiple markers higher taxonomic resolution, (d) avoid touchdown profiles, (e) fixed annealing temperature each pair when comparing across or institutes, (f) minimum three replicates, (g) both negative positive controls. Although implementation still faces several technical complexities, foresee wide-ranging advances near future, including improved bioinformatics assignment, sequencing longer fragments whole-genome information. Despite involved if appropriate controls included along data generation process, it clear that provides valuable tool assessments.

Язык: Английский

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