Environmental DNA

Oxford University Press eBooks, Год журнала: 2018, Номер unknown

Опубликована: Фев. 15, 2018

Abstract Environmental DNA (eDNA), i.e. released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on distribution or feeding habits of species. It has therefore great potential for applications ecology biodiversity management. However, this research field is fast-moving, involves different areas expertise currently lacks approaches, which calls an up-to-date comprehensive synthesis. monitoring covers current methods based eDNA, with particular focus “eDNA metabarcoding”. Intended scientists managers, it provides background allow design sound experiments. revisits all steps necessary produce high-quality metabarcoding data such as sampling, metabarcode design, optimization PCR sequencing protocols, well analysis large datasets. All these are presented discussing challenges eDNA-based approaches infer parameters ecological processes. The last chapters book review how been used so far unravel novel patterns diversity space time, detect species, answer new questions various ecosystems organisms. constitutes essential reading graduate students, researchers practitioners who do not have strong molecular genetics willing use eDNA biomonitoring.

Язык: Английский

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Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Май 16, 2019

Abstract Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared wild counterparts. To resolve this disagreement, we analyze new, large, and highly diverse animal distal 16 S rRNA microbiome dataset, comprises 80% animals includes members of Mammalia, Aves, Reptilia, Amphibia, Actinopterygii. We decouple effects host evolutionary history diet diversity show that each factor modulates aspects diversity. Moreover, particular taxa associated with phylogeny or Mammalia stronger signal cophylogeny. Finally, find environmental filtering microbe-microbe interactions differ among clades. These findings provide robust assessment processes driving intestine.

Язык: Английский

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The hologenome concept of evolution after 10 years

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

Опубликована: Апрель 25, 2018

The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selection operates. whole: anatomically, metabolically, immunologically, developmentally, during evolution. Consideration of hologenome independent in evolution has led better understanding underappreciated modes genetic variation is comprised two complimentary parts: host microbiome genomes. Changes either genome result variations that be selected for or against. highly conserved, changes within it occur slowly, whereas dynamic change rapidly response environment by increasing reducing particular microbes, acquisition novel horizontal gene transfer, mutation. Recent experiments showing microbiota play initial role speciation have been suggested mode enhancing Some transferred offspring variety mechanisms. Strain-specific DNA analysis shown at least some maintained across hundreds thousands generations, implying existence microbial core. We argue rapid could allow holobionts adapt survive under changing environmental conditions thus providing time necessary evolve. As Darwin wrote, "It not strongest species survives but most adaptable".

Язык: Английский

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Caterpillars lack a resident gut microbiome

Proceedings of the National Academy of Sciences, Год журнала: 2017, Номер 114(36), С. 9641 - 9646

Опубликована: Авг. 22, 2017

Many animals are inhabited by microbial symbionts that influence their hosts' development, physiology, ecological interactions, and evolutionary diversification. However, firm evidence for the existence functional importance of resident microbiomes in larval Lepidoptera (caterpillars) is lacking, despite fact these insects enormously diverse, major agricultural pests, dominant herbivores many ecosystems. Using 16S rRNA gene sequencing quantitative PCR, we characterized gut wild leaf-feeding caterpillars United States Costa Rica, representing 124 species from 15 families. Compared with other vertebrates assayed using same methods, microbes detected caterpillar guts were unusually low-density variable among individuals. Furthermore, abundance composition leaf-associated reflected feces consuming plants. Thus, ingested food present (although possibly dead or dormant) gut, but host-specific, largely absent. To test whether transient might still contribute to feeding conducted an experiment on field-collected model Manduca sexta Antibiotic suppression bacterial activity did not significantly affect weight gain, survival. The high pH, simple structure, fast transit times typify digestive physiology may prevent colonization. Moreover, host-encoded detoxification mechanisms likely render unnecessary herbivory. Caterpillars illustrate potential benefits independence symbionts, a lifestyle be widespread animals.

Язык: Английский

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The human microbiome in evolution

BMC Biology, Год журнала: 2017, Номер 15(1)

Опубликована: Дек. 1, 2017

The trillions of microbes living in the gut—the gut microbiota—play an important role human biology and disease. While much has been done to explore its diversity, a full understanding our microbiomes demands evolutionary perspective. In this review, we compare from populations, placing them context humanity’s near distant animal relatives. We discuss potential mechanisms generate host-specific microbiome configurations consequences disrupting those configurations. Finally, propose that broader phylogenetic perspective is useful for underlying human–microbiome interactions.

Язык: Английский

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Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

Nature Communications, Год журнала: 2018, Номер 9(1)

Опубликована: Ноя. 16, 2018

Scleractinian corals' microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. show that are anatomically compartmentalized both modern ecology evolutionary assembly. Coral mucus, tissue, skeleton differ community composition, richness, response to vs. environmental drivers. also find evidence coral-microbe phylosymbiosis, which microbiome composition richness reflect phylogeny. Surprisingly, the represents most biodiverse microbiome, shows strongest phylosymbiosis. Interactions between phylogeny significantly abundance four groups bacteria-including Endozoicomonas-like bacteria, divide into host-generalist host-specific subclades. Together these results trace symbiosis across anatomy during a basal animal lineage.

Язык: Английский

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Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

The ISME Journal, Год журнала: 2018, Номер 13(3), С. 576 - 587

Опубликована: Июль 11, 2018

Язык: Английский

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Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats

mBio, Год журнала: 2020, Номер 11(1)

Опубликована: Янв. 6, 2020

In this comprehensive survey of microbiomes >900 species, including 315 mammals and 491 birds, we find a striking convergence the birds animals that fly. nonflying mammals, diet short-term evolutionary relatedness drive microbiome, many microbial species are specific to particular kind mammal, but flying break pattern with microbes shared across different little correlation either or hosts. This finding suggests adaptation flight breaks long-held relationships between hosts their microbes.

Язык: Английский

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Applying the core microbiome to understand host–microbe systems

Journal of Animal Ecology, Год журнала: 2020, Номер 89(7), С. 1549 - 1558

Опубликована: Апрель 5, 2020

Abstract The host‐associated core microbiome was originally coined to refer common groups of microbes or genes that were likely be particularly important for host biological function. However, the term has evolved encompass variable definitions across studies, often identifying key with respect their spatial distribution, temporal stability ecological influence, as well contribution function and fitness. A major barrier reaching a consensus over how define its relevance biological, evolutionary theory is lack precise terminology associated definitions, persistent association Common, microbiomes can together generate insights into processes act independently function, while functional host‐adapted cores distinguish between facultative near‐obligate symbionts differ in effects on This commentary summarizes five broad have been applied literature, highlighting strengths limitations advancing our understanding host–microbe systems, noting where they are overlap, discussing potential No one definition capture range population. Applied together, reveal different layers microbial organization from which we begin understand govern interactions.

Язык: Английский

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Microbiomes as sources of emergent host phenotypes

Science, Год журнала: 2019, Номер 365(6460), С. 1405 - 1409

Опубликована: Сен. 26, 2019

Microbial communities associated with animals exert powerful influences on host physiology, regulating metabolism and immune function, as well complex behaviors. The importance of host–microbiome interactions for maintaining homeostasis promoting health raises evolutionarily complicated questions about how their microbiomes have coevolved, these relationships affect the ways that interact environment. Here, we review literature contributions factors to microbial community structure corresponding emergent phenotypes. We focus in particular animal behaviors a basis understanding potential roles microbiome shaping neurobiology.

Язык: Английский

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