The sponge holobiont in a changing ocean: from microbes to ecosystems

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

Опубликована: Март 9, 2018

The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, microbiota, interactions among them. Accordingly, ecological concepts can be applied to understand host-derived processes govern dynamics interactive networks within holobiont. In marine systems, holobionts further integrated into larger more ecosystems, concept referred as "nested ecosystems." this review, we discuss dynamic interact at multiple scales respond environmental change. We focus on symbiosis sponges their communities—a resulted one most diverse environment. recent years, sponge microbiology remarkably advanced terms curated databases, standardized protocols, information functions microbiota. Like Russian doll, these translated holobiont impact surrounding ecosystem. For example, sponge-associated metabolisms, fueled by high filtering capacity substantially affect biogeochemical cycling key nutrients like carbon, nitrogen, phosphorous. Since increasingly threatened anthropogenic stressors jeopardize stability ecosystem, link between perturbations, dysbiosis, diseases. Experimental studies suggest community composition is tightly linked health, but whether dysbiosis cause or consequence collapse remains unresolved. Moreover, potential role microbiome mediating for acclimate adapt change unknown. Future should aim identify mechanisms underlying scales, from develop management strategies preserve provided our present future oceans.

Язык: Английский

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Gut microbiome, big data and machine learning to promote precision medicine for cancer

Nature Reviews Gastroenterology & Hepatology, Год журнала: 2020, Номер 17(10), С. 635 - 648

Опубликована: Июль 9, 2020

Язык: Английский

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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?

Zoology, Год журнала: 2018, Номер 127, С. 1 - 19

Опубликована: Фев. 15, 2018

From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant animal hosts, ultimately forming a metaorganism consisting uni- or multicellular host community associated microorganisms. Research on host–microbe interactions has become emerging cross-disciplinary field. In both vertebrates invertebrates complex microbiome confers immunological, metabolic behavioural benefits; conversely, its disturbance can contribute development disease states. However, molecular cellular mechanisms controlling within poorly understood many key between organisms remain unknown. this perspective article, we outline some issues in interspecies particular address question how metaorganisms react adapt inputs from extreme environments such as deserts, intertidal zone, oligothrophic seas, hydrothermal vents.

Язык: Английский

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Application of Machine Learning in Microbiology

Frontiers in Microbiology, Год журнала: 2019, Номер 10

Опубликована: Апрель 18, 2019

Microorganisms are ubiquitous and closely related to people's daily lives. Since they were first discovered in the 19th century, researchers have shown great interest microorganisms. People studied microorganisms through cultivation, but this method is expensive time consuming. However, cultivation cannot keep a pace with development of high-throughput sequencing technology. To deal problem, machine learning methods been widely applied field microbiology. Literature reviews that can be used many aspects microbiology research, especially classification problems, for exploring interaction between surrounding environment. In study, we summarize application

Язык: Английский

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A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction

Frontiers in Genetics, Год журнала: 2019, Номер 10

Опубликована: Июнь 25, 2019

With the growing importance of microbiome research, there is increasing evidence that host variation in microbial communities associated with overall health. Advancement genetic sequencing methods for microbiomes has coincided improvements machine learning, important implications disease risk prediction humans. One aspect specific to use taxonomy-informed feature selection. In this review non-experts, we explore most commonly used learning methods, and evaluate their accuracy as applied trait prediction. Methods are described at an introductory level, R/Python code analyses provided.

Язык: Английский

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Machine learning and deep learning applications in microbiome research

ISME Communications, Год журнала: 2022, Номер 2(1)

Опубликована: Окт. 6, 2022

Abstract The many microbial communities around us form interactive and dynamic ecosystems called microbiomes. Though concealed from the naked eye, microbiomes govern influence macroscopic systems including human health, plant resilience, biogeochemical cycling. Such feats have attracted interest scientific community, which has recently turned to machine learning deep methods interrogate microbiome elucidate relationships between its composition function. Here, we provide an overview of how latest studies harness inductive prowess artificial intelligence methods. We start by highlighting that data – being compositional, sparse, high-dimensional necessitates special treatment. then introduce traditional novel discuss their strengths applications. Finally, outlook pipelines, focusing on bottlenecks considerations address them.

Язык: Английский

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Potential for Artificial Intelligence (AI) and Machine Learning (ML) Applications in Biodiversity Conservation, Managing Forests, and Related Services in India

Sustainability, Год журнала: 2022, Номер 14(12), С. 7154 - 7154

Опубликована: Июнь 10, 2022

The recent advancement in data science coupled with the revolution digital and satellite technology has improved potential for artificial intelligence (AI) applications forestry wildlife sectors. India shares 7% of global forest cover is 8th most biodiverse region world. However, rapid expansion developmental projects, agriculture, urban areas threaten country’s rich biodiversity. Therefore, adoption new technologies like AI Indian forests biodiversity sectors can help effective monitoring, management, conservation resources. We conducted a systematic search literature related to application machine learning algorithms (ML) sector across globe (using ISI Web Science Google Scholar). Additionally, we also collected on AI-based startups non-profits understand growth conservation, services. Here, first provide overview research conservation. Next, discuss challenges Overall, find that been slow compared developed, other developing countries. improving access big biodiversity, cloud computing, improve India. hope this synthesis will motivate officials, scientists, conservationists explore management.

Язык: Английский

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Modularity and predicted functions of the global sponge-microbiome network

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

Опубликована: Март 1, 2019

Defining the organisation of species interaction networks and unveiling processes behind their assembly is fundamental to understanding patterns biodiversity, community stability ecosystem functioning. Marine sponges host complex communities microorganisms that contribute health survival, yet mechanisms microbiome are largely unknown. We present global marine sponge-microbiome network reveal a modular in both structure function. Modules linked by few sponge share microbes with other around world. Further, we provide evidence abiotic factors influence structuring when considering all present, but biotic interactions drive more intimately associated 'core' microorganisms. These findings suggest ecological evolutionary at play host-microbe assembly. expect be consistent across multicellular hosts throughout tree life.

Язык: Английский

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The sponge microbiome within the greater coral reef microbial metacommunity

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

Опубликована: Апрель 9, 2019

Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in greater coral reef metacommunity. Here, we present an extensive survey of prokaryote communities a wide range biotopes from Indo-Pacific environments. We find large variation operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing most diverse communities. These share higher percentage number OTUs sediment are particularly enriched members phylum Planctomycetes. Despite having lower OTU sponges greatest (>90%) >100 sequences environment (sediment and/or seawater) although there considerable among species. Our results, furthermore, highlight that microorganisms shared multiple biotopes, that, compositionally distinct, community does not appear to be as sponge-specific previously thought.

Язык: Английский

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Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts

The ISME Journal, Год журнала: 2019, Номер 13(5), С. 1209 - 1225

Опубликована: Янв. 15, 2019

Abstract Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics imaging analyses revealed unusually high amounts MOX symbionts hosts group previously assumed to have low abundances. These belonged Marine Methylotrophic Group 2 clade. They are host-specific likely vertically transmitted, based on presence embryos streamlined genomes, which lacked genes typical related free-living MOX. Moreover, known play role host–symbiont interactions, such as those encode eukaryote-like proteins, were abundant expressed. Methane assimilation by was one most highly expressed metabolic pathways sponges. Molecular stable carbon isotope patterns lipids confirmed methane-derived incorporated into hosts. Our results sponges, although distantly related, independently established specific, symbioses closely methanotrophs. This convergence symbiont acquisition underscores strong selective advantage for these sponges harboring bacteria food-limited deep sea.

Язык: Английский

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