From the raw bar to the bench: Bivalves as models for human health

Robledo, José A. Fernández; Yadavalli, Raghavendra; Allam, Bassem; Espinosa, Emmanuelle Pales; Gerdol, Marco; Greco, Samuele; Stevick, Rebecca J.; Gomez‐Chiarri, Marta; Zhang, Ying; Heil, Cynthia A.; Tracy, Adrienne N.; Bishop‐Bailey, David; Metzger, Michael J.

doi:10.1016/j.dci.2018.11.020

Cited by 51 publications

(22 citation statements)

References 403 publications

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“…The potential similarity in function of microbes involved in N and P cycling between oyster gut and seawater/sediment may be explained by unique aspects of the physiology and anatomy of bivalves like oysters. Bivalves are ectotherms with an open circulatory system, and perform high levels of filtration when actively feeding [64,65]. Therefore, we hypothesize that the particular nutrients (N, P compounds) and conditions (DO, pH) driving N and P cycling, must be, overall, similar in the oyster gut to the ambient water environment.…”

Section: Discussionmentioning

confidence: 99%

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

2021

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Background Oysters in coastal environments are subject to fluctuating environmental conditions that may impact the ecosystem services they provide. Oyster-associated microbiomes are responsible for some of these services, particularly nutrient cycling in benthic habitats. The effects of climate change on host-associated microbiome composition are well-known, but functional changes and how they may impact host physiology and ecosystem functioning are poorly characterized. We investigated how environmental parameters affect oyster-associated microbial community structure and function along a trophic gradient in Narragansett Bay, Rhode Island, USA. Adult eastern oyster, Crassostrea virginica, gut and seawater samples were collected at 5 sites along this estuarine nutrient gradient in August 2017. Samples were analyzed by 16S rRNA gene sequencing to characterize bacterial community structures and metatranscriptomes were sequenced to determine oyster gut microbiome responses to local environments. Results There were significant differences in bacterial community structure between the eastern oyster gut and water samples, suggesting selection of certain taxa by the oyster host. Increasing salinity, pH, and dissolved oxygen, and decreasing nitrate, nitrite and phosphate concentrations were observed along the North to South gradient. Transcriptionally active bacterial taxa were similar for the different sites, but expression of oyster-associated microbial genes involved in nutrient (nitrogen and phosphorus) cycling varied throughout the Bay, reflecting the local nutrient regimes and prevailing environmental conditions. Conclusions The observed shifts in microbial community composition and function inform how estuarine conditions affect host-associated microbiomes and their ecosystem services. As the effects of estuarine acidification are expected to increase due to the combined effects of eutrophication, coastal pollution, and climate change, it is important to determine relationships between host health, microbial community structure, and environmental conditions in benthic communities.

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Section: Discussionmentioning

confidence: 99%

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

2021

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“…Since their initial diversification in the early Cambrian (Paleozoic Era), bivalves successfully colonized a variety of aquatic environments, from cold-water seas, to freshwater basins and deep anoxic vents, with some species showing an invasive behavior [24,25,26,27]. A number of bivalve species have been investigated for their peculiar adaptation strategies [28], innate immune systems [29], and bio-inspired applications [30] as well as for their use as models for human health [31]. Today, few bivalve genome drafts are available, whereas more than 2,100 transcriptomic datasets have been deposited in public databases (NCBI SRA archive, accessed in November 2018).…”

Section: Introductionmentioning

confidence: 99%

A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data

Rosani

Shapiro

Venier

et al. 2019

Viruses

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Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4% of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated with bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. Single Nucleotide Polymorphism (SNP) analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses.

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“…In nature, M. arenaria is known to develop a potentially transmissible leukemia that has been described as an alternative invertebrate model for cancer ( Walker et al. 2011 ; Fernandez Robledo et al. 2019 ).…”

Section: Introductionmentioning

confidence: 99%

The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis

Plachetzki

Pankey

MacManes

et al. 2020

Genome Biology and Evolution

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Apoptosis is a fundamental feature of multicellular animals and is best understood in mammals, flies, and nematodes, with the invertebrate models being thought to represent a condition of ancestral simplicity. However, the existence of a leukemia-like cancer in the softshell clam Mya arenaria provides an opportunity to re-evaluate the evolution of the genetic machinery of apoptosis. Here we report the whole genome sequence for M. arenaria which we leverage with existing data to test evolutionary hypotheses on the origins of apoptosis in animals. We show that the ancestral bilaterian p53 locus, a master regulator of apoptosis, possessed a complex domain structure, in contrast to that of extant ecdysozoan p53s. Further, ecdysozoan taxa, but not chordates or lophotrochozoans like M. arenaria, show a widespread reduction in apoptosis gene copy number. Finally, phylogenetic exploration of apoptosis gene copy number reveals a striking linkage with p53 domain complexity across species. Our results challenge the current understanding of the evolution of apoptosis and highlight the ancestral complexity of the bilaterian apoptotic tool kit and its subsequent dismantlement during the ecdysozoan radiation.

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From the raw bar to the bench: Bivalves as models for human health

Cited by 51 publications

References 403 publications

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data

The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis

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