Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community

Griffin, Tyler W.; Baer, Julia; Ward, J. Evan

doi:10.1007/s00248-020-01553-2

Cited by 21 publications

(23 citation statements)

References 55 publications

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“…As a result of the sampling scheme, the gut communities collected in these experiments were likely resident microbes. For all bivalves, dissections were conducted at least 12 h after the final feeding event, allowing a sufficient time for voidance of transient microbiota in the feces (Griffin et al, 2021). Furthermore, the microbial communities associated with seawater in the microcosms of the mussel trial showed little overlap with the communities ultimately detected in gut samples (Figure S4).…”

Section: Discussionmentioning

confidence: 99%

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An examination of the use of antibiotics as a method to experimentally perturb the microbiota of suspension‐feeding bivalves

Griffin

Pierce

Nigro

et al. 2021

Invertebrate Biology

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Suspension-feeding bivalves are critical members of aquatic ecosystems worldwide, which is why research into their host-associated microbiota is growing. Experiments that artificially diminish the native microbial communities of bivalves in vivo will be increasingly necessary to evaluate the functional role of microbes within their hosts.Previous methods to manipulate the microbiome of bivalves lack standardization and, often, verification of successful disturbance. The goal of this study was to evaluate antibiotic administration as a method for perturbing the gut microbiome of bivalves in two separate, but related, experiments. In the first, a mixture of antibiotics was delivered to eastern oysters for 4 days to probe effects on gut microbial carbon usage, diversity, and taxonomic composition. In the second, the same antibiotic mixture was administered to blue mussels for 21 days to probe effects on microbial abundance, diversity, and taxonomic composition. In both experiments, animals were administered antibiotics in isolation, and stringent sterilization methods were employed, which included sterilized seawater and microalgal food. The results of the oyster experiment revealed that antibiotics substantially reduced microbial carbon usage and perturbed community composition. In the mussel experiment, antibiotics lowered microbial abundance and species richness and significantly altered community composition. Taken together, results from the two experiments demonstrate that antibiotics can be used to effectively alter the function and composition of the gut microbial community of bivalves. Future research that aims to perturb the microbiomes of suspension-feeding animals should incorporate aspects similar to the protocols described herein. Additionally, future studies must include verification, ideally high-throughput DNA sequencing coupled with microbial quantification, that the antibiotic perturbation was successful.

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Section: Discussionmentioning

confidence: 99%

“…Although the functional role of Mycoplasmatales, especially Mycoplasma spp. and close relatives, is unconfirmed, their relative dominance in the gut of M. edulis in situ suggests an important symbiotic role (Griffin et al, 2021). Thus, the depletion of Mycoplasmatales in antibiotic-treated mussels is highly indicative of a perturbed state.…”

Section: Discussionmentioning

confidence: 99%

An examination of the use of antibiotics as a method to experimentally perturb the microbiota of suspension‐feeding bivalves

Griffin

Pierce

Nigro

et al. 2021

Invertebrate Biology

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“…It has always been controversial whether the bacterial community of the GIT can be represented by that of the feces. Studies on humans [ 45 ], bats [ 46 ], and blue mussels [ 47 ] have all demonstrated significant differences between the fecal and gut microbial communities. In this study, the bacterial community characteristics of different segments of the GIT, the stomach, small intestine, cecum, and rectum, are significantly different.…”

Section: Discussionmentioning

confidence: 99%

Microbial Biogeography along the Gastrointestinal Tract Segments of Sympatric Subterranean Rodents (Eospalax baileyi and Eospalax cansus)

Liu

Yan

Wang

et al. 2021

Animals

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In this study, based on high-throughput sequencing technology, the biodiversity and the community structure of microbiota in different GIT segments (the stomach, small intestine, cecum and rectum) of plateau zokors and Gansu zokors were studied and compared. A source tracking analysis for the microbial communities of different GIT segments was carried out using the fast expectation–maximization microbial source tracking (FEAST) method. We found that, for both species, the microbial community richness and diversity of the small intestine were almost the lowest while those of the cecum were the highest among the four segments of the GIT. Beta diversity analyses revealed that the bacterial community structures of different GIT segments were significantly different. As for the comparison between species, the bacterial community compositions of the whole GIT, as well as for each segment, were all significantly different. Source tracking conducted on both zokors indicated that the soil has little effect on the bacterial community of the GIT. A fairly high percentage of rectum source for the bacterial community of the stomach indicated that both zokors may engage in coprophagy.

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“…using biodeposit samples to represent the gut microbiota), as a clear distinction is found between the fecal microbiome and the gut microbiome of filter feeding bivalves, e.g. the blue mussel, Mytilus edulis [31]. Thus, a successful application of metagenomics in oyster microbiome studies requires the development of customized protocols for the enrichment of microbial DNA from the oyster host tissues.…”

Section: Introductionmentioning

confidence: 99%

Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome

Pimentel

Dufault‐Thompson

Russo

et al. 2020

Preprint

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Marine invertebrate microbiomes play important roles in various host and ecological processes. However, a mechanistic understanding of host-microbe interactions is so far only available for a handful of model organisms. Here, an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica, was performed using 16S rRNA gene amplicon profiling, shotgun metagenomics, and genome-scale metabolic reconstruction. A relatively low number of amplicon sequence variants (ASVs) were observed in oyster tissues compared to water samples, while high variability was observed across individual oysters and among different tissue types. Targeted metagenomic sequencing of the gut microbiota led to further characterization of a dominant bacterial taxon, the class Mollicutes, which was captured by the reconstruction of a metagenome-assembled genome (MAG). Genome-scale metabolic reconstruction of the oyster Mollicutes MAG revealed a reduced set of metabolic functions and a high reliance on the uptake of host-derived nutrients. A chitin degradation and an arginine deiminase pathway were unique to the MAG as compared to other closely related Mycoplasma genomes, indicating a distinct mechanism of carbon and energy acquisition by the oyster- associated Mollicutes. A systematic reanalysis of public eastern oyster-derived microbiome data revealed the Mollicutes as a ubiquitous taxon among adult oysters despite their general absence in larvae and biodeposit samples, suggesting potential horizontal transmission via an unknown mechanism.IMPORTANCEDespite well-documented biological significance of invertebrate microbiomes, a detailed taxonomic and functional characterization is frequently missing from many non-model marine invertebrates. By using 16S rRNA gene-based community profiling, shotgun metagenomics, and genome-scale metabolic reconstruction, this study provides an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica. Community profiling revealed a surprisingly low richness, as compared to surrounding seawater, and high variability among different tissue types and individuals. Reconstruction of a Mollicutes MAG enabled the phylogenomic positioning and functional characterization of the oyster-associated Mollicutes. Comparative analysis of the adult oyster gut, biodeposits, and oyster larvae samples indicated the potentially ubiquitous associations of the Mollicutes taxon with adult oysters. To the best of our knowledge, this study represented the first metagenomics derived functional inference of the eastern oyster microbiome. An integrated analytical procedure was developed for the functional characterization of microbiomes in other non-model host species.

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Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community

Cited by 21 publications

References 55 publications

An examination of the use of antibiotics as a method to experimentally perturb the microbiota of suspension‐feeding bivalves

An examination of the use of antibiotics as a method to experimentally perturb the microbiota of suspension‐feeding bivalves

Microbial Biogeography along the Gastrointestinal Tract Segments of Sympatric Subterranean Rodents (Eospalax baileyi and Eospalax cansus)

Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome

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