“Unraveling the Gut Microbiome of the Genus Herichthys (Pisces: Cichlidae): What Can We Learn from Museum Specimens?”

Mejía, Omar; Sánchez-Quinto, Andrés; Gómez-Acata, Selene; Pérez‐Miranda, Fabian; Falcón, Luisa I.

doi:10.1007/s00284-022-03047-5

Cited by 2 publications

(2 citation statements)

References 48 publications

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“…In the animal kingdom, studies are however not limited to mammals, several papers have for instance reported the composition of the gut microbiome of specimens of other animal taxa preserved in alcohol in natural history collections. This is the case of related Mexican Herichthys endemic fish species that; for several specimens; were stored for about 50 years in alcohol (Mejía et al., 2022 ), or for terrestrial snails, several of which collected 98 years before analysis (Chalifour et al., 2022 ). As in the case of dental calculus, mineralized structures are however more likely to preserve DNA for longer periods.…”

Section: Host‐associated Ancient Microbial Communitiesmentioning

confidence: 99%

Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities

Grasso,

Bianciotto,

Marmeisse

2024

Microbial Biotechnology

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By deciphering information encoded in degraded ancient DNA extracted from up to million‐years‐old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. Assembly of full‐length genomes of ancient pathogen lineages allows not only to follow historical epidemics in space and time but also to identify the acquisition of genetic features that represent landmarks in the evolution of the host–microbe interaction. Analysis of microbial community DNA extracted from essentially human paleo‐artefacts (paleofeces, dental calculi) evaluates the relative contribution of diet, lifestyle and geography on the taxonomic and functional diversity of these guilds in which have been identified species that may have gone extinct in today's human microbiome. As for non‐host‐associated environmental samples, such as stratified sediment cores, analysis of their DNA illustrates how and at which pace microbial communities are affected by local or widespread environmental disturbance. Description of pre‐disturbance microbial diversity patterns can aid in evaluating the relevance and effectiveness of remediation policies. We finally discuss how recent achievements in paleomicrobiology could contribute to microbial biotechnology in the fields of medical microbiology and food science to trace the domestication of microorganisms used in food processing or to illustrate the historic evolution of food processing microbial consortia.

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Section: Host‐associated Ancient Microbial Communitiesmentioning

confidence: 99%

Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities

Grasso,

Bianciotto,

Marmeisse

2024

Microbial Biotechnology

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“…One area of recent methodological focus for molecular analysis of preserved specimens is the specimen-associated microbial community or microbiome. Characterizing the microbiome of fluid-preserved museum specimens is a rapidly increasing area of focus due to its relevance in biology broadly, but especially in the disciplines of ecology and evolution [ 5 , 6 ]. The most common way to characterize host-associated microbiomes is through nucleic acid isolation followed by 16S rRNA gene sequencing.…”

Section: Introductionmentioning

confidence: 99%

Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens

Madison,

LaBumbard,

Woodhams

2023

PLoS ONE

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The use of museum specimens for research in microbial evolutionary ecology remains an under-utilized investigative dimension with important potential. Despite this potential, there remain barriers in methodology and analysis to the wide-spread adoption of museum specimens for such studies. Here, we hypothesized that there would be significant differences in taxonomic prediction and related diversity among sample type (museum or fresh) and sequencing strategy (medium-depth shotgun metagenomic or 16S rRNA gene). We found dramatically higher predicted diversity from shotgun metagenomics when compared to 16S rRNA gene sequencing in museum and fresh samples, with this differential being larger in museum specimens. Broadly confirming these hypotheses, the highest diversity found in fresh samples was with shotgun sequencing using the Rep200 reference inclusive of viruses and microeukaryotes, followed by the WoL reference database. In museum-specimens, community diversity metrics also differed significantly between sequencing strategies, with the alpha-diversity ACE differential being significantly greater than the same comparisons made for fresh specimens. Beta diversity results were more variable, with significance dependent on reference databases used. Taken together, these findings demonstrate important differences in diversity results and prompt important considerations for future experiments and downstream analyses aiming to incorporate microbiome datasets from museum specimens.

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“Unraveling the Gut Microbiome of the Genus Herichthys (Pisces: Cichlidae): What Can We Learn from Museum Specimens?”

Cited by 2 publications

References 48 publications

Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities

Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities

Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens

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