ArticlePloS one2023
Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Forensic Microbiomics and Trace Microbial Evidence: Molecular Innovations for Linking Suspects, Objects, and Environments.Microorganisms · 2026Review
- Plant-Derived Foods and Medicines as Modulators of the Gut Microbiome: Molecular Interactions and Implications for Disease and Therapy.Molecules (Basel, Switzerland) · 2026Review
- Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.Environmental microbiology reports · 2026Article
- Metagenomic Insights into the Effects of Dietary Thymol on the Structure and Function of the Rumen Microbial Community in Beef Steers Consuming Forage.Animals : an open access journal from MDPI · 2026Article
- Functional shotgun metagenomic insights into gut microbial pathway and enzyme disruptions linking metabolism, affect, cognition, and suicidal ideation in major depressive disorder.Acta neuropsychiatrica · 2026Article
- Advancing the study of microbial symbionts of amphibians and reptiles.Frontiers in amphibian and reptile science · 2026Article
- Comparative metagenomic analysis of gut microbiota inFrontiers in insect science · 2026Article
- Microbial Evolution and Systematics: Archaea and Bacteria.Progress in molecular and subcellular biology · 2026Review
- A realistic simulation-based benchmark of microbiome normalization in sample stratification and taxa-level analysis.Frontiers in bioinformatics · 2026Article
- Dual-approach analysis of gut microbiome in patients with type 1 diabetes and diabetic kidney disease.Annals of medicine · 2025Article
- Unveiling the Allium ampeloprasum rhizosphere microbiome and its functional dataset under different fertilization systems.BMC genomic data · 2025Article
- VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.Briefings in bioinformatics · 2025Article
- Bioinformatics Research in Bacterial Genomics and Metagenomics.Current issues in molecular biology · 2025Article
- Implication of Gut Mycobiome and Virome in Type-2 Diabetes Mellitus: Uncovering the Hidden Players.Phenomics (Cham, Switzerland) · 2025Review
- The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.Frontiers in microbiology · 2025Article
- Beneficial perspective onFrontiers in immunology · 2025Review
- Metagenomic insights into the microbial community of the Buhera soda pans, Zimbabwe.BMC microbiology · 2024Article
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Abstract
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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