Evaluation of Sample Preservation Approaches for Better Insect Microbiome Research According to Next-Generation and Third-Generation Sequencing

Yang, Ziwen; Men, Yu; Zhang, Jing; Liu, Zhihui; Luo, Jiu-Yang; Wang, Yanhui; Li, Wenjun; Xie, Qiang

doi:10.1007/s00248-021-01727-6

Cited by 13 publications

(9 citation statements)

References 48 publications

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“…The location explained more of the variance when compared to the binary explanatory variable of the presence of preservation (whether a sample was preserved at all [1 month, 6 month, 9-month treatments] or never preserved [fresh and starved treatments]). In another short-term study only preserving specimens up to 60 days, the effect of preservation was also detected in PERMANOVAs in explaining microbiome compositions [ 36 ]. However, this study also tested different storage mediums (e.g., ethanol, freezing, RNA Later, etc.)…”

Section: Discussionmentioning

confidence: 99%

“…There may be some microbial taxa that do not preserve well in 80% ethanol and are thus less represented in the preserved samples, also explaining why richness is lower in those short-term samples. However, multiple studies have shown that ethanol preservation is the ideal method for preserving microbiomes [36,39]. Additionally, although we believe ethanol was the only preservative used in our samples, in some older museum specimens, formalin was initially used to preserve specimens, starting in 1891 and gaining popularity into the first quarter of the twentieth century [40].…”

Section: Microbial Composition Preservation and Gut Microbiome Commun...mentioning

confidence: 99%

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Gut microbiome of century-old snail specimens stable across time in preservation

Chalifour

Elder

2022

Microbiome

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Background Museum biological specimens provide a unique means of gathering ecological information that spans wide temporal ranges. Museum specimens can also provide information on the microbial communities that persist within the host specimen. Together, these provide researchers valuable opportunities to study long-term trends and mechanisms of microbial community change. The effects of decades-long museum preservation on host-microbial communities have not been systematically assessed. The University of Colorado’s Museum of Natural History has densely sampled Oreohelix strigosa (Rocky Mountainsnail) for the past century; many are preserved in ethanol, which provides an excellent opportunity to explore how the microbiome changes across time in preservation. Results We used 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing to examine Oreohelix strigosa gut microbiomes from museum specimens across a 98-year range, as well as within short-term preservation treatments collected in 2018. Treatment groups included samples extracted fresh, without preservation; samples starved prior to extraction; and samples preserved for 1 month, 6 months, and 9 months. General microbiome composition was similar across all years. Sample groups belonging to specific years, or specific short-term treatments, showed unique associations with select bacterial taxa. Collection year was not a significant predictor of microbial richness, though unpreserved short-term treatments showed significantly higher richness than preserved treatments. While the year was a significant factor in microbiome composition, it did not explain much of the variation across samples. The location was a significant driver of community composition and explained more of the variability. Conclusions This study is the first to examine animal host-associated microbiome change across a period of nearly one century. Generally, geographic location was a greater factor in shaping gut microbiome composition, rather than a year collected. Consistent patterns across this temporal range indicate that historic specimens can answer many ecological questions surrounding the host-associated microbiome.

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Section: Discussionmentioning

confidence: 99%

Section: Microbial Composition Preservation and Gut Microbiome Commun...mentioning

confidence: 99%

Gut microbiome of century-old snail specimens stable across time in preservation

Chalifour

Elder

2022

Microbiome

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“…Location explained more of the variance when compared to the binary explanatory variable of the presence of preservation (whether a sample was preserved at all [1 month, 6 month, 9 month treatments], or never preserved [fresh and starved treatments]). In another short-term study only preserving specimens up to 60 days, the effect of preservation was also detected in their PERMANOVAs in explaining microbiome compositions [15]. However, this short-term study also tested different storage mediums (e.g.…”

Section: Microbial Composition Preservation and Gut Microbiome Commun...mentioning

confidence: 95%

“…Generally, while some Polymerase Chain Reaction (PCR) success is age-dependent, it is possible to obtain viable genetic information from host specimens up to hundreds of years old. In fact, xation, storage, sample conservation and documentation of the specimens' history, rather than extraction methodology, are often the more crucial factors for successful use of historic DNA [13,14,15]. While microbiome compositions in animal hosts are not signi cantly altered by short-term preservation [14], the effects of decades-long preservation require further study.…”

Section: Introductionmentioning

confidence: 99%

Gut Microbiome of Century-Old Snail Specimens Stable Across Time in Preservation

Chalifour

Elder

2022

Preprint

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Background Oreohelix strigosa (Rocky Mountainsnail) is a land snail found in the talus slopes of the Rocky Mountains. The University of Colorado’s Museum of Natural History has densely sampled Oreohelix for the past century; many are preserved in ethanol and available for molecular research. While microbiome compositions in other systems are not affected by short-term field season preservation, the effects of decades-long preservation have yet to be assessed. Results We used 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing to examine Oreohelix strigosa gut microbiomes from museum specimens across a 98-year range, as well as within short term preservation treatments collected in 2018. Treatment groups included samples extracted fresh, without preservation; samples starved prior to extraction; and samples preserved for 1 month, 6 months, and 9 months. General microbiome composition was similar across all years. Sample groups belonging to specific years, or specific short-term treatments, showed unique associations with select bacterial taxa. Collection year was not a significant predictor of microbial richness, though unpreserved short-term treatments showed significantly higher richness than preserved treatments. While year was a significant factor in microbiome composition, it did not explain much of the variation across samples. Other factors like location collected and drought index were also significant drivers of community composition and explained as much or more of the variability. Conclusions This study is the first to examine animal host associated microbiome change across a period of nearly one century. Generally, geographic location was a greater factor in shaping gut microbiome composition, rather than year collected. Consistent patterns across this temporal range indicate that historic specimens can answer many ecological questions surrounding the host associated microbiome.

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“…Except for the bacterial diversity of the superfamily Gerroidea in Gerromorpha, and the bacterial and fungal diversity of Cimicomorpha and Pentatomomorpha, the bacterial and fungal communities of the remaining true bugs studied here have never been included in microbial studies. In the technical aspect, both full-length bacterial 16S and fungal ITS amplicons were sequenced by the PacBio platform, which could minimize the overestimation or underestimation of community diversity ( 40 , 41 ).…”

Section: Discussionmentioning

confidence: 99%

Symbiotic Microorganisms and Their Different Association Types in Aquatic and Semiaquatic Bugs

et al. 2022

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Evaluation of Sample Preservation Approaches for Better Insect Microbiome Research According to Next-Generation and Third-Generation Sequencing

Cited by 13 publications

References 48 publications

Gut microbiome of century-old snail specimens stable across time in preservation

Gut microbiome of century-old snail specimens stable across time in preservation

Gut Microbiome of Century-Old Snail Specimens Stable Across Time in Preservation

Symbiotic Microorganisms and Their Different Association Types in Aquatic and Semiaquatic Bugs

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