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Nunes JS, Pimentel-Vera LN, Silva SB, de Bem Prunes B, Rados PV, Visioli F. Comparison of different DNA preservation solutions for oral cytological samples. Arch Oral Biol 2024; 158:105867. [PMID: 38056230 DOI: 10.1016/j.archoralbio.2023.105867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
OBJECTIVE The objective of this study was to compare the DNA preservation capacity of buccal mucosa exfoliated cells when stored in different solutions under varying time and temperature conditions. DESIGN DNA preservation solutions, including Dimethyl sulphoxide disodium-EDTA-saturated NaCl (DESS), Tris-EDTA-NaCl-Tween20 buffer (TENT), Nucleic Acid Preservation Buffer (NAP), and phosphate-buffered saline (PBS), were prepared. Buccal mucosa cells from a single patient were collected, dispensed into these solutions, and stored at room temperature (RT) and 4 °C for 24 h, 72 h, 30 days, 90 days, and 180 days. DNA was extracted using the salting-out method and the QIAamp DNA Mini Kit. DNA concentration and purity were determined using the QuBit device and NanoDrop, while DNA integrity was assessed using the Agilent 4200 TapeStation system. The ability to amplify the IFNA primer was also evaluated by PCR. RESULTS The salting-out method yielded better concentration and purity results, with PBS, TENT, and DESS buffers demonstrating superior concentration values when stored at 4 °C, resulting in mean values exceeding 10 ng/μL for up to 30 days. DESS consistently exhibited the best integrity values over time for both temperature conditions. Amplification capacity was enhanced when samples were stored at 4 °C. When stored at RT, PBS achieved 100% amplification within 24 h. NAP yielded the poorest results. CONCLUSION In the context of long-term preservation, the DESS buffer emerges as the most effective solution, maintaining requisite DNA quality and quantity standards for up to 30 days at RT and up to 3 months at 4 °C.
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Affiliation(s)
- Júlia Silveira Nunes
- Department of Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | | | - Sabrina Barcelos Silva
- Department of Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Bianca de Bem Prunes
- Department of Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Pantelis Varvaki Rados
- Department of Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fernanda Visioli
- Department of Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.
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2
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Kyle KE, Puckett SP, Caraballo-Rodríguez AM, Rivera-Chávez J, Samples RM, Earp CE, Raja HA, Pearce CJ, Ernst M, van der Hooft JJJ, Adams ME, Oberlies NH, Dorrestein PC, Klassen JL, Balunas MJ. Trachymyrmex septentrionalis ants promote fungus garden hygiene using Trichoderma-derived metabolite cues. Proc Natl Acad Sci U S A 2023; 120:e2219373120. [PMID: 37319116 PMCID: PMC10288546 DOI: 10.1073/pnas.2219373120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/04/2023] [Indexed: 06/17/2023] Open
Abstract
Fungus-growing ants depend on a fungal mutualist that can fall prey to fungal pathogens. This mutualist is cultivated by these ants in structures called fungus gardens. Ants exhibit weeding behaviors that keep their fungus gardens healthy by physically removing compromised pieces. However, how ants detect diseases of their fungus gardens is unknown. Here, we applied the logic of Koch's postulates using environmental fungal community gene sequencing, fungal isolation, and laboratory infection experiments to establish that Trichoderma spp. can act as previously unrecognized pathogens of Trachymyrmex septentrionalis fungus gardens. Our environmental data showed that Trichoderma are the most abundant noncultivar fungi in wild T. septentrionalis fungus gardens. We further determined that metabolites produced by Trichoderma induce an ant weeding response that mirrors their response to live Trichoderma. Combining ant behavioral experiments with bioactivity-guided fractionation and statistical prioritization of metabolites in Trichoderma extracts demonstrated that T. septentrionalis ants weed in response to peptaibols, a specific class of secondary metabolites known to be produced by Trichoderma fungi. Similar assays conducted using purified peptaibols, including the two previously undescribed peptaibols trichokindins VIII and IX, suggested that weeding is likely induced by peptaibols as a class rather than by a single peptaibol metabolite. In addition to their presence in laboratory experiments, we detected peptaibols in wild fungus gardens. Our combination of environmental data and laboratory infection experiments strongly support that peptaibols act as chemical cues of Trichoderma pathogenesis in T. septentrionalis fungus gardens.
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Affiliation(s)
- Kathleen E. Kyle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT06269
| | - Sara P. Puckett
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093-0657
| | - José Rivera-Chávez
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402
- Department of Natural Products, Instituto de Química, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, 04510, Mexico
| | - Robert M. Samples
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269
- Department of Chemistry, University of Connecticut, Storrs, CT06269
| | - Cody E. Earp
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402
| | | | - Madeleine Ernst
- Department of Congenital Disorders, Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Statens Serum Institut, 2300Copenhagen, Denmark
| | - Justin J. J. van der Hooft
- Bioinformatics Group, Wageningen University & Research, 6708PBWageningen, the Netherlands
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Madison E. Adams
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT06269
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093-0657
- Department of Pharmacology, University of California San Diego, La Jolla, CA92093-0657
- Department of Pediatrics, University of California San Diego, La Jolla, CA92093-0657
| | - Jonathan L. Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT06269
| | - Marcy J. Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI48109
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3
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Abstract
Within social insect colonies, microbiomes often differ between castes due to their different functional roles and between colony locations. Trachymyrmex septentrionalis fungus-growing ants form colonies throughout the eastern United States and northern Mexico that include workers, female and male alates (unmated reproductive castes), larvae, and pupae. How T. septentrionalis microbiomes vary across this geographic range and between castes is unknown. Our sampling of individual ants from colonies across the eastern United States revealed a conserved T. septentrionalis worker ant microbiome and revealed that worker ant microbiomes are more conserved within colonies than between them. A deeper sampling of individual ants from two colonies that included all available castes (pupae, larvae, workers, and female and male alates), from both before and after adaptation to controlled laboratory conditions, revealed that ant microbiomes from each colony, caste, and rearing condition were typically conserved within but not between each sampling category. Tenericute bacterial symbionts were especially abundant in these ant microbiomes and varied widely in abundance between sampling categories. This study demonstrates how individual insect colonies primarily drive the composition of their microbiomes and shows that these microbiomes are further modified by developmental differences between insect castes and the different environmental conditions experienced by each colony. IMPORTANCE This study investigates microbiome assembly in the fungus-growing ant Trachymyrmex septentrionalis, showing how colony, caste, and lab adaptation influence the microbiome and revealing unique patterns of mollicute symbiont abundance. We find that ant microbiomes differ strongly between colonies but less so within colonies. Microbiomes of different castes and following lab adaptation also differ in a colony-specific manner. This study advances our understanding of the nature of individuality in social insect microbiomes and cautions against the common practice of only sampling a limited number of populations to understand microbiome diversity and function.
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4
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Hua H, Meydan C, Afshin EE, Lili LN, D’Adamo CR, Rickard N, Dudley JT, Price ND, Zhang B, Mason CE. A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling. Front Immunol 2022; 13:889702. [PMID: 35711426 PMCID: PMC9196042 DOI: 10.3389/fimmu.2022.889702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.
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Affiliation(s)
- Hui Hua
- Thorne HealthTech, New York, NY, United States
- *Correspondence: Hui Hua, ; Christopher E. Mason,
| | - Cem Meydan
- Thorne HealthTech, New York, NY, United States
| | | | | | - Christopher R. D’Adamo
- Department of Family and Community Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | | | - Nathan D. Price
- Thorne HealthTech, New York, NY, United States
- Institute for Systems Biology, Seattle, WA, United States
| | - Bodi Zhang
- Thorne HealthTech, New York, NY, United States
| | - Christopher E. Mason
- Thorne HealthTech, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, United States
- *Correspondence: Hui Hua, ; Christopher E. Mason,
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5
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Sorensen JW, Zinke LA, ter Horst AM, Santos-Medellín C, Schroeder A, Emerson JB. DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes. mSystems 2021; 6:e0061421. [PMID: 34491084 PMCID: PMC8547471 DOI: 10.1128/msystems.00614-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
The small genomes of most viruses make it difficult to fully capture viral diversity in metagenomes dominated by DNA from cellular organisms. Viral size fraction metagenomics (viromics) protocols facilitate the enrichment of viral DNA from environmental samples, and these protocols typically include DNase treatment of the post-0.2-μm-filtered viromic fraction to remove contaminating free DNA prior to virion lysis. However, DNase may also remove desirable viral genomic DNA (e.g., contained in virions compromised due to frozen storage or laboratory processing), suggesting that DNase-untreated viromes might be useful in some cases. In order to understand how virome preparation with and without DNase treatment influences the resultant data, here, we compared 15 soil viromes (7 DNase treated and 8 untreated) from 8 samples collected from agricultural fields prior to tomato planting. DNase-treated viromes yielded significantly more assembled viral contigs, contained significantly less nonviral microbial DNA, and recovered more viral populations (viral operational taxonomic units [vOTUs]) through read mapping. However, DNase-treated and untreated viromes were statistically indistinguishable in terms of ecological patterns across viral communities. Although the results suggest that DNase treatment is preferable where possible, in comparison to previously reported total metagenomes from the same samples, both DNase-treated and untreated viromes were significantly enriched in viral signatures by all metrics compared, including a 225-times-higher proportion of viral reads in untreated viromes compared to total metagenomes. Thus, even without DNase treatment, viromics was preferable to total metagenomics for capturing viral diversity in these soils, suggesting that preparation of DNase-untreated viromes can be worthwhile when DNase treatment is not possible. IMPORTANCE Viromics is becoming an increasingly popular method for characterizing soil viral communities. DNase treatment of the viral size fraction prior to DNA extraction is meant to reduce contaminating free DNA and is a common step within viromics protocols to ensure that sequences are of viral origin. However, some samples may not be amenable to DNase treatment due to viral particles being compromised either in storage (i.e., frozen) or during other sample processing steps. To date, the effect of DNase treatment on the recovery of viruses and downstream ecological interpretations of soil viral communities is not thoroughly understood. This work sheds light on these questions and indicates that while DNase treatment of soil viromes improves the recovery of viral populations, this improvement is modest in comparison to the gains made by viromics over total soil metagenomics. Furthermore, DNase treatment may not be necessary to observe the ecological patterns structuring soil viral communities.
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Affiliation(s)
- Jackson W. Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Laura A. Zinke
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Anneliek M. ter Horst
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | | | - Alena Schroeder
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Joanne B. Emerson
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
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6
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Carvalhais LC, Dennis PG, Poudel A, Birt HWG, Bhuiyan SA, Card SD, Joyce PA. Simple solution to preserve plant samples for microbiome analyses. Mol Ecol Resour 2021; 22:1055-1064. [PMID: 34695303 DOI: 10.1111/1755-0998.13538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 09/28/2021] [Accepted: 10/19/2021] [Indexed: 11/27/2022]
Abstract
Culture-independent survey techniques are fundamental tools when assessing plant microbiomes. These methods rely on DNA that is carefully preserved after collecting samples to achieve meaningful results. Immediately freezing samples to -80°C after collection is considered one of the most robust methods for preserving samples before DNA extraction but is often impractical. Preservation solutions can solve this problem, but commercially available products are expensive, and there is limited data comparing their efficacy with other preservation methods. In this study, we compared the impact of three methods of sample preservation on plant microbiome surveys: (1) RNAlater, a proprietary preservative, (2) a home-made salt-saturated dimethyl sulphoxide preservation solution (DESS), and (3) freezing at -80°C. DESS-preserved samples, stored at room temperature for up to four weeks, did not show any significant differences to samples frozen at -80°C, while RNAlater inflated bacterial alpha diversity. Preservation treatments did not distinctively influence fungal alpha diversity. Our results demonstrate that DESS is a versatile and inexpensive preservative of DNA in plant material for diversity analyses of fungi and bacteria.
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Affiliation(s)
- Lilia C Carvalhais
- Sugar Research Australia Ltd., Indooroopilly, Qld, Australia.,Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Brisbane, Qld, Australia.,School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Qld, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Amrit Poudel
- Sugar Research Australia Ltd., Indooroopilly, Qld, Australia
| | - Henry W G Birt
- School of Earth and Environmental Sciences, University of Queensland, Brisbane, Qld, Australia
| | - Shamsul A Bhuiyan
- Sugar Research Australia Ltd., Indooroopilly, Qld, Australia.,Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Brisbane, Qld, Australia
| | - Stuart D Card
- Resilient Agriculture, AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Priya A Joyce
- Sugar Research Australia Ltd., Indooroopilly, Qld, Australia.,The University of Queensland, Brisbane, Qld, Australia
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7
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Green EA, Smedley SR, Klassen JL. North American Fireflies Host Low Bacterial Diversity. MICROBIAL ECOLOGY 2021; 82:793-804. [PMID: 33609143 DOI: 10.1007/s00248-021-01718-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Although there are numerous studies of firefly mating flashes, lantern bioluminescence, and anti-predation lucibufagin metabolites, almost nothing is known about their microbiome. We therefore used 16S rRNA community amplicon sequencing to characterize the gut and body microbiomes of four North American firefly taxa: Ellychnia corrusca, the Photuris versicolor species complex, Pyractomena borealis, and Pyropyga decipiens. These firefly microbiomes all have very low species diversity, often dominated by a single species, and each firefly type has a characteristic microbiome. Although the microbiomes of male and female fireflies did not differ from each other, Ph. versicolor gut and body microbiomes did, with their gut microbiomes being enriched in Pseudomonas and Acinetobacter. Ellychnia corrusca egg and adult microbiomes were unique except for a single egg microbiome that shared a community type with E. corrusca adults, which could suggest microbial transmission from mother to offspring. Mollicutes that had been previously isolated from fireflies were common in our firefly microbiomes. These results set the stage for further research concerning the function and transmission of these bacterial symbionts.
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Affiliation(s)
- Emily A Green
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | | | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
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8
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Zaiko A, Greenfield P, Abbott C, von Ammon U, Bilewitch J, Bunce M, Cristescu ME, Chariton A, Dowle E, Geller J, Ardura Gutierrez A, Hajibabaei M, Haggard E, Inglis GJ, Lavery SD, Samuiloviene A, Simpson T, Stat M, Stephenson S, Sutherland J, Thakur V, Westfall K, Wood SA, Wright M, Zhang G, Pochon X. Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment. Mol Ecol Resour 2021; 22:519-538. [PMID: 34398515 DOI: 10.1111/1755-0998.13485] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/21/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022]
Abstract
Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future biodiversity studies using metabarcoding.
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Affiliation(s)
- Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia.,Environmental (e)DNA and Biomonitoring Lab, Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Cathryn Abbott
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ulla von Ammon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Jaret Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hataitai, Wellington, New Zealand
| | - Michael Bunce
- Environmental Protection Authority, Wellington, New Zealand
| | | | - Anthony Chariton
- Environmental (e)DNA and Biomonitoring Lab, Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Eddy Dowle
- School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jonathan Geller
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | | | | | - Emmet Haggard
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | - Graeme J Inglis
- National Institute of Water & Atmospheric Research Ltd (NIWA), Christchurch, New Zealand
| | - Shane D Lavery
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Tiffany Simpson
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Michael Stat
- The University of Newcastle, Newcastle, New South Wales, Australia
| | - Sarah Stephenson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Judy Sutherland
- National Institute of Water & Atmospheric Research Ltd (NIWA), Hataitai, Wellington, New Zealand
| | - Vibha Thakur
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kristen Westfall
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | | | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
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9
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Pavlovska M, Prekrasna I, Parnikoza I, Dykyi E. Soil Sample Preservation Strategy Affects the Microbial Community Structure. Microbes Environ 2021; 36. [PMID: 33563868 PMCID: PMC7966943 DOI: 10.1264/jsme2.me20134] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Sample preservation is a critical procedure in any research that relies on molecular tools and is conducted in remote areas. Sample preservation options include low and room temperature storage, which require freezing equipment and specific buffering solutions, respectively. The aim of the present study was to investigate whether DNA/RNA Shield 1x from Zymo Research and DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution performed similarly to snap freezing in liquid nitrogen. Soil samples were stored for 1 month in each of the buffers and without any solution at a range of temperatures: –20, +4, and +23°C. All treatments were compared to the “optimal treatment”, namely, snap freezing in liquid nitrogen. The quality and quantity of DNA were analyzed, and the microbial community structure was investigated in all samples. The results obtained indicated that the quantity and integrity of DNA was preserved well in all samples; however, the taxonomic distribution was skewed in samples stored without any solution at ambient temperatures, particularly when analyses were performed at lower taxonomic levels. Although both solutions performed equally well, sequencing output and OTU numbers in DESS-treated samples were closer to those snap frozen with liquid nitrogen. Furthermore, DNA/RNA Shield-stored samples performed better for the preservation of rare taxa.
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Affiliation(s)
- Mariia Pavlovska
- State Institution National Antarctic Scientific Center.,National University of Life and Environmental Sciences of Ukraine
| | | | | | - Evgen Dykyi
- State Institution National Antarctic Scientific Center
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10
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Stracke K, Adisakwattana P, Phuanukoonnon S, Yoonuan T, Poodeepiyasawat A, Dekumyoy P, Chaisiri K, Roth Schulze A, Wilcox S, Karunajeewa H, Traub RJ, Jex AR. Effective low-cost preservation of human stools in field-based studies for helminth and microbiota analysis. Int J Parasitol 2021; 51:741-748. [PMID: 33774039 DOI: 10.1016/j.ijpara.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/19/2022]
Abstract
Molecular studies of gastrointestinal infections or microbiotas require either rapid sample processing or effective interim preservation. This is difficult in remote settings in low-income countries, where the majority of the global infectious disease burden exists. Processing or freezing of samples immediately upon collection is often not feasible and the cost of commercial preservatives is prohibitive. We compared fresh freezing (the 'gold standard' method), with low-cost chemical preservation in (i) a salt-based buffer consisting of DMSO, EDTA and NaCl (DESS) or (ii) 2.5% potassium dichromate (PD), for soil-transmitted helminth detection and microbiota characterisation in pre-school and school-aged children from north-western Thailand. Fresh frozen samples were frozen at -20°C on collection and maintained at -80°C within ~3 days of collection until molecular analysis, with international shipping on dry ice. In contrast, chemically preserved samples were collected and stored at ~4°C, transported on wet ice and only stored at -20°C on arrival in Australia ~8 weeks after collection, with international shipping on wet ice. DESS and PD provided better sensitivity for STH diagnosis, estimating higher infection rates (>80% for Ascaris lumbricoides and >60% for Trichuris trichiura; versus 56% and 15% for these parasites in fresh frozen samples) and egg abundance (inferred as gene copy number estimates). All methods performed similarly for microbiota preservation, showing no significant differences in alpha-diversity based on overall richness or inverted Simpson's Index. All three methods performed similarly for RNA and protein preservation in a small subset of samples. Overall, DESS provided the best performance, with the added benefit of being non-toxic, compared with PD, hence making it particularly applicable for studies in remote and resource-poor settings.
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Affiliation(s)
- Katharina Stracke
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Department of Medical Biology, The Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Poom Adisakwattana
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Suparat Phuanukoonnon
- Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tippayarat Yoonuan
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Akkarin Poodeepiyasawat
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paron Dekumyoy
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kittipong Chaisiri
- Department of Helminthology, Faculty for Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Harin Karunajeewa
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Department of Medicine - Western Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca J Traub
- Faculty for Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Aaron R Jex
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Faculty for Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
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A Recent Overview of Microbes and Microbiome Preservation. Indian J Microbiol 2020; 60:297-309. [PMID: 32655197 DOI: 10.1007/s12088-020-00880-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 05/06/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes are mediators in almost all ecosystem processes and act as a pivotal game changer in various ecological activities, globally. Therefore, understanding of microbial community structure and related functions in different environmental and micro-environmental niches is not only critical, but also a matter of greatest importance. Due to our inability to cultivate and preserve all sorts of microorganisms, we are losing some ecologically and industrially relevant components of microbial community, due to extinction caused by environmental and climatic variations with time. Intact sample and microbiome preservation are crucial for future cultivation as well as to study the effects of ecological and climatic variations on community functionality and shift with time, using OMICS. Although, methods for pure culture preservation are almost optimized, the techniques of microbiome preservation still remain as an unsolved challenge for microbiologists due to technical and physiological constraints. Present article discusses, recent approaches of microbial preservation with special reference to intact sample, mixed culture and microbiome preservation. It also incorporates recent practices used to achieve the highest viability and metabolic activities in long-term preserved microbiome.
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12
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Vavourakis CD, Mehrshad M, Balkema C, van Hall R, Andrei AŞ, Ghai R, Sorokin DY, Muyzer G. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake. BMC Biol 2019; 17:69. [PMID: 31438955 PMCID: PMC6704655 DOI: 10.1186/s12915-019-0688-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/09/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions. RESULTS Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes. CONCLUSIONS The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.
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Affiliation(s)
- Charlotte D Vavourakis
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Cherel Balkema
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Rutger van Hall
- Department of Ecosystem & Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
- Department of Biotechnology, Environmental Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands.
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Gołębiewski M, Tretyn A. Generating amplicon reads for microbial community assessment with next‐generation sequencing. J Appl Microbiol 2019; 128:330-354. [DOI: 10.1111/jam.14380] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022]
Affiliation(s)
- M. Gołębiewski
- Plant Physiology and Biotechnology Nicolaus Copernicus University Toruń Poland
- Centre for Modern Interdisciplinary Technologies Nicolaus Copernicus University Toruń Poland
| | - A. Tretyn
- Plant Physiology and Biotechnology Nicolaus Copernicus University Toruń Poland
- Centre for Modern Interdisciplinary Technologies Nicolaus Copernicus University Toruń Poland
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