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Dong W, Tomita K, Sawada A, Hasebe M, Inoue M, Momose K, Nakamura T, Teraoka H. Possible Shifts in the Genetic Diversity of Red-crowned Cranes ( Grus japonensis) in Hokkaido, Japan: Indications of Continental Gene Flow. Animals (Basel) 2024; 14:1633. [PMID: 38891680 PMCID: PMC11171382 DOI: 10.3390/ani14111633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Red-crowned cranes (Grus japonensis) consist of two distinct groups: the continental population and the island population. The island population, localized in Hokkaido, Japan, exhibits very low genetic diversity due to its rapid recovery from the brink of extinction. Our previous research in 2018 highlighted a possible mating between a male from the continental population, with the Gj5 haplotype, and a female from the island population, with the Gj2 haplotype, at Hitominuma Sawmp shore in northern Hokkaido. The present study attempted to unravel the distribution of their offspring by examining the major histocompatibility complex (MHC) of this mixed breeding pair compared with samples collected from cranes in northern and southeastern Hokkaido between 2008 and 2022. The analysis identified 55 MHC types, including 10 known types in a dataset of 89 crane samples, based on amino acid sequences. A total of 58 MHC types were recognized, based on nucleotide sequences, as there were many cases in which the same amino acid sequence had different nucleotide sequences. The five DNA types of MHC in the Hitominuma Swamp male were predominantly identified in eight cranes from northern Hokkaido and one chick from southeastern Hokkaido. In addition, population genetic analysis, based on insertion/deletion (InDel) polymorphisms, indicates distinct population differentiation between the northern and southeastern regions of Hokkaido. These results suggest that genetic contributions from the continental red-crowned crane population have already been integrated into the Hokkaido populations, with a more pronounced influence in northern Hokkaido.
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Affiliation(s)
- Wenjing Dong
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (W.D.); (K.T.); (T.N.)
| | - Kai Tomita
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (W.D.); (K.T.); (T.N.)
| | - Akira Sawada
- Faculty of Human Sciences, Waseda University, Tokorozawa 359-1192, Japan;
| | - Makoto Hasebe
- NPO Sarobetsu Eco Network, Toyotomi 098-4100, Japan;
| | - Masako Inoue
- NPO Red-crowned Crane Conservancy, Kushiro 085-0036, Japan; (M.I.); (K.M.)
| | - Kunikazu Momose
- NPO Red-crowned Crane Conservancy, Kushiro 085-0036, Japan; (M.I.); (K.M.)
| | - Tatsuro Nakamura
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (W.D.); (K.T.); (T.N.)
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (W.D.); (K.T.); (T.N.)
- NPO Red-crowned Crane Conservancy, Kushiro 085-0036, Japan; (M.I.); (K.M.)
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2
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Dang X, Hanson BA, Orban ZS, Jimenez M, Suchy S, Koralnik IJ. Characterization of the brain virome in human immunodeficiency virus infection and substance use disorder. PLoS One 2024; 19:e0299891. [PMID: 38630782 PMCID: PMC11023569 DOI: 10.1371/journal.pone.0299891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/17/2024] [Indexed: 04/19/2024] Open
Abstract
Viruses can infect the brain in individuals with and without HIV-infection: however, the brain virome is poorly characterized. Metabolic alterations have been identified which predispose people to substance use disorder (SUD), but whether these could be triggered by viral infection of the brain is unknown. We used a target-enrichment, deep sequencing platform and bioinformatic pipeline named "ViroFind", for the unbiased characterization of DNA and RNA viruses in brain samples obtained from the National Neuro-AIDS Tissue Consortium. We analyzed fresh frozen post-mortem prefrontal cortex from 72 individuals without known viral infection of the brain, including 16 HIV+/SUD+, 20 HIV+/SUD-, 16 HIV-/SUD+, and 20 HIV-/SUD-. The average age was 52.3 y and 62.5% were males. We identified sequences from 26 viruses belonging to 11 viral taxa. These included viruses with and without known pathogenic potential or tropism to the nervous system, with sequence coverage ranging from 0.03 to 99.73% of the viral genomes. In SUD+ people, HIV-infection was associated with a higher total number of viruses, and HIV+/SUD+ compared to HIV-/SUD+ individuals had an increased frequency of Adenovirus (68.8 vs 0%; p<0.001) and Epstein-Barr virus (EBV) (43.8 vs 6.3%; p=0.037) as well as an increase in Torque Teno virus (TTV) burden. Conversely, in HIV+ people, SUD was associated with an increase in frequency of Hepatitis C virus, (25 in HIV+/SUD+ vs 0% in HIV+/SUD-; p=0.031). Finally, HIV+/SUD- compared to HIV-/SUD- individuals had an increased frequency of EBV (50 vs 0%; p<0.001) and an increase in TTV viral burden, but a decreased Adenovirus viral burden. These data demonstrate an unexpectedly high variety in the human brain virome, identifying targets for future research into the impact of these taxa on the central nervous system. ViroFind could become a valuable tool for monitoring viral dynamics in various compartments, monitoring outbreaks, and informing vaccine development.
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Affiliation(s)
- Xin Dang
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Barbara A. Hanson
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Zachary S. Orban
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Millenia Jimenez
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Stephen Suchy
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Igor J. Koralnik
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
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Stocker T, Ward MP, Šlapeta J. Nationwide USA re-analysis of amplicon metabarcoding targeting β-tubulin isoform-1 reveals absence of benzimidazole resistant SNPs in Ancylostoma braziliense, Ancylostoma tubaeforme and Uncinaria stenocephala. Vet Parasitol 2024; 327:110118. [PMID: 38278035 DOI: 10.1016/j.vetpar.2024.110118] [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: 11/08/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Nationwide sampling by Venkatesan and colleagues (2023) described the resistance status of the canine hookworm, Ancylostoma caninum, to benzimidazoles across the USA via β-tubulin isotype-1 amplicon metabarcoding. In this study, we aimed to use the existing public amplicon metabarcoding data and mine it for the presence of β-tubulin isotype-1 sequences that belong to hookworm species other than A. caninum. Through bioinformatics analysis we assigned species to A. caninum, Ancylostoma braziliense, Ancylostoma tubaeforme and Uncinaria stenocephala. All non-A. caninum sequences contained only the benzimidazole susceptible residues of β-tubulin isotype-1. Using two β-tubulin isotype-1 metabarcoding sequence data (assay targeting 134 and 167 codons, and assay targeting 198 and 200 codons), 2.0% (6/307) and 2.9% (9/310) individual samples had hookworms other than A. caninum (A. braziliense n = 5, A. tubaeforme n = 4 and U. stenocephala n = 2), respectively. We identified one sample containing A. braziliense in each of the Northeastern region and Midwestern region, and in three samples from the Southern region. Presence of A. tubaeforme in dog faeces is considered as pseudoparasitism. There were no statistically significant regional differences for the distribution of each species, for either of the two assays independently or combined (χ2 tests, P > 0.05). Our work demonstrates the utility of the amplicon metabarcoding for the identification of species through antemortem assays, thus resolving the dilemma of assigning hookworm species based on either post-mortem or egg sizes for the identification of hookworms.
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Affiliation(s)
- Thomas Stocker
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia
| | - Michael P Ward
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia; The University of Sydney Institute for Infectious Diseases, New South Wales 2006, Australia.
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Daouti E, Neidel V, Carbonne B, Vašková H, Traugott M, Wallinger C, Bommarco R, Feit B, Bohan DA, Saska P, Skuhrovec J, Vasconcelos S, Petit S, van der Werf W, Jonsson M. Functional redundancy of weed seed predation is reduced by intensified agriculture. Ecol Lett 2024; 27:e14411. [PMID: 38577993 DOI: 10.1111/ele.14411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 01/19/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
Intensified agriculture, a driver of biodiversity loss, can diminish ecosystem functions and their stability. Biodiversity can increase functional redundancy and is expected to stabilize ecosystem functions. Few studies, however, have explored how agricultural intensity affects functional redundancy and its link with ecosystem function stability. Here, within a continental-wide study, we assess how functional redundancy of seed predation is affected by agricultural intensity and landscape simplification. By combining carabid abundances with molecular gut content data, functional redundancy of seed predation was quantified for 65 weed genera across 60 fields in four European countries. Across weed genera, functional redundancy was reduced with high field management intensity and simplified crop rotations. Moreover, functional redundancy increased the spatial stability of weed seed predation at the field scale. We found that ecosystem functions are vulnerable to disturbances in intensively managed agroecosystems, providing empirical evidence of the importance of biodiversity for stable ecosystem functions across space.
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Affiliation(s)
- Eirini Daouti
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Veronika Neidel
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | | | - Hana Vašková
- Functional Diversity in Agro-Ecosystems, Crop Research Institute, Praha 6, Ruzyně, Czech Republic
| | - Michael Traugott
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Corinna Wallinger
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Riccardo Bommarco
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Benjamin Feit
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - David A Bohan
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne Franche-Comté, Dijon, France
| | - Pavel Saska
- Functional Diversity in Agro-Ecosystems, Crop Research Institute, Praha 6, Ruzyně, Czech Republic
| | - Jiří Skuhrovec
- Functional Diversity in Agro-Ecosystems, Crop Research Institute, Praha 6, Ruzyně, Czech Republic
| | - Sasha Vasconcelos
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sandrine Petit
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne Franche-Comté, Dijon, France
| | - Wopke van der Werf
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Mattias Jonsson
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Yokokawa A, Dong W, Momose K, Iima H, Yoshino T, Izumi K, Kawai Y, Amano T, Nakamura T, Sawada A, Endoh D, Nakajima N, Teraoka H. Analysis of Crop Consumption Using Scatological Samples from the Red-Crowned Crane Grus japonensis in Eastern Hokkaido, Japan. Animals (Basel) 2023; 13:3167. [PMID: 37893891 PMCID: PMC10603659 DOI: 10.3390/ani13203167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Total DNA extracts from the intestinal contents of 60 flying red-crowned cranes (juveniles, subadults and adults) found dead in 2006-2021, and the feces of 25 chicks collected in June and July of 2016-2018, were used for PCR reactions with primers specific for 16 crops, followed by high-throughput sequencing. The most predominant crop detected was corn in adult and subadult cranes (61.7%). Other grains (barley, wheat, soybean) (5.0-8.3%) and vegetables (tomatoes, Chinese cabbage, etc.) (1.7-6.7%) were also detected in flying cranes. Surprisingly, some of the detected crops were not grown in the Kushiro and Nemuro regions. There was no significant difference in crop intake status in winter and that in other seasons for most of the crops. Corn (28.0%), soybeans (8.0%), wheat and beet (4.0%) were detected in crane chicks in summer, though the detection rates were generally lower than those in flying cranes. Alfalfa, which is not grown in eastern Hokkaido but is used in some cattle feed, was detected in some cranes. Rice, buckwheat, adzuki beans, common beans, potatoes and carrots were not detected at any life stage, indicating the preferences of red-crowned cranes. The results suggest that red-crowned cranes in Hokkaido are dependent on dairy farmers for their feed supply.
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Affiliation(s)
- Ayaka Yokokawa
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (A.Y.); (W.D.); (T.N.); (D.E.)
| | - Wenjing Dong
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (A.Y.); (W.D.); (T.N.); (D.E.)
| | - Kunikazu Momose
- NPO Red-Crowned Crane Conservancy, 9-21 Wakatake-Cho, Kushiro 085-0036, Japan;
| | - Hiroko Iima
- Kushiro Zoo, 11 Shimoninishibetsu, Kushiro 085-0204, Japan; (H.I.); (T.Y.)
| | - Tomoo Yoshino
- Kushiro Zoo, 11 Shimoninishibetsu, Kushiro 085-0204, Japan; (H.I.); (T.Y.)
| | - Kenichi Izumi
- College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (K.I.); (T.A.)
| | - Yusuke Kawai
- Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada-cho Nishi, Obihiro 080-8555, Japan;
| | - Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (K.I.); (T.A.)
| | - Tatsuro Nakamura
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (A.Y.); (W.D.); (T.N.); (D.E.)
| | - Akira Sawada
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan; (A.S.); (N.N.)
| | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (A.Y.); (W.D.); (T.N.); (D.E.)
| | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan; (A.S.); (N.N.)
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (A.Y.); (W.D.); (T.N.); (D.E.)
- NPO Red-Crowned Crane Conservancy, 9-21 Wakatake-Cho, Kushiro 085-0036, Japan;
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Keenum I, Player R, Kralj J, Servetas S, Sussman MD, Russell JA, Stone J, Chandrapati S, Sozhamannan S. Amplicon Sequencing Minimal Information (ASqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications. J AOAC Int 2023; 106:1424-1430. [PMID: 37067472 PMCID: PMC10472743 DOI: 10.1093/jaoacint/qsad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023]
Abstract
BACKGROUND Accurate, high-confidence data is critical for assessing potential biothreat incidents. In a biothreat event, false-negative and -positive results have serious consequences. Worst case scenarios can result in unnecessary shutdowns or fatalities at an exorbitant monetary and psychological cost, respectively. Quantitative PCR assays for agents of interest have been successfully used for routine biosurveillance. Recently, there has been increased impetus for adoption of amplicon sequencing (AS) for biosurveillance because it enables discrimination of true positives from near-neighbor false positives, as well as broad, simultaneous detection of many targets in many pathogens in a high-throughput scheme. However, the high sensitivity of AS can lead to false positives. Appropriate controls and workflow reporting can help address these challenges. OBJECTIVES Data reporting standards are critical to data trustworthiness. The standards presented herein aim to provide a framework for method quality assessment in biodetection. METHODS We present a set of standards, Amplicon Sequencing Minimal Information (ASqMI), developed under the auspices of the AOAC INTERNATIONAL Stakeholder Program on Agent Detection Assays for making actionable calls in biosurveillance applications. In addition to the first minimum information guidelines for AS, we provide a controls checklist and scoring scheme to assure AS run quality and assess potential sample contamination. RESULTS Adoption of the ASqMI guidelines will improve data quality, help track workflow performance, and ultimately provide decision makers confidence to trust the results of this new and powerful technology. CONCLUSION AS workflows can provide robust, confident calls for biodetection; however, due diligence in reporting and controls are needed. The ASqMI guideline is the first AS minimum reporting guidance document that also provides the means for end users to evaluate their workflows to improve confidence. HIGHLIGHTS Standardized reporting guidance for actionable calls is critical to ensuring trustworthy data.
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Affiliation(s)
- Ishi Keenum
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Robert Player
- The Johns Hopkins University, Applied Physics Laboratory, Laurel, MD 20723, USA
- Datirium, LLC, Cincinnati, OH 45526, USA
| | - Jason Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Stephanie Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Michael D Sussman
- US Department of Agriculture, Agricultural Analytics Division, Livestock and Poultry Programs, Agricultural Marketing Service, Washington, DC 20250 USA
| | | | | | | | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD 21702, USA
- Joint Research and Development, Inc., Stafford, VA 22556, USA
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Johnson MS, Venkataram S, Kryazhimskiy S. Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes. J Mol Evol 2023; 91:263-280. [PMID: 36651964 PMCID: PMC10276077 DOI: 10.1007/s00239-022-10083-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Abstract
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.
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Affiliation(s)
- Milo S Johnson
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA.
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Guenay-Greunke Y, Trager H, Bohan DA, Traugott M, Wallinger C. Consumer identity but not food availability affects carabid diet in cereal crops. JOURNAL OF PEST SCIENCE 2023; 97:281-296. [PMID: 38223748 PMCID: PMC10784395 DOI: 10.1007/s10340-023-01620-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 01/16/2024]
Abstract
Understanding trophic interactions in agroecosystems is crucial for harnessing ecosystem services such as pest control, thus enabling a reduction in pesticide use. Carabid beetles (Coleoptera: Carabidae) have the potential to regulate not only insect pests but also weed seeds and slugs. The aim of this study was to investigate the food choice of different carabid species in the experimental setting of a cereal field with varying seed and slug prey availability during the season. In addition to varying food availability, the effects of species identity and season on carabid food choice should also be closely examined. Therefore, the gut contents of 1,120 beetles of eight carabid species were screened for the DNA of plants, aphids, springtails, earthworms and slugs via diagnostic multiplex PCR and a nested metabarcoding approach for plant species identification. Plant DNA was detected far more often (72%) than the various animal prey types (less than 12.5% each). Within the plant detections, 80 weed species were identified in the metabarcoding, with Galinsoga parviflora/quadriradiata (Galinsoga spp.-quickweeds) as the most frequently detected species. Carabid food choice was driven by their species identity and seasonality, while no effect of increased availability of seeds and slugs on their food choice was detected. While weed seeds seem to be an important food source for carabids, their availability does not directly affect the carabid diet. The importance of consumer identity and seasonality highlight the need for a diverse carabid species community for resilient pest control services. Supplementary Information The online version contains supplementary material available at 10.1007/s10340-023-01620-w.
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Affiliation(s)
- Yasemin Guenay-Greunke
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
- Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020 Innsbruck, Austria
| | - Harald Trager
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - David A. Bohan
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Michael Traugott
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Corinna Wallinger
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
- Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020 Innsbruck, Austria
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9
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Neidel V, Traugott M. Laboratory protocol is important to improve the correlation between target copies and metabarcoding read numbers of seed DNA in ground beetle regurgitates. Sci Rep 2023; 13:1995. [PMID: 36737468 PMCID: PMC9898267 DOI: 10.1038/s41598-023-29019-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
DNA metabarcoding is increasingly important for studying feeding interactions, yet it remains unresolved whether reporting read counts or occurrences is to be preferred. To address this issue for gut content samples, basic experimental data on the relationship between read numbers and initial prey DNA amounts and how both change over digestion time is needed. Using regurgitates of the carabid Pseudoophonus rufipes the digestion of Taraxacum officinale seeds was documented for 128 h post-feeding to determine how the number of (1) seed DNA copies and (2) metabarcoding reads change over digestion time, and (3) how they correlate to each other. Additionally, we tested (4) whether PCR cycle-numbers during library preparation affect this correlation. The number of copies and reads both decreased with digestion time, but variation between samples was high. Read and copy numbers correlated when using a library preparation protocol with 35 cycles (R2 = 42.0%), yet a reduction to 30 cycles might significantly improve this correlation, as indicated by additional PCR testing. Our findings show that protocol optimization is important to reduce technical distortions of read numbers in metabarcoding analysis. However, high inter-sample variation, likely due to variable digestive efficiency of individual consumers, can blur the relationship between the amount of food consumed and metabarcoding read numbers.
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Affiliation(s)
- Veronika Neidel
- Applied Animal Ecology Research Unit, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
| | - Michael Traugott
- Applied Animal Ecology Research Unit, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
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10
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Klapper R, Velasco A, Döring M, Schröder U, Sotelo CG, Brinks E, Muñoz-Colmenero M. A next-generation sequencing approach for the detection of mixed species in canned tuna. Food Chem X 2023; 17:100560. [PMID: 36845509 PMCID: PMC9943852 DOI: 10.1016/j.fochx.2023.100560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/02/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Tuna cans are relevant seafood products for which mixtures of different tuna species are not allowed according to European regulations. In order to support the prevention of food fraud and mislabelling, a next-generation sequencing methodology based on mitochondrial cytochrome b and control region markers has been tested. Analyses of defined mixtures of DNA, fresh tissue and canned tissue revealed a qualitative and, to some extent, semiquantitative identification of tuna species. While the choice of the bioinformatic pipeline had no influence in the results (p = 0.71), quantitative differences occurred depending on the treatment of the sample, marker, species, and mixture (p < 0.01). The results revealed that matrix-specific calibrators or normalization models should also be used in NGS. The method represents an important step towards a semiquantitative method for routine control of this analytically challenging food matrix. Tests of commercial samples uncovered mixed species in some cans, being not in compliance with EU regulations.
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Affiliation(s)
- Regina Klapper
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, National Reference Centre for Authentic Food, E.-C.-Baumann-Straße 20, 95326 Kulmbach, Germany,Corresponding author.
| | - Amaya Velasco
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Maik Döring
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, National Reference Centre for Authentic Food, E.-C.-Baumann-Straße 20, 95326 Kulmbach, Germany
| | - Ute Schröder
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Milk and Fish Products, Palmaille 9, 22767 Hamburg, Germany
| | - Carmen G. Sotelo
- Instituto de Investigaciones Marinas (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Erik Brinks
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Department of Microbiology and Biotechnology, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
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Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022; 11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.
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Affiliation(s)
- Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - Orla O’Sullivan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - John G. Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence:
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12
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Wu Y, Ke Y, Chan Y, Wang G, Kuo L. Integrating tissue-direct PCR into genetic identification: An upgraded molecular ecology approach to survey fern gametophytes in the field. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11462. [PMID: 35495191 PMCID: PMC9039786 DOI: 10.1002/aps3.11462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 02/11/2021] [Accepted: 12/02/2021] [Indexed: 05/14/2023]
Abstract
PREMISE The gametophytes of different fern species collected in the field can be difficult to distinguish because of their morphological similarities. Nonetheless, emerging molecular ecology techniques are starting to be used to tackle such limitations. Here, using case studies and a detailed protocol, we demonstrate a convenient methodology, tissue-direct PCR (TD-PCR), that foregoes a traditional DNA extraction and facilitates the identification of fern gametophytes, as well as enabling the elucidation of their natural distribution. METHODS Based on updated plastome information, we designed a universal primer set targeting the trnL-L-F region, which is effective across extant ferns. We used this primer set to perform TD-PCR on the case-studied populations of Taiwanese Lomariopsis gametophytes, using the generated sequences for their identification. In the case study concerning the microhabitat preference of Vaginularia junghuhnii, we designed and used a taxon-specific primer set. RESULTS Compared with approaches requiring DNA extraction, the use of TD-PCR with either universal or taxon-specific primers could save significant time, money, labor, and research materials in the genetic identification of fern gametophytes. DISCUSSION The use of modern genetic tools can aid in the identification of fern gametophytes. An updated TD-PCR strategy not only facilitates the DNA-based identification of gametophytes, but also promotes new avenues of research for investigating these plants in the field.
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Affiliation(s)
- Yi‐Hsuan Wu
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Ya‐Ting Ke
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Yuan‐Yao Chan
- College of Biological Science and TechnologyNational Yang Ming Chiao Tung UniversityHsinchu CityTaiwan
| | - Goang‐Jiun Wang
- Department of Life Science, College of Life ScienceNational Taiwan UniversityTaipei CityTaiwan
- Present address:
Goang‐Jiun Wang, Fab12 Phase7 (RD fab)Taiwan Semiconductor Manufacturing CompanyHsinchu CountyTaiwan
| | - Li‐Yaung Kuo
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
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13
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Optimization of Protocol for Construction of Fungal ITS Amplicon Library for High-Throughput Illumina Sequencing to Study the Mycobiome of Aspen Leaves. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.
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