References

Arıkan M and Muth T. Integrated multi-omics analyses of microbial communities: a review of the current state and future directions. Mol. Omics, 2023, 19, 607. https://doi.org/10.1039/D3MO00089C

Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ, Creer S. Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour. 2022 May;22(4):1231-1246. https://doi.org/10.1111/1755-0998.13512

Bokulich, N.A., Kaehler, B.D., Rideout, J.R. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6, 90 (2018). https://doi.org/10.1186/s40168-018-0470-z

Bolyen E, Rideout JR, Dillon MR et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37, 852–857 (2019). https://doi.org/10.1038/s41587-019-0209-9

Callahan B, McMurdie P, Rosen M et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 (2016). https://doi.org/10.1038/nmeth.3869

Compson ZG, McClenaghan B, Singer GA, Fahner NA, and Hajibabaei M, 2020. Metabarcoding from microbes to mammals: comprehensive bioassessment on a global scale. Frontiers in Ecology and Evolution, 8, p.581835. https://doi.org/10.3389/fevo.2020.581835

Couradeau E, Sasse J, Goudeau D. et al. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nat Commun 10, 2770 (2019). https://doi.org/10.1038/s41467-019-10542-0

Crick F. Central dogma of molecular biology. Nature. 1970 Aug 8;227(5258):561-3. https://doi.org/10.1038/227561a0.

Daliri EB-M, Ofosu FK, Chelliah R, Lee BH, Oh D-H. Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies. Biomolecules. 2021; 11(2):300. https://doi.org/10.3390/biom11020300

Deagle BE, Kirkwood R, and Jarman SN (2009). Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology, 18(9), 2022–2038. Portico. https://doi.org/10.1111/j.1365-294x.2009.04158.x

Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, et al. Towards Robust and Repeatable Sampling Methods in eDNA‐based Studies. Molecular Ecology Resources 18, no. 5 (June 14, 2018): 940–52. https://doi.org/10.1111/1755-0998.12907

Doble CJ, Hipperson H, Salzburger W, et al. Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika. Environmental DNA. 2020; 2: 24–41. https://doi.org/10.1002/edn3.43

Edgar RC, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, Volume 26, Issue 19, October 2010, Pages 2460–2461, https://doi.org/10.1093/bioinformatics/btq461

Edgar R, UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10, 996–998 (2013). https://doi.org/10.1038/nmeth.2604

Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, del Campo J, Dolan JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WHCF, Lara E, Le Bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet AL, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R, The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy, Nucleic Acids Res., 41 (2013), pp. 597-604. https://doi.org/10.1093/nar/gks116 

Gurbich TA, Almeida A, Beracochea M, et al. MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues. Journal of Molecular Biology. 2023 Jul;435(14):168016. https://doi.org/10.1016/j.jmb.2023.168016.

Hakimzadeh A, AbdalaAsbun A, Albanese D, Bernard M, Buchner D, Callahan B, Caporaso JG, Curd E, Djemiel C, BrandströmDurling M, Elbrecht V, Gold Z, Gweon HS, Hajibabaei M, Hildebrand F, Mikryukov V, Normandeau E, Özkurt E, M Palmer J … Anslan S (2024). A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Molecular Ecology Resources, 24, e13847. https://doi.org/10.1111/1755-0998.13847

Hleap JS, Littlefair JE, Steinke D, Hebert PDN and Cristescu ME (2021), Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes. Mol Ecol Resour, 21: 2190-2203. https://doi.org/10.1111/1755-0998.13407

Kasper S. A Beginner’s Guide to Interpreting Results from Biostatistics; 2023; https://doi.org/10.6019/tol.biostatistics-w.2023.00001.1

Kaspar S. Biostatistics: A practical introduction. European Bioinformatics Institute (EMBL-EBI); 2022. https://doi.org/10.6019/tol.biostatistics-t.2022.00001.1

Kõljalg U, Abarenkov K, Nilsson R, Larsson K, Taylor A (2019) The UNITE Database for Molecular Identification and for Communicating Fungal Species. Biodiversity Information Science and Standards 3: e37402. https://doi.org/10.3897/biss.3.37402

Kovaka S, Ou S, Jenike, KM et al. Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing. Nat Methods 20, 12–16 (2023). https://doi.org/10.1038/s41592-022-01716-8

Lan F, Demaree B, Ahmed N, Abate AR. Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat Biotechnol. 2017 Jul;35(7):640-646. https://doi.org/10.1038/nbt.3880.

Leempoel K, Hebert T, and Hadly EA. A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity. Proc Biol Sci. 2020 Jan 15;287(1918):20192353. https://doi.org/10.1098/rspb.2019.2353

Leray M, Knowlton N, Machida R J, (2022). MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences. Environmental DNA, 4, 894–907. https://doi.org/10.1002/edn3.303

Lynggaard C, Bertelsen MF, Jensen CV, Johnson MS, Frøslev TG, Olsen MT, and Bohmann K. Airborne environmental DNA for terrestrial vertebrate community monitoring. Curr Biol. 2022 Feb 7;32(3):701-707.e5. https://doi.org/10.1016/j.cub.2021.12.014

Mahmoud M, Huang Y, Garimella K. et al. Utility of long-read sequencing for All of Us. Nat Commun 15, 837 (2024). https://doi.org/10.1038/s41467-024-44804-3

Martínez Arbas S, Busi SB, Queirós P, de Nies L, Herold M, May P, Wilmes P, Muller EEL, Narayanasamy S. Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies. Front Genet. 2021 Jun 14;12:666244. https://doi.org/10.3389/fgene.2021.666244.

Marx, V. Method of the year: long-read sequencing. Nat Methods 20, 6–11 (2023). https://doi.org/10.1038/s41592-022-01730-w

Oehler, J.B., Wright, H., Stark, Z. et al. The application of long-read sequencing in clinical settings. Hum Genomics 17, 73 (2023). https://doi.org/10.1186/s40246-023-00522-3

Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM, Reier Ü and Zobel M, (2010), The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist, 188: 223-241. https://doi.org/10.1111/j.1469-8137.2010.03334.x

Paoli L, Ruscheweyh HJ, Forneris CC et al. Biosynthetic potential of the global ocean microbiome. Nature 607, 111–118 (2022). https://doi.org/10.1038/s41586-022-04862-3

Patten BC. Systems ecology and environmentalism: Getting the science right. Part I: Facets for a more holistic Nature Book of ecology, Ecological Modelling, Volume 293, 2014, Pages 4-21, ISSN 0304-3800, https://doi.org/10.1016/j.ecolmodel.2014.04.010.

Pawlowski J, Apothéloz‐Perret‐Gentil L, and Altermatt F, 2020. Environmental DNA: What’s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring. Molecular Ecology, 29(22), pp.4258-4264. https://doi.org/10.1111/mec.15643

Porter TM, (2023). terrimporter/12SvertebrateClassifier: 12S Vertebrate North American Classifier v3.0.0-ref (v3.0.0-ref). Zenodo. https://doi.org/10.5281/zenodo.7888133

Press release. NobelPrize.org. Nobel Prize Outreach AB 2024. Tue. 9 Jul 2024. https://www.nobelprize.org/prizes/chemistry/2022/press-release/

Prodan A, Tremaroli V, Brolin H, Zwinderman AH, Nieuwdorp M, Levin E. Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing. PLoS One. 2020 Jan 16;15(1):e0227434. https://doi.org/10.1371/journal.pone.0227434

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D590–D596, https://doi.org/10.1093/nar/gks1219

Richardson L, Allen B, Baldi G, et al. MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Research. 2023 Jan;51(D1):D753-D759. https://doi.org/10.1093/nar/gkac1080

Rimet F, Gusev E, Kahlert M. et al. Diat.barcode, an open-access curated barcode library for diatoms. Sci Rep 9, 15116 (2019). https://doi.org/10.1038/s41598-019-51500-6

S Sellers G, Di Muri C, Gómez A, Hänfling B. Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types v2. 2018 Jun 2. http://dx.doi.org/10.17504/protocols.io.qn9dvh6

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Appl Environ Microbiol 75. https://doi.org/10.1128/AEM.01541-09

Scholier T, Lavrinienko A, Brila I, Tukalenko E, Hindström R, Vasylenko A, Cayol C, Ecke F, Singh NJ, Forsman JT, Tolvanen A, Matala J, Huitu O, Kallio ER, Koskela E, Mappes T, and Watts PC (2023). Urban forest soils harbour distinct and more diverse communities of bacteria and fungi compared to less disturbed forest soils. Molecular Ecology, 32, 504–517. https://doi.org/10.1111/mec.16754

Simons DL, Hipperson H, Webb T, Mieszkowska N. eDNA water sampling in remote rocky shore environments v1. 2023 Jan 16. http://dx.doi.org/10.17504/protocols.io.4r3l27nkqg1y/v1

Taberlet, P., Bonin, A., Zinger, L. and Coissac, E., 2018. Environmental DNA: For biodiversity research and monitoring. Oxford University Press. https://doi.org/10.1093/oso/9780198767220.001.0001

Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E (2012) Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples. PLoS ONE 7(8): e41732. https://doi.org/10.1371/journal.pone.0041732

Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7. https://doi.org/10.1128/AEM.00062-07

Willis, A. Statistical Thinking for Microbial Ecology. Apr. 2024. https://doi.org/10.6019/tol.stats-ecology-w.2024.00001.1

Zhu T, Sato Y, Sado T, Miya M, Iwasaki W, MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years, Molecular Biology and Evolution, Volume 40, Issue 3, March 2023, msad035, https://doi.org/10.1093/molbev/msad035