Mediagraphy
Aivelo, T., and A. Norberg. 2018. Parasite–microbiota interactions
potentially affect intestinal communities in wild mammals. Journal of
Animal Ecology 87:438–447.
Belda, E., B. Coulibaly, A. Fofana, A. H. Beavogui, S. F. Traore, D. M.
Gohl, K. D. Vernick, and M. M. Riehle. 2017. Preferential suppression of
Anopheles gambiae host sequences allows detection of the mosquito
eukaryotic microbiome. Scientific Reports 7:3241.
Berry, O., C. Bulman, M. Bunce, M. Coghlan, D. C. Murray, and R. D.
Ward. 2015. Comparison of morphological and DNA metabarcoding analyses
of diets in exploited marine fishes. Marine Ecology Progress Series
540:167–181.
Boessenkool, S., L. S. Epp, J. Haile, E. Bellemain, M. Edwards, E.
Coissac, E. Willerslev, and C. Brochmann. 2012. Blocking human
contaminant DNA during PCR allows amplification of rare mammal species
from sedimentary ancient DNA. Molecular Ecology 21:1806–1815.
Callahan, B. J., P. J. McMurdie, M. J. Rosen, A. W. Han, A. J. A.
Johnson, and S. P. Holmes. 2016. DADA2: High-resolution sample inference
from Illumina amplicon data. Nature Methods 13:581–583.
Clerissi, C., S. Brunet, J. Vidal-Dupiol, M. Adjeroud, P. Lepage, L.
Guillou, J.-M. Escoubas, and E. Toulza. 2018. Protists Within Corals:
The Hidden Diversity. Frontiers in Microbiology 9:2043.
Fu, Y., J. A. Foden, C. Khayter, M. L. Maeder, D. Reyon, J. K. Joung,
and J. D. Sander. 2013. High-frequency off-target mutagenesis induced by
CRISPR-Cas nucleases in human cells. Nature Biotechnology 31:822–826.
Green, S. J., and D. Minz. 2005. Suicide Polymerase Endonuclease
Restriction, a Novel Technique for Enhancing PCR Amplification of Minor
DNA Templates. Applied and Environmental Microbiology 71:4721–4727.
Guedegbe, H. J., E. Miambi, A. Pando, J. Roman, P. Houngnandan, and C.
Rouland-Lefevre. 2009. Occurrence of fungi in combs of fungus-growing
termites (Isoptera: Termitidae, Macrotermitinae). Mycological Research
113:1039–1045.
Hadziavdic, K., K. Lekang, A. Lanzen, I. Jonassen, E. M. Thompson, and
C. Troedsson. 2014. Characterization of the 18S rRNA Gene for Designing
Universal Eukaryote Specific Primers. PLoS ONE 9.
Hugerth, L. W., E. E. L. Muller, Y. O. O. Hu, L. A. M. Lebrun, H. Roume,
D. Lundin, P. Wilmes, and A. F. Andersson. 2014. Systematic Design of
18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial
Consortia. PLOS ONE 9:e95567.
Kodio, A., E. Menu, and S. Ranque. 2020. Eukaryotic and Prokaryotic
Microbiota Interactions. Microorganisms 8:2018.
Koester, M., and R. Gergs. 2017. Laboratory Protocol for Genetic Gut
Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA
Primers. JoVE (Journal of Visualized Experiments):e56132.
Kounosu, A., K. Murase, A. Yoshida, H. Maruyama, and T. Kikuchi. 2019.
Improved 18S and 28S rDNA primer sets for NGS-based parasite detection.
Scientific Reports 9:15789.
Leung, J. M., S. A. Budischak, H. C. The, C. Hansen, R. Bowcutt, R.
Neill, M. Shellman, P. Loke, and A. L. Graham. 2018. Rapid environmental
effects on gut nematode susceptibility in rewilded mice. Plos Biology
16:e2004108.
Liu, C., R.-J. Qi, J.-Z. Jiang, M.-Q. Zhang, and J.-Y. Wang. 2019.
Development of a Blocking Primer to Inhibit the PCR Amplification of the
18S rDNA Sequences of Litopenaeus vannamei and Its Efficacy inCrassostrea hongkongensis . Frontiers in Microbiology 10.
Madeira, F., Y. M. Park, J. Lee, N. Buso, T. Gur, N. Madhusoodanan, P.
Basutkar, A. R. N. Tivey, S. C. Potter, R. D. Finn, and R. Lopez. 2019.
The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic
acids research 47:W636–W641.
Mann, A. E., F. Mazel, M. A. Lemay, E. Morien, V. Billy, M. Kowalewski,
A. Di Fiore, A. Link, T. L. Goldberg, S. Tecot, A. L. Baden, A. Gomez,
M. L. Sauther, F. P. Cuozzo, G. A. O. Rice, N. J. Dominy, R. Stumpf, R.
J. Lewis, L. Swedell, K. Amato, and L. Wegener Parfrey. 2020.
Biodiversity of protists and nematodes in the wild nonhuman primate gut.
The ISME Journal 14:609–622.
Martin, M. 2011. Cutadapt removes adapter sequences from high-throughput
sequencing reads. EMBnet.journal 17:10–12.
Mayer, T., A. Mari, J. Almario, M. Murillo-Roos, H. Syed M. Abdullah, N.
Dombrowski, S. Hacquard, E. M. Kemen, and M. T. Agler. 2021. Obtaining
deeper insights into microbiome diversity using a simple method to block
host and nontargets in amplicon sequencing. Molecular Ecology Resources
21:1952–1965.
McMurdie, P. J., and S. Holmes. 2013. phyloseq: An R Package for
Reproducible Interactive Analysis and Graphics of Microbiome Census
Data. PLOS ONE 8:e61217.
Okonechnikov, K., O. Golosova, M. Fursov, and the UGENE team. 2012.
Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics
28:1166–1167.
Paradis, E., J. Claude, and K. Strimmer. 2004. APE: Analyses of
Phylogenetics and Evolution in R language. Bioinformatics 20:289–290.
Paradis E, Schliep K (2019). “ape 5.0: an environment for modern
phylogenetics and evolutionary analyses in R.” Bioinformatics, 35,
526-528. (n.d.). .
Pires, T., D. Campos, C. Röpke, J. Sodré, S. Amadio, and J. Zuanon.
2015. Ecology and life-history of Mesonauta festivus : biological
traits of a broad ranged and abundant Neotropical cichlid. Environmental
Biology of Fishes 98:789–799.
Rojahn, J., D. M. Gleeson, E. Furlan, T. Haeusler, and J. Bylemans.
2021. Improving the detection of rare native fish species in
environmental DNA metabarcoding surveys. Aquatic Conservation: Marine
and Freshwater Ecosystems 31:990–997.
Satbige, A. S., V. R. Kasaralikar, S. C. Halmandge, and C. Rajendran.
2017. Nyctotherus sp . infection in pet turtle: a case report.
Journal of Parasitic Diseases 41:590–592.
Scheifler, M., M. Ruiz-Rodríguez, S. Sanchez-Brosseau, E. Magnanou, M.
T. Suzuki, N. West, S. Duperron, and Y. Desdevises. 2019.
Characterization of ecto- and endoparasite communities of wild
Mediterranean teleosts by a metabarcoding approach. PLOS ONE
14:e0221475.
Severo-Neto, F., and O. Froehlich. 2015. Cleaning behaviour of the
cichlid Mesonauta festivus in the Pantanal wetlands: evidence of
a potential freshwater cleaning station. Marine and Freshwater Behaviour
and Physiology 49:1–6.
Stewart, S. D., D. Kelly, L. Biessy, O. Laroche, and S. A. Wood. 2021.
Individual diet specialization drives population trophic niche responses
to environmental change in a predator fish population. Food Webs
27:e00193.
Su, M., H. Liu, X. Liang, L. Gui, and J. Zhang. 2018. Dietary Analysis
of Marine Fish Species: Enhancing the Detection of Prey-Specific DNA
Sequences via High-Throughput Sequencing Using Blocking Primers.
Estuaries and Coasts 41:560–571.
Suzuki, J., S. Kobayashi, N. Yoshida, Y. Azuma, N. Kobayashi-Ogata, D.
P. Kartikasari, Y. Yanagawa, and S. Iwata. 2020. Phylogenetic position
of Nyctotherus teleacus isolated from a tortoise
(Astrochelys radiata ) and its electron microscopic features.
Journal of Veterinary Medical Science 82:699–703.
Sylvain, F.-É., A. Holland, É. Audet‐Gilbert, A. L. Val, and N. Derome.
2019. Amazon fish bacterial communities show structural convergence
along widespread hydrochemical gradients. Molecular Ecology
28:3612–3626.
Trujillo-González, A., T. Li, J. Potts, S. Nicol, V. Allain, S. C.
Godwin, E. Vourey, A. Portal, B. Kumasi, T. Usu, A. Rodrigo, and D.
Gleeson. 2022. Can Stomach Content and Microbiomes of Tuna Provide Near
Real-Time Detection of Ecosystem Composition in the Pacific Ocean?
Frontiers in Marine Science 9.
Vestheim, H., and S. N. Jarman. 2008. Blocking primers to enhance PCR
amplification of rare sequences in mixed samples – a case study on prey
DNA in Antarctic krill stomachs. Frontiers in Zoology 5:12.
Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naïve
Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New
Bacterial Taxonomy. Applied and Environmental Microbiology
73:5261–5267.
Zhong, K. X., A. Cho, C. M. Deeg, A. M. Chan, and C. A. Suttle. 2021.
Revealing the composition of the eukaryotic microbiome of oyster spat by
CRISPR-Cas Selective Amplicon Sequencing (CCSAS). Microbiome 9:1–17.