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Literature

 
 
Please find below a selection of scientific peer reviewed papers where the next generation sequencing department of Microsynth has been involved.

Targeted Sequencing

Amplicon Metagenomics
 
2024
  • Raul Rivera-Chacon, Cátia Pacífico, Sara Ricci, Renee M. Petri, Nicole Reisinger, Qendrim Zebeli, Ezequias Castillo-Lopez, Prolonged feeding of high-concentrate diet remodels the hindgut microbiome and modulates nutrient degradation in the rumen and the total gastrointestinal tract of cows, Journal of Dairy Science, Volume 107, Issue 11, 2024, Pages 9235-9250, ISSN 0022-0302, https://doi.org/10.3168/jds.2024-24919.
  • Zélia Bontemps, Mylène Hugoni, Yvan Moënne-Loccoz, Ecological impact of mechanical cleaning method to curb black stain alterations on Paleolithic cave walls, International Biodeterioration & Biodegradation, Volume 191, 2024, 105797, ISSN 0964-8305, https://doi.org/10.1016/j.ibiod.2024.105797.
  • Schlunck G, Maier P, Maier B, Maier W, Strempel S, Reinhard T, Heinzelmann S. Next-Generation Sequencing of the Human Aqueous Humour Microbiome. Int J Mol Sci. 2024 Jun 1;25(11):6128. doi: 10.3390/ijms25116128. PMID: 38892316; PMCID: PMC11173048.
  • Pushkareva E, Elster J, Kudoh S, Imura S and Becker B (2024) Microbial community composition of terrestrial habitats in East Antarctica with a focus on microphototrophs. Front. Microbiol. 14:1323148. doi: 10.3389/fmicb.2023.1323148
  • Mariana Erthal rocha, Norberto Mangiavacchi, Marcia Marques et al. Succession from acetoclastic to hydrogenotrophic microbial community during sewage sludge anaerobic digestion for bioenergy production, 05 January 2024, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-3722725/v1]
2022
  • Springer, A., Wagner, L., Koehler, S. et al. Modulation of the porcine intestinal microbiota in the course of Ascaris suum infection. Parasites Vectors 15, 433 (2022). https://doi.org/10.1186/s13071-022-05535-w
  • Ricci, S., Petri, R.M., Pacífico, C. et al. Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism. Sci Rep 12, 13812 (2022). https://doi.org/10.1038/s41598-022-17445-z
2019
  • Matthias T. Buhmann, Dominik Abt, Oliver Nolte, Thomas R. Neu, Sebastian Strempel, Werner C. Albrich, Patrick Betschart, Valentin Zumstein, Antonia Neels, Katharina Maniura-Weber, Qun Ren (2019) Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load. Microbiome 7:60, https://doi.org/10.1186/s40168-019-0674-x
2017
  • Petri RM, Pourazad P, Khiaosa-ard R, Klevenhusen F, Metzler-Zebeli BU, Zebeli Q (2017) Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling. PLoS ONE 12(8): e0182271. https://doi.org/10.1371/journal.pone.0182271
  • Schären, M. et al., Differential effects of monensin and a blend of essential oils on rumen microbiota composition of transition dairy cows, Journal of Dairy Science , Volume 100 , Issue 4 , 2765 - 2783
  • Schären M, Kiri K, Riede S, Gardener M, Meyer U, Hummel J, Urich T, Breves G and Dänicke S (2017) Alterations in the Rumen Liquid-, Particle- and Epithelium-Associated Microbiota of Dairy Cows during the Transition from a Silage- and Concentrate-Based Ration to Pasture in Spring.
    Front. Microbiol. 8:744. doi: 10.3389/fmicb.2017.00744
2015
  • Wilkins, L. G. E. et al. Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures. Sci. Rep. 5, 17084; doi: 10.1038/srep17084 (2015).
CRISPR/Cas9
 
2020
  • Pharmacological validation of targets regulating CD14 during macrophage differentiation, Jimenez-Duran, Gisela et al., eBioMedicine, Volume 61, 103039
2016
  • Cross, B. C. S. et al. Increasing the performance of pooled CRISPR–Cas9 drop-out screening. Sci. Rep. 6, 31782; doi: 10.1038/srep31782 (2016).
2015
  • Ulrike Mock, Rafał Machowicz, Ilona Hauber, Stefan Horn, Pierre Abramowski, Belinda Berdien, Joachim Hauber, Boris Fehse; mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5, Nucleic Acids Research, Volume 43, Issue 11, 23 June 2015, Pages 5560–5571, https://doi.org/10.1093/nar/gkv469
ChIP Seq
 
2020
  • Sunny, D.E., Hammer, E., Strempel, S. et al. Nup133 and ERα mediate the differential effects of hyperoxia-induced damage in male and female OPCs. Mol Cell Pediatr 7, 10 (2020). https://doi.org/10.1186/s40348-020-00102-8

Transcriptome Sequencing

Reference Transcriptome
 
2024
  • Murovec, U., Accetto, T. Transcriptomic analysis of polysaccharide utilization loci reveals substrate preferences in ruminal generalists Segatella bryantii TF1-3 and Xylanibacter ruminicola KHP1. BMC Genomics 25, 495 (2024). https://doi.org/10.1186/s12864-024-10421-z
2017
  • Neves, R.C., Guimaraes, J.C., Strempel, S. et al., Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis, Org Divers Evol (2017) 17: 111. https://doi.org/10.1007/s13127-016-0315-1

 

Metatranscriptomics

2021

  • Huang Y,Straub D,Blackwell N, Kappler A, Kleindienst S. 2021. Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS. Appl Environ Microbiol 87:e00496-21
    https://doi.org/10.1128/AEM.00496-21
RNA Seq
 
2020
  • Balogh, E. et al. Pseudouridylation defect due to DKC1 and NOP10 mutations causes nephrotic syndrome with cataracts, hearing impairment, and enterocolitis. Proc. Natl. Acad. Sci. U. S. A. 117, 15137–15147 (2020). https://www.pnas.org/doi/full/10.1073/pnas.2002328117
2016
2015
  • Sandrine Borgeaud, Lisa C. Metzger, Tiziana Scrignari, Melanie Blokesch, The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer, Science 02 Jan 2015: Vol. 347, Issue 6217, pp. 63-67. DOI: 10.1126/science.1260064
Small RNA Seq
 

2020

  • Boubaker G, Strempel S, Hemphill A, Müller N, Wang J, Gottstein B, et al. (2020) Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice. PLoS Negl Trop Dis 14(5): e0007640. https://doi.org/10.1371/journal.pntd.0007640
2018
  • Bhupesh K. Prusty, Nitish Gulve, Suvagata Roy Chowdhury, Michael Schuster, Sebastian Strempel, Vincent Descamps, Thomas Rudel (2018) HHV-6 encoded small non-coding RNAs define an intermediate and early stage in viral reactivation, npj Genomic Medicine 3:25, https://www.nature.com/articles/s41525-018-0064-5

Genome Sequencing

2024
  • Zsolt Balázs, Panagiotis Balermpas, Ivna Ivanković, Jonas Willmann, Todor Gitchev, Asher Bryant, Matthias Guckenberger, Michael Krauthammer, Nicolaus Andratschke,
    Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy, Radiotherapy and Oncology,
    Volume 197, 2024, 110364, ISSN 0167-8140, https://doi.org/10.1016/j.radonc.2024.110364.
  • Ana B. García-Martín, Lisandra Aguilar-Bultet, Elena Gómez-Sanz, Monica Alt Hug, Reto Furger, Lucas Eichenberger, Ruth Schindler, Ingrid Steffen, Adrian Egli, Tanja Stadler, Claudia Bagutti, Sarah Tschudin-Sutter, Prospective One-Health investigation into low-abundant extended-spectrum β-lactamase producing Enterobacterales enables detection of potential dissemination events and persistence, Science of The Total Environment, Volume 950, 2024, 175078, ISSN 0048-9697, https://doi.org/10.1016/j.scitotenv.2024.175078. (https://www.sciencedirect.com/science/article/pii/S0048969724052288)
2022
  • Jean-Baptiste Vuillemenot, Maxime Bour, Racha Beyrouthy, Richard Bonnet, Maria-Halima Laaberki, Xavier Charpentier, Raymond Ruimy, Patrick Plésiat, Anaïs Potron, Genomic analysis of CTX-M-115 and OXA-23/-72 co-producing Acinetobacter baumannii, and their potential to spread resistance genes by natural transformation, Journal of Antimicrobial Chemotherapy, Volume 77, Issue 6, June 2022, Pages 1542–1552, https://doi.org/10.1093/jac/dkac099
2019
  • Noémie Matthey, Sandrine Stutzmann, Candice Stoudmann, Nicolas Guex, Christian Iseli, Melanie Blokesch (2019) Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae. eLife 8:e48212 DOI: 10.7554/eLife.48212
2015
  • Grass, R. N., Heckel, R., Puddu, M., Paunescu, D. and Stark, W. J. (2015), Robust Chemical Preservation of Digital Information on DNA in Silica with Error-Correcting Codes. Angew. Chem. Int. Ed., 54: 2552–2555. doi:10.1002/anie.201411378
 

Whole Genome Metagenomics

2024

  • Genath, A., Hackmann, C., Denkel, L. et al. The genetic relationship between human and pet isolates: a core genome multilocus sequence analysis of multidrug-resistant bacteria. Antimicrob Resist Infect Control 13, 107 (2024). https://doi.org/10.1186/s13756-024-01457-7

Oxford Nanopore Sequencing

2024
  • Cecile Lorrain, Alice Feurtey, Julien Alassimone et al. A novel genome-wide association approach reveals wheat pathogen genes involved in host specialization, 04 June 2024, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-4486034/v1]
  • Bultreys, A. & Gheysen I, (2023). High diversity of Curtobacterium flaccumfaciens in poinsettia and detection of three pathogenicity plasmids for identification of C. f. pv. poinsettiae. Phytobiomes Journal, https://doi.org/10.1094/PBIOMES-10-23-0104-R.

2022

  • Nüesch-Inderbinen Magdalena, Tresch Silvan, Zurfluh Katrin, Cernela Nicole, Biggel Michael, Stephan Roger. Finding of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in wild game meat originating from several European countries: predominance of Moellerella wisconsensis producing CTX-M-1, November 2021. Euro Surveill. 2022;27(49):pii=2200343. https://doi.org/10.2807/1560-7917.ES.2022.27.49.2200343