Details zur Publikation

Kategorie Textpublikation
Referenztyp Zeitschriften
DOI 10.3390/microorganisms11010175
Lizenz creative commons licence
Titel (primär) Combining flow cytometry and metagenomics improves recovery of metagenome-assembled genomes in a cell culture from activated sludge
Autor Abdulkadir, N.; Saraiva, J.P.; Schattenberg, F.; Brizola Toscan, R.; Borim Correa, F.; Harms, H.; Müller, S.; Nunes da Rocha, U.
Quelle Microorganisms
Erscheinungsjahr 2023
Department UMB
Band/Volume 11
Heft 1
Seite von art. 175
Sprache englisch
Topic T7 Bioeconomy
Supplements https://www.mdpi.com/article/10.3390/microorganisms11010175/s1
Keywords cell sorting; flow cytometry; metagenome-assembled genomes; metagenomics
Abstract The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry cell sorting with bioinformatics tools to recover metagenome-assembled genomes. We used a cell culture of a wastewater microbial community as our model system. Cells were separated based on fluorescence signals via flow cytometry cell sorting into sub-communities: dominant gates, low abundant gates, and outer gates into subsets of the original community. Metagenome sequencing was performed for all groups. The unsorted community was used as control. We recovered a total of 24 metagenome-assembled genomes (MAGs) representing 11 species-level genome operational taxonomic units (gOTUs). In addition, 57 ribosomal operational taxonomic units (rOTUs) affiliated with 29 taxa at species level were reconstructed from metagenomic libraries. Our approach suggests a two-fold increase in the resolution when comparing sorted and unsorted communities. Our results also indicate that species abundance is one determinant of genome recovery from metagenomes as we can recover taxa in the sorted libraries that are not present in the unsorted community. In conclusion, a combination of cell sorting and metagenomics allows the recovery of MAGs undetected without cell sorting.
dauerhafte UFZ-Verlinkung https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=25962
Abdulkadir, N., Saraiva, J.P., Schattenberg, F., Brizola Toscan, R., Borim Correa, F., Harms, H., Müller, S., Nunes da Rocha, U. (2023):
Combining flow cytometry and metagenomics improves recovery of metagenome-assembled genomes in a cell culture from activated sludge
Microorganisms 11 (1), art. 175 10.3390/microorganisms11010175