PacBio-Based Protocol for Bacterial Genome Assembly

Motyka-Pomagruk, Agata; Żołędowska, Sabina; Kabza, Michał; Łojkowska, Ewa

doi:10.1007/978-1-0716-1099-2_1

Cited by 1 publication

(1 citation statement)

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“…Furthermore, we observed that, on average, 32.71% (±8.39) of reads from each library were not mapped to any MAG. Thus, the extraction of higher yields and higher-quality DNA [ 51 ] may also help circumvent some of these issues. Integrating flow cytometry and metagenomics shows a higher resolution in deciphering microbial community composition by decreasing community complexity, including long-read sequencing data leading to improved genome-centric analyses of microbial communities.…”

Section: Discussionmentioning

confidence: 99%

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge

et al. 2023

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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.

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Section: Discussionmentioning

confidence: 99%