Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach

Chen, Yu-Hsiang; Chiang, Pei‐Wen; Rogozin, D. Yu.; Degermendzhy, Andrey G.; Chiu, Hsiu‐Hui; Tang, Sen‐Lin

doi:10.1038/s42003-021-02510-6

Cited by 16 publications

(16 citation statements)

References 99 publications

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“…al. spiked environmental DNA with DNA of a known bacterium as the authors described their DNA amount as insufficient for Nanopore sequencing [23]. In similar fashion, the so-called CarrierSeq protocol includes the addition of 1000 ng of Lambda phage DNA to the target DNA, which could be metagenomic DNA for sequencing; in such an approach Mojarro et al used 0.2 ng Bacillus subtilis DNA as 10 the target, which resulted in only 777 Nanopore-reads (out of 718,432) that mapped to the target genome of B. subtilis [38].…”

Section: Discussionmentioning

confidence: 99%

Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction

Simon

Schmidt

Griesdorn

et al. 2023

Preprint

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Background: While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs. Results: We generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies. Conclusion: Our results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.

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Section: Discussionmentioning

confidence: 99%

Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction

Simon

Schmidt

Griesdorn

et al. 2023

Preprint

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“…Improvements to long-read sequencing such as PacBio or Nanopore technologies lead to better metagenome assembly. They can be combined synergistically with low error rate short reads to accurately retrieve repetitive genome regions (Chen et al, 2021;Damme et al, 2021). Long reads using the most recent technologies can suffice alone for reconstructing high-quality MAGs (Sereika et al, 2022).…”

Section: Molecular Tools To Uncover the Functional Potential Of The M...mentioning

confidence: 99%

The functional microbiome of grapevine throughout plant evolutionary history and lifetime

Fournier

Pellan

Barroso-Bergadà

et al. 2022

Advances in Ecological Research

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“…Prosthecochloris spp. were found in diverse environments including hydrogen sulfide-rich mud, hot spring sediment and coral skeletons ( Gorlenko, 1970 ; Imhoff, 2003 ; Beatty et al, 2005 ; Nabhan et al, 2016 ; Cai et al, 2017 ; Thiel et al, 2017 ; Grouzdev et al, 2018 ; Bryantseva et al, 2019 ; Yang et al, 2019 ; Kyndt et al, 2020 ; Athen et al, 2021 ; Chen et al, 2021a , b ). The major difference between coral-associated and other non-coral-associated Prosthecochloris remains poorly understood, although preliminary analysis of coral-associated Prosthecochloris was performed previously ( Chen et al, 2021b ).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris

et al. 2023

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Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.

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Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach

Cited by 16 publications

References 99 publications

Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction

Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction

The functional microbiome of grapevine throughout plant evolutionary history and lifetime

Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris

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