Complete Genome Sequence of Stenotrophomonas maltophilia Strain CF13, Recovered from Sputum from an Australian Cystic Fibrosis Patient

Hamidian, Mohammad; Lazenby, James; To, Joyce; Hartstein, Rebecca M.; Soares, J.A.H.; McNamara, Samantha; Whitchurch, Cynthia B.

doi:10.1128/mra.00628-20

Cited by 2 publications

(1 citation statement)

References 23 publications

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“…Hackflex has been widely validated and used in the context of whole-genome sequencing for bacterial isolates [4][5][6][7][8][9][10][11] and amplicon sequencing [12]. Although Hackflex has been used in metagenomic analyses, its accuracy has only been tested in the context of simple mock communities containing seven species of known relative abundances [13,14].…”

Section: Introductionmentioning

confidence: 99%

Hackflex library preparation enables low-cost metagenomic profiling

Goldman,

Sanders,

Sprockett

et al. 2024

Preprint

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Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

show abstract

Section: Introductionmentioning

confidence: 99%

Hackflex library preparation enables low-cost metagenomic profiling

Goldman,

Sanders,

Sprockett

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Hackflex library preparation enables low-cost metagenomic profiling

Goldman,

Sanders,

Sprockett

et al. 2024

ISME Communications

View full text Add to dashboard Cite

Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

show abstract

Complete Genome Sequence of Stenotrophomonas maltophilia Strain CF13, Recovered from Sputum from an Australian Cystic Fibrosis Patient

Abstract: Stenotrophomonas maltophilia isolate CF13 is a multidrug-resistant isolate that was recovered in Sydney, Australia, in 2011, from a sputum sample from an individual with cystic fibrosis. The genome sequence of CF13 was completed using long- and short-read technologies.

Cited by 2 publications

References 23 publications

Hackflex library preparation enables low-cost metagenomic profiling

Hackflex library preparation enables low-cost metagenomic profiling

Hackflex library preparation enables low-cost metagenomic profiling

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