Identification and Analysis of Essential Genes in Streptococcus mutans with Transposon Sequencing

Walker, Alejandro R.; Shields, Robert C.

doi:10.1007/978-1-0716-1720-5_13

Cited by 3 publications

(2 citation statements)

References 24 publications

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“…A current method to determine essential genes is to use a high-throughput method known as transposon sequencing (TnSeq) (Van Opijnen et al, 2009). This technique has been used to assess bacteria fitness under different conditions (Klein et al, 2015; Narayanan et al, 2017; Turner et al, 2014) and has also been applied to identify the essential genome of other bacterial species that colonize the oral cavity and the upper respiratory tract such as Streptococcus mutans (Walker and Shields, 2022), Aggregatibacter actinomycetemcomitans (Narayanan et al, 2017), Porphyromonas gingivalis (Klein et al, 2015), Treponema denticola (Yang et al, 2008), and Haemophilus influenzae (Gawronski et al, 2009). In addition to TnSeq, transcriptomes can shed light on the adaptation of an organism to its environment and allow for hypotheses generation for mechanisms that may be essential for fitness in that environment.…”

Section: Introductionmentioning

confidence: 99%

“…This technique has been used to assess bacteria fitness under different conditions (Klein et al, 2015;Narayanan et al, 2017;Turner et al, 2014) and has also been applied to identify the essential genome of other bacterial species that colonize the oral cavity and the upper respiratory tract such as Streptococcus mutans (Walker and Shields, 2022), Aggregatibacter actinomycetemcomitans (Narayanan et al, 2017), Porphyromonas gingivalis (Klein et al, 2015), Treponema denticola (Yang et al, 2008), and Haemophilus influenzae (Gawronski et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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Essential genes forHaemophilus parainfluenzaesurvival and biofilm growth

de Palma,

Powers,

McPartland

et al. 2024

Preprint

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Haemophilus parainfluenzae (Hp) is a Gram-negative, pleomorphic rod, highly prevalent and abundant as a commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the tongue dorsum, keratinized gingiva, and the supragingival plaque biofilm. As a member of the HACEK group, Hp is also known to cause infective endocarditis. Additionally, case reports have identified Hp as the causative agent of meningitis, septic arthritis, chronic osteomyelitis, septicemia, and a variety of other infectious diseases. Little is known about how Hp interacts with its neighbors in the healthy biofilm nor about its mechanisms of pathogenesis as an extraoral opportunistic pathogen. To address these unknowns, we identified the essential genomes of two Hp strains and the conditionally essential genes for their growth in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and a commensal oral isolate EL1 (Hp EL1), we show that the essential genome of Hp 392 and Hp EL1 is composed of 395 and 384 genes, respectively. The core essential genome, consisting of 341 essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains of Hp. Additionally, RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic biofilm survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo oral habitat. Further, the creation of this library presents a valuable tool for further investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Essential genes forHaemophilus parainfluenzaesurvival and biofilm growth

de Palma,

Powers,

McPartland

et al. 2024

Preprint

View full text Add to dashboard Cite

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Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto

Jiang,

Zhao,

Wang

et al. 2024

Gene

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Essential genes for Haemophilus parainfluenzae survival and biofilm growth

de Palma,

Powers,

McPartland

et al. 2024

mSystems

View full text Add to dashboard Cite

Haemophilus parainfluenzae ( Hp ) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain ( Hp 392) and oral isolate EL1 ( Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat. IMPORTANCE Haemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.

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Identification and Analysis of Essential Genes in Streptococcus mutans with Transposon Sequencing

Cited by 3 publications

References 24 publications

Essential genes forHaemophilus parainfluenzaesurvival and biofilm growth

Essential genes forHaemophilus parainfluenzaesurvival and biofilm growth

Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto

Essential genes for Haemophilus parainfluenzae survival and biofilm growth

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