FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced
            <i>Fusobacterium</i>
            Genomes Improves Gene Identification and Characterization

Sanders, Blake E.; Umaña, Ariana; Lemkul, Justin A.; Slade, Daniel J.

doi:10.1128/msphere.00228-18

Cited by 16 publications

(24 citation statements)

References 22 publications

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“…We show that all of the contigs mapped, with our genome completing previous gaps. The new build adds 62 kb to the completed genome, and we show in a companion manuscript that this results in the correction of a significant portion of previously misannotated genes around contig ends ( 13 ). The accuracy of our genome compared to mapped base pairs from the draft genome assembly at NCBI (GCF_000178895.1) shows 99.99% base identification as determined by Geneious version 9.1.4.…”

Section: Resultsmentioning

confidence: 99%

“…These data can found in easily searchable and downloadable formats on the FusoPortal website under their respective genomes. We highlight in detail in a companion paper that these genomes are much more accurate for annotating large genes (>3 kb), many of which belong to the type 5 secreted autotransporter family of validated virulence proteins ( 11 , 12 , 13 ).…”

Section: Resultsmentioning

confidence: 99%

“…We have used a previously validated pipeline for sequencing and annotation and applied this to create a library of Fusobacterium genomes. Drafts of these genomes previously consisted of 6 to 67 contigs, and in many cases we found that these draft genomes contained errors in open-reading frame annotations of long genes (>3 kb) ( 13 ). The newly completed genomes presented in this report are highly accurate, consist of one complete chromosome, and are freely available on our newly initiated FusoPortal website.…”

Section: Resultsmentioning

confidence: 99%

“…The methods described here are expanded versions of those found in our related work ( 13 ), which describes the FusoPortal genome repository.…”

Section: Methodsmentioning

confidence: 99%

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Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction

Todd

Settlage

Lahmers

et al. 2018

mSphere

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Fusobacterium spp. are Gram-negative, oral bacteria that are increasingly associated with human pathologies as diverse as periodontitis, preterm birth, and colorectal cancer. While a recent surge in F. nucleatum research has increased our understanding of this human pathogen, a lack of complete genomes has hindered the identification and characterization of associated host-pathogen virulence factors. Here we report the first eight complete Fusobacterium genomes sequenced using an Oxford Nanopore MinION and Illumina sequencing pipeline and assembled using the open-source program Unicycler. These genomes are highly accurate, and seven of the genomes represent the first complete sequences for each strain. In summary, the FusoPortal resource provides a publicly available resource that will guide future genetic, bioinformatic, and biochemical experiments to characterize this genus of emerging human pathogens.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…The methods described here are expanded versions of those found in our related work ( 13 ), which describes the FusoPortal genome repository.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction

Todd

Settlage

Lahmers

et al. 2018

mSphere

Self Cite

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“…The reason for this lack of molecular studies in Fusobacterium is its well-known genetic recalcitrance, with only four strains of F. nucleatum yielding chromosomal modification (15,(26)(27)(28). To aid in our understanding of virulence at the genetic and molecular level, we recently completed nine Fusobacterium genomes and created the FusoPortal database that includes detailed genomic and bioinformatic analysis of this emerging pathogen (29,30). These genomes were used here to identify and correct protein families of the autotransporter, FadA, and MORN2 domaincontaining proteins, all of which are predicted to play key roles in cellular binding and invasion.…”

mentioning

confidence: 99%

Utilizing Whole Fusobacterium Genomes To Identify, Correct, and Characterize Potential Virulence Protein Families

et al. 2019

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Fusobacterium spp. are Gram-negative, anaerobic, opportunistic pathogens involved in multiple diseases, including a link between the oral pathogen Fusobacterium nucleatum and the progression and severity of colorectal cancer. The identification and characterization of virulence factors in the genus Fusobacterium has been greatly hindered by a lack of properly assembled and annotated genomes. Using newly completed genomes from nine strains and seven species of Fusobacterium, we report the identification and corrected annotation of verified and potential virulence factors from the type 5 secreted autotransporter, FadA, and MORN2 protein families, with a focus on the genetically tractable strain F. nucleatum subsp. nucleatum ATCC 23726 and type strain F. nucleatum subsp. nucleatum ATCC 25586. Within the autotransporters, we used sequence similarity networks to identify protein subsets and show a clear differentiation between the prediction of outer membrane adhesins, serine proteases, and proteins with unknown function. These data have identified unique subsets of type 5a autotransporters, which are key proteins associated with virulence in F. nucleatum. However, we coupled our bioinformatic data with bacterial binding assays to show that a predicted weakly invasive strain of F. necrophorum that lacks a Fap2 autotransporter adhesin strongly binds human colonocytes. These analyses confirm a gap in our understanding of how autotransporters, MORN2 domain proteins, and FadA adhesins contribute to host interactions and invasion. In summary, we identify candidate virulence genes in Fusobacterium, and caution that experimental validation of host-microbe interactions should complement bioinformatic predictions to increase our understanding of virulence protein contributions in Fusobacterium infections and disease. IMPORTANCE Fusobacterium spp. are emerging pathogens that contribute to mammalian and human diseases, including colorectal cancer. Despite a validated connection with disease, few proteins have been characterized that define a direct molecular mechanism for Fusobacterium pathogenesis. We report a comprehensive examination of virulence-associated protein families in multiple Fusobacterium species and show that complete genomes facilitate the correction and identification of multiple, large type 5a secreted autotransporter genes in previously misannotated or fragmented genomes. In addition, we use protein sequence similarity networks and human cell interaction experiments to show that previously predicted noninvasive strains can indeed bind to and potentially invade human cells and that this could be due to the expansion of specific virulence proteins that drive Fusobacterium infections and disease.

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Detection of Tylosin Resistance in Fusobacterium necrophorum subspecies necrophorum

Schwarz,

Mathieu,

Laverde Gomez

et al. 2024

ACS Agric. Sci. Technol.

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In-feed tylosin, a macrolide, is widely used to prevent liver abscessation in feedlot cattle by repressing growth of ruminal Fusobacterium necrophorum. Although tylosin has been used for almost five decades, no resistant F. necrophorum subsp. necrophorum strain has ever been isolated. Here, we report two strains (FN37 and FN38) previously isolated from abscessed livers containing several antibiotic resistance genes: cfr(C), tet(O), ant(6)-Ia, and erm(B), the latter of which confers resistance to macrolides via modification of the ribosome. To evaluate if erm(B) conferred a phenotypic advantage, four strains (deposited strain ATCC 25286, ruminal isolate FNC, and abscess isolates FN37 and FN38) were tested for their responses to tylosin. The two erm(B)-harboring strains showed resistance at concentrations commonly found within the ruminal compartment under current dosing guidelines, and in the case of FN38, up to 100 μg/mL tylosin was tolerated. Tylosin susceptibility varied depending on the growth phase (stationary vs logarithmic) and preconditioning (growth in medium containing tylosin at a concentration of 1 μg/mL) of the inoculum in all four strains, but the two harboring the erm(B) gene demonstrated robust resistance. This discovery along with whole genome sequencing and preliminary annotation indicates horizontal gene transfer and acquisition of resistance genes, highlighting the need to revisit antimicrobial strategies for the feedlot cattle industry.

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FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization

Cited by 16 publications

References 22 publications

Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction

Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction

Utilizing Whole Fusobacterium Genomes To Identify, Correct, and Characterize Potential Virulence Protein Families

Detection of Tylosin Resistance in Fusobacterium necrophorum subspecies necrophorum

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