<i>Fusobacterium</i>
            Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction

Todd, S. Michelle; Settlage, Robert E.; Lahmers, Kevin K.; Slade, Daniel J.

doi:10.1128/msphere.00269-18

Cited by 24 publications

(16 citation statements)

References 22 publications

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“…Many of these proteins are predicted surface adhesins with homology to Fap2, a key protein involved in F. nucleatum-induced colorectal cancer modulation. We subsequently sequenced and completed a total of nine Fusobacterium genomes and previously showed that genes larger than 3 kb had a high error rate, as validated in this study for the T5aSS proteins (29,30,34). A comparison of all annotations of T5aSS to T5dSS autotransporters for strains F. nucleatum 25586 and F. nucleatum 23726 can be found in Table S1 in the supplemental material.…”

Section: Resultssupporting

confidence: 54%

“…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.…”

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confidence: 99%

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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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Section: Resultssupporting

confidence: 54%

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confidence: 99%

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

et al. 2019

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“…Detailed sequencing statistics and assembly methods are reported in a concurrent publication by Todd and colleagues ( 17 ). Briefly, genomic DNA was isolated from Fusobacterium cultures and sequenced using MinION (Oxford Nanopore Technologies) and Illumina platforms.…”

Section: Methodsmentioning

confidence: 99%

“…All accession numbers for data are provided in Table 1 . In addition, all raw sequencing data have been deposited in the NCBI sequence read archive (SRA) as documented in a companion manuscript accompanying this report ( 17 ).…”

Section: Methodsmentioning

confidence: 99%

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

Sanders

Umaña

Lemkul

et al. 2018

mSphere

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In this report, we describe a hybrid MinION whole-genome sequencing pipeline and the genomic characteristics of the first eight Fusobacterium strains deposited in the FusoPortal database. This collection of highly accurate and complete genomes drastically improves upon previous multicontig assemblies by correcting and newly identifying a significant number of open reading frames. We believe that the availability of this resource will result in the discovery of proteins and molecular mechanisms used by an oral pathogen, with the potential to further our understanding of how Fusobacterium nucleatum contributes to a repertoire of diseases, including periodontitis, preterm birth, and colorectal cancer.

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“…Therefore, due to the limited reading length, the short read-based sequencing approach using the Illumina platform is not optimal for the de novo assembly of whole genome. However, because of the high reading accuracy, this platform is suitable for guided assembly and read mapping combined with long read technology (Oxford Nanopore Technologies, ONT) [21]. The combination of these two platforms creates a robust pipeline, which ensures highly contiguous assembly and high consensus accuracy, making accurate gene identification and characterization possible.…”

Section: Introductionmentioning

confidence: 99%

A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

Szczerba

Dudziak

Krawczyk

et al. 2020

IJMS

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Enterobacter sp. LU1, a wild-type bacterium originating from goat rumen, proved to be a potential succinic acid producer in previous studies. Here, the first complete genome of this strain was obtained and analyzed from a biotechnological perspective. A hybrid sequencing approach combining short (Illumina MiSeq) and long (ONT MinION) reads allowed us to obtain a single continuous chromosome 4,636,526 bp in size, with an average 55.6% GC content that lacked plasmids. A total of 4425 genes, including 4283 protein-coding genes, 25 ribosomal RNA (rRNA)-, 84 transfer RNA (tRNA)-, and 5 non-coding RNA (ncRNA)-encoding genes and 49 pseudogenes, were predicted. It has been shown that genes involved in transport and metabolism of carbohydrates and amino acids and the transcription process constitute the major group of genes, according to the Clusters of Orthologous Groups of proteins (COGs) database. The genetic ability of the LU1 strain to metabolize a wide range of industrially relevant carbon sources has been confirmed. The genome exploration indicated that Enterobacter sp. LU1 possesses all genes that encode the enzymes involved in the glycerol metabolism pathway. It has also been shown that succinate can be produced as an end product of fermentation via the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. The transport system involved in succinate excretion into the growth medium and the genes involved in the response to osmotic and oxidative stress have also been recognized. Furthermore, three intact prophage regions ~70.3 kb, ~20.9 kb, and ~49.8 kb in length, 45 genomic islands (GIs), and two clustered regularly interspaced short palindromic repeats (CRISPR) were recognized in the genome. Sequencing and genome analysis of Enterobacter sp. LU1 confirms many earlier results based on physiological experiments and provides insight into their genetic background. All of these findings illustrate that the LU1 strain has great potential to be an efficient platform for bio-based succinate production.

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

Cited by 24 publications

References 22 publications

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

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

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

A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

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