Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium

Fusobacterium nucleatum is a prominent member of the oral microbiota and is a common cause of human infection. F. nucleatum includes five subspecies: polymorphum, nucleatum, vincentii, fusiforme, and animalis. F. nucleatum subsp. polymorphum ATCC 10953 has been well characterized phenotypically and, in contrast to previously sequenced strains, is amenable to gene transfer. We sequenced and annotated the 2,429,698 bp genome of F. nucleatum subsp. polymorphum ATCC 10953. Plasmid pFN3 from the strain was also sequenced and analyzed. When compared to the other two available fusobacterial genomes (F. nucleatum subsp. nucleatum, and F. nucleatum subsp. vincentii) 627 open reading frames unique to F. nucleatum subsp. polymorphum ATCC 10953 were identified. A large percentage of these mapped within one of 28 regions or islands containing five or more genes. Seventeen percent of the clustered proteins that demonstrated similarity were most similar to proteins from the clostridia, with others being most similar to proteins from other gram-positive organisms such as Bacillus and Streptococcus. A ten kilobase region homologous to the Salmonella typhimurium propanediol utilization locus was identified, as was a prophage and integrated conjugal plasmid. The genome contains five composite ribozyme/transposons, similar to the CdISt IStrons described in Clostridium difficile. IStrons are not present in the other fusobacterial genomes. These findings indicate that F. nucleatum subsp. polymorphum is proficient at horizontal gene transfer and that exchange with the Firmicutes, particularly the Clostridia, is common.     

Characteristics of Fusobacterium ulcerans,a New and Unusual Species Compared with Fusobacterium varium and Fusobacterium mortiferum

Fusobacterium ulcerans is a newly described obligately anaerobic Gram-negative, non-spore-forming rod [1] that has been isolated from tropical ulcers. Two morphotypes were described: one resemblingFusobacterium varium and the other Fusobacterium mortiferum[1]. Because of the weak or negative fermentation reactions of most fusobacteria, the standard carbohydrate tests used for identification of anaerobe organisms are of little use for identification, and other rapid and simple methods are needed. We characterized eight F. ulcerans strains using conventional biochemical testing. We further analysed these strains by PCR employing a single non-specific primer AP3 and by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) of whole cell proteins. PCR using a self-designed pair of primers for the amplification of the spacer (intergenic) region between the 16S and 23S rRNA genes, led to the development of genetic markers for species identification. All F. ulcerans clinical isolates appeared very similar to each other in all the test parameters, but were distinctly different from the type strains of the two phenotypically similar species, F. mortiferum and F. varium. High similarity in PCR- and protein-profiles also raise the possibility that all these F. ulcerans strains came from one clone. We noted significant differences among the strains of F. mortiferum and F. varium.     

Reproductive versatility in legumes: the case of amphicarpy in Trifolium polymorphum

Amphicarpy is a fascinating reproductive strategy, defined as fruit produced both below the soil surface and as aerial fruit on the same plant. Trifolium polymorphum is a grassland species subject to herbivory that combines amphicarpy with vegetative reproduction through stolons. Underground flowers have been described as obligate autogamous and aerial ones as self‐compatible allogamous, with aerial floral traits favouring cross‐pollination. In the present work we performed different pollination treatments on aerial flowers to analyse rates of pollen tube development and offspring fitness, measured as fruit set, seed production and germination percentage. This last variable was compared to that of seeds produced underground. No significant differences were found between fruit set in self‐ and cross‐pollinations. Seed production was higher in self‐pollinations, which is consistent with the higher rate of pollen tube development observed in self‐crosses. Spontaneous self‐pollination is limited in aerial flowers; thus pollen transfer by means of a vector is required even within the same flower. Germination tests showed that aerial seeds produced after self‐ and cross‐pollination did not differ in fitness, but underground seeds had higher germination percentage than aerial ones. Thus, we conclude that T. polymorphum has a mixed mating system. In grasslands with heavy grazing pressure, clonal propagation and underground seed production ensure persistence in the field. An intermediate level of selfing in aerial flowers ensures offspring, but morphological (herkogamy) and functional (dicogamy) floral traits maintain a window to incorporate genetic variability, allowing the species to tolerate temporal and spatial pressures.     

The leukotoxin operon of Fusobacterium necrophorum is not present in other species of Fusobacterium

The complete nucleotide sequence of the leukotoxin operon of Fusobacterium necrophorum has been determined. The operon consists of three genes (lktBAC) of which the leukotoxin structural gene is the middle determinant. Southern and western blot analyses and flow cytometry analysis for biological activity of the culture supernatants were carried out to determine if the leukotoxin is present in other species of the genus Fusobacterium. Only the two subspecies of F. necrophorum were found to possess the leukotoxin locus and produce the toxin. The human periodontal pathogen, F. nucleatum does not produce detectable leukotoxin. The F. necrophorum leukotoxin was found to be active against human neutrophils.     

Phospholipids of Fusobacterium spp.

The aim of this study was to analyse individual polar lipid analogues, within each lipid family present, of fusobacteria using fast atom bombardment mass spectrometry (FAB-MS). Polar lipid extracts were prepared, washed and dried. Samples, dispersed in a matrix of m -nitrobenzyl alcohol, were analysed by negative ion FAB-MS using xenon as the reagent gas. Major anion peaks observed in the low mass region of mass/charge (m/z), 211, 221, 225, 227, 239, 241, 249, 251, 253, 255, 273, 277, 279, 281, 289 and 291, were consistent with the presence of C_13:1, C_14:3, C_14:1, C_14:0, C_15:1, C_15:0, C_16:3, C_16:2, C_16:1, C_16:0, unknown, C_18:3, C_18:2, C_18:1, unknown and C_19:3 carboxylate anions. In the high mass region, major anion peaks observed with m/z 644, 646, 648, 660, 662, 672, 673, 674, 686, 688, 689, 690, 698, 700, 701, 703, 714, 716, 717 and 719 were consistent with the presence of phosphatidylethanolamine (PE) (29:2), PE (29:1), PE (29:0), PE (30:1), PE (30:0), PE (31:2), first isotope of PE (31:2), PE (31:1), PE (32:2), PE (32:1), first isotope peak of PE (32:1), PE (30:0), PE (33:3), PE (33:2), phosphatidylglycerol (PG) (31:3), PG (31:2), PE (34:2), PE (34:1), PG (32:2) and PG (32:1). We conclude that FAB-MS can provide data on individual analogues of PE and PG from Fusobacterium spp. not readily obtained by other means. Furthermore, the phospholipid profile is diagnostic for the genus.     

Chemotypes of Fusobacterium nucleatum lipopolysaccharides

Lipopolysaccharides (LPS) were isolated from 20 strains of Fusobacterium nucleatum and examined by paper chromatography, gas liquid chromatography and colorimetric methods for the presence of neutral sugars, amino sugars and 2-keto-3-dexoxy-octonate (KDO). The LPS had in common glucosamine, L-glycero-D-manno-heptose, glucose and KDO. The KDO content was low. Galatose, rhamnose and D-glycero-D-manno-heptose were found in some strains. Based on the sugar composition of the LPS, the F. nucleatum strains could be classified into six chemotypes.     

Partial characterization of Fusobacterium necrophorum protease

Partial characterization of Fusobacterium necrophorum protease was investigated. The protease was partially purified by gel filtration with Toyopearl HW 55. The final preparation was inactivated completely by heating at 60 degrees C for 30 min and inhibited by ascorbic acid, sodium thioglycollate and p-hydromercuribenzoate. Antibody response to the protease was demonstrated in mice receiving 10(4) CFU of F. necrophorum.     

Phenotypic and genotypic analyses of clinical Fusobacterium nucleatum and Fusobacterium periodonticum isolates from the human gut

Fusobacterium nucleatum is a Gram-negative anaerobic rod that is part of the normal human microflora, and has also been associated with various infections. Bacterial strains belonging to the species are typically heterogeneous in both phenotype and genotype, which can hinder their identification in a clinical setting. The majority of F. nucleatum isolates originate from oral sites, however the species is also a resident of the human gastrointestinal tract. The aim of this study was to compare F. nucleatum isolates from human intestinal biopsy samples to try and determine whether isolates from this site are divergent from oral isolates. We used a variety of phenotypic and genotypic markers to compare 21 F. nucleatum and Fusobacterium periodonticum isolates from the GI tract to oral isolates and recognized type strains in order to study heterogeneity within this set. 16S rDNA and rpoB gene sequence analysis allowed us to build phylogenetic trees that consistently placed isolates into distinct clusters. 16S rDNA copy number analyses using Denaturing Gradient Gel Electrophoresis (DGGE) demonstrated potential for use as a method to examine clonality amongst species. Phenotypic analyses gave variable results that were generally unhelpful in distinguishing between phylogenetic clusters. Our results suggest that a) F. periodonticum isolates are not restricted to the oral niche; b) phenotypic classification is not sufficient to subspeciate isolates; c) heterogeneity within the species is extensive but constrained; and d) F. nucleatum isolates from the gut tend to identify with the animalis subspecies.     

Fusobacterium nucleatum subsp. fusiforme subsp. nov. and Fusobacterium nucleatum subsp. animalis subsp. nov. as additional subspecies within Fusobacterium nucleatum.

Using a variety of physiological, biochemical, and molecular systematic analyses, we have shown previously that there are four groups within the species Fusobacterium nucleatum. Two of these groups of strains correspond to the recently proposed taxa F. nucleatum subsp. nucleatum and F. nucleatum subsp. polymorphum. In this paper we show that the two remaining groups are distinct and formally propose that they should be recognized as F. nucleatum subsp. fusiforme (type strain, NCTC 11326) and F. nucleatum subsp. animalis (type strain, NCTC 12276). The tests which we used did not allow a full assessment of the status of F. nucleatum subsp. vincentii compared with F. nucleatum subsp. nucleatum.     

Differentiation of Bacteroides from Sphaerophorus and Fusobacterium

This paper is concerned with new findings in the comparative study of the genera, Bacteroides, Sphaerophorus and Fusobacterium. Victoria blue 4R and barbiturates were found to be effective in differentiating the genera by their discriminative inhibition of the growth. A new character, glutamic acid decarboxylation, was found in Bacteroides but neither in Sphaerophorus nor in Fusobacterium. The procedure for this test was presented. In the classification of newly isolated fecal strains this test and other differential features were compared. An improved method for the threonine deamination test was reported. The use of these characters and tests would be a step in the improvement of the present incomplete classification of gram-negative anaerobic non-sporulating rods.     

Morphology of Bacteriophage-Like Particles from Fusobacterium symbiosum

The morphology of bacteriophage-like particles from the strict anaerobe Fusobacterium symbiosum is described. Attempts to demonstrate plaque formation on the host strain of F. symbiosum and other related species were unsuccessful.     

A selective medium for Fusobacterium spp

A new selective medium (JVN) for the isolation of Fusobacterium spp. from clinical material is described. The medium incorporates josamycin, vancomycin and norfloxacin (at 3, 4 and 1 microgram/ml, respectively) as the selective agents, plus 5% defibrinated horse blood in Fastidious Anaerobe Agar Base (Lab M). This formula allowed luxuriant growth of all 82 strains (eight recognized species) of fusobacteria tested, while significantly inhibiting 51/51 (100%) strains of facultative anaerobes and 45/51 (88%) strains of other obligate anaerobes. JVN medium allowed the successful isolation of strains of Fusobacterium naviforme, F. nucleatum and F. necrophorum from the gingivae of 9/16 healthy volunteers, and strains of F. varium and F. mortiferum from faecal suspensions seeded with these organisms.     

Surface EMG pattern recognition for real-time control of a wrist exoskeleton

Background  

Surface electromyography (sEMG) signals have been used in numerous studies for the classification of hand gestures and movements and successfully implemented in the position control of different prosthetic hands for amputees. sEMG could also potentially be used for controlling wearable devices which could assist persons with reduced muscle mass, such as those suffering from sarcopenia. While using sEMG for position control, estimation of the intended torque of the user could also provide sufficient information for an effective force control of the hand prosthesis or assistive device. This paper presents the use of pattern recognition to estimate the torque applied by a human wrist and its real-time implementation to control a novel two degree of freedom wrist exoskeleton prototype (WEP), which was specifically developed for this work.