Ignacio Bolivar

Noma: an “infectious” disease of unknown aetiology

Noma (cancrum oris) is a devastating gangrenous disease that leads to severe tissue destruction in the face and is associated with high morbidity and mortality. It is seen almost exclusively in young children living in remote areas of less developed countries, particularly in Africa. The exact prevalence of the disease is unknown, but a conservative estimate is that 770000 people are currently affected by noma sequelae. The cause remains unknown, but a combination of several elements of a plausible aetiology has been identified: malnutrition, a compromised immune system, poor oral hygiene and a lesion of the gingival mucosal barrier, and an unidentified bacterial factor acting as a trigger for the disease. This review discusses the epidemiology, clinical features, current understanding of the pathophysiology, and treatment of the acute phase and sequelae requiring reconstructive surgery. Noma may be preventable if recognised at an early stage. Further research is needed to identify more exactly the causative agents.

Molecular evidence that Reticulomyxa filosa is a freshwater naked foraminifer.

ABSTRACT Reticulomyxa filosa is a freshwater protist possessing fine granular, branching and anastomosing pseudopodia and therefore traditionally placed in the class Granuloreticulosea, order Athalamida, as a sister group to the order Foraminiferida. Recent studies have revealed remarkable similarities in pseudopodial motility and ultrastructure between R. filosa and foraminifera (e.g. Allogromia laticollaris), prompting us to conduct a molecular phylogenetic analysis of these seemingly disparate organisms. We sequenced the complete small‐subunit of the ribosomal DNA of the cultured strain of R. filosa and compared it to the corresponding sequences of other protists including 12 species of foraminifera. We also sequenced and analyzed the actin coding genes from R. filosa and two species of foraminifera, Allogromia sp. and Ammonia sp. the analysis of both data sets clearly shows that R. filosa branches within the clade of foraminifera, suggesting that R. filosa is in fact a freshwater naked foraminiferan.

Novel Microarray Design Strategy To Study Complex Bacterial Communities

ABSTRACT Assessing bacterial flora composition appears to be of increasing importance to fields as diverse as physiology, development, medicine, epidemiology, the environment, and the food industry. We report here the development and validation of an original microarray strategy that allows analysis of the phylogenic composition of complex bacterial mixtures. The microarray contains ∼9,500 feature elements targeting 16S rRNA gene-specific regions. Probe design was performed by selecting oligonucleotide sequences specific to each node of the seven levels of the bacterial phylogenetic tree (domain, phylum, class, order, family, genus, and species). This approach, based on sequence information, allows analysis of the bacterial contents of complex bacterial mixtures to detect both known and unknown microorganisms. The presence of unknown organisms can be suspected and mapped on the phylogenetic tree, indicating where to refine analysis. Initial proof-of-concept experiments were performed on oral bacterial communities. Our results show that this hierarchical approach can reveal minor changes (≤1%) in gingival flora content when samples collected in individuals from similar geographical origins are compared.

Bacterial Diversity in Oral Samples of Children in Niger with Acute Noma, Acute Necrotizing Gingivitis, and Healthy Controls

Background Noma is a gangrenous disease that leads to severe disfigurement of the face with high morbidity and mortality, but its etiology remains unknown. Young children in developing countries are almost exclusively affected. The purpose of the study was to record and compare bacterial diversity in oral samples from children with or without acute noma or acute necrotizing gingivitis from a defined geographical region in Niger by culture-independent molecular methods. Methods and Principal Findings Gingival samples from 23 healthy children, nine children with acute necrotizing gingivitis, and 23 children with acute noma (both healthy and diseased oral sites) were amplified using “universal” PCR primers for the 16 S rRNA gene and pooled according to category (noma, healthy, or acute necrotizing gingivitis), gender, and site status (diseased or control site). Seven libraries were generated. A total of 1237 partial 16 S rRNA sequences representing 339 bacterial species or phylotypes at a 98–99% identity level were obtained. Analysis of bacterial composition and frequency showed that diseased (noma or acute necrotizing gingivitis) and healthy site bacterial communities are composed of similar bacteria, but differ in the prevalence of a limited group of phylotypes. Large increases in counts of Prevotella intermedia and members of the Peptostreptococcus genus are associated with disease. In contrast, no clear-cut differences were found between noma and non-noma libraries. Conclusions Similarities between acute necrotizing gingivitis and noma samples support the hypothesis that the disease could evolve from acute necrotizing gingivitis in certain children for reasons still to be elucidated. This study revealed oral microbiological patterns associated with noma and acute necrotizing gingivitis, but no evidence was found for a specific infection-triggering agent.

ACTIN PHYLOGENY OF FORAMINIFERA

Molecular phylogenies of foraminifera are commonly inferred from the small subunit rRNA (SSU) genes, which can easily be obtained from single cells isolated from environmental samples. The SSU phylogenies, however, are often biased by heterogeneity of substitution rates, and their resolution of higher level relationships is often very low. The sequences of protein-coding genes provide an important alternative source of phylogenetic information, yet their availability from foraminifera has been limited until now. Here, we report the first extensive protein sequence data for foraminifera, which comprises 90 actin sequences for 27 species representing five major foraminiferan groups. Our analysis enables grouping foraminiferan actins into two main paralogs, ACT1 (actin type 1) and ACT2 (actin type 2), and several actin-deviating proteins. Phylogenetic analyses of ACT1 and ACT2 confirm the general structure of foraminiferan phylogenies inferred from SSU rDNA sequences. In particular, actin phylogenies support (1) the paraphyly of monothalamous foraminifera, including the allogromiids, astrorhizids and athalamids; (2) the independent divergence of miliolids and their close relationship to Miliammina ; (3) the monophyly of rotalids; and (4) the rotaliid ancestry of globigerinids. Some foraminiferan taxa can be distinguished in actin sequences by the presence of group-specific introns (rotaliids, allogromiids) or absence of any introns (soritids ACT1).

Naked foraminiferans revealed

It is generally assumed that the first fossil appearance of a group of organisms corresponds to its evolutionary origin. But we have molecular evidence that extant members of the most abundant microfossil-forming group, the Foraminifera, include ‘naked’ amoeboid species, indicating that ancestral foraminiferans could be unfossilized. This means that the origin of the group might be much earlier than has been deduced from the fossil record. This might help to explain the conflicting molecular and fossil data on the origin of the Foraminifera.

DNA analysis of “Ammonia beccarii” morphotypes: one or more species?

Abstract Partial large subunit ribosomal DNA (LSU rDNA) sequences were obtained from six morphotypes of “ Ammonia beccarii s.l.” collected from different localities. Each morphotype is characterized by a different LSU rDNA sequence. Sequences of similar morphotypes from geographically distant regions resemble each other more than sequences of different morphotypes from the same locality. DNA analysis and morphologic comparisons allow the distinction of three species: A. tepida A. beccarii and A. parkinsoniana .

Tempo and mode of spliceosomal intron evolution in actin of foraminifera.

Spliceosomal introns are present in almost all eukaryotic genes, yet little is known about their origin and turnover in the majority of eukaryotic phyla. There is no agreement whether most introns are ancestral and have been lost in some lineage or have been gained recently. We addressed this question by analyzing the spatial and temporal distribution of introns in actins of foraminifera, a group of testate protists whose exceptionally rich fossil record permits the calibration of molecular phylogenies to date intron origins. We identified 24 introns dispersed along the sequence of two foraminiferan actin paralogues and actin deviating proteins, an unconventional type of fast-evolving actin found in some foraminifera. Comparison of intron positions indicates that 20 of 24 introns are specific to foraminifera. Four introns shared between foraminifera and other eukaryotes were interpreted as parallel gains because they have been found only in single species belonging to phylogenetically distinctive lineages. Moreover, additional recent intron gain due to the transfer between the actin paralogues was observed in two cultured species. Based on a relaxed molecular clock timescale, we conclude that intron gains in actin took place throughout the evolution of foraminifera, with the oldest introns inserted between 550 and 500 million years ago and the youngest ones acquired less than 100 million years ago.

Microarray analysis of microbiota of gingival lesions in noma patients.

Noma (cancrum oris) is a gangrenous disease of unknown etiology affecting the maxillo-facial region of young children in extremely limited resource countries. In an attempt to better understand the microbiological events occurring during this disease, we used phylogenetic and low-density microarrays targeting the 16S rRNA gene to characterize the gingival flora of acute noma and acute necrotizing gingivitis (ANG) lesions, and compared them to healthy control subjects of the same geographical and social background. Our observations raise doubts about Fusobacterium necrophorum, a previously suspected causative agent of noma, as this species was not associated with noma lesions. Various oral pathogens were more abundant in noma lesions, notably Atopobium spp., Prevotella intermedia, Peptostreptococcus spp., Streptococcus pyogenes and Streptococcus anginosus. On the other hand, pathogens associated with periodontal diseases such as Aggregatibacter actinomycetemcomitans, Capnocytophaga spp., Porphyromonas spp. and Fusobacteriales were more abundant in healthy controls. Importantly, the overall loss of bacterial diversity observed in noma samples as well as its homology to that of ANG microbiota supports the hypothesis that ANG might be the immediate step preceding noma.

Streptococcus sinensis Endocarditis outside Hong Kong

Streptococcus sinensis has been described as a causative organism for infective endocarditis in 3 Chinese patients from Hong Kong. We describe a closely related strain in an Italian patient with chronic rheumatic heart disease. The case illustrates that S. sinensis is a worldwide emerging pathogen.