Detection of a putative novel Wolinella species in patients with squamous cell carcinoma of the esophagus

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

A plea for linguistic accuracy - also for Candidatus taxa

While all names of new taxa submitted to the International Journal of Systematic and Evolutionary Microbiology, either in direct submissions or in validation requests for names effectively published elsewhere, are subject to nomenclatural review to ensure that they are acceptable based on the rules of the International Code of Nomenclature of Prokaryotes, the names of Candidatus taxa have not been subjected to such a review. Formally, this was not necessary because the rank of Candidatus is not covered by the Code, and the names lack the priority afforded validly published names. However, many Candidatus taxa of different ranks are widely discussed in the scientific literature, and a proposal to incorporate the nomenclature of uncultured prokaryotes under the provisions of the Code is currently pending. Therefore, an evaluation of the names of Candidatus taxa published thus far is very timely. Out of the ~400 Candidatus names found in the literature, 120 contradict the current rules of the Code or are otherwise problematic. A list of those names of Candidatus taxa that need correction is presented here and alternative names that agree with the provisions of the Code are proposed.

Evaluation of the Helicobacteraceae in the oral cavity of dogs

OBJECTIVE

To determine the Helicobacter spp present in the oral cavity of dogs and the relationship of those organisms with gastric Helicobacter spp to better define the potential for dog-human and dog-dog transmission.

SAMPLE

Saliva and dental plaque from 28 dogs and gastric biopsy specimens from a subset of 8 dogs.

PROCEDURES

PCR-based screening for Helicobacter spp was conducted on samples obtained from the oral cavity of 28 dogs. Comparative analysis was conducted on Helicobacteraceae 16S rDNA clone libraries from the oral cavity and stomach of a subset of 8 dogs (5 vomiting and 3 healthy) that had positive PCR results for Helicobacter spp.

RESULTS

Helicobacteraceae DNA was identified in the oral cavity of 24 of 28 dogs. Analysis of cloned 16S rDNA amplicons from 8 dogs revealed that Wolinella spp was the most common (8/8 dogs) and abundant (52/57 [91%] clones) member of the Helicobacteraceae family in the oral cavity. Only 2 of 8 dogs harbored Helicobacter spp in the oral cavity, and 1 of those was coinfected with Helicobacter heilmannii and Helicobacter felis in samples obtained from the stomach and saliva. Evaluation of oral cavity DNA with Wolinella-specific PCR primers yielded positive results for 16 of 20 other dogs (24/28 samples were positive for Wolinella spp).

CONCLUSIONS AND CLINICAL RELEVANCE

Wolinella spp rather than Helicobacter spp were the predominant Helicobacteraceae in the oral cavity of dogs. The oral cavity of dogs was apparently not a zoonotically important reservoir of Helicobacter spp that were non-Helicobacter pylori organisms.

Bioactive metabolites from the South African marine mollusk Trimusculus costatus

A reinvestigation of extracts of the endemic South African intertidal limpet Trimusculus costatus yielded the known labdane diterpenes 6beta,7alpha-diacetoxylabda-8,13 E-dien-15-ol ( 1) and 2alpha,6beta,7alpha-triacetoxylabda-8,13 E-dien-15-ol ( 2) and three new metabolites, 6beta,7alpha,15-triacetoxylabda-8,13 E-diene ( 3), 3alpha,11-dihydroxy-9,11-seco-cholest-4,7-dien-6,9-dione ( 4), and cholest-7-en-3,5,7-triol ( 5). Chiral derivatization and X-ray analysis were used to confirm the labdane absolute configuration of 2. Compounds 1, 2 and 4 exhibited moderate activity (3-25 microM) against the WHCO1 human esophageal cancer cell line.

Non-pylori Helicobacteraceae in the upper digestive tract of asymptomatic Venezuelan subjects: detection of Helicobacter cetorum-like and Candidatus Wolinella africanus-like DNA

BACKGROUND

The spectrum of human non-pylori Helicobacter infections is expanding, with species such as H. heilmannii and H. felis occasionally being associated with gastritis. However, the existence of non-pylori Helicobacter colonization in asymptomatic subjects has not been evaluated. The aim of this study was to investigate whether Helicobacter species other than pylori are present in the upper digestive tract of asymptomatic human subjects.

MATERIALS AND METHODS

A Helicobacteraceae-specific semi-nested polymerase chain reaction (PCR) assay was used to detect Helicobacter-like organisms in the upper digestive tract of 91 Venezuelan volunteers (aged 18-68 years, 41 females, 50 males). Species were identified by denaturing gradient gel electrophoresis analysis and sequencing of the PCR products.

RESULTS

We detected DNA sharing 99-100% sequence identity in over 300-400 bp with the 16S rRNA genes of H. pylori, H. cetorum, and Candidatus Wolinella africanus in 76%, 16%, and 15% of the subjects, respectively. Multiple colonization was documented in 10% of the subjects: H. cetorum and Candidatus W. africanus (4%), H. pylori and Candidatus W. africanus (4%), and H. pylori and H. cetorum (2%).

CONCLUSIONS

Our results suggest that non-pylori Helicobacteraceae colonization is relatively common in the Venezuelan asymptomatic population. This is the first report documenting the presence of H. cetorum DNA in the human upper digestive tract, and the second report of the recently discovered Candidatus W. africanus.

Identification of disulfide reductases in Campylobacterales: a bioinformatics investigation

Disulfide reductases of host-colonising bacteria are involved in the expression of virulence factors, resistance to drugs, and elimination of toxic compounds. Large-scale genome analyses of 281 prokaryotes identified CXXC and CXXC-derived motifs in each microorganism. The total number of these motifs showed correlations with genome size and oxygen tolerance of the prokaryotes. Specific bioinformatic analyses served to identify putative disulfide reductases in the Campylobacterales Campylobacter jejuni, Helicobacter pylori, Wolinella succinogenes and Arcobacter butzleri which colonise the gastrointestinal tract of higher animals. Three filters applied to the genomes of these species yielded 35, 25, 28 and 34 genes, respectively, encoding proteins with the characteristics of disulfide reductases. Ten proteins were common to the four species, including four belonging to the thioredoxin system. The presence of thioredoxin reductase activities was detected in the four bacterial species by observing dithiobis-2-nitrobenzoic acid reduction with beta-nicotinamide adenine dinucleotide phosphate as cofactor. Phylogenetic analyses of the thioredoxin reductases TrxB(1) and TrxB(2) of the four Campylobacterales were performed. Their TrxB(1) proteins were more closely related to those of Firmicutes than to the corresponding proteins of other Proteobacteria. The Campylobacterales TrxB(2) proteins were closer to glutathione reductases of other organisms than to their respective TrxB(1) proteins. The phylogenetic features of the Campylobacterales thioredoxin reductases suggested a special role for these enzymes in the physiology of these bacteria.

Wolinella succinogenes response to ox-bile stress

The bacterium Wolinella succinogenes is the only known species of its genus. It was first isolated from cow ruminal fluid, and in cattle, it dwells in the reticulum and rumen compartments of the stomach. The global protein response of W. succinogenes to ox-bile was investigated with the aim to understand bile-tolerance mechanisms of the bacterium. Bacteria were grown in liquid media supplemented with different bile concentrations to determine its effects on growth and morphology. Proteomic analyses served to identify 14 proteins whose expression was modulated by the presence of 0.2% bile. Quantitative real-time PCR analyses of the expression of selected genes were employed to obtain independent confirmation of the proteomics data. Proteins differentially expressed revealed metabolic pathways involved in the adaptation of W. succinogenes to bile. The data suggested that bile stress elicited complex physiological responses rather than just specific pathways, and identified proteins previously unknown to be involved in the adaptation of bacteria to bile.

Low prevalence of Helicobacteraceae in gall-stone disease and gall-bladder carcinoma in the German population

Colonisation of the hepatobiliary system with bile-resistant Helicobacter spp. has been proposed as a novel risk-factor in the pathogenesis of gall-bladder carcinoma (GBC). There are reports that biliary Helicobacter colonisation is frequent in countries with a high incidence of gall-bladder carcinoma. However, the prevalence of Helicobacteraceae in the gall-bladders of patients with GBC in Germany, a region with a low incidence of GBC, is unknown. Therefore, gall-bladder tissue from 99 patients who had undergone cholecystectomy was tested, including 57 cases of gall-stone disease (GSD), 20 cases of GBC, and 22 control patients. The presence of Helicobacter spp. was investigated by culture, immunohistochemistry and a group-specific PCR targeting the 16S rRNA gene of all currently known Helicobacteraceae. Of the 99 cases investigated, only one patient with GSD was PCR-positive for Helicobacteraceae. For this individual, sequence analysis of the 16S rRNA gene showed that it had homology closest to the 16S rRNA sequence of Helicobacter ganmani. Helicobacteraceae were not detected by culture or immunohistochemistry. The low prevalence of Helicobacteraceae in the gall-bladders investigated suggests that Helicobacteraceae do not play a predominant role in the pathogenesis of GSD and GBC in the German population. The low prevalence could be a possible explanation for a relatively low incidence of GBC in the German population, despite the fact that GSD, the major risk-factor for GBC, is highly prevalent.

Bioinformatic study of bile responses inCampylobacterales

Campylobacter, Helicobacter and Wolinella are genera of the order Campylobacterales, belonging to the class Epsilonproteobacteria. Their habitats are various niches in the gastrointestinal tract of higher animals, where they may come into contact with bile. Microorganisms in these environments require mechanisms of resistance to the surface-active amphipathic molecules with potent antimicrobial activities present in bile. This review summarizes current knowledge on the molecular responses to bile by Campylobacterales and other bacterial species that inhabit the intestinal tract and belong to the phyla Proteobacteria, Bacteriodetes, Firmicutes and Actinobacteria. To date, 125 specific genes have been implicated in bile responses, of which 10 are found in Campylobacterales. Genome database searches, analyses of protein sequence and domain similarities, and gene ontology data integration were performed to compare the responses to bile of these bacteria. The results showed that 33 proteins of bacteria belonging to the four phyla had similarities equal to or greater than 50-46% proteins of Campylobacterales. Domain architecture analyses revealed that 151 Campylobacterales proteins had similar domain composition and organization to 60 proteins known to participate in the tolerance to bile in other bacteria. The proteins CmeB, CmeF and CbrR of Campylobacter jejuni involved in bile tolerance were homologous to 42 proteins identified in the Proteobacteria, Bacteriodetes and Firmicutes. On the other hand, the proteins CiaB, CmeA, CmeC, CmeD, CmeE and FlaAsigma(28) also involved in the response to bile of C. jejuni, did not have homologues in other bacteria. Among the bacteria inhabiting the gastrointestinal tract, the Campylobacterales seem to have evolved some mechanisms of bile resistance similar to those of other bacteria, as well as other mechanisms that appear to be characteristic of this order.

Prevalence and spread of enterohepatic Helicobacter species in mice reared in a specific-pathogen-free animal facility

Infections with enterohepatic Helicobacter species (EHS) can change the results of animal experiments. However, there is little information about the prevalence of EHS in noncommercial animal facilities. The aim of this study was to investigate the prevalence and the spread of EHS in specific-pathogen-free (SPF) mice. Fecal samples of 40 mouse lines were analyzed for members of the family Helicobacteraceae using a group-specific PCR targeting the 16S rRNA gene. Additional experiments were carried out to evaluate the spread of EHS among mice harbored in different caging systems. Helicobacter species were detected in 87.5% of the mouse lines tested. Five different Helicobacter species were identified: H. ganmani, H. hepaticus, H. typhlonicus, and the putative Helicobacter species represented by the isolates hamster B and MIT 98-5357. Helicobacter infection did not spread between animals in neighboring cages when individually ventilated cages were used; in contrast, when the mice were reared in open-air cages, EHS were found to spread from cage to cage. However, the spread was prevented by adding polycarbonate filter tops to the cages. When Helicobacter-negative and infected mice shared the same cage, transmission of the infection occurred in 100% within 2 weeks. Furthermore, we found that mice from commercial breeding facilities may carry undetected Helicobacter infections. Taken together, we show that infection with EHS may frequently occur and spread easily in mice reared under SPF conditions despite extensive safety precautions. Moreover, there is a high prevalence of rather uncommon Helicobacter species that may be a consequence of the current routine procedures used for health screening of SPF mice.

Application of horizontal staircase electrophoresis in agarose minigels to the random intergenic spacer analysis of clinical samples

The random intergenic spacer analysis is a recently developed technique for the study of microbial populations. The bacterial intergenic spacer (ITS) is located between 16S rRNA and 23S rRNA genes and presents different length and sequence among bacterial species. Therefore, the amplicons can be separated by electrophoresis commonly performed at low voltage during several hours. Although this technique is especially useful for unculturable microorganisms, it has not been applied before to clinical sample analysis. As these samples have a limited number of bacterial species, the size of the gels may be reduced to facilitate their handling and to reduce the running time. To obtain maximum separation among the ITS bands, we analysed in this work different electrophoretical conditions including staircase electrophoresis, a technique based on the application of several voltage steps. The results obtained showed a different behaviour of the electrical resistance during the performance of submarine horizontal and vertical staircase electrophoresis. In the first case the resistance decreased during most of the running time whereas in the second case it increased. Here, we show that the performance of horizontal staircase electrophoresis reduces the running time more than 80% with respect to conventional electrophoresis at low voltages. This procedure was applied to the separation of ITS bands from bacterial DNA present in a tissue from a vocal cord biopsy. The sequencing of these bands allowed their identification. This new procedure may be very useful in the rapid diagnosis of bacteria present in human, animal and plant tissues.

Species of the family Helicobacteraceae detected in an Australian sea lion (Neophoca cinerea) with chronic gastritis

We describe the first case of gastritis in a male Australian sea lion (Neophoca cinerea) in which members of the family Helicobacteraceae, particularly the genus Wolinella, were detected. The sea lion exhibited clinical signs of gastrointestinal disease, including abdominal pain, lack of appetite, and lethargy. Examination of one ileal and five gastric biopsy specimens collected over a 10-year period revealed persistent fibrosis and/or superficial focal erosion and ulceration of the lamina propria. Spiral-shaped organisms 5 to 12 microm long were observed in two of the gut biopsy specimens. While Helicobacter species were detected by PCR in one of the gastric biopsy specimens, Wolinella species were detected in four of the five gastric specimens, including those in which spiral-shaped organisms were observed. Comparisons of biopsy specimen ribosomal DNA sequences with those obtained from the feces of this animal, the gastric tissue of a clinically healthy individual, and the feces of several other cohoused sea lions and fur seals revealed a separate and possibly novel gastric Helicobacter species. A possibly novel Wolinella species, along with Wolinella succinogenes, was also identified. These findings highlight the pathogenic potential of other members of this family in the etiopathogenesis of gastric disease in these animals.

Identification of enterohepatic Helicobacter species in patients suffering from inflammatory bowel disease

Using a group-specific PCR assay, we investigated the presence of enterohepatic Helicobacter species in gut specimens from patients with inflammatory bowel disease. Enterohepatic Helicobacter species were detected in 12% (3 of 25) of the patients with Crohn's disease, in 17% (3 of 18) of the ulcerative colitis samples, and in 4% (1 of 23) of the controls.