Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics

Proposal of Helicobacter higonensis sp. nov. isolated from a human clinical specimen, and emended description of Helicobacter valdiviensis Collado, 2014

We have previously isolated a gram-negative microaerophilic strain, PAGU2000T from a patient presenting with a fever in Kumamoto Prefecture, Japan. The present study aimed to comprehensively analyze the taxonomy of the isolated strain using a polyphasic approach. The 16S rRNA gene sequence analysis indicated that the strain was a member of enterohepatic Helicobacter. The strain PAGU2000T shared a 97.5% 16S rRNA gene nucleotide identity with Helicobacter valdiviensis, and this taxonomic position was confirmed by phylogenetic analysis of the GyrA amino acid sequences. The proposed strain PAGU2000T has a 1.482 Mbp chromosome with a DNA G + C content of 31.3 mol% and encodes 1520 predicted coding sequences. The average nucleotide identity between the strain PAGU2000T and type strain of H. valdiviensis was 70.3%, which was lower than the recommended threshold of 95% for species delineation. The strain PAGU2000T was a motile, non-spore-forming, and spiral-shaped bacterium, exhibiting catalase and oxidase activities but not urease and nitrate reduction. This study demonstrates that the isolate represents a novel species within enterohepatic Helicobacter, for which the name Helicobacter higonensis is proposed (type strain: PAGU2000T = GTC 16811T = LMG 33095T). In this study, we describe the phenotypic and morphological features of this strain and propose an emended description of some biochemical traits of H. valdiviensis.

Anaplasmataceae presence in Amblyomma calcaratum associated with anteaters (Tamandua tetradactyla) in the rainforest ecoregion, Argentina

Bacteria of the sister genera Ehrlichia and Anaplasma (Anaplasmataceae) are obligate intracellular Alphaproteobacteria that are transmitted mostly through arthropod vectors. These agents can infect different vertebrate cells, depending on the species involved, and can cause diseases in animals and humans. In this study, we evaluated the presence of Anaplasmataceae bacteria in Amblyomma calcaratum ticks collected from a road-killed Tamandua tetradactyla in the Rainforest ecoregion in Argentina. All samples were screened for Anaplasmataceae DNA using a real-time PCR assay targeting the 16S rRNA gene. Evidence of Anaplasmataceae DNA was detected in three out of thirty-nine Am. calcaratum ticks. Phylogenetic analysis of a portion of 16S rRNA gene positioned one sample (Ehrlichia sp. strain Ac124) with Ehrlichia sequences and the other two samples with Anaplasma sequences; Anaplasma sp. strain Ac145 close to Anaplasma odocoilei and Anaplasma sp. strain Ac152 in an ancestral position to most Anaplasma species. The groEL sequence obtained showed that Ehrlichia sp. strain Ac124 was phylogenetically related to Ehrlichia sp. strain Iberá reported infecting Amblyomma tigrinum from Iberá wetlands in Argentina. Phylogenetic analysis using the rpoB sequence positioned Anaplasma sp. strain Ac145 close to the canine pathogen Anaplasma platys, while Anaplasma sp. strain Ac152 was positioned close to the bovine pathogen Anaplasma marginale. In this study, three Anaplasmataceae agents were detected in adults of Am. calcaratum associated with a T. tetradactyla. These results suggest that the number of Anaplasmataceae species, as well as their distribution, is largely unknown.

Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria

Digital PCR combined with high resolution melt (HRM) is an emerging method for identifying pathogenic bacteria with single cell resolution via species-specific digital melt curves. Currently, the development of such digital PCR-HRM assays entails first identifying PCR primers to target hypervariable gene regions within the target bacteria panel, next performing bulk-based PCR-HRM to examine whether the resulting species-specific melt curves possess sufficient interspecies variability (i.e., variability between bacterial species), and then digitizing the bulk-based PCR-HRM assays with melt curves that have high interspecies variability via microfluidics. In this work, we first report our discovery that the current development workflow can be inadequate because a bulk-based PCR-HRM assay that produces melt curves with high interspecies variability can, in fact, lead to a digital PCR-HRM assay that produces digital melt curves with unwanted intraspecies variability (i.e., variability within the same bacterial species), consequently hampering bacteria identification accuracy. Our subsequent investigation reveals that such intraspecies variability in digital melt curves can arise from PCR primers that target nonidentical gene copies or amplify nonspecifically. We then show that computational in silico HRM opens a window to inspect both interspecies and intraspecies variabilities and thus provides the missing link between bulk-based PCR-HRM and digital PCR-HRM. Through this new development workflow, we report a new digital PCR-HRM assay with improved bacteria identification accuracy. More broadly, this work can serve as the foundation for enhancing the development of future digital PCR-HRM assays toward identifying causative pathogens and combating infectious diseases.

Divide and conquer: genetics, mechanism, and evolution of the ferrous iron transporter Feo in Helicobacter pylori

Introduction

Feo is the most widespread and conserved system for ferrous iron uptake in bacteria, and it is important for virulence in several gastrointestinal pathogens. However, its mechanism remains poorly understood. Hitherto, most studies regarding the Feo system were focused on Gammaproteobacterial models, which possess three feo genes (feoA, B, and C) clustered in an operon. We found that the human pathogen Helicobacter pylori possesses a unique arrangement of the feo genes, in which only feoA and feoB are present and encoded in distant loci. In this study, we examined the functional significance of this arrangement.

Methods

Requirement and regulation of the individual H. pylori feo genes were assessed through in vivo assays and gene expression profiling. The evolutionary history of feo was inferred via phylogenetic reconstruction, and AlphaFold was used for predicting the FeoA-FeoB interaction.

Results and Discussion

Both feoA and feoB are required for Feo function, and feoB is likely subjected to tight regulation in response to iron and nickel by Fur and NikR, respectively. Also, we established that feoA is encoded in an operon that emerged in the common ancestor of most, but not all, helicobacters, and this resulted in feoA transcription being controlled by two independent promoters. The H. pylori Feo system offers a new model to understand ferrous iron transport in bacterial pathogens.

Helicobacter kumamotonensis sp. nov., isolated from human clinical specimens

A Gram-stain-negative, spiral bacterium (PAGU 1991^T) was isolated from the blood of a patient with diffuse large B-cell lymphoma. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was very closely related to Helicobacter equorum LMG 23362^T (99.1 % similarity), originally isolated from a faecal sample from a healthy horse. PAGU 1991^T was also very closely related to PAGU 1750 in our strain library (=CCUG 41437) with 99.7 % similarity. Additional phylogenetic analyses based on the 23S rRNA gene sequence and GyrA amino acid sequence further supported the close relationship between the two human isolates (PAGU 1991^T and PAGU 1750) and the horse strain. However, a phylogenetic analysis based on 16S rRNA showed that the two human isolates formed a lineage that was distinct from the horse strain (less than 99.2 % similarity). In silico whole-genome comparisons based on digital DNA-DNA hybridization, average nucleotide identity based on blast and orthologous average nucleotide identity using usearch between the two human isolates and the type strain of H. equorum showed values of less than 52.40, 93.47, and 93.50 %, respectively, whereas those between the two human isolates were 75.8, 97.2, and 97.2 %, respectively. These data clearly demonstrated that the two human isolates formed a single species, distinct from H. equorum. Morphologically, the human isolates could be distinguished by the type of flagella; the human isolates showed a bipolar sheathed flagellum, whereas that of H. equorum was monopolar. Biochemically, the human isolate was characterized by growth at 42 °C under microaerobic conditions and nitrate reduction unability. We conclude that the two human isolates, obtained from geographically and temporally distinct sources, were a novel species, for which we propose the name Helicobacter kumamotonensis sp. nov., with the type strain PAGU 1991^T (=GTC 16810^T=CCUG 75774^T).

The virtual microbiome: A computational framework to evaluate microbiome analyses

Microbiomes have been the focus of a substantial research effort in the last decades. The composition of microbial populations is normally determined by comparing DNA sequences sampled from those populations with the sequences stored in genomic databases. Therefore, the amount of information available in databanks should be expected to constrain the accuracy of microbiome analyses. Albeit normally ignored in microbiome studies, this constraint could severely compromise the reliability of microbiome data. To test this hypothesis, we generated virtual bacterial populations that exhibit the ecological structure of real-world microbiomes. Confronting the analyses of virtual microbiomes with their original composition revealed critical issues in the current approach to characterizing microbiomes, issues that were empirically confirmed by analyzing the microbiome of Galleria mellonella larvae. To reduce the uncertainty of microbiome data, the effort in the field must be channeled towards significantly increasing the amount of available genomic information and optimizing the use of this information.

Validation of Multiplex PCR and Serology Detecting Helicobacter Species in Mice

High-throughput multiplexed assays are needed to simplify detection of Helicobacter species in experimental infection and routine health monitoring of laboratory mice. Therefore, fluorescent bead-based hybridization assays for Helicobacter sp. DNA and serology were developed. Multiplex PCR amplicons (H. hepaticus, H. bilis, H. typhlonius, H. pylori, H. muridarum, H. pullorum, H. cinaedi, H. heilmanii, C. jejuni) and antibodies against H. pylori, H. hepaticus, H. bilis were assessed in naturally and experimentally infected mice, and results compared to conventional PCR. Species-specific and sensitive detection of seven Helicobacter spp. <100 copies/PCR, and of two species <1000 copies/PCR was successfully established in the Helicobacter multiplex DNA finder. The novel assay was highly comparable with conventional PCR (kappa = 0.98, 95%CI: 0.94-1.00). Antibody detection of H. hepaticus and H. bilis showed low sensitivity (71% and 62%, respectively) and cross-reactivity in H. typhlonius-infected mice. Infection experiments showed that antibodies develop earliest two weeks after DNA detection in feces. In conclusion, detection of Helicobacter antibodies showed low sensitivity depending on the timing relative to infection. However, Helicobacter multiplex DNA finder is a sensitive and specific high-throughput assay applicable in routine health monitoring for laboratory animals.

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

BACKGROUND

The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82].

RESULTS

At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%).

CONCLUSIONS

Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.

Gastric Helicobacter species associated with dogs, cats and pigs: significance for public and animal health

This article focuses on the pathogenic significance of Helicobacter species naturally colonizing the stomach of dogs, cats and pigs. These gastric "non-Helicobacter (H.) pylori Helicobacter species" (NHPH) are less well-known than the human adapted H. pylori. Helicobacter suis has been associated with gastritis and decreased daily weight gain in pigs. Several studies also attribute a role to this pathogen in the development of hyperkeratosis and ulceration of the non-glandular stratified squamous epithelium of the pars oesophagea of the porcine stomach. The stomach of dogs and cats can be colonized by several Helicobacter species but their pathogenic significance for these animals is probably low. Helicobacter suis as well as several canine and feline gastric Helicobacter species may also infect humans, resulting in gastritis, peptic and duodenal ulcers, and low-grade mucosa-associated lymphoid tissue lymphoma. These agents may be transmitted to humans most likely through direct or indirect contact with dogs, cats and pigs. Additional possible transmission routes include consumption of water and, for H. suis, also consumption of contaminated pork. It has been described that standard H. pylori eradication therapy is usually also effective to eradicate the NHPH in human patients, although acquired antimicrobial resistance may occasionally occur and porcine H. suis strains are intrinsically less susceptible to aminopenicillins than non-human primate H. suis strains and other gastric Helicobacter species. Virulence factors of H. suis and the canine and feline gastric Helicobacter species include urease activity, motility, chemotaxis, adhesins and gamma-glutamyl transpeptidase. These NHPH, however, lack orthologs of cytotoxin-associated gene pathogenicity island and vacuolating cytotoxin A, which are major virulence factors in H. pylori. It can be concluded that besides H. pylori, gastric Helicobacter species associated with dogs, cats and pigs are also clinically relevant in humans. Although recent research has provided better insights regarding pathogenic mechanisms and treatment strategies, a lot remains to be investigated, including true prevalence rates, exact modes of transmission and molecular pathways underlying disease development and progression.

Helicobacter Species and Their Association with Gastric Pathology in a Cohort of Dogs with Chronic Gastrointestinal Signs

Prevalence of individual Helicobacter species, data evaluating their association with gastric pathology and comparison of accuracy of diagnostic techniques are limited. The aims of this study were to determine the prevalence of gastric Helicobacter species, their association with gastric pathology, and to compare diagnostic techniques. Gastric biopsies from 84 privately-owned dogs with chronic gastrointestinal signs were obtained endoscopically. Helicobacters were detected using PCR, cytology, urease test, and histopathology. PCR detected helicobacters in 71.4% of dogs. Helicobacter heilmannii sensu stricto (s.s.) was the predominant species. Mixed infection was detected in 40% of PCR positive dogs. Gastritis was diagnosed in 38.5% of Helicobacter positive and 47.4% of Helicobacter negative dogs. Mono-infection was associated with 2.4 times increased odds of having more severe inflammation compared to mixed infection. Erosions and ulcers were common endoscopic lesions. Cytology had sensitivity/specificity of 88.3/91.7%. Association between infection and lymphoid follicular hyperplasia was demonstrated.

Helicobacter cyclurae sp. Nov., Isolated From Endangered Blue Iguanas (Cyclura lewisi)

Blue iguanas (Cyclura lewisi) are endangered reptiles found only on Grand Cayman. Previously, DNA for a novel Helicobacter species GCBI1 was detected in sick and dead iguanas. In the current study, fecal and cloacal swab samples were obtained from 25 iguanas. Through molecular and microbiological techniques, a novel Helicobacter species was cultured from feces and characterized, for whom we propose the name Helicobacter cyclurae. This novel helicobacter had a prevalence of 56% by PCR and 20% by culture in samples analyzed. The type strain MIT 16-1353 was catalase, oxidase, and gamma-glutamyl transpeptidase positive. By electron microscopy, H. cyclurae has a curved rod morphology and a single sheathed polar flagellum. Phylogenetic analysis using 16S rRNA, gyrB, and hsp60 indicated that these strains were most closely related to Helicobacter sp. 12502256-12 previously isolated from lizards. H. cyclurae has a 1.91-Mb genome with a GC content of 33.37%. There were 1,969 genes with four notable virulence genes: high temperature requirement-A protein-secreted serine protease, gamma-glutamyl transpeptidase, fibronectin/fibrinogen binding protein, and neutrophil-activating protein. Whole-genome phylogeny, average nucleotide identity, and digital DNA–DNA hybridization analysis confirmed that H. cyclurae is a novel species, and the first helicobacter cultured and characterized from blue iguanas.

Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes

Characterization of the bacterial composition and functional repertoires of microbiome samples is the most common application of metagenomics. Although deep whole-metagenome shotgun sequencing (WMS) provides high taxonomic resolution, it is generally cost-prohibitive for large longitudinal investigations. Until now, 16S rRNA gene amplicon sequencing (16S) has been the most widely used approach and usually cooperates with WMS to achieve cost-efficiency. However, the accuracy of 16S results and its consistency with WMS data have not been fully elaborated, especially by complicated microbiomes with defined compositional information. Here, we constructed two complex artificial microbiomes, which comprised more than 60 human gut bacterial species with even or varied abundance. Utilizing real fecal samples and mock communities, we provided solid evidence demonstrating that 16S results were of poor consistency with WMS data, and its accuracy was not satisfactory. In contrast, shallow whole-metagenome shotgun sequencing (shallow WMS, S-WMS) with a sequencing depth of 1 Gb provided outputs that highly resembled WMS data at both genus and species levels and presented much higher accuracy taxonomic assignments and functional predictions than 16S, thereby representing a better and cost-efficient alternative to 16S for large-scale microbiome studies.

Substrate usage determines carbon flux via the citrate cycle in Helicobacter pylori

Helicobacter pylori displays a worldwide infection rate of about 50%. The Gram-negative bacterium is the main reason for gastric cancer and other severe diseases. Despite considerable knowledge about the metabolic inventory of H. pylori, carbon fluxes through the citrate cycle (TCA cycle) remained enigmatic. In this study, different ¹³ C-labeled substrates were supplied as carbon sources to H. pylori during microaerophilic growth in a complex medium. After growth, ¹³ C-excess and ¹³ C-distribution were determined in multiple metabolites using GC-MS analysis. [U-¹³ C₆ ]Glucose was efficiently converted into glyceraldehyde but only less into TCA cycle-related metabolites. In contrast, [U-¹³ C₅ ]glutamate, [U-¹³ C₄ ]succinate, and [U-¹³ C₄ ]aspartate were incorporated at high levels into intermediates of the TCA cycle. The comparative analysis of the ¹³ C-distributions indicated an adaptive TCA cycle fully operating in the closed oxidative direction with rapid equilibrium fluxes between oxaloacetate-succinate and α-ketoglutarate-citrate. ¹³ C-Profiles of the four-carbon intermediates in the TCA cycle, especially of malate, together with the observation of an isocitrate lyase activity by in vitro assays, suggested carbon fluxes via a glyoxylate bypass. In conjunction with the lack of enzymes for anaplerotic CO₂ fixation, the glyoxylate bypass could be relevant to fill up the TCA cycle with carbon atoms derived from acetyl-CoA.

Enterohepatic Helicobacter species - clinical importance, host range, and zoonotic potential

The genus Helicobacter defined just over 30 years ago, is a highly diverse and fast-growing group of bacteria that are able to persistently colonize a wide range of animals. The members of this genus are subdivided into two groups with different ecological niches, associated pathologies, and phylogenetic relationships: the gastric Helicobacter (GH) and the enterohepatic Helicobacter (EHH) species. Although GH have been mostly studied, EHH species have become increasingly important as emerging human pathogens and potential zoonotic agents in the last years. This group of bacteria has been associated with the development of several diseases in humans from acute pathologies like gastroenteritis to chronic pathologies that include inflammatory bowel disease, and liver and gallbladder diseases. However, their reservoirs, as well as their routes of transmission, have not been well established yet. Therefore, this review summarizes the current knowledge of taxonomy, epidemiology, and clinical role of the EHH group.

Systemic Helicobacter infection and associated mortalities in endangered Grand Cayman blue iguanas (Cyclura lewisi) and introduced green iguanas (Iguana iguana)

The Blue Iguana Recovery Programme maintains a captive breeding and head-starting program for endangered Grand Cayman blue iguanas (Cyclura lewisi) on Grand Cayman, Cayman Islands. In May 2015, program staff encountered two lethargic wild Grand Cayman blue iguanas within the Queen Elizabeth II Botanic Park (QEIIBP). Spiral-shaped bacteria were identified on peripheral blood smears from both animals, which molecular diagnostics identified as a novel Helicobacter species (provisionary name Helicobacter sp. GCBI1). Between March 2015 and February 2017, 11 Grand Cayman blue iguanas were identified with the infection. Two of these were found dead and nine were treated; five of the nine treated animals survived the initial infection. Phylogenetic analysis of the 16S rRNA gene suggests Helicobacter sp. GCBI1 is most closely related to Helicobacter spp. in chelonians. We developed a Taqman qPCR assay specific for Helicobacter sp. GCBI1 to screen tissue and/or blood samples from clinical cases, fecal and cloacal samples from clinically healthy Grand Cayman blue iguanas, including previously infected and recovered iguanas, and iguanas housed adjacent to clinical cases. Fecal and/or cloacal swab samples were all negative, suggesting that Grand Cayman blue iguanas do not asymptomatically carry this organism nor shed this pathogen per cloaca post infection. Retrospective analysis of a 2014 mortality event affecting green iguanas (Iguana iguana) from a separate Grand Cayman location identified Helicobacter sp. GCBI1 in two of three cases. The source of infection and mode of transmission are yet to be confirmed. Analysis of rainfall data reveal that all infections occurred during a multi-year dry period, and most occurred shortly after the first rains at the end of seasonal drought. Additionally, further screening has identified Helicobacter sp. GCBI1 from choanal swabs of clinically normal green iguanas in the QEIIBP, suggesting they could be asymptomatic carriers and a potential source of the pathogen.

Exploring the role of healthy dogs as hosts of enterohepatic Helicobacter species using cultivation-dependent and -independent approaches

Enterohepatic Helicobacter (EHH) species have been increasingly associated with acute gastroenteritis, inflammatory bowel disease and hepatobiliary diseases in humans. However, their host range and transmission routes are poorly understood. Therefore, the aim of this study was to determine the presence of EHH in healthy dogs using both cultivation-dependent and -independent methods. Three hundred and ninety faecal samples from domestic dogs without gastrointestinal symptoms were analysed between June 2018 and July 2019 in Valdivia (South of Chile). Samples were inoculated on selective medium and in parallel were filtrated over an antibiotic-free blood agar. Both media were incubated in a microaerobic atmosphere at 37°C for 7 days. Colonies were identified by PCR and phylogenetic analysis. A subset of 50 samples (half of them positive for EHH by cultivation and the remaining half negative) was analysed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) for direct detection. Cultivation method detected EHH in 15.4% (60/390) of the samples, being the most prevalent species H. canis (5.8%, 23/390) and H. canicola (5.1%, 20/390), followed by H. bilis (3.6%, 14/390) and 'H. winghamensis' (1.3%, 5/390). In contrast, PCR-DGGE method detected Helicobacter DNA in almost all (96%, 48/50) tested samples. On the other hand, the method used also allowed to isolate other Campylobacterales, in fact 44.3% (173/390) of the samples were positive for Campylobacter upsaliensis (43.3%, 169/390) followed by C. jejuni (2.0%, 8/390). Moreover, two strains that presented Campylobacter-like morphology were finally identified as Anaerobiospirillum succiniciproducens. Our results indicate that healthy domestic dogs commonly carry EHH and other Campylobacter species. However, further studies are needed to determine whether and how these Helicobacter and Campylobacter species can be transmitted to humans.

Helicobacter monodelphidis sp. nov. and Helicobacter didelphidarum sp. nov., isolated from grey short-tailed opossums (Monodelphis domestica) with endemic cloacal prolapses

In a search for potential causes of increased prolapse incidence in grey short-tailed opossum colonies, samples from the gastrointestinal tracts of 94 clinically normal opossums with rectal prolapses were screened for Helicobacter species by culture and PCR. Forty strains of two novel Helicobacter species which differed from the established Helicobacter taxa were isolated from opossums with and without prolapses. One of the Helicobacter species was spiral-shaped and urease-negative whereas the other Helicobacter strain had fusiform morphology with periplasmic fibres and was urease-positive. 16S rRNA gene sequence analysis revealed that all the isolates had over 99 % sequence identity with each other, and were most closely related to Helicobacter canadensis. Strains from the two novel Helicobacter species were subjected to gyrB and hsp60 gene and whole genome sequence analyses. These two novel Helicobacter species formed separate phylogenetic clades, divergent from other known Helicobacter species. The bacteria were confirmed as novel Helicobacter species based on digital DNA-DNA hybridization and average nucleotide identity analysis of their genomes, for which we propose the names Helicobacter monodelphidis sp. nov. with the type strain MIT 15-1451^T (=LMG 29780^T=NCTC 14189^T) and Helicobacter didelphidarum sp. nov with type strain MIT 17-337^T (=LMG 31024^T=NCTC 14188^T).

First report of PCR-based detection of Helicobacter species DNA in Camelus dromedarius in Egypt

Background and Aim:

Helicobacter species infections have epidemiological and zoonotic impacts, and different species of Helicobacter have been implicated in infecting humans and animals. The aim of this study was to investigate Helicobacter species infections in Camelus dromedarius.

Materials and Methods:

Fecal samples were collected from 32 camels from 9 camel farms located at Ismailia Governorate, Egypt. The collected samples were investigated by bacteriological isolation and conventional polymerase chain reaction (PCR) assays targeting the 16S ribosomal RNA gene.

Results:

Although Helicobacter species could not be isolated from all the examined samples, Helicobacter DNA was detected in 2 (22.22%) of the 9 camel farms. Of the 32 camel fecal samples examined, 4 (12.5%) were positive for Helicobacter species as analyzed by the PCR assay.

Conclusion:

To the best of our knowledge, this is the first report of PCR-based detection of Helicobacter species infections in C. dromedarius. Further epidemiological studies are required to clarify Helicobacter species infections in camels.

A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes

It is well established nowadays that among prokaryotes, various families of orthologous genes exhibit conflicting evolutionary history. A prime factor for this conflict is horizontal gene transfer (HGT) - the transfer of genetic material not via vertical descent. Thus, the prevalence of HGT is challenging the meaningfulness of the classical Tree of Life concept. Here we present a comprehensive study of HGT representing the entire prokaryotic world. We mainly rely on a novel analytic approach for analyzing an aggregate of gene histories, by means of the quartet plurality distribution (QPD) that we develop. Through the analysis of real and simulated data, QPD is used to reveal evidence of a barrier against HGT, separating the archaea from the bacteria and making HGT between the two domains, in general, quite rare. In contrast, bacteria's confined HGT is substantially more frequent than archaea's. Our approach also reveals that despite intensive HGT, a strong tree-like signal can be extracted, corroborating several previous works. Thus, QPD, which enables one to analytically combine information from an aggregate of gene trees, can be used for understanding patterns and rates of HGT in prokaryotes, as well as for validating or refuting models of horizontal genetic transfers and evolution in general.

Helicobacter labacensis sp. nov., Helicobacter mehlei sp. nov., and Helicobacter vulpis sp. nov., isolated from gastric mucosa of red foxes (Vulpes vulpes)

Six Helicobacter-like isolates were recovered from 15 gastric mucosa samples of red foxes (Vulpes vulpes) shot by hunters in the surroundings of Ljubljana, Slovenia. Gram-negative, tightly coiled, intensely motile, 7-15 µm long and ≤1 µm wide bacteria grew on the biphasic blood agar plates. By using a genus-specific polymerase chain reaction (PCR), all isolates were confirmed as Helicobacter sp. and subsequently subjected to whole-genome sequencing (WGS). Five isolates showed a genome-wide average nucleotide identity (ANI) value of <95 % to the previously described Helicobacter species and one isolate was classified as Helicobacter felis. In the five unidentified isolates, the 16S rRNA gene sequence similarity to the type strains of all Helicobacter species ranged from 98.6 to 98.9 %. Their taxonomic status was established using a polyphasic taxonomic approach comprising the core genome-based phylogeny, morphological and phenotypic characteristics, including an analysis of matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectra. Phylogeny revealed the existence of three novel and well-supported clusters, with Helicobacter bizzozeronii and Helicobacter baculiformis being the most closely related species. The isolates also differed from the previously described species in their MALDI-TOF profiles and some biochemical characteristics. In conclusion, the data presented herein indicate that the obtained isolates, excluding H. felis isolate, represent three novel Helicobacter species, for which the names Helicobacter labacensis sp. nov., Helicobacter mehlei sp. nov., and Helicobacter vulpis sp. nov. are proposed, with isolates L9^T (=DSM 108823^T=CRBIP 111719^T), L15^T (=DSM 108730^T=CCUG 72910^T) and L2^T (=DSM 108727^T=CCUG 72909^T) as type strains, respectively.

Taxonomic classification and abundance estimation using 16S and WGS-A comparison using controlled reference samples

The assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S data are alleviated. However, due to the computationally intensive data analyses and higher sequencing costs, WGS based metagenomics remains a less popular option. Selecting the experiment type that provides a comprehensive, yet manageable amount of information is a challenge encountered in many metagenomics studies. In this work, we created a series of artificial bacterial mixes, each with a different distribution of skin-associated microbial species. These mixes were used to estimate the resolution of two different metagenomic experiments - 16S and WGS - and to evaluate several different bioinformatics approaches for taxonomic read classification. In all test cases, WGS approaches provide much more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. Furthermore, we demonstrate that a 16S dataset, analysed using different state of the art techniques and reference databases, can produce widely different results. In light of the fact that most forensic metagenomic analysis are still performed using 16S data, our results are especially important.

Whole-Genome Sequencing and Bioinformatics as Pertinent Tools to Support Helicobacteracae Taxonomy, Based on Three Strains Suspected to Belong to Novel Helicobacter Species

The present study describes three putative novel species received at the French National Reference Center for Campylobacters & Helicobacters (CNRCH). The CNRCH 2005/566H strain was isolated in 2005 from the feces of a patient with a hepatocellular carcinoma and gastroenteritis. Strain 48519 was isolated in 2017 from the blood of a male patient suffering from a bacteremia. Strain Cn23e was isolated from a gastric biopsy from a dog suffering from chronic gastritis. Biochemical and growth characteristics and electron microscopy for these three strains were studied. Their genomes were also sequenced. gyrA based phylogeny built with 72 nucleotide sequences placed CNRCH 2005/566H among the unsheathed enterohepatic helicobacters, close to Helicobacter valdiviensis; strain 48519 among the sheathed enterohepatic helicobacters, close to Helicobacter cinaedi; and strain Cn23e among gastric helicobacters, close to Helicobacter felis. 16S rRNA gene phylogeny showed similar results, but with weak discriminant strength. Average nucleotide identity and in silico DNA–DNA hybridization analyses revealed that CNRCH 2005/566H and 48519 strains belong to new putative species, but confirmed that Cn23e corresponds to H. felis. Cn23e was able to infect C57BL6 mice and to induce gastric inflammation. The genomics data, together with their different morphological and biochemical characteristics, revealed that these two strains represent novel Helicobacter species. We propose the following names: ‘Helicobacter burdigaliensis,’ with the type strain CNRCH 2005/566H ( =CECT 8850 =CIP 111660), and ‘Helicobacter labetoulli,’ with the type strain 48519 ( =CCUG 73475 =CIP 1111659). This study highlights that the diversity of the Helicobacteraceae family remains to be fully explored.

Comparison of media and growth conditions for culturing enterohepatic Helicobacter species

This research aims to compare the culturing conditions for enterohepatic Helicobacter, evaluating culture media, incubation atmosphere and susceptibility to antimicrobials used to generate selective conditions. Four common media for the closely related genus Campylobacter (Columbia, Bolton, Brucella and CCDA agar), as well as the need for hydrogen in the microaerobic incubation atmosphere, were evaluated. Serial dilutions of 13 strains belonging to six species (H. apodemus, H. bilis, H. canicola, H. canis, H. equorum and Helicobacter sp.) were inoculated in each media and incubated at 37°C for 48 to 96 h using CampyGen (OXOID) and gaseous exchange (including hydrogen) in parallel. Columbia or Brucella agars were the most appropriate for culturing EHH (P < 0·05). However, there was no significant difference between the atmospheres evaluated (P = 0·13). In addition, minimal inhibitory concentration for six antibiotics showed that all isolates were resistant to trimethoprim, whereas for the rest of the antibiotics (cephalothin, cefoperazone, cefsulodin, teicoplanin and vancomycin) the inhibition range was between 8 and 64 μg ml^{- 1} . Our findings suggest that Columbia or Brucella media, regardless of the use of hydrogen, can be used for the EHH isolation. In addition, the concentration of antibiotics included in commercial campylobacteria supplements is suitable for EHH species recovery. SIGNIFICANCE AND IMPACT OF THE STUDY: Enterohepatic Helicobacter (EHH) infections have been associated with several diseases in humans such as acute gastroenteritis, inflammatory bowel disease and hepatobiliary diseases. Although they are frequently detected in clinical samples by molecular methods, only occasionally they are isolated using culture conditions described for the taxonomic related pathogen Campylobacter sp. This is because the optimal conditions for the isolation of EHH have not yet been described, which results in an underestimation of the prevalence and clinical importance of these emerging pathogens. Therefore, this study provides insight for culturing EHH species.

Mixed Borrelia burgdorferi and Helicobacter pylori Biofilms in Morgellons Disease Dermatological Specimens

BACKGROUND

Morgellons disease (MD) is a dermopathy that is associated with tick-borne illness. It is characterized by spontaneously developing skin lesions containing embedded or projecting filaments, and patients may also experience symptoms resembling those of Lyme disease (LD) including musculoskeletal, neurological and cardiovascular manifestations. Various species of Borrelia and co-infecting pathogens have been detected in body fluids and tissue specimens from MD patients. We sought to investigate the coexistence of Borrelia burgdorferi (Bb) and Helicobacter pylori (Hp) in skin specimens from MD subjects, and to characterize their association with mixed amyloid biofilm development.

METHODS

Testing for Bb and Hp was performed on dermatological specimens from 14 MD patients using tissue culture, immunohistochemical (IHC) staining, polymerase chain reaction (PCR) testing, fluorescent in situ hybridization (FISH) and confocal microscopy. Markers for amyloid and biofilm formation were investigated using histochemical and IHC staining.

RESULTS

Bb and Hp were detected in dermatological tissue taken from MD lesions. Bb and Hp tended to co-localize in foci within the epithelial tissue. Skin sections exhibiting foci of co-infecting Bb and Hp contained amyloid markers including β-amyloid protein, thioflavin and phosphorylated tau. The biofilm marker alginate was also found in the sections.

CONCLUSIONS

Mixed Bb and Hp biofilms containing β-amyloid and phosphorylated tau may play a role in the evolution of MD.

Comparative genomics analysis to differentiate metabolic and virulence gene potential in gastric versus enterohepatic Helicobacter species

Background

The genus Helicobacter are gram-negative, microaerobic, flagellated, mucus-inhabiting bacteria associated with gastrointestinal inflammation and classified as gastric or enterohepatic Helicobacter species (EHS) according to host species and colonization niche. While there are over 30 official species, little is known about the physiology and pathogenic mechanisms of EHS, which account for most in the genus, as well as what genetic factors differentiate gastric versus EHS, given they inhabit different hosts and colonization niches. The objective of this study was to perform a whole-genus comparative analysis of over 100 gastric versus EHS genomes in order to identify genetic determinants that distinguish these Helicobacter species and provide insights about their evolution/adaptation to different hosts, colonization niches, and mechanisms of virulence.

Results

Whole-genome phylogeny organized Helicobacter species according to their presumed gastric or EHS classification. Analysis of orthologs revealed substantial heterogeneity in physiological and virulence-related genes between gastric and EHS genomes. Metabolic reconstruction predicted that unlike gastric species, EHS appear asaccharolytic and dependent on amino/organic acids to fuel metabolism. Additionally, gastric species lack de novo biosynthetic pathways for several amino acids and purines found in EHS and instead rely on environmental uptake/salvage pathways. Comparison of virulence factor genes between gastric and EHS genomes identified overlapping yet distinct profiles and included canonical cytotoxins, outer membrane proteins, secretion systems, and survival factors.

Conclusions

The major differences in predicted metabolic function suggest gastric species and EHS may have evolved for survival in the nutrient-rich stomach versus the nutrient-devoid environments, respectively. Contrasting virulence factor gene profiles indicate gastric species and EHS may utilize different pathogenic mechanisms to chronically infect hosts and cause inflammation and tissue damage. The findings from this study provide new insights into the genetic differences underlying gastric versus EHS and support the need for future experimental studies to characterize these pathogens.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5171-2) contains supplementary material, which is available to authorized users.

A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality

Extracting the strength of the tree signal that is encompassed by a collection of gene trees is an exceptionally challenging problem in phylogenomics. Often, this problem not only involves the construction of individual phylogenies based on different genes, which may be a difficult endeavor on its own, but is also exacerbated by many factors that create conflicts between the evolutionary histories of different gene families, such as duplications or losses of genes; hybridization events; incomplete lineage sorting; and horizontal gene transfer, the latter two play central roles in the evolution of eukaryotes and prokaryotes, respectively. In this work, we tackle the aforementioned problem by focusing on quartet trees, which are the most basic unit of information in the context of unrooted phylogenies. In the first part, we show how a theorem of Janson that generalizes the classical Hoeffding inequality can be used to develop a statistical test involving quartets. In the second part, we study real and simulated data using this theoretical advancement, thus demonstrating how the significance of the differences between sets of quartets can be assessed. Our results are particularly intriguing since they nonstandardly require the analysis of dependent random variables.

Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence

Since the discovery of the human pathogen Helicobacter pylori, various other Helicobacter species have been identified in the stomach of domesticated and wild mammals. To better understand the evolutionary history of these ecologically similar but genetically distinct species, we analyzed 108 gastric Helicobacter genomes and included 54 enterohepatic Helicobacter genomes for comparison purposes. An admixture analysis supported the presence of an ecological barrier, preventing the genetic exchange between the gastric and enterohepatic Helicobacter species, and unraveled many gene flow events within and across species residing in the stomach. As pets can be colonized by multiple gastric Helicobacter species, the genetic exchange between the canine and feline strains was evident, with H. heilmannii and H. bizzozeronii showing the highest interspecies recombination. An admixture between H. pylori (in particular, the ancestral African strains), H. acinonychis from wild felines and H. cetorum from marine mammals was also identified. Because these latter species do not share the same host, this phenomenon is most likely a remaining signal of shared ancestry. A reconstruction of the time of divergence of the gastric Helicobacter spp. revealed that the domestic animal-related Helicobacter species evolved in parallel with H. pylori and its two closest relatives (H. acinonychis and H. cetorum), rather than together.

Droplet Digital PCR-Based Detection of Clarithromycin Resistance in Helicobacter pylori Isolates Reveals Frequent Heteroresistance

Chronic infection with Helicobacter pylori causes peptic ulcers and stomach cancer in a subset of infected individuals. While standard eradication therapy includes multiple antibiotics, treatment failure due to resistance is an increasing clinical problem. Accurate assessment of H. pylori antimicrobial resistance has been limited by slow growth and sampling of few isolates per subject. We established a method to simultaneously quantify H. pylori clarithromycin-resistant (mutant) and -susceptible (wild-type) 23S rRNA gene alleles in both stomach and stool samples using droplet digital PCR (ddPCR). In 49 subjects, we assessed the performance of these assays alongside clarithromycin MIC testing of up to 16 H. pylori isolates per subject and included both cancer (25 subjects) and noncancer (24 subjects) cases. Gastric ddPCR and H. pylori culture showed agreement with urea breath test (UBT) detection of infection in 94% and 88% of subjects, respectively, while stool ddPCR showed agreement with UBT in 92% of subjects. Based on MIC testing of 43 culture-positive cases, 20 subjects had only susceptible isolates, 14 had a mix of susceptible and resistant isolates, and 9 had only resistant isolates. ddPCR of gastric samples indicated that 21 subjects had only wild-type alleles, 13 had a mixed genotype, and 9 had only mutant alleles. Stool ddPCR detected mutant alleles in four subjects for which mutant alleles were not detected by stomach ddPCR, and no resistant isolates were cultured. Our results indicate that ddPCR detects H. pylori clarithromycin resistance-associated genotypes, especially in the context of heteroresistance.

Reconstruction of real and simulated phylogenies based on quartet plurality inference

BACKGROUND

Deciphering the history of life on Earth has long been regarded as one of the most central tasks in biology. In past years, widespread discordance between the evolutionary histories of different groups of orthologous genes of prokaryotes have been revealed, primarily due to horizontal gene transfers (HGTs). Nonetheless, evidence that support a strong tree-like signal of evolution have been uncovered, despite the presence of HGT events. Therefore, a challenging task is to distill this tree-like signal from the noise induced by all sources of non-tree-like events.

RESULTS

In this work we tackle this question, using real and simulated data. We first tighten a recent related theoretical result in this field. In a simulation study, we infer individual quartet topologies, and then use the inferred quartets to reconstruct simulated species trees. We demonstrate that accurate tree reconstruction is feasible despite surprisingly high rates of HGT. In a real data study, we construct phylogenies of two sets of prokaryotes, and show that our tree reconstruction scheme is comparable with (and complementary better than) other commonly used methods.

CONCLUSIONS

Using a blend of theoretical and empirical investigations, our study proves the feasibility of accurate quartet-based phylogenetic reconstruction, the vast impact of HGT events notwithstanding.

Diversity and microevolution of CRISPR loci in Helicobacter cinaedi

Helicobacter cinaedi is associated with nosocomial infections. The CRISPR-Cas system provides adaptive immunity against foreign genetic elements. We investigated the CRISPR-Cas system in H. cinaedi to assess the potential of the CRISPR-based microevolution of H. cinaedi strains. A genotyping method based on CRISPR spacer organization was carried out using 42 H. cinaedi strains. The results of sequence analysis showed that the H. cinaedi strains used in this study had two CRISPR loci (CRISPR1 and CRISPR2). The lengths of the consensus direct repeat sequences in CRISPR1 and CRISPR2 were both 36 bp-long, and 224 spacers were found in the 42 H. cinaedi strains. Analysis of the organization and sequence similarity of the spacers of the H. cinaedi strains showed that CRISPR arrays could be divided into 7 different genotypes. Each genotype had a different ancestral spacer, and spacer acquisition/deletion events occurred while isolates were spreading. Spacer polymorphisms of conserved arrays across the strains were instrumental for differentiating closely-related strains collected from the same hospital. MLST had little variability, while the CRISPR sequences showed remarkable diversity. Our data revealed the structural features of H. cinaedi CRISPR loci for the first time. CRISPR sequences constitute a valuable basis for genotyping, provide insights into the divergence and relatedness between closely-related strains, and reflect the microevolutionary process of H. cinaedi.

Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host

Reptiles have been shown to host a significant Helicobacter diversity. In order to survive, reptile-associated Helicobacter lineages need to be adapted to the thermally dynamic environment encountered in a poikilothermic host. The whole genomes of reptile-associated Helicobacter lineages can provide insights in Helicobacter host adaptation and coevolution. These aspects were explored by comparing the genomes of reptile-, bird-, and mammal-associated Helicobacter lineages. Based on average nucleotide identity, all reptile-associated Helicobacter lineages in this study could be considered distinct species. A whole genome-based phylogeny showed two distinct clades, one associated with chelonians and one associated with lizards. The phylogeny indicates initial adaptation to an anatomical niche, which is followed by an ancient host jump and subsequent diversification. Furthermore, the ability to grow at low temperatures, which might reflect thermal adaptation to a reptilian host, originated at least twice in Helicobacter evolution. A putative tricarballylate catabolism locus was specifically present in Campylobacter and Helicobacter isolates from reptiles. The phylogeny of reptile-associated Helicobacter parallels host association, indicating a high level of host specificity. The high diversity and deep branching within these clades supports long-term coevolution with, and extensive radiation within the respective reptilian host type.

Ordered orthology as a tool in prokaryotic evolutionary inference

Molecular data is accumulated at exponentially increasing pace. This deluge of information should have brought us closer to resolving one of the most fundamental issues in biology - deciphering the history of life on Earth. So far, however, this abundance of data only seems to blur our understanding of the problem. This is largely due to horizontal gene transfer (HGT), the transfer of genetic material between evolutionarily unrelated organisms that transforms the prokaryotic tree into a network of relationships. Recently, we developed a method to infer evolutionary relationships among closely related species where the conventional evolutionary markers do not provide a strong enough signal. The method relies on the loss of synteny, gene order conservation among species that provides a stronger signal, sufficient to classify even strains of a given species. Here we elaborate on this method and suggest further uses of it in the context of detecting HGT events and genome architecture.

Convex recoloring as an evolutionary marker

With the availability of enormous quantities of genetic data it has become common to construct very accurate trees describing the evolutionary history of the species under study, as well as every single gene of these species. These trees allow us to examine the evolutionary compliance of given markers (characters). A marker compliant with the history of the species investigated, has undergone mutations along the species tree branches, such that every subtree of that tree exhibits a different state. Convex recoloring (CR) uses combinatorial representation to measure the adequacy of a taxonomic classifier to a given tree. Despite its biological origins, research on CR has been almost exclusively dedicated to mathematical properties of the problem, or variants of it with little, if any, relationship to taxonomy. In this work we return to the origins of CR. We put CR in a statistical framework and introduce and learn the notion of the statistical significance of a character. We apply this measure to two data sets - Passerine birds and prokaryotes, and four examples. These examples demonstrate various applications of CR, from evolutionary relatedness, through lateral evolution, to supertree construction. The above study was done with a new software that we provide, containing algorithmic improvement with a graphical output of a (optimally) recolored tree.

AVAILABILITY

A code implementing the features and a README is available at http://research.haifa.ac.il/ssagi/software/convexrecoloring.zip.

Proposal of Helicobacter canicola sp. nov., previously identified as Helicobacter cinaedi, isolated from canines

During the course of our taxonomic investigation of Helicobacter cinaedi, it was realized that the strains isolated from dogs, which have been identified as H. cinaedi, showed different biochemical traits than did the isolates obtained from humans. None of the three dog isolates could reduce nitrate to nitrite, whereas all of the human H. cinaedi isolates could do so. The dog isolates showed a strong positive alkaline phosphatase reaction and could grow at 42°C, however the human isolates showed negative to very weak responses to those tests. The GyrA protein based phylogenetic analysis showed that the three isolates from dogs formed a slightly distinct cluster from the human isolate cluster. Phylogenetic analysis of the 16S rRNA, 23S rRNA, gyrB, and hsp60 gene sequences further confirmed that the dog isolates differed from the human H. cinaedi isolate cluster. The whole-genome in silico DNA similarities of each isolate based on their full genome sequences revealed that the isolates from dogs shared more than 94.9% ANIb (average nucleotide identity based on BLAST), while 94.0% ANIb were found between the isolates from dogs and the humans, including the H. cinaedi type strain ATCC BAA-847(T) (=CCUG 18818(T)). From these data, we propose a new species, 'H. canicola' sp. nov., for the isolates from dogs. The type strain is PAGU 1410(T) (CCUG 33887(T)=LMG 29580(T)).

Helicobacter bilis and Helicobacter trogontum: infectious causes of abortion in sheep

The aim of our study was to determine the association of Helicobacter spp. that had flexispira morphology with ovine abortion, and to understand the importance of these organisms as a cause of ovine abortion in New Zealand. A retrospective diagnostic survey was carried out on laboratory submissions from ovine abortion outbreaks. A comparison was made of the proportion of laboratory submissions where Helicobacter spp. were detected from flocks that had no other agent identified (group A) with a group that had a known cause of abortion identified (group B). This latter group was considered to be a negative control, given the premise that Helicobacter spp. were not causing abortions and that Helicobacter spp. should be present at a lower rate in the group. Where no diagnosis had been made, aborted material was positive for Helicobacter spp. with flexispira morphology in 8 submissions (20%, 8/40) from 5 of the 31 survey farms (16%, 5/31). Helicobacter spp. were not detected in any of the 18 submissions from the 17 control farms (group B). Helicobacter spp. were confirmed by 16S ribosomal RNA sequencing of 3 of the Helicobacter spp. isolated by culture from the livers of aborted sheep fetuses, and 7 of the 8 where samples were positive in a Helicobacter PCR assay. The Helicobacter spp. were identified as Helicobacter trogontum (Flexispira taxon 5 genotype) and Helicobacter bilis (Flexispira taxon 8 genotype). The findings support Helicobacter spp. being a probable causative agent of ovine abortions in New Zealand.

The GyrA encoded gene: A pertinent marker for the phylogenetic revision of Helicobacter genus

Phylogeny of Epsilonproteobacteria is based on sequencing of the 16S rRNA gene. However, this gene is not sufficiently discriminatory in Helicobacter species and alternative markers would be useful. In this study, the 16S rRNA, gyrA, hsp60, gyrB, and ureA-ureB gene sequences, as well as GyrA, HSP60 and GyrB protein sequences were analyzed as tools to support Helicobacter species phylogeny: 72 Helicobacter strains, belonging to 41 species of which 36 are validated species, were included. Results of the phylogenetic reconstructions of the GyrA gene encoded protein (approximately 730 residues) indicated the most stable trees to bootstrap resampling with a good separation of Helicobacter taxa, especially between gastric and enterohepatic species. Moreover, the GyrA tree revealed high similarity with that of the gyrB and ureA-ureB genes (restricted to urease-positive Helicobacter species). However, some differences in clustering were observed when compared to the hsp60 and 23S rRNA gene trees. Altogether, these revised phylogenies (except the 16S rRNA gene for enterohepatic Helicobacters) enabled reliable clustering of Helicobacter cinaedi and 'Flexispira' strains, determined a reliable position for Helicobacter mustelae (except the hsp60 gene) and for novel Helicobacter species proposed such as 'Helicobacter sanguini', 'Helicobacter apodemus' or 'Helicobacter winghamensis', and suggest that Helicobacter species MIT 09-6949 and MIT 05-5293 isolated from rodents constitute novel species. Although they are not commonly used to study the phylogeny of Epsilonproteobacteria, protein sequences and, in particular, the GyrA protein sequence may constitute pertinent phylogenetic markers for Helicobacter genus.

[Role of animal gastric Helicobacter species in human gastric pathology]

Animal Helicobacter species other than Helicobacter pylori are also able to cause human gastritis, gastric ulcers, and MALT lymphomas. Animal Helicobacter species are presented with typical spiral fastidious microorganisms colonizing the gastric mucosa of different animals. Bacteria initially received their provisional name Helicobacter heilmannii, and out of them at least five species colonizing the gastric mucosa of pigs, cats, and dogs were isolated later on. A high proportion of these diseases are shown to be zoonotic. Transmission of pathogens occurs by contact. The factors of bacterial pathogenicity remain little studied.

Helicobacteraceae in Bulk Tank Milk of Dairy Herds from Northern Italy

Helicobacter pylori is responsible for gastritis and gastric adenocarcinoma in humans, but the routes of transmission of this bacterium have not been clearly defined. Few studies led to supposing that H. pylori could be transmitted through raw milk, and no one investigated the presence of other Helicobacteraceae in milk. In the current work, the presence of Helicobacteraceae was investigated in the bulk tank milk of dairy cattle herds located in northern Italy both by direct plating onto H. pylori selective medium and by screening PCR for Helicobacteraceae, followed by specific PCRs for H. pylori, Wolinella spp., and “Candidatus Helicobacter bovis.” Three out of 163 bulk milk samples tested positive for Helicobacteraceae, but not for the subsequent PCRs. H. pylori was not isolated in any case. However, given similar growth conditions, Arcobacter butzleri, A. cryaerophilus, and A. skirrowii were recovered. In conclusion, the prevalence of Helicobacteraceae in raw milk was negligible (1.8%), and H. pylori was not identified in any of the positive samples, suggesting that, at least in the farming conditions of the investigated area, bovine milk does not represent a potential source of infection.

Co-infection of the Siberian hamster (Phodopus sungorus) with a novel Helicobacter sp. and Campylobacter sp

We report the isolation of a novel helicobacter isolated from the caecum of the Siberian hamster (Phodopus sungorus). Sequence analysis showed 97% sequence similarity to Helicobacter ganmani. In addition, we report the co-infection of these Siberian hamsters with a Campylobacter sp. and a second Helicobacter sp. with 99% sequence similarity to Helicobacter sp. flexispira taxon 8 (Helicobacter bilis), a species isolated previously from patients with bacteraemia. Gross necropsy and histopathology did not reveal any overt pathological lesions of the liver and gastrointestinal tract that could be attributed to the Helicobacter or Campylobacter spp. infections. This is the first helicobacter to be identified in the Siberian hamster and the first report of co-infection of Helicobacter spp. and Campylobacter sp. in asymptomatic Siberian hamsters.

Biosorption of heavy metals by Pseudomonas species isolated from sugar industry

Heavy metal-resistant bacteria can be efficient bioremediators of metals and may provide an alternative or additional method to conventional methods of metal removal. In this study, 10 bacterial isolates were isolated from soil samples of a sugar industry, located at Peshawar, Pakistan. Morphological, physiological, and biochemical characteristics of these isolates were observed. Sequence analysis (16S ribosomal RNA) revealed that isolated strains were closely related to the species belonging to the genera Pseudomonas, Arthrobacter, Exiguobacterium, Citrobacter, and Enterobacter Bacterial isolates were resistant with a minimum inhibitory concentration (500-900 ppm) to lead ion (Pb(2+)), (500-600 ppm) nickel ion (Ni(2+)), (500-800 ppm) copper ion (Cu(2+)), and (600-800 ppm) chromium ion (Cr(3+)) in solid media. Furthermore, biosorption of metals proved considerable removal of heavy metals by isolated metal-resistant strains. Pseudomonas sp. reduced 37% (Pb(2+)), 32% (Ni(2+)), 29% (Cu(2+)), and 32% (Cr(3+)) and was thus found to be most effective, whereas Enterobacter sp. reduced 19% (Pb(2+)), 7% (Ni(2+)), 14% (Cu(2+)), and 21% (Cr(3+)) and was found to be least effective. While average reduction of Pb(2+), Ni(2+), Cu(2+), and Cr(3+) by Citrobacter sp. was found to be 24%, 18%, 23%, and 27%, respectively, among recognized species. This study revealed that Pseudomonas sp. may provide a new microbial community that can be used for enhanced remediation of contaminated environment.

Helicobacter himalayensis sp. nov. isolated from gastric mucosa of Marmota himalayana

A Gram-stain-negative, microaerophilic strain, 80(YS1)T, with a spiral-shaped morphology and 1-2 sheathed flagella at each end of the cells was isolated from the gastric mucosa of Marmota himalayana, the animal reservoir of Yersinia pestis in China, on the Qinghai-Tibet Plateau. The strain grew at 30, 35 and 42 °C, but not at 25 °C. Growth was in the form of a thinly spreading film on brain heart infusion agar containing 8 % sheep blood under microaerobic conditions. The strain did not hydrolyse urea or hippurate, and did not grow on media containing 1 % glycine. It reduced nitrate to nitrite, and was catalase- and alkaline-phosphatase-positive, susceptible to nalidixic acid and resistant to cefalotin. It was positive for genus-specific PCR for the genus Helicobacter, but could not be classified to any recognized species according biochemical tests results. Therefore, a phylogenetic study based on 16S rRNA, 23S rRNA, 60 kDa heat-shock protein (hsp60) and gyrase subunit B (gyrB) genes was conducted. The 16S rRNA gene sequence (1468 bp) analysis showed that strain 80(YS1)T was most closely related to Helicobacter marmotae (96.7 % similarity). The 23S rRNA gene sequence (2879 bp) analysis showed that the strain was most closely related to Helicobacter canis (96 % similarity). The complete gyrB gene sequence (2325 bp) analysis showed that it was related phylogenetically to Helicobacter cinaedi (79.4 % similarity) and H. marmotae (79.1 % similarity). Analysis of the partial sequence of the hsp60 gene of strain 80(YS1)T showed closest similarity to the sequences of Helicobacter equorum (82 %) and H. cinaedi (81 %), respectively. However, there was no hsp60 sequence of H. marmotae available for analysis. The data of morphological, biochemical and phylogenetic characteristics all supported that this strain represents a novel species. The name Helicobacter himalayensis sp. nov. is proposed for this novel species with the type strain 80(YS1)T ( = CGMCC 1.12864T = DSM 28742T).

Identification of Helicobacter spp. in gastrointestinal tract, pancreas and hepatobiliary system of stray cats

The aim of the present study was to determine the presence of Helicobacter species in different parts of gastrointestinal tract, hepatobiliary system and pancreas of stray cats. Six different sites at the level of genus, gastric (H. heilmannii and H. felis) and enterohepatic species of Helicobacter were investigated in six cats using species-specific primers by polymerase chain reaction (PCR). Interestingly, DNA of enterohepatic spp. was detected in 1/6 duodenum, 2/6 colon and 1/6 pancreas specimens. Results of sequencing revealed that all of these four positive samples belong to Helicobacter canis. While cats have not been considered as a potential zoonotic danger for non-pylori Helicobacter infections, the results of current study show prompt re-evaluation of that view. To the best of our knowledge, this is the first study about distribution of Helicobcater spp. in gastrointestinal tract of cats.

Biology and Diseases of Dogs

Historically, the dog played an important role as a laboratory animal in biomedical research. Although numbers are declining, the use of dogs continues to be common in pharmacokinetics and cardiovascular studies. The normal biology of the dog as both a laboratory and a companion animal has been well studied and reference values are presented here as a clinical and experimental resource. This provides the necessary background to discuss the spontaneous diseases, including infectious and neoplastic conditions, prevalent in purpose bred as well as random source dogs used in biomedical research. In addition, diseases and conditions that arise secondary to the housing and experimental manipulation of dogs is discussed with emphasis on treatment and prevention.

Low occurrence of Helicobacter DNA in tropical wild birds, Venezuela

Enteric Helicobacter species (Helicobacter pullorum, Helicobacter pametensis, Helicobacter canadensis, Helicobacter anseris, and Helicobacter brantae) have been found in birds from temperate latitudes. We evaluated the occurrence of Helicobacter spp. in terrestrial wild birds from Venezuela. A fragment of 16S rRNA gene was amplified by PCR with Helicobacter genus-specific primers. Helicobacter spp. were detected in four of 80 fecal and in three of 42 intestinal tissue samples. Analyses of 16S and 23S rRNA gene sequences confirm for the first time the presence of Helicobacter in tropical terrestrial wild birds. However, the occurrence of Helicobacter was low, suggesting these bacteria may be uncommon in the populations we studied.

Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions

Background and objective

In addition to the well-known phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Spirochaetes, Fusobacteria, Tenericutes, and Chylamydiae, the oral microbiomes of mammals contain species from the lesser-known phyla or candidate divisions, including Synergistetes, TM7, Chlorobi, Chloroflexi, GN02, SR1, and WPS-2. The objectives of this study were to create phyla-selective 16S rDNA PCR primer pairs, create selective 16S rDNA clone libraries, identify novel oral taxa, and update canine and human oral microbiome databases.

Design

16S rRNA gene sequences for members of the lesser-known phyla were downloaded from GenBank and Greengenes databases and aligned with sequences in our RNA databases. Primers with potential phylum level selectivity were designed heuristically with the goal of producing nearly full-length 16S rDNA amplicons. The specificity of primer pairs was examined by making clone libraries from PCR amplicons and determining phyla identity by BLASTN analysis.

Results

Phylum-selective primer pairs were identified that allowed construction of clone libraries with 96–100% specificity for each of the lesser-known phyla. From these clone libraries, seven human and two canine novel oral taxa were identified and added to their respective taxonomic databases. For each phylum, genome sequences closest to human oral taxa were identified and added to the Human Oral Microbiome Database to facilitate metagenomic, transcriptomic, and proteomic studies that involve tiling sequences to the most closely related taxon. While examining ribosomal operons in lesser-known phyla from single-cell genomes and metagenomes, we identified a novel rRNA operon order (23S-5S-16S) in three SR1 genomes and the splitting of the 23S rRNA gene by an I-CeuI-like homing endonuclease in a WPS-2 genome.

Conclusions

This study developed useful primer pairs for making phylum-selective 16S rRNA clone libraries. Phylum-specific libraries were shown to be useful for identifying previously unrecognized taxa in lesser-known phyla and would be useful for future environmental and host-associated studies.

Horizontal transfers and gene losses in the phospholipid pathway of bartonella reveal clues about early ecological niches

Bartonellae are mammalian pathogens vectored by blood-feeding arthropods. Although of increasing medical importance, little is known about their ecological past, and host associations are underexplored. Previous studies suggest an influence of horizontal gene transfers in ecological niche colonization by acquisition of host pathogenicity genes. We here expand these analyses to metabolic pathways of 28 Bartonella genomes, and experimentally explore the distribution of bartonellae in 21 species of blood-feeding arthropods. Across genomes, repeated gene losses and horizontal gains in the phospholipid pathway were found. The evolutionary timing of these patterns suggests functional consequences likely leading to an early intracellular lifestyle for stem bartonellae. Comparative phylogenomic analyses discover three independent lineage-specific reacquisitions of a core metabolic gene—NAD(P)H-dependent glycerol-3-phosphate dehydrogenase (gpsA)—from Gammaproteobacteria and Epsilonproteobacteria. Transferred genes are significantly closely related to invertebrate Arsenophonus-, and Serratia-like endosymbionts, and mammalian Helicobacter-like pathogens, supporting a cellular association with arthropods and mammals at the base of extant Bartonella spp. Our studies suggest that the horizontal reacquisitions had a key impact on bartonellae lineage specific ecological and functional evolution.

Clinical and bacteriological characteristics of Helicobacter cinaedi infection

Helicobacter cinaedi was first isolated from rectal cultures from homosexual men in 1984. In the 1980s to mid 1990s, the microorganism was mainly isolated from samples from homosexual men or immunocompromised patients; however, during the last two decades, H. cinaedi has been isolated from immunocompromised and from immunocompetent individuals worldwide. In Japan, the isolation of this microorganism was first reported in 2003. Since then, many cases have been reported in hospitals across the country. Despite many reports, the etiological properties and pathogenicity of H. cinaedi remain elusive; however, we are increasingly able to recognize some of the features and the clinical relevance of infection. In particular, a long incubation period is essential for detection in an automatic blood culture system and many of the recent isolates are resistant to both macrolides and quinolones. Furthermore, there is an association between infection and severe or chronic illnesses, such as meningitis or arteriosclerosis, in addition to mild diseases such as fever, abdominal pain, gastroenteritis, proctitis, diarrhea, erysipelas, cellulitis, arthritis, and bacteremia. In this review, we introduce the current knowledge and our latest findings relating to H. cinaedi.

Pathogenic properties of enterohepatic Helicobacter spp. isolated from rhesus macaques with intestinal adenocarcinoma

Considerable progress has been made in understanding the roles of Helicobacter pylori in inflammation and gastric cancer; however, far less is known about the roles of enterohepatic Helicobacter species (EHS) in carcinogenesis and their zoonotic or pathogenic potential. We determined the prevalence of EHS infection in a cohort of geriatric rhesus monkeys in which intestinal adenocarcinoma (IAC) is common and investigated the association between EHS infection and IAC. The cohort consisted of 36 animals, 14 of which (age 26-35 years) had IAC. Of the 36 rhesus, 35 (97%) were positive for EHS using PCR or bacterial isolation from faeces, colonic or tumour tissues. Only a single rhesus, which had IAC, was negative for EHS by all detection methods. The EHS identified by 16S rRNA sequencing in this study were from three Helicobacter taxa: Helicobacter macacae (previously rhesus monkey taxon 1), Helicobacter sp. rhesus monkey taxon 2, previously described from strain MIT 99-5507, and Helicobacter sp. rhesus monkey taxon 4, related to Helicobacter fennelliae. Thirteen of 14 monkeys with IAC were positive for either H. macacae (7/13, 54%), EHS rhesus monkey taxon 4 (4/13, 31%) or a mixture of the two EHS (2/13, 15%). These results indicate that EHS are prevalent among aged rhesus macaques with IAC. Using Helicobacter genus-specific florescent in situ hybridization, EHS were detected on the surface of colonic epithelia of infected monkeys. All Helicobacter isolates, including H. macacae, effectively adhered to, invaded, and significantly induced proinflammatory genes, including IL-8, IL-6, TNF-α and iNOS, while downregulating genes involved in the function of inflammasomes, particularly IL-1β, CASPASE-1, NRLP3, NLRP6 and NLRC4 in the human colonic T84 cell line (P<0.0001). These results suggest that EHS may represent an aetiological agent mediating diarrhoea, chronic inflammation, and possibly intestinal cancer in non-human primates, and may play a role in similar disease syndromes in humans. Downregulation of inflammasome function may represent an EHS strategy for long-term persistence in the host and play a role in inducing pathological changes in the host's lower bowel.