Emergence of diverse Helicobacter species in the pathogenesis of gastric and enterohepatic diseases

Helicobacter cinaedi bacterium association with atherosclerosis and other diseases

Helicobacter is a genus of spiral-shaped Gram-negative enterohepatic bacteria whose members are capable of causing bacteremia in humans. One of the poorly studied members of this genus is the bacterium Helicobacter cinaedi. This microorganism was first isolated from human fecal samples in 1984. Although it was long considered to be associated with only immunocompromised patients, more evidence in recent years has implicated H. cinaedi in causing serious pathologies in immunocompetent populations. In addition, H. cinaedi is also reported to be associated with a few chronic or severe illnesses, such as atherosclerosis, which in turn can lead to the development of other cardiovascular pathologies: one of the leading causes of mortality worldwide. Helicobacter cinaedi often goes unnoticed in standard diagnostic methods due to its slow growth under microaerobic conditions. This often leads to significant underdetection and hence undermines the role of this bacterium in the pathogenesis of various diseases and the extent of its spread in humans. In this review, we have compiled information on pathologies associated with H. cinaedi, the occurrence of the bacterium in humans and animals, and the latest developments in diagnosing the bacterium and treating associated diseases.

Fine-scale geographic difference of the endangered Big-headed Turtle (Platysternon megacephalum) fecal microbiota, and comparison with the syntopic Beale's Eyed Turtle (Sacalia bealei)

BACKGROUND

Studies have elucidated the importance of gut microbiota for an organism, but we are still learning about the important influencing factors. Several factors have been identified in helping shape the microbiome of a host, and in this study we focus on two factors-geography and host. We characterize the fecal microbiota of the Big-headed Turtle (Platysternon megacephalum) and compare across a relatively fine geographic scale (three populations within an 8-km radius) and between two syntopic hosts (P. megacephalum and Sacalia bealei). Both species are endangered, which limits the number of samples we include in the study. Despite this limitation, these data serve as baseline data for healthy, wild fecal microbiotas of two endangered turtle species to aid in conservation management.

RESULTS

For geography, the beta diversity of fecal microbiota differed between the most distant sites. The genus Citrobacter significantly differs between sites, which may indicate a difference in food availability, environmental microbiota, or both. Also, we identify the common core microbiome for Platysternon across Hong Kong as the shared taxa across the three sites. Additionally, beta diversity differs between host species. Since the two species are from the same site and encounter the same environmental microbiota, we infer that there is a host effect on the fecal microbiota, such as diet or the recruitment of host-adapted bacteria. Lastly, functional analyses found metabolism pathways (KEGG level 1) to be the most common, and pathways (KEGG level 3) to be statistically significant between sites, but statistically indistinguishable between species at the same site.

CONCLUSIONS

We find that fecal microbiota can significantly differ at a fine geographic scale and between syntopic hosts. Also, the function of fecal microbiota seems to be strongly affected by geographic site, rather than species. This study characterizes the identity and function of the fecal microbiota of two endangered turtle species, from what is likely their last remaining wild populations. These data of healthy, wild fecal microbiota will serve as a baseline for comparison and contribute to the conservation of these two endangered species.

Zearalenone-14-glucoside specifically promotes dysplasia of Gut-Associated Lymphoid Tissue: A natural product for constructing intestinal nodular lymphatic hyperplasia model

INTRODUCTION

Zearalenone-14-glucoside (Z14G) is a modified mycotoxin that widely contaminates food across the world. Our preliminary experiment showed that Z14G degrades to zearalenone (ZEN) in the intestine exerting toxicity. Notably, oral administration of Z14G in rats induces intestinal nodular lymphatic hyperplasia.

OBJECTIVES

To investigate the mechanism of Z14G intestinal toxicity and how it differs from ZEN toxicity. We conducted a precise toxicology study on the intestine of rats exposed to Z14G and ZEN using multi-omics technology.

METHODS

Rats were exposed to ZEN (5 mg/kg), Z14G-L (5 mg/kg), Z14G-H (10 mg/kg), and pseudo germ free (PGF)-Z14G-H (10 mg/kg) for 14 days. Histopathological studies were performed on intestines from each group and compared. Metagenomic, metabolomic, and proteomic analyses were performed on rat feces, serum, and intestines, respectively.

RESULTS

Histopathological studies showed that Z14G exposure resulted in dysplasia of gut-associated lymphoid tissue (GALT) compared to ZEN exposure. The elimination of gut microbes in the PGF-Z14G-H group alleviated or eliminated Z14G-induced intestinal toxicity and GALT dysplasia. Metagenomic analysis revealed that Z14G exposure significantly promoted the proliferation of Bifidobacterium and Bacteroides compared to ZEN. Metabolomic analysis showed that Z14G exposure significantly reduced bile acid, while proteomic analysis found that Z14G exposure significantly reduced the expression of C-type lectins compared to ZEN.

CONCLUSIONS

Our experimental results and previous research suggest that Z14G is hydrolyzed to ZEN by Bifidobacterium and Bacteroides promoting their co-trophic proliferation. This leads to inactivation of lectins by hyperproliferative Bacteroides when ZEN caused intestinal involvement, resulting in abnormal lymphocyte homing and ultimately GALT dysplasia. It is noteworthy that Z14G is a promising model drug to establish rat models of intestinal nodular lymphatic hyperplasia (INLH), which is of great significance for studying the pathogenesis, drug screening and clinical application of INLH.

[Detection of Helicobacter species in humans and their dog]

Helicobacter is a genus of Gram-negative bacteria that colonizes the stomach of humans and dogs, among other mammals. The most frequent species found in the gastric mucosa of man is H. pylori, however, there are other species of Helicobacter in the stomach of humans, such as H. suis, H. bizzozeronii, H. felis, H. salomonis and H. heilmannii sensu stricto, named non H. pylori Helicobacter (NHPH) some of which also colonize the dog's stomach. The detection of NHPH in the stomach mucosa of humans with gastric disease, and in a high percentage of dogs, suggests the possibility that these animals play an important role in the pathogenesis and transmission of infection to man, postulating the path of transmission oral-oral or fecal-oral. The aim of this study was to determine whether people with signs of chronic gastritis who have Helicobacter spp. and who own dogs as pets, share the same species with them. The presence of Helicobacter spp. in gastric samples of 30 people with clinical signs of chronic gastritis and histopathological diagnosis of gastric infection with Helicobacter spp. was analyzed by PCR. The presence of Helicobacter spp. was also studied in the dogs of these people. Then, the species of Helicobacter presented was determined in both. In human gastric samples, H. pylori was the only species found, while in dogs, samples were H. bizzozeronii, H. felis, H. salomonis and H. heilmannii. In this work the same species were not found in dogs and their owners.

Helicobacter spp. are prevalent in wild mice and protect from lethal Citrobacter rodentium infection in the absence of adaptive immunity

Transfer of the gut microbiota from wild to laboratory mice alters the host's immune status and enhances resistance to infectious and metabolic diseases, but understanding of which microbes and how they promote host fitness is only emerging. Our analysis of metagenomic sequencing data reveals that Helicobacter spp. are enriched in wild compared with specific-pathogen-free (SPF) and conventionally housed mice, with multiple species commonly co-colonizing their hosts. We create laboratory mice harboring three non-SPF Helicobacter spp. to evaluate their effect on mucosal immunity and colonization resistance to the enteropathogen Citrobacter rodentium. Our experiments reveal that Helicobacter spp. interfere with C. rodentium colonization and attenuate C. rodentium-induced gut inflammation in wild-type (WT) mice, even preventing lethal infection in Rag2-/- SPF mice. Further analyses suggest that Helicobacter spp. interfere with tissue attachment of C. rodentium, putatively by reducing the availability of mucus-derived sugars. These results unveil pivotal protective functions of wild mouse microbiota constituents against intestinal infection.

Omega-3-Rich Fish-Oil-Influenced Mouse Gut Microbiome Shaped by Intermittent Consumption of Beef

Beef consumption can provide various amino acids, lipids, vitamins, and minerals; however, excessive intake causes metabolic disorders and increases the probability of obesity, atherosclerosis, and colorectal cancer. The intake of omega-3 fatty acids can ameliorate metabolic disorders by lowering blood glucose and triglyceride levels. In the present study, we investigated the effect of omega-3-rich fish oil on body performance and the gut microbiome in a beef-rich diet. Four-week-old C57BL/6 mice were distributed into four groups (chow diet [Chow], chow with beef diet [Beef], chow with omega-3 diet [Cw3], and chow with beef and omega-3 diet [Bw3]). We observed that body weight was unaltered between groups, and serum triglyceride levels were reduced in the omega-3 supplemented groups. The beta diversity indices, unweighted UniFrac distance (P = 0.001), and Jaccard distance (P = 0.001) showed statistically significant differences, and the principal coordinates analysis plot showed a clear separation between groups. In addition, the taxonomic comparison revealed that beef consumption increased numerous potentially pathogenic bacteria, including Escherichia-Shigella, Mucispirillum, Helicobacter, and Desulfovibrio, which were decreased following omega-3 supplementation. Metabolic comparison based on 16S rRNA revealed that energy and glucose metabolism were higher in omega-3 supplemented groups. Our findings suggest that the omega-3 supplementation under intermittent beef consumption contributes to changes in the gut microbiome and microbial metabolic pathways.

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).

Population- and Gender-Based Investigation for Prevalence of Helicobacter pylori in Dhamar, Yemen

Among 35 species of genus Helicobacter, H. pylori is the most common causative agent of human gastritis, peptic ulcer, and gastric cancer. The infection can spread through direct human-to-human contact, fecal-oral route, and contaminated water. The study was designed to investigate the rate of prevalence of H. pylori in the population of Dhamar, Yemen. In this one-year study, 460 including 250 male and 210 female stool specimens were collected between January to December 2020 in Dhamar Governorate, Yemen. Of the total 460, 215 rural (male: n = 120 and female: n = 95) and 245 urban (male: n = 130 and female: n = 115) specimens were investigated for identification of H. pylori by serological test using Helicobacter pylori stool antigen (HpSA) test. In addition, for comparing an improved recovery of H. pylori, conventional culture-based isolation was also carried out using three selective media. Modified Campy-blood Agar (MCA), Belo Horizonte Agar (BHA), and Egg yolk Emulsion (EYE) medium supplemented with antimicrobial agents including vancomycin (10 mg/L), cefsulodin (5 mg/L), trimethoprim (5 mg/L), and amphotericin B (5 mg/L) and isolates were phenotypically characterized. The HpSA test results revealed that of the total 460 specimens, 89 (19.3%) were positive for H. pylori with relatively low in male (n = 43; 17.2%) as compared to the female (n = 46; 21.9%) specimens. After 3-10 days of incubation, H. pylori was recovered at a variable rate on each selective (MCA: 16.5%; BHA: 15.0%; EYE: 13.0%) media. However, culture-based assay results showed less recovery (n = 81; 17.6%) with no significant difference among all selective media tested and between genders (male: n = 39; 15.6%; female: n = 42; 20.0%). The infection rate was comparatively higher in rural (n = 45; 20.9%) as compared to urban (n = 36; 14.7%) population. Overall, the study data showed the prevalence of infection in both genders of all age groups. The present study showed a relatively high rate of infection of H. pylori in the Dhamar population. The serological identification and culture-based methods are important for rapid detection, aid in treatment, and developing policies for the control and eradication of H. pylori infection and to prevent the disease in different age groups in Yemen.

Ginsenoside Rg1 modulates intestinal microbiota and supports re-generation of immune cells in dexamethasone-treated mice

Ginsenoside Rg1 is one of the major ginsenosides found in roots of Panax ginseng and Panax notoginseng. Ginsenoside Rg1 is known to possess various biological activities including immunity enhancement activity. However, it is not clear whether the regulation of immune function by Rg1 is related to the intestinal microbiota. In the present study, the immuno-modulatory and gut microbiota-reshaping effects of ginsenoside Rg1 were evaluated. Ginsenoside Rg1 acts as an immune-enhancing agent to increase spleen index and the number of T, B and dendritic cells in dexamethasone (Dex)-treated mice. Ginsenoside Rg1 also increased the production of sIgA and regulated the expression of interleukin 2 (IL-2), IL-4, IL-10 and IFN-γ. Meanwhile, Rg1 administration regulated the structure of intestinal microbiota. The relative abundance of mouse intestinal microbial groups, such as Alistipes, Ruminococcaceae, Lachnospiraceae, and Roseburia were increased by Rg1 administration, whereas a decrease in the potential pathogens like Helicobacteraceae, Dubosiella, Mycoplasma, Alloprevotella, Allobaculum was observed. Moreover, Rg1 metabolites of Lachnospiraceae bacterium enhanced the proliferation of CD4+ T cells and T regulatory (Treg) cells. Ginsenoside Rg1 improved the inflammatory condition of the colonic tissue and repaired the destructed mucosal barrier. This study suggested that Rg1 strengthens immunity with regulating the homeostasis of intestinal microbiota in mice.

Methylation-Independent Chemotaxis Systems Are the Norm for Gastric-Colonizing Helicobacter Species

Many bacteria and archaea rely on chemotaxis signal transduction systems for optimal fitness. These complex, multiprotein signaling systems have core components found in all chemotactic microbes, as well as variable proteins found in only some species. We do not yet understand why these variations exist or whether there are specific niches that favor particular chemotaxis signaling organization. One variation is in the presence/absence of the chemotaxis methylation adaptation enzymes CheB and CheR. Genes for CheB and CheR are missing in the gastric pathogen Helicobacter pylori but present in related Helicobacter that colonize the liver or intestine. In this work, we asked whether there was a general pattern of CheB/CheR across multiple Helicobacter species. Helicobacter spp. all possess chemotactic behavior, based on the presence of genes for core signaling proteins CheA, CheW, and chemoreceptors. Genes for the CheB and CheR proteins, in contrast, were variably present. Niche mapping supported the idea that these genes were present in enterohepatic Helicobacter species and absent in gastric ones. We then analyzed whether there were differences between gastric and enterohepatic species in the CheB/CheR chemoreceptor target methylation sites. Indeed, these sites were less conserved in gastric species that lack CheB/CheR. Lastly, we determined that cheB and cheR could serve as markers to indicate whether an unknown Helicobacter species was of enterohepatic or gastric origin. Overall, these findings suggest the interesting idea that methylation-based adaptation is not required in specific environments, particularly the stomach. IMPORTANCE Chemotaxis signal transduction systems are common in the archaeal and bacterial world, but not all systems contain the same components. The rationale for this system variation remains unknown. In this report, comparative genomics analysis showed that the presence/absence of CheR and CheB is one main variation within the Helicobacter genus, and it is strongly associated with the niche of Helicobacter species: gastric Helicobacter species, which infect animal stomachs, have lost their CheB and CheR, while enterohepatic Helicobacter species, which infect the liver and intestine, retain them. This study not only provides an example that a chemotaxis system variant is associated with particular niches but also proposes that CheB and CheR are new markers distinguishing gastric from enterohepatic Helicobacter species.

Pan-Genome-Assisted Computational Design of a Multi-Epitopes-Based Vaccine Candidate against Helicobacter cinaedi

Helicobacter cinaedi is a Gram-negative bacterium from the family Helicobacteraceae and genus Helicobacter. The pathogen is a causative agent of gastroenteritis, cellulitis, and bacteremia. The increasing antibiotic resistance pattern of the pathogen prompts the efforts to develop a vaccine to prevent dissemination of the bacteria and stop the spread of antibiotic resistance (AR) determinants. Herein, a pan-genome analysis of the pathogen strains was performed to shed light on its core genome and its exploration for potential vaccine targets. In total, four vaccine candidates (TonB dependent receptor, flagellar hook protein FlgE, Hcp family type VI secretion system effector, flagellar motor protein MotB) were identified as promising vaccine candidates and subsequently subjected to an epitopes' mapping phase. These vaccine candidates are part of the pathogen core genome: they are essential, localized at the pathogen surface, and are antigenic. Immunoinformatics was further applied on the selected vaccine proteins to predict potential antigenic, non-allergic, non-toxic, virulent, and DRB*0101 epitopes. The selected epitopes were then fused using linkers to structure a multi-epitopes' vaccine construct. Molecular docking simulations were conducted to determine a designed vaccine binding stability with TLR5 innate immune receptor. Further, binding free energy by MMGB/PBSA and WaterSwap was employed to examine atomic level interaction energies. The designed vaccine also stimulated strong humoral and cellular immune responses as well as interferon and cytokines' production. In a nutshell, the designed vaccine is promising in terms of immune responses' stimulation and could be an ideal candidate for experimental analysis due to favorable physicochemical properties.

Within-community variation of interspecific divergence patterns in passerine gut microbiota

Gut microbiota (GM) often exhibit variation between different host species and co-divergence with hosts' phylogeny. Identifying these patterns is a key for understanding the mechanisms that shaped symbiosis between GM and its hosts. Therefore, both GM-host species specificity and GM-host co-divergence have been investigated by numerous studies. However, most of them neglected a possibility that different groups of bacteria within GM can vary in the tightness of their association with the host. Consequently, unlike most of these studies, we aimed to directly address how the strength of GM-host species specificity and GM-host co-divergence vary across different GM clades. We decomposed GM communities of 52 passerine species (394 individuals), characterized by 16S rRNA amplicon sequence variant (ASV) profiles, into monophyletic Binned Taxonomic units (BTUs). Subsequently, we analyzed strength of host species specificity and correlation with host phylogeny separately for resulting BTUs. We found that most BTUs exhibited significant host-species specificity in their composition. Notably, BTUs exhibiting high host-species specificity comprised bacterial taxa known to impact host's physiology and immune system. However, BTUs rarely displayed significant co-divergence with host phylogeny, suggesting that passerine GM evolution is not shaped primarily through a shared evolutionary history between the host and its gut microbes.

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.

The Role of Gut Microbiota in Gastrointestinal Tract Cancers

Disturbances in gastrointestinal (GI) microbiota could play a significant role in the development of GI cancers, but the underlying mechanisms remain largely unclear. While some bacteria seem to facilitate carcinogenesis, others appear to be protective. So far only one bacterium (Helicobacter pylori) has been classified by the International Agency for Cancer Research as carcinogenic in humans but many other are the subject of intense research. Most studies on the role of microbiota in GI tract oncogenesis focus on pancreatic and colorectal cancers with the following three species: Helicobacter pylori, Escherichia coli, and Porphyromonas gingivalis as likely causative factors. This review summarizes the role of bacteria in GI tract oncogenesis.

A unique aromatic cluster near the active site of H. pylori CPA is essential for catalytic function

Polyamines are essential for cell growth and proliferation. In plants and many bacteria, including Helicobacter pylori, the parent polyamine putrescine is only produced through the metabolism of N-carbamoylputrescine by N-carbamoylputrescine amidase (CPA). Thus, CPA is a crucial intermediate enzyme. Moreover, the absence of CPA in humans makes its presence in H. pylori a potential target for the development of new therapeutics against this pathogen. Despite this enzyme's presence in plants and bacteria, its function is not completely explored. Using structure-guided biochemical and biophysical studies on H. pylori CPA, we discovered an aromatic cluster containing four conserved tryptophans near the catalytic site and elucidated its role. Mutational studies revealed that they are individually vital to enzyme function. Unlike wild-type, which forms a hexamer, the Trp to Ala mutants only formed dimers. Interestingly, two other conserved residues, Gln155 and Asp278, interact with the tryptophan cluster and perform similar roles. Our results indicate that aromatic-aromatic and H-bonding contacts between the residues (Trp156-Trp273, Trp196-Gln155, and Trp153-Asp278) play a crucial role in stimulating activity through hexamer formation. Additionally, Trp156 is essential to generating a catalytically efficient hexamer. These results suggest dual roles for the tryptophans; in hexamer formation and in generating its functionally active form, thereby providing a mechanistic understanding into the role of the cluster. We also elucidated the catalytic roles of Glu43, Lys115, and Cys152, which are present at the active site. Our findings highlight, for the first time, the importance of a tryptophan cluster in H. pylori CPA that can be exploited to design therapeutic inhibitors.

Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis

It is now well established that the Gram-negative bacterium, Helicobacter pylori, causes gastritis in humans. In recent years, it has become apparent that the so-called non-pylori Helicobacters, normally infecting pigs, cats, and dogs, may also be involved in human pathology via zoonotic transmission. Indeed, more than 30 species of non-pylori Helicobacters have been identified thus far. One such organism is Helicobacter canadensis, an emerging pathogen whose genome sequence was published in 2009. Given our long-standing interest in the biosynthesis of N-formylated sugars found in the O-antigens of some Gram-negative bacteria, we were curious as to whether H. canadensis produces such unusual carbohydrates. Here, we demonstrate using both biochemical and structural techniques that the proteins encoded by the HCAN_0198, HCAN_0204, and HCAN_0200 genes in H. canadensis, correspond to a 3,4-ketoisomerase, a pyridoxal 5'-phosphate aminotransferase, and an N-formyltransferase, respectively. For this investigation, five high-resolution X-ray structures were determined and the kinetic parameters for the isomerase and the N-formyltransferase were measured. Based on these data, we suggest that the unusual sugar, 3-formamido-3,6-dideoxy-d-glucose, will most likely be found in the O-antigen of H. canadensis. Whether N-formylated sugars found in the O-antigen contribute to virulence is presently unclear, but it is intriguing that they have been observed in such pathogens as Francisella tularensis, Mycobacterium tuberculosis, and Brucella melitensis.

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.

An evolutionary non-conserved motif in Helicobacter pylori arginase mediates positioning of the loop containing the catalytic residue for catalysis

The binuclear metalloenzyme Helicobacter pylori arginase is important for pathogenesis of the bacterium in the human stomach. Despite conservation of the catalytic residues, this single Trp enzyme has an insertion sequence (-153ESEEKAWQKLCSL165-) that is extremely crucial to function. This sequence contains the critical residues, which are conserved in the homolog of other Helicobacter gastric pathogens. However, the underlying basis for the role of this motif in catalytic function is not completely understood. Here, we used biochemical, biophysical and molecular dynamics simulations studies to determine that Glu155 of this stretch interacts with both Lys57 and Ser152. These interactions are essential for positioning of the motif through Trp159, which is located near Glu155 (His122-Trp159-Tyr125 contact is essential to tertiary structural integrity). The individual or double mutation of Lys57 and Ser152 to Ala considerably reduces catalytic activity with Lys57 to Ala being more significant, indicating they are crucial to function. Our data suggest that the Lys57-Glu155-Ser152 interaction influences the positioning of the loop containing the catalytic His133 so that this His can participate in catalysis, thereby providing a mechanistic understanding into the role of this motif in catalytic function. Lys57 was also found only in the arginases of other Helicobacter gastric pathogens. Based on the non-conserved motif, we found a new molecule, which specifically inhibits this enzyme. Thus, the present study not only provides a molecular basis into the role of this motif in function, but also offers an opportunity for the design of inhibitors with greater efficacy.

Differentiation of Gastric Helicobacter Species Using MALDI-TOF Mass Spectrometry

Gastric helicobacters (Helicobacter (H.) pylori and non-H. pylori Helicobacter species (NHPHs)) colonize the stomach of humans and/or animals. Helicobacter species identification is essential since many of them are recognized as human and/or animal pathogens. Currently, Helicobacter species can only be differentiated using molecular methods. Differentiation between NHPHs using MALDI-TOF MS has not been described before, probably because these species are poorly represented in current MALDI-TOF MS databases. Therefore, we identified 93 gastric Helicobacter isolates of 10 different Helicobacter species using MALDI-TOF MS in order to establish a more elaborate Helicobacter reference database. While the MALDI Biotyper database was not able to correctly identify any of the isolates, the in-house database correctly identified all individual mass spectra and resulted in 82% correct species identification based on the two highest log score matches (with log scores ≥2). In addition, a dendrogram was constructed using all newly created main spectrum profiles. Nine main clusters were formed, with some phylogenetically closely related Helicobacter species clustering closely together and well-defined subclusters being observed in specific species. Current results suggest that MALDI-TOF MS allows rapid differentiation between gastric Helicobacter species, provided that an extensive database is at hand and variation due to growth conditions and agar-medium-related peaks are taken into account.

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 delphinicola sp. nov., isolated from common bottlenose dolphins Tursiops truncatus with gastric diseases

Gastritis and gastric ulcers are well-recognized symptoms in cetaceans, and the genus Helicobacter is considered as the main cause. In this study, we examined the gastric fluid of captive common bottlenose dolphins Tursiops truncatus with gastric diseases in order to isolate the organisms responsible for diagnosis and treatment. Four Gram-negative, rod-shaped isolates (TSBT, TSH1, TSZ, and TSH3) with tightly coiled spirals with 2-4 turns and 2-6 bipolar, sheathed flagella, were obtained from gastric fluids of common bottlenose dolphins with gastric diseases. Phylogenetic analysis, based on 16S rRNA, atpA, and 60 kDa heat-shock protein (hsp60) genes, demonstrated that these isolates form a novel lineage within the genus Helicobacter. Analyses of 16S rRNA, atpA, and hsp60 gene sequences showed that isolate TSBT was most closely related to H. cetorum MIT99-5656T (98.5% similarity), H. pylori ATCC 43504T (76.7% similarity), and H. pylori ATCC 43504T (78.0% similarity), respectively. Type strains of Helicobacter showing resistance to 2% NaCl have not been reported previously; however, these novel isolates were resistant to 2% NaCl. Culture supernatant of some isolates induced intracellular vacuolization in mammalian cultured cells. These data, together with the different morphological and biochemical characteristics of the isolates, reveal that these isolates represent a novel species for which we propose the name Helicobacter delphinicola sp. nov. with type strain TSBT (= JCM 32789T = TSD-183T). Future studies will confirm whether H. delphinicola plays a role in lesion etiopathogenesis in cetaceans.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Structure of cytotoxic associated antigen A protein of Helicobacter pylori from Bali and Lombok isolates of Indonesia

Background and Aim:

Helicobacterpylori is a well-known zoonotic agent with worldwide distribution. In Indonesia, only one report regarding the variation within the cytotoxic associated antigen A (CagA) protein of H. pylori has been described in the literature, which was conducted in Manado, South Sulawesi. There remains no report concerning the structure of this protein, particularly for the Bali and Lombok isolates. The objective of this study was to investigate the diversity of H. pylori CagA amino acid sequences of Bali and Lombok isolates, to predict their molecular structures and conduct toxicity examination of CagA on gastric cells.

Materials and Methods:

A total of 36 samples were used in equal proportions for each pathologic condition. DNA extraction was performed to subculture H. pylori Bali isolates. The amplification of the CagA 3′ variable region was carried out using the primers P1 (5′-GATAACAGGCAAGCTTTTTGAGG-3′) and P2 (5′-CTGCAAAAGATTGTTTGGCAG-3′). The W2, W9, and W35 fragments were selected as a representation of H. pylori Bali isolates, which were modeled through the threading modeling approach using I-TASSER.

Results:

According to the 12 CagA sequences obtained and phylogenetic analyses, the H. pylori strain originating from Bali can be grouped within the East Asian genotypes and is identical to the Lombok strain. In addition, the Bali isolates are phylogenetically more closely related to Southeast Asian strains, particularly the Filipino strain. The relationship between degree of inflammation induced and CagA-positive infection was not statistically significant.

Conclusion:

The structure of the H. pylori Bali isolate is identical to that of Lombok isolate, which belongs to the same group of East Asian genotypes, and bacterial virulence is not related to structure.

Transient and Persistent Gastric Microbiome: Adherence of Bacteria in Gastric Cancer and Dyspeptic Patient Biopsies after Washing

Helicobacter pylori is a common colonizer of the human stomach, and long-term colonization has been related to development of atrophic gastritis, peptic ulcers and gastric cancer. The increased gastric pH caused by H. pylori colonization, treatment with antibiotics or proton pump inhibitors (PPI) may allow growth of other bacteria. Previous studies have detected non-Helicobacter bacteria in stomach biopsies, but no conclusion has been made of whether these represent a transient contamination or a persistent microbiota. The aim of this study was to evaluate the transient and persistent bacterial communities of gastric biopsies. The washed or unwashed gastric biopsies were investigated by cultivation and microbiota analysis (16S rRNA gene-targeted amplicon sequencing) for the distribution of H. pylori and other non-Helicobacter bacteria. The number of cultured non-Helicobacter bacteria decreased in the washed biopsies, suggesting that they might be a transient contamination. No significant differences in the bacterial diversity were observed in the microbiome analysis between unwashed and washed biopsies. However, the bacterial diversity in biopsies shown H. pylori-positive and H. pylori-negative were significantly different, implying that H. pylori is the major modulator of the gastric microbiome. Further large-scale studies are required to investigate the transient and persistent gastric microbiota.

A comparative proteomic approach using metabolic pathways for the identification of potential drug targets against Helicobacter pylori

BACKGROUND

Helicobacter pylori is the most highlighted pathogen across the globe especially in developing countries. Severe gastric problems like ulcers, cancers are associated with H. pylori and its prevalence is widespread. Evolution in the genome and cross-resistance with different antibiotics are the major reason of its survival and pandemic resistance against current regimens.

OBJECTIVES

To prioritize potential drug target against H. pylori by comparing metabolic pathways of its available strains.

METHODS

We used various computational tools to extract metabolic sets of all available (61) strains of H. pylori and performed pan genomics and subtractive genomics analysis to prioritize potential drug target. Additionally, the protein interaction and detailed structure-based studies were performed for further characterization of protein.

RESULTS

We found 41 strains showing similar set of metabolic pathways. However, 19 strains were found with unique set of metabolic pathways. The metabolic set of these 19 strains revealed 83 unique proteins and BLAST against human proteome further funneled them to 38 non-homologous proteins. The druggability and essentiality testing further converged our findings to a single unique protein as a potential drug target against H. pylori.

CONCLUSION

We prioritized one protein-based drug target which upon subject to applied protocol was found as close homolog of the Saccharopine dehydrogenase. Our study has opened further avenues of research regarding the discovery of new drug targets against H. pylori.

Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists

Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.

Effects of Rhodotorula mucilaginosa fermentation product on the laying performance, egg quality, jejunal mucosal morphology and intestinal microbiota of hens

AIM

The aim of this study was to investigate the effects of dietary supplementation of Rhodotorula mucilaginosa solid-state fermentation product (RSFP) on the laying performance, egg quality and intestinal microbial flora of hens.

METHODS AND RESULTS

In this study, 40-week-old Roman laying hens (n = 216) were randomly assigned to one of the four groups: the control (CON) group, fed 87.5% basal diet +12.5% fermentation substrate; the 0.5% RSFP group, fed 87.5% basal diet +12.0% fermentation substrate +0.5% RSFP; the 2.5% RSFP group, fed 87.5% basal diet +10.0% fermentation substrate +2.5% RSFP; and the 12.5% RSFP group, fed 87.5% basal diet +12.5% RSFP. The effect of each treatment was analysed in six replicates of nine hens. The experimental period was 31 days, which included a 3-day adaptation period. After 31 days of feeding, one hen from each replicate was randomly selected and killed, and the jejunum and digesta in the cecum were collected for the determination of the intestinal morphology and microbial flora respectively. Daily egg mass in the 2.5 and 12.5% RSFP groups and egg production and feed conversion ratio in the 12.5% RSFP group were higher than those in control group (P < 0.05). The yolk colour was improved in hens fed RSFP-supplemented diets (P < 0.05). Hens fed RSFP-supplemented diet showed a decrease in the relative abundances of Proteobacteria, Bacteroides, Helicobacteraceae, Helicobacter and Lachnospiraceae UCG-002, but an increase in the relative abundance of Prevotellaceae UCG-001 in the cecum (P < 0.05).

CONCLUSION

Dietary RSFP supplementation improved the laying performance, egg quality and intestinal microflora of hens.

SIGNIFICANCE AND IMPACT OF THE STUDY

Dietary supplementing diet with Rhodotorula mucilaginosa solid-state fermentation product, which is rich in carotenoids, improved the yolk colour and increased the carotenoid content, thereby improving the intestinal health of hens.

Helicobacter pylori: Survival in cultivable and non-cultivable form in artificially contaminated Mytilus galloprovincialis

Several studies report the presence of Helicobacter pylori (H. pylori) in seawater either free or attached to planktonic organism. After considering the role played by plankton in the food chain of most aquatic ecosystems and the possible role that seafood products can assume in the transmission of H. pylori to humans, the aim of this study was to assess the survival of H. pylori in artificially contaminated Mytilus galloprovincialis (M. galloprovincialis). A traditional culture method and a reverse transcriptase-PCR (RT-PCR) assay were employed to detect the mRNA of known virulence factor (VacA) which can be considered use a marker of bacterial viability. The obtained results clearly show that H. pylori is able to survive in artificially contaminated mussels for 6 days (2 days in a cultivable form and 4 days in a non-cultivable form).

Multi-step genomic dissection of a suspected intra-hospital Helicobacter cinaedi outbreak

Helicobacter cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a suspected intra-hospital outbreak of H. cinaedi that occurred in a hospital in Japan. The outbreak was recognized by the infectious control team (ICT) of the hospital as a sudden increase in H. cinaedi bacteraemia. ICT defined this outbreak case based on 16S rRNA sequence data and epidemiological information, but were unable to determine the source and route of the infections. We therefore re-investigated this case using whole-genome sequencing (WGS). We first performed a species-wide analysis using publicly available genome sequences to understand the level of genomic diversity of this under-studied species. The clusters identified were then separately analysed using the genome sequence of a representative strain in each cluster as a reference. These analyses provided a high-level phylogenetic resolution of each cluster, identified a confident set of outbreak isolates, and discriminated them from other closely related but distinct clones, which were locally circulating and invaded the hospital during the same period. By considering the epidemiological data, possible strain transmission chains were inferred, which highlighted the role of asymptomatic carriers or environmental contamination. The emergence of a subclone with increased resistance to fluoroquinolones in the outbreak was also recognized. Our results demonstrate the impact of the use of a closely related genome as a reference to maximize the power of WGS.

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.

Living in Cold Blood: Arcobacter, Campylobacter, and Helicobacter in Reptiles

Species of the Epsilonproteobacteria genera Arcobacter, Campylobacter, and Helicobacter are commonly associated with vertebrate hosts and some are considered significant pathogens. Vertebrate-associated Epsilonproteobacteria are often considered to be largely confined to endothermic mammals and birds. Recent studies have shown that ectothermic reptiles display a distinct and largely unique Epsilonproteobacteria community, including taxa which can cause disease in humans. Several Arcobacter taxa are widespread amongst reptiles and often show a broad host range. Reptiles carry a large diversity of unique and novel Helicobacter taxa, which apparently evolved in an ectothermic host. Some species, such as Campylobacter fetus, display a distinct intraspecies host dichotomy, with genetically divergent lineages occurring either in mammals or reptiles. These taxa can provide valuable insights in host adaptation and co-evolution between symbiont and host. Here, we present an overview of the biodiversity, ecology, epidemiology, and evolution of reptile-associated Epsilonproteobacteria from a broader vertebrate host perspective.

Identification of Helicobacter pylori in Saliva of Patients with and without Gastritis by Polymerase Chain Reaction

Aims and Objective:

The aim of this study was to identify the presence of Helicobacter pylori in saliva of patients with and without gastritis by polymerase chain reaction (PCR) method.

Materials and Methods:

The study comprised 20 patients in Group I presenting with various symptoms of gastritis and 10 asymptomatic subjects in Group II. The intestinal endoscopy antral biopsies were collected from 20 symptomatic patients with gastroduodenal disorders. The saliva specimens were taken from all patients before endoscopy. PCR was performed using genomic DNA, isolated from the saliva and the biopsies of the patients as the template to detect the presence of the 16S ribosomal RNA gene in H. pylori.

Results:

In Group I, 10 (50%) cases of clinical gastritis were positive for H. pylori by endoscopy biopsy and 10 (50%) were negative. Of the 10 endoscopy biopsy positive cases for H. pylori, eight were PCR positive in saliva and two were negative. Of the 10 endoscopy biopsy negative cases, three were PCR positive for H. pylori in saliva and seven were negative. In Groups II, four were symptomatic for gastritis and six were negative. Of the six gastritis negative cases, three were PCR positive, four were gastritis positive, and three were PCR positive. Sensitivity and specificity of PCR were found to be 80% and 70%, respectively. The positive predictive and negative predictive values of PCR in saliva were 72.7% and 77.7%, respectively.

Conclusion:

PCR analysis of saliva may be handy in identification of H. pylori and serves as a noninvasive technique to diagnose and monitor the prognosis.

Presence of gastric Helicobacter species in children suffering from gastric disorders in Southern Turkey

BACKGROUND

Infections with gastric Helicobacter spp. are associated with gastritis, peptic ulceration, and malignancies. Helicobacter pylori is the most prevalent Helicobacter species colonizing the human stomach. Other gastric non-H. pylori helicobacters (NHPHs) have been described in 0.2%-6% of human patients with gastric disorders. Nevertheless, due to difficulties in the diagnosis of NHPH infections and lack of routine screening, this is most likely an underestimation of their true prevalence. To the best of our knowledge, no studies have been performed in the presence of Helicobacter spp. in children suffering from gastric disorders in Southern Turkey.

MATERIALS AND METHODS

In total, 110 children with gastric complaints were examined at the Cukurova University Balcali hospital, Turkey. Gastroscopy was performed to evaluate the presence of gastric mucosal lesions. Biopsies of the pyloric gland zone were taken for histopathological analysis, rapid urease testing, and presence of Helicobacter spp. DNA by PCR.

RESULTS

Based on the PCR results, the prevalence of Helicobacter spp. was 32.7% (36/110). H. pylori was found in 30.9% (34/110), H. suis in 1.8% (2/110), and H. heilmannii/H. ailurogastricus in 0.9% (1/110) of the human patients. A mixed infection with H. pylori and H. suis was present in one patient. The presence of mucosal abnormalities, such as nodular inflammation, ulceration, and hyperemia, as well as gastritis, was significantly higher in Helicobacter spp. positive patients.

CONCLUSION

Helicobacter pylori, H. suis, and H. heilmannii/H. ailurogastricus were present in children with gastric complaints. Infection with these pathogens may be involved in the development of gastritis and ulceration.

Helicobacter pylori: A foodborne pathogen?

Helicobacter pylori (H. pylori) is an organism that is widespread in the human population and is sometimes responsible for some of the most common chronic clinical disorders of the upper gastrointestinal tract in humans, such as chronic-active gastritis, duodenal and gastric ulcer disease, low-grade B-cell mucosa associated lymphoid tissue lymphoma of the stomach, and gastric adenocarcinoma, which is the third leading cause of cancer death worldwide. The routes of infection have not yet been firmly established, and different routes of transmission have been suggested, although the most commonly accepted hypothesis is that infection takes place through the faecal-oral route and that contaminated water and foods might play an important role in transmission of the microorganism to humans. Furthermore, several authors have considered H. pylori to be a foodborne pathogen because of some of its microbiological and epidemiological characteristics. H. pylori has been detected in drinking water, seawater, vegetables and foods of animal origin. H. pylori survives in complex foodstuffs such as milk, vegetables and ready-to-eat foods. This review article presents an overview of the present knowledge on the microbiological aspects in terms of phenotypic characteristics and growth requirements of H. pylori, focusing on the potential role that foodstuffs and water may play in the transmission of the pathogen to humans and the methods successfully used for the detection of this microorganism in foodstuffs and water.

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.

Effect of lactulose intervention on gut microbiota and short chain fatty acid composition of C57BL/6J mice

Gut microbiota have strong connections with health. Lactulose has been shown to regulate gut microbiota and benefit host health. In this study, the effect of short‐term (3 week) intervention of lactulose on gut microbiota was investigated. Gut microbiota were detected from mouse feces by 16S rRNA high‐throughput sequencing, and short chain fatty acids (SCFAs) were detected by gas chromatography‐mass spectrometry (GC‐MS). Lactulose intervention enhanced the α‐diversity of the gut microbiota; increased the abundance of hydrogen‐producing bacteria Prevotellaceae and Rikenellaceae, probiotics Bifidobacteriaceae and Lactobacillaceae, and mucin‐degrading bacteria Akkermansia and Helicobacter; decreased the abundance of harmful bacteria Desulfovibrionaceae and branched‐chain SCFAs (BCFAs). These results suggest that lactulose intervention effectively increased the diversity and improved the structure of the intestinal microbiota, which may be beneficial for host health.

Getting to the Heart of the Matter: A 20-Year-Old Man With Fever, Rash, and Chest Pain

Infection with Helicobacter cinaedi can encompass a wide spectrum of clinical manifestations, including fever, rash, endocarditis, osteomyelitis, and meningitis. The present case demonstrates the ability of H cinaedi to masquerade as acute rheumatic fever and represents the first reported case of cardiac tamponade caused by H cinaedi.

Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements

Background

The genome of the gastric pathogen Helicobacter pylori is characterised by considerable variation of both gene sequence and content, much of which is contained within three large genomic islands comprising the cag pathogenicity island (cagPAI) and two mobile integrative and conjugative elements (ICEs) termed tfs3 and tfs4. All three islands are implicated as virulence factors, although whereas the cagPAI is well characterised, understanding of how the tfs elements influence H. pylori interactions with different human hosts is significantly confounded by limited definition of their distribution, diversity and structural representation in the global H. pylori population.

Results

To gain a global perspective of tfs ICE population dynamics we established a bioinformatics workflow to extract and precisely define the full tfs pan-gene content contained within a global collection of 221 draft and complete H. pylori genome sequences. Complete (ca. 35-55kbp) and remnant tfs ICE clusters were reconstructed from a dataset comprising > 12,000 genes, from which orthologous gene complements and distinct alleles descriptive of different tfs ICE types were defined and classified in comparative analyses. The genetic variation within defined ICE modular segments was subsequently used to provide a complete description of tfs ICE diversity and a comprehensive assessment of their phylogeographic context. Our further examination of the apparent ICE modular types identified an ancient and complex history of ICE residence, mobility and interaction within particular H. pylori phylogeographic lineages and further, provided evidence of both contemporary inter-lineage and inter-species ICE transfer and displacement.

Conclusions

Our collective results establish a clear view of tfs ICE diversity and phylogeographic representation in the global H. pylori population, and provide a robust contextual framework for elucidating the functional role of the tfs ICEs particularly as it relates to the risk of gastric disease associated with different tfs ICE genotypes.

Electronic supplementary material

The online version of this article (10.1186/s13100-018-0109-4) contains supplementary material, which is available to authorized users.

Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon

Marine invertebrates associate with diverse microorganisms. Microorganisms even inhabit coelomic fluid (CF), namely, the fluid filling the main body cavity of echinoderms. The CF microbiota potentially impacts host health and disease. Here, we analysed the CF microbiota in two common coastal starfish species, Patiria pectinifera and Asterias amurensis. Although microbial community structures were highly variable among individual starfish, those of P. pectinifera were compositionally similar to those in the surrounding seawater. By contrast, many A. amurensis individuals harboured unique microbes in the CF, which was dominated by the unclassified Thiotrichales or previously unknown Helicobacter-related taxon. In some individuals, the Helicobacter-related taxon was the most abundant genus-level taxon, accounting for up to 97.3% of reads obtained from the CF microbial community. Fluorescence in situ hybridization using a Helicobacter-related-taxon-specific probe suggested that probe-reactive cells in A. amurensis were spiral-shaped, morphologically similar to known Helicobacter species. Electron microscopy revealed that the spiral cells had a prosthecate-like polar appendage that has never been reported in Helicobacter species. Although culture of Helicobacter-related taxon was unsuccessful, this is the first report of the dominance of a Helicobacter-related taxon in invertebrates and non-digestive organs, reshaping our knowledge of the phylogeography of Helicobacter-related taxa.

Effects of Medium- and Long-Chain Triacylglycerols on Lipid Metabolism and Gut Microbiota Composition in C57BL/6J Mice

Obesity is related to an increasing risk of chronic diseases. Medium- and long-chain triacylglycerols (MLCT) have been recognized as a promising choice to reduce body weight. In this study, three MLCT with different contents of medium-chain fatty acids (MCFA) (10-30%, w/w) were prepared, and their effects on lipid metabolism and fecal gut microbiota composition of C57BL/6J mice were systematically investigated. MLCT with 30% (w/w) MCFA showed the best performance in decreasing body weight gain as well as optimizing serum lipid parameters and liver triacylglycerol content. The expression levels of genes encoding enzymes for fatty acid degradation increased markedly and expression levels of genes encoding enzymes for de novo fatty acid biosynthesis decreased significantly in the liver of mice treated with MLCT containing 30% (w/w) MCFA. Interestingly, the dietary intake of a high fat diet containing MLCT did significantly decrease the ratio of Firmicutes to Bacteroidetes and down-regulate the relative abundance of Proteobacteria that may attribute to weight loss. Furthermore, we found a notable increase in the total short-chain fatty acid (SCFA) content in feces of mice on a MLCT containing diet. All these results may be concomitantly responsible for the antiobesity effect of MLCT with relatively high contents of MCFA.

Individual differences in stress vulnerability: The role of gut pathobionts in stress-induced colitis

Chronic subordinate colony housing (CSC), an established mouse model for chronic psychosocial stress, promotes a microbial signature of gut inflammation, characterized by expansion of Proteobacteria, specifically Helicobacter spp., in association with colitis development. However, whether the presence of Helicobacter spp. during CSC is critically required for colitis development is unknown. Notably, during previous CSC studies performed at Regensburg University (University 1), male specific-pathogen-free (SPF) CSC mice lived in continuous subordination to a physically present and Helicobacter spp.-positive resident. Therefore, it is likely that CSC mice were colonized, during the CSC procedure, with Helicobacter spp. originating from the dominant resident. In the present study we show that employing SPF CSC mice and Helicobacter spp.-free SPF residents at Ulm University (University 2), results in physiological responses that are typical of chronic psychosocial stress, including increased adrenal and decreased thymus weights, decreased adrenal in vitro adrenocorticotropic hormone (ACTH) responsiveness, and increased anxiety-related behavior. However, in contrast to previous studies that used Helicobacter spp.-positive resident mice, use of Helicobacter spp.-negative resident mice failed to induce spontaneous colitis in SPF CSC mice. Consistent with the hypothesis that the latter is due to a lack of Helicobacter spp. transmission from dominant residents to subordinate mice during the CSC procedure, colonization of SPF residents with Helicobacter typhlonius at University 2, prior to the start of the CSC model, rescued the colitis-inducing potential of CSC exposure. Furthermore, using SPF CSC mice and H. typhlonius-free SPF residents at University 1 prevented CSC-induced colitis. In summary, our data support the hypothesis that the presence or absence of exposure to certain pathobionts contributes to individual variability in susceptibility to stress-/trauma-associated pathologies and to reproducibility of stress-related outcomes between laboratories.

Arginase of Helicobacter Gastric Pathogens Uses a Unique Set of Non-catalytic Residues for Catalysis

Helicobacter pylori arginase, a bimetallic enzyme, is crucial for pathogenesis of the bacterium in human stomach. Despite conservation of the signature motifs in all arginases, the H. pylori homolog has a non-conserved motif (¹⁵³ESEEKAWQKLCSL¹⁶⁵), whose role was recently shown to be critical for its stability and function. The sequence analysis also reveals the presence of this motif with critical residues in the homolog of other Helicobacter gastric pathogens. However, the underlying mechanism for its significance in catalytic function is not clearly understood. Using H. pylori arginase, our studies reveal that the interactions of His122 and Tyr125 with Trp159 are indispensable for tertiary structural intactness through optimal positioning of the motif and thus for the catalytic function. The single and double mutants of His122 and Tyr125 not only enhanced the solvent accessibility and conformational flexibility of Trp159 in the holo protein, but also showed complete loss of catalytic activity. An intact bimetallic center and unaltered substrate binding indicate that proper positioning of the motif by aromatic-aromatic contact is vital for the generation of a catalytically active conformation. Additionally, the metal ions provide higher stability to the holo protein. We also identified the presence of these two residues exclusively in arginase of other Helicobacter gastric pathogens, which may have similar function. Therefore, to the best of our knowledge, these findings highlight for the first time that arginase of all Helicobacter gastric pathogens utilizes a unique non-catalytic triad for catalysis, which could be exploited for therapeutics.

Nod2: The intestinal gate keeper

Nucleotide-binding oligomerization domain 2 (NOD2) is an intracellular pattern recognition receptor that senses bacterial peptidoglycan (PGN)-conserved motifs in cytosol and stimulates host immune response. The association of NOD2 mutations with a number of inflammatory pathologies, including Crohn disease (CD), Graft-versus-host disease (GVHD), and Blau syndrome, highlights its pivotal role in host–pathogen interactions and inflammatory response. Stimulation of NOD2 by its ligand (muramyl dipeptide) activates pro-inflammatory pathways such as nuclear factor-κB (NF-κB), mitogen-activated protein kinases (MAPKs), and Caspase-1. A loss of NOD2 function may result in a failure in the control of microbial infection, thereby initiating systemic responses and aberrant inflammation. Because the ligand of Nod2 is conserved in both gram-positive and gram-negative bacteria, NOD2 detects a wide variety of microorganisms. Furthermore, current literature evidences that NOD2 is also able to control viruses’ and parasites’ infections. In this review, we present and discuss recent developments about the role of NOD2 in shaping the gut commensal microbiota and pathogens, including bacteria, viruses, and parasites, and the mechanisms by which Nod2 mutations participate in disease occurrence.

A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria

Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfur-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we found epsilonproteobacterial sequences in metatranscriptomes, metagenomes and 16S rRNA clone libraries as well as by polymerase chain reaction screening of Bathymodiolus species sampled from vents and seeps around the world. These epsilonproteobacterial sequences were closely related, indicating that the association is highly specific. The Bathymodiolus-associated epsilonproteobacterial 16S rRNA sequences were at most 87.6% identical to the closest cultured relative, and 91.2% identical to the closest sequences in public databases. This clade therefore represents a novel family within the Epsilonproteobacteria. Fluorescence in situ hybridization and transmission electron microscopy showed that the bacteria are filamentous epibionts associated with the gill epithelia in two Bathymodiolus species. In animals that host highly specific symbioses with one or a few types of endosymbionts, other less-abundant members of the microbiota can be easily overlooked. Our work highlights how widespread and specific associations with less-abundant microbes can be. Possibly, these microbes play an important role in the survival and health of their animal hosts.

The Complexity of Simplicity: Role of Sex, Development and Environment in the Modulation of the Stress Response

Anecdotally, we all know that stress is 'complicated', although most stress research is undertaken using incredibly simplified models that may not allow us to fully understand the underlying interactive mechanisms present in the 'real world'. This attempt at simplification, although sometimes necessary, may explain some of the difficulties faced when integrating basic science findings with the clinical and epidemiological data on stress and stress-related disorders. In a symposium held at the 2015 International Society for Psychoneuroendocrinology meeting in Edinburgh, UK, a series of speakers explored 'The Many Pathways to Plasticity in the Stress System', specifically focusing on variables that, in many cases, are eliminated from studies of stress to provide increased experimental control. Specifically, four speakers tackled the complex contributions of 'Sex, Development and Environment' in stress research, and reported published and unpublished evidence from work conducted in their own laboratories demonstrating that, in our race for simplicity in experimentation, the stories that we tell become all the more complex.