Classification of a Brevundimonas strain detectable after PCR with a Helicobacter-specific primer pair

Changes of gut microbiota in pregnant sows induced by 5-Aminolevulinic acid

Sow health is related to farm productivity and sustainability, but the increased resistance of bacteria to antibiotics in the pig industry has led to a decline in resistance to disease and environmental pollution. 5-Aminolevulinic acid (5-ALA) is considered a feed additive to replace antibiotics, but the effect of 5-ALA on gut microbiota has not been studied. In this study, we fed 12 healthy Landrace × Large White two-line hybrid sows with different concentrations of 5-ALA; blood and fecal samples were obtained after 110 days of pregnancy, and 16S rRNA amplicon sequencing was performed. The alpha diversity of the gut microbiota in sows was not significant among the sows fed different concentrations of 5-ALA. PCoA revealed a significant (P < 0.05) difference in the gut microbiota composition with different 5-ALA groups. LEfSe revealed that 5-ALA increased relative abundance of Streptococcus, while Myroides was enriched in CK group. Functional prediction of Tax4Fun showed that different concentrations of 5-ALA significantly (P < 0.05) increased the mean relative abundance of KEGG pathways involved in core microbiota cellular processes, environmental information processing, and genetic information processing. In summary, 5-ALA changed bacterial community composition of gut microbiota, reduced colonization of some pathogenes and increased the relative abundance of some probiotics. These results provide a theoretical basis for the healthy breeding of pigs.

Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity

Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.

Exploring gastric bacterial community in young pigs

Microbiota plays an important role in the homeostasis of the gastrointestinal tract. Understanding the variations of the commensal microbiota composition is crucial for a more efficient control of enteric infectious diseases and for the reduction of the use of antibiotics in animal production, which are the main points of interest for improved animal healthcare and welfare and for consumer health protection. Even though the intestinal microbiota has been extensively studied, little is known about the gastric microbiota. This pilot study was aimed at a descriptive analysis of the gastric microbiota in healthy pigs and at the identification of any differences among four potentially distinct microbial niches in the stomach. Gastric mucosal samples from the oxyntic area, the pylorus and the gastric groove, and a sample of gastric contents were collected from four healthy weaned pigs. Bacterial DNA was isolated and extracted from each sample and amplicons from the V6 region of the 16S rRNA gene were sequenced using Ion Torrent PGM. The data were analysed by an "unsupervised" and a "supervised" approach in the Ribosomal Database Project (RDP) pipeline. Proteobacteria was the dominant phylum in all the samples. Differences in bacterial community composition were found between mucosal and content samples (one-way ANOSIM pairwise post hoc test, p < 0.05); instead, the different mucosal regions did not show differences between them. The mucosal samples were characterised by Herbiconiux and Brevundimonas, two genera which include cellulolytic and xylanolytic strains. Nevertheless, additional larger trials are needed to support the data presented in this pilot study and to increase the knowledge regarding the resident microbiota of the stomach.

Diagnosis of Helicobacter spp. infection in canine stomach

A total of 75 biopsied samples of cardia, fundus, body, and pyloric antrum from necropsied dogs that were submitted to the Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University from April 2003 to June 2004 were investigated. The objectives of this study were to determine the prevalence of Helicobacter spp. in canine stomach by polymerase chain reaction (PCR) in comparison to histochemistry versus immunohistochemistry (IHC), and to correlate these diagnostic methods with the clinical significance in infected dogs. Histopathological results revealed 60.0% (45/75) of samples to be positive, and consisted of mild gastritis in 64.44% (29/45), moderate gastritis in 11.11% (5/45), and severe gastritis in 24.44% (11/45). The proportion showing no histopathological lesions was 40.0% (30/75). Helicobacter spp. were localized to the luminal crypt in 18.67% (14/75), gastric pit in 22.67% (17/75), gastric gland in 21.33% (16/75), and gastric epithelium in 8% (6/75). The percentages of positive samples of Helicobacter spp. diagnosed by hematoxylin and eosin stain (H&E), Warthin Starry stain (WSS), IHC with rabbit polyclonal anti-H. pylori antibody, and PCR were 17.3% (13/75), 46.7% (35/75), 30.7% (23/75), and 10.7% (8/75), respectively. No significant differences weree observed in histopathological changes in portions of the stomach (p>0.05). The diagnosis of Helicobacter spp. by PCR in comparison to that by WSS and IHC was not significantly different (p>0.05). There were no relationships between pathological studies using H&E, WSS, and IHC, and especially between PCR and clinical signs of Helicobacter spp. infections in canine stomachs (p>0.05). The present study revealed significantly different levels of correlation for Helicobacter spp. detection between H&E and WSS (p<0.001). Results indicate that the method of choice for diagnosis of Helicobacter spp. infection in canine stomach is dependent on the purpose of study and appropriate specimen collection.

Bacteriophages of freshwater Brevundimonas vesicularis isolates

Nine strains of Brevundimonas vesicularis were isolated from surface water of three ponds in Bielefeld, Germany. With those strains as indicators seven bacteriophages with different host ranges were isolated. Molecular characterization showed that all phages contained linear double-stranded DNA with a similar genome size of about 37 kb. Restriction analysis and hybridization of phage DNAs revealed that three of these phages are closely related to each other. These phages had morphologies typical of the family Siphoviridae. Their genomes contained cohesive ends. Four phages were classified into the family of Podoviridae. Restriction analysis of the DNAs of these phages did not reveal any similarities. The DNA of these phages were terminally redundant. All phages were unable to transduce plasmids or marker genes.

PCR-based genetic evidence for occurrence of Helicobacter pylori and novel Helicobacter species in the canine gastric mucosa

The canine gastric mucosa is known to be a habitat for various Helicobacter species. So far, five Helicobacter species have been described from the canine gastric mucosa, but histological studies have demonstrated a greater variety. In order to gain more information on diversity of canine gastric mucosa colonising helicobacters, biopsy samples of four pet dogs were examined by DNA-based techniques. PCR with a primer pair binding specifically to the 16S rDNA of the species of the genus Helicobacter and generating a fragment of approximately 400 bp indicated the presence of Helicobacter strains in the stomachs of the four dogs. PCR products were cloned into Escherichia coli DH10B and PCR-re-amplified 16S rDNA fragments were subjected to amplified ribosomal DNA restriction analysis (ARDRA) employing restriction enzyme HhaI. Restriction profiles indicated the presence of at least two different Helicobacter species in two dogs. Partial sequences of 16S rDNA of six clones were compared with sequences available in the EMBL data bank. Two sequences obtained from different dogs were identical with the corresponding sequences of Helicobacter pylori strains. Three sequences showed highest but moderate similarity values to H. pylori (96.6-98.0%) and one sequence to Helicobacter salomonis (97.3%). In contrast to previous reports our data implicate that the gastric mucosa of dogs may be colonised by strains of H. pylori or a very closely related species but they also confirm indications for the presence of so far uncultivated species of Helicobacter.

Extragastric Helicobacter species

The genus Helicobacter has expanded at a rapid pace and no fewer than 31 species have been named since the proposal of the genus in 1989. Of these 31 species, 22 are principally associated with extragastric niches and there is increasing interest in the role of these taxa in diseases of humans and animals. Substantial evidence attests to certain species playing a role in the pathogenesis of enteric, hepatic and biliary disorders and some taxa demonstrate zoonotic potential. The importance of extragastric Helicobacters is likely to be an important topic for research in the near future. Here, important papers published in the field this last year are reviewed.