Detection of Helicobacter in the fecal material of the endangered Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis

The bacteria of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) are site-specific and distinct from freshwater environment

Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. Romboutsia, Plesiomonas, Actinobacillus, Candidatus Arthromitus dominated in the intestine (fecal and rectal samples). Fusobacterium, Streptococcus, and Acinetobacter dominated in the oral. The dominant genera in the blowhole include Suttonella, Psychrobacter, and two uncultured genera. Psychrobacter, Flavobacterium, and Acinetobacter were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.

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.

Changes in the fecal microbiome of the Yangtze finless porpoise during a short-term therapeutic treatment

The fecal microbiome is an integral part of aquatic mammals, like an inner organ. But we know very little about this inner organ of the threatened aquatic species, Yangtze finless porpoise (YFP). Four YFPs were placed into a purse seine for skin ulceration treatment, and this opportunity was taken to nurse the animals closer. In particular, we collected the feces of the YFPs before and after the paired healing and therapeutic treatment, along with samples of their fish diet and water habitat, to explore the changes in their fecal microbiome. Firmicutes (20.9–96.1%), Proteobacteria (3.8–78.7%), Actinobacteria (0.1–35.0%) and Tenericutes (0.8–17.1%) were the most dominant phyla present in the feces. The proportion of Proteobacteria and Actinobacteria increased after the treatment. Firmicutes showed a significant decrease, and most potential pathogens were absent, which reflected the administration of ciprofloxacin hydrochloride. Moreover, environmental shifts can also contribute to changes in the fecal microbiome. These results indicate that certain microbial interactions can be affected by environmental shifts, dietary changes and health-care treatments, which can also help maintain the internal environment of YFPs. These findings will inform the future enhanced protection and management of endangered YFPs and other vulnerable aquatic animals.

Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises (Neophocaena asiaeorientalis sunameri)

Mammalian gastrointestinal (GI) tract microbial communities are critical for host health. However, the microbiota along the GI tract in cetaceans has not been well characterized compared to other animals. In this study, the bacteria and fungi present in the stomach, foregut, hindgut and feces, of East Asian finless porpoises (Neophocaena asiaeorientalis sunameri, EAFPs) were characterized using high-throughput sequencing analysis. The bacterial and fungal diversity and richness in the stomach, hindgut and fecal samples tended to be higher than those in the foregut. Bacterial taxonomic compositions found in the hindgut and feces were different from those seen in the stomach and foregut. A greater proportion of strict anaerobic bacteria including Clostridia, Fusobacteria, and Ruminococcaceae were found in the hindgut and fecal samples. The fungal communities present in stomach samples differed from those detected in other regions to some extent. Zygomycota and Neocallimastigomycota were more predominant in the stomach. Some potential pathogens, such as Helicobacter spp. and Vibrio spp., were commonly present along the GI tract. Our study confirms that the fecal microbiota can represent the whole GI tract to some extent because of their relatively higher microbial diversity and presence of potential pathogens. Our study provides the first comprehensive characterization of the EAFPs GI microbiota, expanding on the current knowledge about the bacterial diversity in the GI tract of cetaceans. In addition, this is the first study characterizing the fungal diversity of any species of porpoise.

Presence of Helicobacter and Campylobacter species in faecal samples from zoo mammals

Helicobacter and Campylobacter species (spp.) colonize the gastrointestinal tract of various domesticated animals. Apart from their pathogenic significance in animals, several species are of zoonotic importance as well. For most non-domesticated animal spp., however, little is known on the presence and importance of these agents. Therefore, we investigated the presence of Helicobacter and Campylobacter spp. in marine and terrestrial zoo mammals. Faecal samples of various marine and terrestrial zoo mammals were collected from 6 different zoos in Belgium. These samples were tested for the presence of Helicobacter and Campylobacter spp. by isolation and direct demonstration of DNA using genus-specific PCRs, followed by sequencing of the obtained amplicons. Helicobacter spp. were detected in 12 and Campylobacter spp. in 5 of the 22 faecal samples from marine mammals. In 4 of 5 dolphins, H. cetorum was demonstrated, a well-known pathogen associated with gastritis and gastric ulceration in marine mammals. C. insulaenigrae was isolated from 4 of 6 sea lions and from 1 of 11 seals. To our knowledge, this is the first description of the presence of C. insulaenigrae on the European mainland. Helicobacter spp. were detected in 5 and Campylobacter spp. (mainly C. jejuni subsp. jejuni and C. coli) in 9 of the 26 faecal samples from terrestrial mammals. Potential novel enterohepatic Helicobacter spp. were detected in both marine and terrestrial zoo mammals. For the first time, the presence of several known and unknown Campylobacter and Helicobacter spp. was demonstrated in the gastrointestinal tract of various marine and terrestrial zoo mammals. Further investigation is needed on the pathogenic and zoonotic importance of these species.

Sequence divergence and conservation in genomes of Helicobacter cetorum strains from a dolphin and a whale

Background and Objectives

Strains of Helicobacter cetorum have been cultured from several marine mammals and have been found to be closely related in 16 S rDNA sequence to the human gastric pathogen H. pylori, but their genomes were not characterized further.

Methods

The genomes of H. cetorum strains from a dolphin and a whale were sequenced completely using 454 technology and PCR and capillary sequencing.

Results

These genomes are 1.8 and 1.95 mb in size, some 7–26% larger than H. pylori genomes, and differ markedly from one another in gene content, and sequences and arrangements of shared genes. However, each strain is more related overall to H. pylori and its descendant H. acinonychis than to other known species. These H. cetorum strains lack cag pathogenicity islands, but contain novel alleles of the virulence-associated vacuolating cytotoxin (vacA) gene. Of particular note are (i) an extra triplet of vacA genes with ≤50% protein-level identity to each other in the 5′ two-thirds of the gene needed for host factor interaction; (ii) divergent sets of outer membrane protein genes; (iii) several metabolic genes distinct from those of H. pylori; (iv) genes for an iron-cofactored urease related to those of Helicobacter species from terrestrial carnivores, in addition to genes for a nickel co-factored urease; and (v) members of the slr multigene family, some of which modulate host responses to infection and improve Helicobacter growth with mammalian cells.

Conclusions

Our genome sequence data provide a glimpse into the novelty and great genetic diversity of marine helicobacters. These data should aid further analyses of microbial genome diversity and evolution and infection and disease mechanisms in vast and often fragile ocean ecosystems.

Helicobacter spp. other than H. pylori

Significant advances have been made over the last 12 months in the understanding of the biology of non-H. pylori Helicobacter species (NHPH). Several studies have investigated the association between NHPH and human disease, including Crohn's disease, lithiasis, liver disease, coronary disease, gastritis, and pyoderma gangrenosum-like ulcers. Novel Helicobacter taxa were identified in new vertebrate hosts, and new methodologies in the fields of identification of Helicobacter spp. and evaluation of antibiotic resistance were described. The genome of the first human-derived gastric NHPH strain (Helicobacter bizzozeronii CIII-1) was sequenced, and several studies elucidated functions of different genes in NHPH. A number of important investigations regarding pathogenesis and immunopathobiology of NHPH infections have been published including the description of a new urease in Helicobacter mustelae. Finally, the effects of the gut microbiota and probiotics on NHPH infections were investigated.