Genomic analysis of Helicobacter himalayensis sp. nov. isolated from Marmota himalayana

Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions

Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g. Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalog of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts-though exceptions, such as the enterohepatic prophages from H. canis, H. equorum, H. jaachi, and the gastric prophage from H. himalayensis-suggesting more complex co-evolutionary dynamics like host jumps, recombination, and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.

Arthrobacter zhaoxinii sp. nov. and Arthrobacter jinronghuae sp. nov., isolated from Marmota himalayana

Four yellow-coloured strains (zg-Y815T/zg-Y108 and zg-Y859T/zg-Y826) were isolated from the intestinal contents of Marmota himalayana and assigned to the 'Arthrobacter citreus group'. The four strains grew optimally on brain heart infusion agar with 5 % defibrinated sheep blood plate at 30 °C, pH 7.0 and with 0.5 % NaCl (w/v). Comparative analysis of their 16S rRNA genes indicated that the two strain pairs belong to the genus Arthrobacter, showing the highest similarity to Arthrobacter yangruifuii 785T (99.52 %), which was further confirmed by the 16S rRNA gene and genome-based phylogenetic analysis. The comparative genomic analysis [digital DNA-DNA hybridization, (dDDH) and average nucleotide identity (ANI)] proved that the four strains are two different species (zg-Y815T/zg-Y108, 71.7 %/96.8 %; zg-Y859T/zg-Y826, 87.3 %/98.5 %) and differ from other known species within the genus Arthrobacter (zg-Y815T, 19.6-32.3 %/77.2-88.0 %; zg-Y859T, 19.5-29.3 %/77.4-86.3 %). Strain pairs zg-Y815T/zg-Y108 and zg-Y859T/zg-Y826 had the same major cellular fatty acids (iso-C16 : 0 and anteiso-C15 : 0), with MK-8(H2) as their dominant respiratory quinone (70.6 and 61.7 %, respectively). The leading polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol. The detected amino acids and cell-wall sugars of the two new species were identical (amino acids: alanine, glutamic acid, and lysine; sugars: rhamnose, galactose, mannose, glucose, and ribose). According to the phylogenetic, phenotypic, and chemotaxonomic analyses, we concluded that the four new strains represented two different novel species in the genus Arthrobacter, for which the names Arthrobacter zhaoxinii sp. nov. (zg-Y815T= GDMCC 1.3494T = JCM 35821T) and Arthrobacter jinronghuae sp. nov. (zg-Y859T = GDMCC 1.3493T = JCM 35822T) are proposed.

Identification of Novel Bartonella washoensis Sequence Type 22 in Marmota himalayana - Jiuquan City, Gansu Province, China, 2021-2022

What is already known about this topic?

The prevalence of rodent-adapted Bartonella species has been increasing significantly. However, the specific Bartonella species carried by Marmota himalayana (M. himalayana), a large rodent species, and the potential risk it poses to human populations remain unknown.

What is added by this report?

Bartonella washoensis (B. washoensis), associated with human endocarditis, was initially identified in M. himalayana, exhibiting a detection rate of approximately one-third and demonstrating a predilection for the heart and lungs. The discovery of the novel Sequence Type 22 has expanded both the isolation source and genetic lineage of B. washoensis.

What are the implications for public health practice?

Individuals residing within the M. himalayana plague focus are at an elevated risk for B. washoensis infection. Consequently, there is a pressing need for public health warnings and efficient clinical case identification in this population.

Canibacter zhuwentaonis sp. nov. and Canibacter zhoujuaniae sp. nov., isolated from Marmota himalayana

Four Gram-stain-positive, facultatively anaerobic, non-motile, non-spore-forming and rod-shaped bacteria (lx-72^T, lx-45, ZJ784^T and ZJ955) were isolated from the respiratory tract or faeces of marmot (Marmota himalayana) from the Qinghai-Tibet Plateau in China. Analysis of the 16S rRNA gene sequences showed that all strains belong to the genus Canibacter and are more related to Canibacter oris CCUG 64069^T (95.1-97.4 % similarity) than to the genus Leucobacter. Both strain pairs grew well at pH 6-9 and 15-42°C, and ZJ784^T/ZJ955 could tolerate slightly higher NaCl (0.5-4.5 %, w/v) than lx-72^T/lx-45(0.5-3.5 %). Based on whole-genome sequences, the average nucleotide identity and digital DNA-DNA hybridization values between our four isolates and their closest relative were below the species delineation thresholds of 70 % and 95-96 %. The common major fatty acids (>10 %) of our four strains were anteiso-C_15 : 0 and anteiso-C_17 : 0. For both new type strains, MK-8(H₄) and MK-9(H₄) were the major isoprenoid quinones, and diphosphatidylglycerol and phosphatidylglycerol were the main polar lipids. The genomic DNA G+C content of all strains was 53.9 mol%. Based on results from the genomic comparison, phylogenetic analysis, and physiological and biochemical characteristics, the four isolates represent two novel species in the genus Canibacter, for which the names Canibacter zhuwentaonis sp. nov. (type strain lx-72^T=KCTC 49658^T=GDMCC 1.2569^T) and Canibacter zhoujuaniae sp. nov. (type strain ZJ784^T=KCTC 49507^T=GDMCC 1.1997^T) are proposed.

Helicobacters and cancer, not only gastric cancer?

The Helicobacter genus actually comprises 46 validly published species divided into two main clades: gastric and enterohepatic Helicobacters. These bacteria colonize alternative sites of the digestive system in animals and humans, and contribute to inflammation and cancers. In humans, Helicobacter infection is mainly related to H. pylori, a gastric pathogen infecting more than half of the world's population, leading to chronic inflammation of the gastric mucosa that can evolve into two types of gastric cancers: gastric adenocarcinomas and gastric MALT lymphoma. In addition, H. pylori but also non-H. pylori Helicobacter infection has been associated with many extra-gastric malignancies. This review focuses on H. pylori and its role in gastric cancers and extra-gastric diseases, as well as malignancies induced by non-H. pylori Helicobacters. Their different virulence factors and their involvement in carcinogenesis is discussed. This review highlights the importance of both gastric and enterohepatic Helicobacters in gastrointestinal and liver cancers.