Corynebacterium heidelbergense sp. nov., isolated from the preen glands of Egyptian geese (Alopochen aegyptiacus)

Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet

BACKGROUND

Goose, descendants of migratory ancestors, have undergone extensive selective breeding, resulting in their remarkable ability to accumulate fat in the liver and exhibit a high tolerance for significant energy intake. As a result, goose offers an excellent model for studying obesity, metabolic disorders, and liver diseases in mammals. Although the impact of the three-dimensional arrangement of chromatin within the cell nucleus on gene expression and transcriptional regulation is widely acknowledged, the precise functions of chromatin architecture reorganization during fat deposition in goose liver tissues still need to be fully comprehended.

RESULTS

In this study, geese exhibited more pronounced changes in the liver index and triglyceride (TG) content following the consumption of the high-fat diet (HFD) than mice without significant signs of inflammation. Additionally, we performed comprehensive analyses on 10 goose liver tissues (5 HFD, 5 normal), including generating high-resolution maps of chromatin architecture, conducting whole-genome gene expression profiling, and identifying H3K27ac peaks in the livers of geese and mice subjected to the HFD. Our results unveiled a multiscale restructuring of chromatin architecture, encompassing Compartment A/B, topologically associated domains, and interactions between promoters and enhancers. The dynamism of the three-dimensional genome architecture, prompted by the HFD, assumed a pivotal role in the transcriptional regulation of crucial genes. Furthermore, we identified genes that regulate chromatin conformation changes, contributing to the metabolic adaptation process of lipid deposition and hepatic fat changes in geese in response to excessive energy intake. Moreover, we conducted a cross-species analysis comparing geese and mice exposed to the HFD, revealing unique characteristics specific to the goose liver compared to a mouse. These chromatin conformation changes help elucidate the observed characteristics of fat deposition and hepatic fat regulation in geese under conditions of excessive energy intake.

CONCLUSIONS

We examined the dynamic modifications in three-dimensional chromatin architecture and gene expression induced by an HFD in goose liver tissues. We conducted a cross-species analysis comparing that of mice. Our results contribute significant insights into the chromatin architecture of goose liver tissues, offering a novel perspective for investigating mammal liver diseases.

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Microbial infection risk predicts antimicrobial potential of avian symbionts

Symbiotic bacteria on animal hosts can prevent pathogenic bacterial infections by several mechanisms. Among them, symbiotic bacteria can indirectly enhance host’s immune responses or, directly, produce antimicrobial substances against pathogens. Due to differences in life-style, different host species are under different risks of microbial infections. Consequently, if symbiotic bacteria are somewhat selected by genetically determined host characteristics, we would expect the antimicrobial properties of bacterial symbionts to vary among host species and to be distributed according to risk of infection. Here we have tested this hypothesis by measuring the antimicrobial ability of the bacterial strains isolated from the uropygial-gland skin of 19 bird species differing in nesting habits, and, therefore, in risk of microbial infection. In accordance with our predictions, intensity and range of antimicrobial effects against the indicator strains assayed varied among bird species, with hole-and open-nesters showing the highest and the lowest values, respectively. Since it is broadly accepted that hole-nesters have higher risks of microbial infection than open nesters, our results suggest that the risk of infection is a strong driver of natural selection to enhance immunocompetence of animals through selecting for antibiotic-producing symbionts. Future research should focus on characterizing symbiotic bacterial communities and detecting coevolutionary processes with particular antibiotic-producing bacteria within-host species.

Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons)

Two novel Gram-positive, non-spore-forming, facultatively anaerobic, non-motile, and short rods to coccoid strains were isolated from the feces of the greater white-fronted geese (Anser albifrons) at Poyang Lake. The 16S rRNA gene sequences of strains 4H37-19^T and 3HC-13 shared highest identity to that of Corynebacterium uropygiale Iso10^T (97.8%). Phylogenetic and phylogenomic analyses indicated that strains 4H37-19^T and 3HC-13 formed an independent clade within genus Corynebacterium and clustered with Corynebacterium uropygiale Iso10^T. The average nucleotide identity and digital DNA-DNA hybridization value between strains 4H37-19^T and 3HC-13 and members within genus Corynebacterium were all below 95% and 70%, respectively. The genomic G + C content of strains 4H37-19^T and 3HC-13 was 52.5%. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), phosphatidylcholine, and phosphatidyl inositol mannosides (PIM) were the major polar lipids, with C_18:1ω9c, C_16:0, and C_18:0 as the major fatty acids, and MK-8 (H4), MK-8(H₂), and MK-9(H₂) as the predominant respiratory quinones. The major whole cell sugar was arabinose, and the cell wall included mycolic acids. The cell wall peptidoglycan contained meso-diaminopimelic acid (meso-DAP). The polyphasic taxonomic data shows that these two strains represent a novel species of the genus Corynebacterium, for which the name Corynebacterium poyangense sp. nov. is proposed. The type strain of Corynebacterium poyangense is 4H37-19^T (=GDMCC 1.1738^T = KACC 21671^T).

Great Tit (Parus major) Uropygial Gland Microbiomes and Their Potential Defensive Roles

The uropygial gland (preen gland) of birds plays an important role in maintaining feather integrity and hygiene. Although a few studies have demonstrated potential defensive roles of bacteria residing within these glands, the diversity and functions of the uropygial gland microbiota are largely unknown. Therefore, we investigated the microbiota of great tit (Parus major) uropygial glands through both isolation of bacteria (culture-dependent) and 16S rRNA amplicon sequencing (culture-independent). Co-culture experiments of selected bacterial isolates with four known feather-degrading bacteria (Bacillus licheniformis, Kocuria rhizophila, Pseudomonas monteilii, and Dermacoccus nishinomiyaensis), two non-feather degrading feather bacteria, one common soil bacterial pathogen and two common fungal pathogens enabled us to evaluate the potential antimicrobial properties of these isolates. Our results show major differences between bacterial communities characterized using culture-dependent and -independent approaches. In the former, we were only able to isolate 12 bacterial genera (dominated by members of the Firmicutes and Actinobacteria), while amplicon sequencing identified 110 bacterial genera (dominated by Firmicutes, Bacteroidetes, and Proteobacteria). Uropygial gland bacterial isolates belonging to the genera Bacillus and Kocuria were able to suppress the growth of four of the nine tested antagonists, attesting to potential defensive roles. However, these bacterial genera were infrequent in our MiSeq results suggesting that the isolated bacteria may not be obligate gland symbionts. Furthermore, bacterial functional predictions using 16S rRNA sequences also revealed the ability of uropygial gland bacteria to produce secondary metabolites with antimicrobial properties, such as terpenes. Our findings support that uropygial gland bacteria may play a role in feather health and that bacterial symbionts might act as defensive microbes. Future investigations of these bacterial communities, with targeted approaches (e.g., bacterial isolation and chemical analyses), are thus warranted to improve our understanding of the evolution and function of these host-microbe interactions.

Birds, feather-degrading bacteria and preen glands: the antimicrobial activity of preen gland secretions from turkeys (Meleagris gallopavo) is amplified by keratinase

The function of uropygial glands (preen glands) has been subject to controversial debates. In this study, we evaluated the antimicrobial potential of preen gland secretions of turkeys (Meleagris gallopavo) against 18 microbial strains by means of diffusion tests, broth microdilutions, checkerboard assays and time-kill curves. Furthermore, we tested the hypothesis that lipids exert direct antimicrobial effects on pathogens. Moreover, we checked for mutualistic relationships between the preen gland bacterium Corynebacterium uropygiale with its hosts. We found that preen gland secretions significantly inhibited the growth of a broad spectrum of bacteria and fungi, particularly when combined with keratinase. Combinations effectively killed multidrug resistant microorganisms in a strongly synergistic manner. Since feather-degrading microorganisms (FDM) express keratinase and thereby disrupt the integrity of the plumage, our data suggests that preen gland secretions of turkeys are specifically activated in the presence of FDM, and specifically eliminate FDM from feathers. However, antimicrobial effects did not originate from lipids, but were mediated by highly polar compounds which might be antimicrobial peptides (AMPs). Finally, C. uropygiale is apparently not involved in the antimicrobial activity of preen gland secretions of turkeys. In conclusion, our results suggest that turkeys can antagonize FDM by amplifying the antimicrobial properties of their preen gland secretions.

Kocuria tytonis sp. nov., isolated from the uropygial gland of an American barn owl (Tyto furcata)

Avian uropygial glands have received increasing attention in recent years, but little is known about micro-organisms in uropygial glands. In this study, we isolated a strain of Gram-stain-positive, non-motile, non-spore-forming cocci, designated 442^T, from the uropygial gland of an American barn owl (Tyto furcata) and characterized it using a polyphasic approach. 16S rRNA gene sequence analysis placed the isolate in the genus Kocuria. The G+C content was 70.8 mol%, the major menaquinone was MK-7(H2) and the predominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. Phylogenetic analyses based on the 16S rRNA gene identified Kocuria rhizophila DSM 11926^T (99.6 % similarity), Kocuria salsicia DSM 24776^T (98.7 %), Kocuria varians DSM 20033^T (98.3 %) and Kocuria marina DSM 16420^T (98.3 %) as the most closely related species. However, average nucleotide identity values below 86 % indicated that the isolate differed from all species hitherto described. Chemotaxonomic analyses and whole-cell protein profiles corroborated these findings. Accordingly, the isolate is considered to be a member of a novel species, for which the name Kocuria tytonis sp. nov. is proposed. The type strain is 442^T (=DSM 104130^T=LMG 29944^T).

Kocuria tytonicola, new bacteria from the preen glands of American barn owls (Tyto furcata)

Although birds are hosts to a large number of microorganisms, microbes have rarely been found in avian oil glands. Here, we report on two strains of a new bacterial species from the preen oil of American barn owls (Tyto furcata). Phenotypic as well as genotypic methods placed the isolates to the genus Kocuria. Strains are non-fastidious, non-lipophilic Gram-positive cocci and can be unambiguously discriminated from their closest relative Kocuria rhizophila DSM 11926^T. In phylogenetic trees, the owl bacteria formed a distinct cluster which was clearly separated from all other known Kocuria species. The same conclusion was drawn from MALDI-TOF MS analyses. Once again, the new bacterial strains were very similar to one another, but exhibited substantial differences when compared to the most closely related species. Besides, the results of the biochemical tests, optimum growth conditions and pigmentation differed from closely related Kocuria spp. Finally, ANIb values of less than 87% provided striking evidence that the isolates recovered from American barn owls represent a hitherto undescribed species, for which we propose the name Kocuria tytonicola sp. nov. The type strain is 489^T (DSM 104133^T=LMG 29945^T, taxonumber TA00340).