Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces

Revisiting host identification of bacteriophage Enc34: from biochemical to molecular

In our 2012 genome announcement (J Virol 86:11403-11404, 2012, https://doi.org/10.1128/JVI.01954-12), we initially identified the host bacterium of bacteriophage Enc34 as Enterobacter cancerogenus using biochemical tests. However, later in-house DNA sequencing revealed that the true host is a strain of Hafnia alvei. Capitalizing on our new DNA-sequencing capabilities, we also refined the genomic termini of Enc34, confirming a 60,496-bp genome with 12-nucleotide 5' cohesive ends.

IMPORTANCE

Our correction reflects the evolving landscape of bacterial identification, where molecular methods have supplanted traditional biochemical tests. This case underscores the significance of revisiting past identifications, as seemingly known bacterial strains may yield unexpected discoveries, necessitating essential updates to the scientific record. Despite the host identity correction, our genome announcement retains importance as the first complete genome sequence of a Hafnia alvei bacteriophage.

Enhancing the therapeutic efficacy of mesenchymal stem cell transplantation in diabetes: Amelioration of mitochondrial dysfunction-induced senescence

Mesenchymal stem cell (MSC) transplantation offers significant potential for the treatment of diabetes mellitus (DM) and its complications. However, hyperglycemic conditions can induce senescence and dysfunction in both transplanted and resident MSCs, thereby limiting their therapeutic potential. Mitochondrial dysfunction and oxidative stress are key contributors to this process in MSCs exposed to hyperglycemia. As such, strategies aimed at mitigating mitochondrial dysfunction could enhance the therapeutic efficacy of MSC transplantation in DM. In this review, we provide an updated overview of how mitochondrial dysfunction mediates MSC senescence. We present experimental evidence for the molecular mechanisms behind high glucose-induced mitochondrial dysfunction in MSCs, which include impairment of mitochondrial biogenesis, mitochondrial calcium regulation, the mitochondrial antioxidant system, mitochondrial fusion-fission dynamics, mitophagy, and intercellular mitochondrial transfer. Furthermore, we propose potential pharmacological candidates that could improve the efficacy of MSC transplantation by enhancing mitochondrial function in patients with DM and related complications.

Host genetic background rather than diet-induced gut microbiota shifts of sympatric black-necked crane, common crane and bar-headed goose

Introduction

Gut microbiota of wild birds are affected by many factors, and host genetic background and diet are considered to be two important factors affecting their structure and function.

Methods

In order to clarify how these two factors influence the gut microbiota, this study selected the sympatric and closely related and similar-sized Black-necked Crane (Grus nigricollis) and Common Crane (Grus grus), as well as the distantly related and significantly different-sized Bar-headed Goose (Anser indicus). The fecal samples identified using sanger sequencing as the above three bird species were subjected to high-throughput sequencing of rbcL gene and 16S rRNA gene to identify the feeding types phytophagous food and gut microbiota.

Results

The results showed significant differences in food diversity between black-necked cranes and Common Cranes, but no significant differences in gut microbiota, Potatoes accounted for approximately 50% of their diets. Bar-headed Geese mainly feed on medicinal plants such as Angelica sinensis, Alternanthera philoxeroides, and Ranunculus repens. Black-necked cranes and Common Cranes, which have a high-starch diet, have a similar degree of enrichment in metabolism and synthesis functions, which is significantly different from Bar-headed Geese with a high-fiber diet. The differences in metabolic pathways among the three bird species are driven by food. The feeding of medicinal plants promotes the health of Bar-headed Geese, indicating that food influences the functional pathways of gut microbiota. Spearman analysis showed that there were few gut microbiota related to food, but almost all metabolic pathways were related to food.

Conclusion

The host genetic background is the dominant factor determining the composition of the microbiota. Monitoring the changes in gut microbiota and feeding types of wild birds through bird feces is of great reference value for the conservation of other endangered species.

Microbiome recognition of virulence-factor-governed interfacial mechanisms in antibiotic resistance and pathogenicity removal by functionalized microbubbles

The frequent occurrence of epidemics around the world gives rise to increasing concerns of the pollution of pathogens and antibiotic resistant bacteria in water. This study investigated the impacts of virulence factors (VFs) on the removal of antibiotic resistant and pathogenic bacteria from municipal wastewater by ozone-free or ozone-encapsulated Fe(III)-coagulant-modified colloidal microbubbles (O3_free-CCMBs or O3-CCMBs). The highly interface-dependent process was initiated with cell-capture on the microbubble surface where the as-collected cells could be further inactivated with the bubble-released ozone and oxidative species if O3-CCMBs were used. The microbiome sequencing analyses denote that the O3_free-CCMB performance of antibiotic resistant and pathogenic bacteria removal was dependent on the virulence phenotypes related to cell-surface properties or structures. The adhesion-related VFs facilitated the effective attachment between cells and the coagulant-modified bubble-surface, which further enhanced cell inactivation by bubble-released ozone. On the contrary, the motility-related VFs might help cells to escape from the bubble capture by locomotion; however, this could be overcome by O3-CCMB-induced oxidative demolition of the movement structures. Besides, the microbubble performance was also impacted with the cell-membrane structure related to antibiotic resistance (i.e., efflux pumps) and the dissolved organic matter through promoting the surface-capture and decreasing the oxidation efficacy. The ozone-encapsulated microbubbles with surface functionalization are robust and promising tools in hampering antibiotic resistance and pathogenicity dissemination from wastewater to surface water environment; and awareness should be raised for the influence of virulence signatures on its performance.

Effects of feeding on different parts of Ailanthus altissima on the intestinal microbiota of Eucryptorrhynchus scrobiculatus and Eucryptorrhynchus brandti (Coleoptera: Curculionidae)

Eucryptorrhynchus brandti and Eucryptorrhynchus scrobiculatus (Coleoptera: Curculionidae) are two monophagous weevil pests that feed on Ailanthus altissima (Mill.) Swingle but differ in their diet niche. In the field, adults of E. brandti prefer to feed on the trunk of A. altissima, whereas adults of E. scrobiculatus prefer to feed on the tender parts. We conducted Illumina sequencing of 16S rRNA to examine changes in bacterial diversity in the adults of these two weevil species after they fed on different parts of A. altissima (trunk, 2–3-year-old branches, annual branches, and petioles). Proteobacteria, Tenericutes, and Firmicutes were the dominant phyla in E. brandti (relative abundance was 50.64, 41.56, and 5.63%, respectively) and E. scrobiculatus (relative abundance was 78.63, 11.91, and 7.41%, respectively). At the genus level, Spiroplasma, endosymbionts2, Unclassified Enterobacteriaceae, and Lactococcus were dominant in E. brandti, and Unclassified Enterobacteriaceae, Wolbachia and Spiroplasma, and endosymbionts2 were dominant in E. scrobiculatus. Linear discriminant analysis effect size analysis revealed microbial biomarkers in the different treatment group of adults of both weevil species. Adults of E. brandti may require the trunk, and adults of E. scrobiculatus may require the petioles and annual branches to maintain the high diversity of their gut microbes. The results of this study indicate that feeding on different parts of A. altissima affects the composition and function of the microbes of E. brandti and the microbial composition of E. scrobiculatus. Variation in the abundance of Wolbachia and Spiroplasma in E. brandti and E. scrobiculatus is associated with dietary niche changes, and this might explain the evolution of reproductive isolation between these two sibling weevil species.

Bacteria and antibiotic resistance detection in fractures of wild birds from wildlife rehabilitation centres in Spain

Anatomic adaptations make birds more prone to open fractures with exposed bone parts losing vascularization. As a result of this exposure, fractures are colonized by different microorganisms, including different types of bacteria, both aerobic and anaerobic, causing osteomyelitis in many cases. For this reason, antibiotic treatment is common. However, carrying out antibiotic treatment without carrying out a previous antibiogram may contribute to increased resistance against antibiotics, especially in migratory wild birds. In this paper, bacterial counts regarding fracture type, bacterial identification and antibiotic resistance have been analysed in wild birds from wildlife rehabilitation centres in Spain. The results obtained showed that open fractures had higher bacterial counts (CFU/mL) than closed ones. Bacteria in family Enterobacteriaceae, identified were Escherichia spp., Enterobacter spp., Shigella spp., Hafnia alvei, Proteus mirabilis, Leclercia adecarboxylata and Pantoea agglomerans. Other bacteria present in wild birds' fractures were Aeromonas spp., Enterococcus spp. Bacillus wiedmannii and Staphylococcus sciuri. All species found presented resistance to at least one of the antibiotics used. Wild birds can be implicated in the introduction, maintenance and global spreading of antibiotic resistant bacteria and represent an emerging public health concern. Results obtained in this paper support the idea that it is necessary to take this fact into account before antibiotic administration to wild animals, since it could increase the number of bacteria resistant to antibiotics.

Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

BACKGROUND

The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.

RESULTS

One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei.

CONCLUSIONS

Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.