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Volume 7,
Issue 4,
2025
Volume 7, Issue 4, 2025
- Research Articles
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Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity
More LessBackground. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus).
Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species.
Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.
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Antibacterial activity of Cinnamomum verum and Thymus vulgaris essential oils on multidrug-resistant zoonotic bacteria isolated from dogs in southern Benin
More LessAntibiotic resistance is a major public health problem. The search for new therapeutic alternatives is becoming urgent. Essential oils are a promising alternative. This study aimed to evaluate the antibacterial activities of essential oils from selected plants on multidrug-resistant zoonotic strains isolated from dogs. Essential oils from dried Thymus vulgaris leaves, Cinnamomum verum bark and Cuminum cyminum seeds were extracted and tested on five multidrug-resistant Escherichia coli and four Staphylococcus aureus isolated from dogs in southern Benin. The study showed that T. vulgaris essential oil was bacteriostatic, with an MIC equal to 2.5 µl ml−1 and a minimum bactericidal concentration (MBC) of 17 µl ml−1 for E. coli strains and 11.25 µl ml−1 for S. aureus strains. Regarding C. verum essential oil, its bacteriostatic power was characterized by an MIC of 1.25 µl ml−1 for the isolates tested and an average MBC of 11.50 µl ml−1 for E. coli and 12.19 µl ml−1 for S. aureus. On the other hand, C. cyminum essential oil was ineffective on the strains investigated. Additionally, T. vulgaris essential oil contained predominantly thymol (36.57%), p-cymene (30.51%) and carvacrol (7.62%), whilst C. verum essential oil contained cinnamaldehyde (88.76%). This study reveals the antibacterial activity of T. vulgaris dry leaf and C. verum bark essential oils on multi-resistant E. coli and S. aureus isolated from dogs. These two essential oils may be alternative candidates for combating antibiotic-resistant E. coli and S. aureus infections.
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- Short Communications
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Detection of vanA genes in vancomycin-susceptible Enterococcus faecium isolates: implications for additional testing
More LessTo assess the frequency of silent vancomycin resistance, phenotypically susceptible Enterococcus faecium isolates underwent genotypic testing using Cepheid’s Xpert vanA/vanB PCR. A total of 6% of isolates had silent vanA genes. However, the clinical relevance of silent van genes and the lack of rapid, random-access genotypic methods poses an ongoing challenge to laboratories.
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Selection and maintenance of mobile linezolid-resistance genes and plasmids carrying them in the presence of florfenicol, an animal-specific antimicrobial
More LessMobile linezolid-resistance genes (optrA, poxtA and cfr) that confer resistance to linezolid and florfenicol have been detected globally in various sources. Linezolid is a last-resort antimicrobial used in human clinical settings, and florfenicol is commonly used in veterinary clinical settings. The present study sought to evaluate the potential of florfenicol in veterinary use to select for linezolid-resistant bacteria. The growth and fitness of linezolid-resistant bacteria harbouring mobile linezolid-resistance genes were assessed in the presence and absence of florfenicol using Enterococcus faecalis and Enterococcus faecium, respectively. The bacterial strains harboured wild and cloning plasmids carrying mobile linezolid-resistance genes, which reduced their susceptibility to linezolid and florfenicol. The acquisition of plasmids carrying mobile linezolid-resistance genes improved bacterial growth in the presence of florfenicol and conferred fitness costs in its absence. Florfenicol imposes a selection pressure on bacteria harbouring plasmids carrying mobile linezolid-resistance genes. Hence, the appropriate use of florfenicol in veterinary clinical settings is important to control the dissemination of mobile linezolid-resistance genes and to ensure the sustained effectiveness of linezolid against multidrug-resistant bacteria, including vancomycin-resistant enterococci in human clinical settings.
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Comparative genomics analysis of six Cutibacterium acnes strains isolated from contaminated platelet concentrates
More LessCutibacterium acnes is a bacterial skin commensal that is often isolated during routine testing of blood products like platelet concentrates (PCs). Due to the slow-growing nature of this bacterium in culture media, C. acnes contaminated PCs are often transfused into vulnerable patients before retrieval of these units can be initiated. This study aimed at obtaining the whole-genome sequence of six C. acnes isolates derived from contaminated PCs, comparing and assessing their genetic backgrounds. Furthermore, the whole genomes of the PC isolates were compared to clinical isolates obtained from different sites and types of infection. The results indicate that these PC isolates assessed belong to four phylotypes, namely IA, IB, II and III. Whole-genome comparisons identified differences in the virulence profiles of the isolates and provide a foundation for future studies aimed at evaluating the risk to transfusion patients by determining whether the expression of virulence factors is impacted in the PC storage environment.
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Novel hot spring Thermoproteota support vertical inheritance of ammonia oxidation and carbon fixation in Nitrososphaeria
More LessAerobic ammonia oxidation is crucial to the nitrogen cycle and is only known to be performed by a small number of bacterial lineages [ammonia-oxidizing bacteria (AOB)] and a single lineage of archaea belonging to the Nitrososphaeria class of Thermoproteota [ammonia-oxidizing Archaea (AOA)]. Most cultivated AOA originate from marine or soil environments, but this may capture only a limited subset of the full diversity of this clade. Here, we describe several genomes of AOA from metagenomic sequencing of a hot spring microbial mat, representing several poorly characterized basal lineages that may be important for understanding the early evolution of archaeal ammonia oxidation. These genomes include a novel genus most closely related to Nitrososphaera as well as novel species belonging to the genera Nitrosotenuis, Nitrososphaera and Nitrosotalea. Furthermore, the distributions and phylogenetic relationships of key metabolic genes support a history of vertical inheritance of ammonia oxidation and carbon fixation from the last common ancestor of crown group AOA.
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- Technical Resources
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Genome sequence of antibiotic-resistant Klebsiella quasipneumoniae FSFC0558: a novel sequence type (ST8212)
More LessKlebsiella quasipneumoniae are Gram-negative bacteria of the family Enterobacteriaceae, distinguished from other members of the Klebsiella genus through a chromosomally encoded extended spectrum β-lactamase, blaOKP . Here, we report a hybrid assembled genome of a novel sequence type of K. quasipneumoniae subspecies similipneumoniae isolated from a faecal sample of a patient with sepsis.
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- Pedagogy
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Opportunities for microbiology citizen science: lessons learnt from three pilot projects
More LessCitizen science (CS) is the partnering of professional scientists and members of the public to answer real-world scientific questions. There has been huge growth in CS over the past two decades, but uptake in microbiology research has, thus far, been relatively limited. In the first part of this article, we discuss how CS is well aligned with microbiology research: sample collection methods can be simplified and used in a variety of environments; projects are expected to appeal to participants as topics are likely to be of relevance to people’s lives and interests, including the health of people and the environment; and projects can also lead to real-world impact, including the identification of new drugs or biotechnological solutions. In the second part of this article, we present our reflections on three pilot projects we have recently completed. In order for the field to grow, people need to share both their successes as well as the challenges they have faced, so that others wanting to use the method can learn from these experiences. We share simplified sampling methods for yeast strains from home brewing and baking, antimicrobial-resistant bacteria on home-grown produce and microbes on chopping boards. However, participation in our projects was limited by a range of factors, including time available and resourcing, which impacted on our ability to generate new knowledge and wider impacts. We provide recommendations for others wishing to run microbiology CS projects, including ensuring appropriate resourcing and considering the ethical implications of projects.
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Prevalence and resistance pattern of uropathogens from community settings of different regions: an experience from India
Sarita Mohapatra, Rajashree Panigrahy, Vibhor Tak, Shwetha J. V., Sneha K. C., Susmita Chaudhuri, Swati Pundir, Deepak Kocher, Hitender Gautam, Seema Sood, Bimal Kumar Das, Arti Kapil, Pankaj Hari, Arvind Kumar, Rajesh Kumari, Mani Kalaivani, Ambica R., Harshal Ramesh Salve, Sumit Malhotra and Shashi Kant
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