Diagnostic performance of Ion 16S metagenomics kit and Ion reporter metagenomics workflow for bacterial pathogen detection in culture-negative clinical specimens from sterile sources

Impact of Polyonchobothrium magnum on health and gut microbial ecology of African catfish (Clarias gariepinus): Insights from morphological, molecular, and microbiological analyses

Parasites pose significant challenges to aquaculture and fisheries industries. Our study focuses on the Polyonchobothrium magnum and African catfish to address a potential health issue in aquaculture, explore host-parasite interactions that can help develop effective management practices to ensure fish health and industry sustainability. P. magnum was isolated from the stomach of African catfish (Clarias gariepinus) as the primary site of infection, with a prevalence of 10%. Most affected fish were heavily infected (8 out of 10). Infection was confirmed by sequencing the PCR-targeted region of the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene, along with light and scanning electron microscopes. The parasite had an elongated scolex with deep bothria, a prominent apical disc wider than the scolex itself, and a four-lobed appearance. The scolex contained a central rostellum divided into two semicircles, bearing 26-30 hooks, with an average of 28. The apical disc had large hooks arranged in four quadrants, with 6-8 hooks each, averaging 7 per quadrant. No neck was observed. Phylogenetic analysis of our sequence showed a 100% match with isolates from Guangzhou, China. In infected fish, the anterior kidney showed increased expression levels of nuclear factor kappa B and lysozyme, but decreased levels of in major histocompatibility complex antigen II. Plasma analysis revealed a significant drop in superoxide dismutase, a rise in interleukin-1 beta, and lower IgM levels compared to non-infected controls. Non-infected fish displayed greater gut microbiota diversity, with dominant families including Moraxellaceae, Enterobacteriaceae, Fusobacteriaceae, and Caulobacteraceae, and prevalent genera such as Acinetobacter, Cetobacterium, and Brevundimonas. In contrast, infected fish exhibited very low diversity, with significantly higher proportions of Enterobacteriaceae (45.99%) and Aeromonadaceae (41.79%) compared to non-infected fish, which had 13.76% and 3.64% respectively. Cetobacterium somerae was prevalent in non-infected fish, while infected fish harboured Aeromonas fluvialis, Plesiomonas shigelloides, and Gallaecimonas xiamenensis. Overall, P. magnum disrupted the immune status and gut microbiota of the host, thereby impacting its health.

Documenting the microbiome diversity and distribution in selected fleas from South Africa with an emphasis on the cat flea, Ctenocephalides f. felis

The factors that influence parasite associated bacterial microbial diversity and the geographic distributions of bacteria are not fully understood. In an effort to gain a deeper understanding of the relationship between the bacterial diversity of Ctenocephalides fleas and host species and the external environment, we conducted a metagenetic analysis of 107 flea samples collected from 8 distinct sampling sites in South Africa. Pooled DNA samples mostly comprising of 2 or 3 individuals sampled from the same host, and belonging to the same genetic cluster, were sequenced using the Ion PGM™ Hi-Q™ Kit and the Ion 316™ Chip v2. Differences were detected in the microbiome compositions between Ctenocephalides felis, Ctenocephalides canis and Ctenocephalides connatus. Although based on a small sample, C. connatus occurring on wildlife harboured a higher bacterial richness when compared to C. felis on domestic animals. Intraspecific differences in the microbial OTU diversity were detected within C. f. felis that occurred on domestic cats and dogs. Different genetic lineages of C. f. felis were similar in microbial compositions but some differences exist in the presence or absence of rare bacteria. Rickettsia and Bartonella OTU's identified in South African cat fleas differ from those identified in the USA and Australia. Intraspecific microbial compositions also differ across geographic sampling sites. Generalized dissimilarity modelling showed that temperature and humidity are potentially important environmental factors explaining the pattern obtained.

Oral microbial dysbiosis in patients with periodontitis and chronic obstructive pulmonary disease

Background

Oral microbiota is closely related to the homeostasis of the oral cavity and lungs. To provide potential information for the prediction, screening, and treatment strategies of individuals, this study compared and investigated the bacterial signatures in periodontitis and chronic obstructive pulmonary disease (COPD).

Materials and methods

We collected subgingival plaque and gingival crevicular fluid samples from 112 individuals (31 healthy controls, 24 patients with periodontitis, 28 patients with COPD, and 29 patients with both periodontitis and COPD). The oral microbiota was analyzed using 16S rRNA gene sequencing and diversity and functional prediction analysis were performed.

Results

We observed higher bacterial richness in individuals with periodontitis in both types of oral samples. Using LEfSe and DESeq2 analyses, we found differentially abundant genera that may be potential biomarkers for each group. Mogibacterium is the predominant genus in COPD. Ten genera, including Desulfovibrio, Filifactor, Fretibacterium, Moraxella, Odoribacter, Pseudoramibacter Pyramidobacter, Scardovia, Shuttleworthia and Treponema were predominant in periodontitis. Bergeyella, Lautropia, Rothia, Propionibacterium and Cardiobacterium were the signature of the healthy controls. The significantly different pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) between healthy controls and other groups were concentrated in genetic information processing, translation, replication and repair, and metabolism of cofactors and vitamins.

Conclusions

We found the significant differences in the bacterial community and functional characterization of oral microbiota in periodontitis, COPD and comorbid diseases. Compared to gingival crevicular fluid, subgingival plaque may be more appropriate for reflecting the difference of subgingival microbiota in periodontitis patients with COPD. These results may provide potentials for predicting, screening, and treatment strategies for individuals with periodontitis and COPD.

Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis

The environment of healthcare institutes (HCIs) potentially affects the internal microecology of medical workers, which is reflected not only in the well-studied gut microbiome but also in the more susceptible oral microbiome. We conducted a prospective cross-sectional cohort study in four hospital departments in Central China. Oropharyngeal swabs from 65 healthcare workers were collected and analyzed using 16S rRNA gene amplicon sequencing. The oral microbiome of healthcare workers exhibited prominent deviations in diversity, microbial structure, and predicted function. The coronary care unit (CCU) samples exhibited robust features and stability, with significantly higher abundances of genera such as Haemophilus, Fusobacterium, and Streptococcus, and a lower abundance of Prevotella. Functional prediction analysis showed that vitamin, nucleotide, and amino acid metabolisms were significantly different among the four departments. The CCU group was at a potential risk of developing periodontal disease owing to the increased abundance of F. nucleatum. Additionally, oral microbial diversification of healthcare workers was related to seniority. We described the oral microbiome profile of healthcare workers in different clinical scenarios and demonstrated that community diversity, structure, and potential functions differed markedly among departments. Intense modulation of the oral microbiome of healthcare workers occurs because of their original departments, especially in the CCU.