Effect of storage temperature and flash-freezing on salivary microbiota profiles based on 16S rRNA-targeted sequencing

16S rRNA sequencing in chronic dacryocystitis

CLINICAL RELEVANCE

The pathogenesis of chronic dacryocystitis (CDC) is associated with a variety of bacteria. Investigating microflora has the potential to provide a theoretical basis for preventing and treating CDC.

BACKGROUND

16S rRNA sequencing is a sequence-based bacterial analysis. The application of 16S rRNA sequencing in CDC is rarely reported.

METHODS

A case-control study of infected and healthy eyes diagnosed as CDC patients was conducted. Seventy-eight patients were divided into A (conjunctival sac secretions from healthy eyes), B (conjunctival sac secretions from affected eyes), and C (lacrimal sac secretions from affected eyes) groups. The flora of samples was analysed with 16S rRNA sequencing, and the data was analysed using QIIME, R, LefSE and other software. The potential functions were analysed by PICRUSt.

RESULTS

A total of 1440 operational taxonomic units (OTUs) were obtained, 139 specific to group A, 220 specific to group B, and 239 specific to group C. There was no significant difference in α index between the three groups. The beta diversity and grouping analysis data indicated that the three groups of flora were similar in species richness and diversity, but there were some differences in composition. In group A, the abundance of Pseudomonadaceae, Chlorobacteria, Moraceae, Staphylococcaceae, Bacillariophyceae, Immunobacterium spp. and Bacillus spp. was higher; in group B, the abundance of Burkholderiaceae, Sphingomonas, Rhizobia, Stalked Bacteria, Sphingomonadaceae, Enterobacteriaceae, Shortwaveomonas spp. was higher; in group C, the abundance of Streptococcus digestiveis, Propionibacterium, Enterobacteriaceae, Anaerobacteriaceae, Propionibacteriaceae, Bacillus spp. Neisseria spp. and Shortactomonas spp. was higher. Six pathways were identified to assess the potential microbial functions.

CONCLUSION

Alterations in the microbiota of the conjunctiva and lacrimal sac are associated with the pathogenesis of CDC, which may provide certain guidance for antibiotic treatment of CDC.

Development of an in-home screening tool for canine periodontitis

Periodontal disease is a common condition in dogs but frequently goes unnoticed by owners. The objective of this study was to develop and validate an in-home screening tool for the detection of canine periodontitis based on the identification of bacterial biomarkers in supragingival plaque. A series of studies were undertaken to establish methods for collecting dental plaque and stabilising its bacterial profile. These were used by owners to collect supragingival plaque samples in a home setting from their dogs (n = 127) whose periodontal health state had been determined by a veterinarian. Samples were screened for the presence of a bacterial biomarker of periodontitis using quantitative polymerase chain reaction (qPCR). Evaluation of six swabs (10 samples each) for plaque collection indicated the CytoSoft™ cytology brush yielded the highest amount of bacterial DNA, determined using a universal bacterial qPCR assay. Evaluation of six stabilisation methods (10-11 samples each) showed no significant differences between air-dried swabs stored at ambient temperatures and those maintained at -80°C for 5 days. qPCR data from plaque samples collected by owners indicated an accuracy at predicting disease of 80.9 %, a specificity of 80.0 % and a sensitivity of 80.9 %. Collection of supragingival plaque by dog owners using the CytoSoft™ cytology brush and postage to a laboratory for qPCR analysis is a practical method of screening for canine periodontitis. The simple, cost-effective method is a viable proposition to enable the detection of periodontitis in client-owned dogs ultimately improving their oral health and quality of life.

Optimal storage time and temperature of human oral samples to minimize microbiome changes: A scoping review

Improper storage times and temperatures negatively impact the quality of biospecimens with oral microbiomes. This study aimed to determine the optimal storage time and temperature for maintaining the integrity of human dental plaque and saliva samples' microbial profiles. A comprehensive search yielded 5433 studies, with 12 meeting inclusion criteria. The number of studies on the storage time and temperature for plaque or saliva samples was extremely limited, with large variability in study designs and analytical tools. The best approach for dental plaque and saliva samples was to immediately freeze fresh specimens at - 80 °C or lower until DNA extraction, with a recommended storage time not exceeding 1-2 years, regardless of temperature. Checkerboard DNA-DNA hybridization-based studies suggested dental plaque storage at - 20 °C for 6 months, but a shorter duration was advised. Based on 16 S rRNA gene sequencing studies, dental plaque samples could be stored at - 80 °C for 6 months in 75 % ethanol or Bead Solution. Dental plaque and saliva samples could be stored at room temperature for 1-2 weeks without significant microbiome changes if stored in appropriate media. Further well-designed randomized controlled studies with longer-storage duration are necessary to establish more definitive guidelines.

Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana)

Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.

Pre-Analytical Factors Affecting Extracellular DNA in Saliva

Salivary DNA is widely used for genetic analyses because of its easy collection. However, its extracellular fraction in particular, similar to the extracellular DNA (ecDNA) in plasma, could be a promising biomarker for oral or systemic diseases. In contrast to genetics, the quantity of salivary ecDNA is of importance and can be affected by the pre-analytical processing of samples, but the details are not known. The aim of our study was to analyze the effects of centrifugation and freezing of saliva on the concentration of ecDNA in saliva. Fifteen healthy volunteers, free of any known systemic or oral diseases, were asked to collect unstimulated saliva samples. Aliquots were centrifuged at 1600× g and frozen or directly processed. The fresh or thawed cell-free saliva samples underwent subsequent centrifugation at 16,000× g. The supernatants were used for DNA isolation and quantification using fluorometry and real-time PCR. While freezing had minimal effects on the salivary ecDNA concentration, another centrifugation step decreased ecDNA considerably in both fresh and frozen samples (by 97.8% and 98.4%, respectively). This was mirrored in the quantitative PCR targeting a nuclear (decrease by 93.5%) and mitochondrial (decrease by 97.7%) ecDNA sequence. In conclusion, in this first study focusing on the technical aspects of salivary ecDNA quantitation, we show that, regardless of its subcellular origin, the concentration of ecDNA in saliva is mainly affected by additional centrifugation and not by the freezing of centrifuged cell-free saliva samples. This suggests that most salivary ecDNA likely is associated with cell debris and apoptotic bodies. Which fraction is affected by a particular disease should be the focus of further targeted studies.

Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques

Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.