AREAS COVERED: The differential bacterial composition identified from BEVs isolated from biofluids between patients and healthy controls may be valuable for detecting diseases. Therefore, BEVs may serve as novel diagnostic markers. Literature search on PubMed and Google Scholar databases was conducted. In this special report, we outline the commonly used approach for investigating BEVs in biofluids, the 16S ribosomal RNA gene sequencing of V3-V4 hypervariable regions, and the recent studies exploring the potential of BEVs as biomarkers for various diseases.
EXPERT OPINION: The emerging field of BEVs offers new possibilities for the diagnosis of various types of diseases, although there remain issues that need to be resolved in this research area to implement BEVs in clinical applications. Hence, it is important for future studies to take these challenges into consideration when investigating the diagnostic value of BEVs.
METHODS: We collected classroom dust from 24 junior high schools in three geographically distanced areas in Malaysia (Johor Bahru, Terengganu and Penang), and conducted culture-independent high-throughput microbiome and untargeted metabolomics/chemical profiling.
RESULTS: 1290 students were surveyed for asthma symptoms (wheeze). In each centre, we found significant variation in the prevalence of wheeze among schools, which could be explained by personal characteristics and air pollutants. Large-scale microbial variations were observed between the three centres; the potential protective bacteria were mainly from phyla Actinobacteria in Johor Bahru, Cyanobacteria in Terengganu and Proteobacteria in Penang. In total, 2633 metabolites and chemicals were characterised. Many metabolites were enriched in low-wheeze schools, including plant secondary metabolites flavonoids/isoflavonoids (isoliquiritigenin, formononetin, astragalin), indole and derivatives (indole, serotonin, 1H-indole-3-carboxaldehyde), and others (biotin, chavicol). A neural network analysis showed that the indole derivatives were co-occurring with the potential protective microbial taxa, including Actinomycetospora, Fischerella and Truepera, suggesting these microorganisms may pose health effects by releasing indole metabolites. A few synthetic chemicals were enriched in high-wheeze schools, including pesticides (2(3H)-benzothiazolethione), fragrances (2-aminobenzoic acid, isovaleric acid), detergents and plastics (phthalic acid), and industrial materials (4,4-sulfonyldiphenol).
CONCLUSIONS: This is the first association study between high-throughput indoor chemical profiling and asthma symptoms. The consistent results from the three centres indicate that indoor metabolites/chemicals could be a better indicator than the indoor microbiome for environmental and health assessments, providing new insights for asthma prediction, prevention and control.
BACKGROUND: Microbial screening is required for all cord blood units (CBUs). Four gram-positive contaminants were documented to survive cryopreservation poorly and isolation of other contaminants were reported.
METHODS: Forty-eight contaminated CBUs detected with either Staphylococcus epidermidis, Corynebacterium species, Peptostreptococcus or Streptococcus species before cryopreservation were used in this study. CBUs were processed, DMSO-infused and microbial screened before cryopreservation. Post-thaw microbial screening was achieved using 1 and 10 ml inoculants in BACTEC culture bottles. Positive bottles were subjected for microbial identification and results were compared with those from pre-freeze.
RESULTS: A higher rate of microbial contamination was found using the 10 ml inoculant. Screening of 11 CBUs did not detect any contaminants while 30 CBUs screened detected more than one unknown contaminants and majority of contaminants were identified to be gram-negative species.
CONCLUSION: A higher inoculation volume used at post-thaw for microbial screening improves contamination detection but leads to the loss of precious cord blood. Some contaminants did not survive cryopreservation or were not identified due to their low microbial levels. Contrasting contaminants found at post-thaw suggest the improvements made in detection and identification of contaminants over the years.
METHODS: Oral swab samples were collected from smokers, smokeless tobacco users, and healthy controls (n = 44). Microbial DNA was extracted and the 16S rRNA gene profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Differentially abundant taxa were identified using DESeq2, while functional metagenomes based on KEGG orthology abundance were inferred using LIMMA.
RESULTS: A significantly higher microbial diversity was observed in smokeless tobacco users and smokers relative to controls (P 1.5; BH adj P