Clinical data on the types of respiratory pathogens which are most frequently engaged in respiratory co-infections of children and adults are lacking. We analyzed 10 years of data on a total of over 15,000 tests for 16 viral and bacterial pathogens detected in clinical samples at the University Hospital of Augsburg, Germany. Co-infection frequencies and their seasonal patterns were examined using a proportional distribution model. Co-infections were detected in 7.3% of samples, with a higher incidence in children and males. The incidence of interbacterial and interviral co-infections was higher than expected, whereas bacterial-viral co-infections were less frequent. H. influenzae, S. pneumoniae, rhinovirus, and respiratory syncytial virus (RSV) were most frequently involved. Most co-infections occurred in winter, but distinct summer peaks were also observed, which occurred even in children, albeit less pronounced than in adults. Seasonality of respiratory (co-)infections decreased with age. Our results suggest to adjust existing testing strategies during high-incidence periods.

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ObjectivesWe evaluated how storing vaginal samples at room temperature in stabilising solutions versus immediate freezing affects 16S rRNA gene amplicon sequencing-based microbiota studies, aiming to simplify home and field collection.
METHODS: Twenty participants self-collected six mid-vaginal swabs that were stored in two nucleic acid preservatives (three in modified Solution C2 (Qiagen) and three in Amies/RNALater (Sigma)) in January-February 2016. From each set, two were immediately frozen (-80°C) and one was shipped to the University of Idaho (Moscow, Idaho) with return shipping to the Institute for Genome Sciences (Baltimore, Maryland). Amplicon sequencing of the 16S rRNA gene was used to characterise the vaginal microbiota, VALENCIA was used to assign community state types (CSTs), and quantitative PCR (qPCR) of 16S rRNA genes was used to estimate bacterial abundance. Cohen\'s Kappa statistic was used to assess within-participant agreement. Bayesian difference of means models assessed within-participant comparisons between shipped and immediately frozen samples.
RESULTS: There were 115 samples available for analysis. Average duration of transit for shipped samples was 8 days (SD: 1.60, range: 6-11). Within-participant comparisons of CSTs between shipped and immediately frozen samples revealed complete concordance (kappa: 1.0) for both preservative solutions. No significant differences comparing shipped and immediately frozen samples were found with taxon-level comparisons or bacterial abundances based on pan-bacterial qPCR.
CONCLUSIONS: Short-term room temperature shipping of vaginal swabs placed in stabilising solutions did not affect vaginal microbiota composition. Home collection with mail-in of vaginal samples may be a reasonable approach for research and clinical purposes to assess the vaginal microbiota.

BACKGROUND: Almonds have prebiotic potential to maintain gut health and regulate glycaemia. Western studies have shown their positive effects on preventing non-communicable diseases like diabetes and cardiovascular diseases. However, there is a lack of research involving Asian Indians, who have a higher predisposition to diabetes due to their unique \'Asian phenotype\'. Therefore, this study aims to evaluate the impact of almond supplementation on glycaemic control and gut health in adults with pre-diabetes in rural India through a randomised clinical trial.
METHODS: A parallel cluster randomised controlled trial with 178 participants with pre-diabetes (assigned 1:1) aged 20-50 years, of both genders, with a body mass index of 18.9-25 kg/m2, will be conducted in rural areas of Chikkaballapur, Kolar and Rural Bangalore districts in India. The intervention group will receive 56 g of almonds as mid-morning snacks for 16 weeks, while the control group will receive cereal/pulse-based traditional isocaloric snacks under the closed supervision of the study investigators. The primary outcome of the study is HbA1c measured at the 16th week. The secondary outcomes-anthropometry, clinical and other biochemical parameters-will be measured at 0th, 8th and 16th weeks, and a subgroup of 120 participants will undergo gut health analysis. Glucagon-like peptide 1 analysis will be conducted on 30 participants at 0th and 16th weeks. Statistical analysis will be performed using SPSS for Windows V.27.0, and both intention-to-treat and per-protocol analyses will be conducted.
BACKGROUND: Ethics approval was obtained from the Institutional Ethics Committee at Ramaiah Medical College, Bangalore, Karnataka, India (DRPEFP7672021). We will obtain the informed written consent of the participants prior to screening and enrolling them in the study. Results from this trial will be disseminated through publication in peer-reviewed journals and scientific gatherings.
BACKGROUND: Clinical Trial Registry of India (CTRI/2023/03/050421).

OBJECTIVE: To compare the subgingival microbiota of patients receiving supportive periodontal care (SPC) with and without subgingival instrumentation, over 2 years.
METHODS: This study was a randomized clinical trial that included 62 participants (50.97 ± 9.26 years old; 40 females) who completed non-surgical periodontal therapy. Participants were randomly assigned to receive oral prophylaxis with oral hygiene instructions alone (test) or in combination with subgingival instrumentation (control) during SPC. Pooled subgingival biofilm samples were obtained from four sites per patient at SPC baseline and at 3, 6, 12, 18, and 24 months. Real-time polymerase chain reaction was used for absolute quantification of Eubacteria and the target bacteria Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. Data were analysed using generalized estimating equations, taking into consideration the clustering of observations within individuals.
RESULTS: No significant differences were found between the experimental groups regarding the mean counts of Eubacteria and target bacteria, as well as the periodontal parameters at the sampled sites. Although significant variability in bacterial counts was present during SPC, all counts after 2 years were not statistically different from those at baseline. Bacterial counts were associated with the presence of plaque, bleeding on probing, mean probing depth ≥3 mm, and follow-up period.
CONCLUSIONS: SPC with or without subgingival instrumentation can result in comparable subgingival microbiological outcomes.
BACKGROUND: clinicaltrials.gov: NCT01598155 (https://clinicaltrials.gov/study/NCT01598155?intr=supragingival%20control&rank=4#study-record-dates).

Constructing metagenome-assembled genomes (MAGs) from complex metagenomic samples involves a series of bioinformatics operations, each requiring deep bioinformatics knowledge. Here, we present a protocol for constructing MAGs and conducting functional profiling to address biological questions. We describe steps for system configuration, data downloads, read processing, removal of human DNA contamination, metagenomic assembly, and statistical quality assessment of the final assembly. Additionally, we detail procedures for the construction and refinement of MAGs, as well as the functional profiling of MAGs.

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The human gut microbiota comprises various microorganisms engaged in intricate interactions among themselves and with the host, affecting its health. While advancements in omics technologies have led to the inference of clear associations between microbiome composition and health conditions, we usually lack a causal and mechanistic understanding of these associations. For modeling mechanisms driving the interactions, we simulated the organism\'s metabolism using in silico genome-scale metabolic models (GEMs). We used multi-objective optimization to predict and explain metabolic interactions among gut microbes and an intestinal epithelial cell. We developed a score integrating model simulation results to predict the type (competition, neutralism, mutualism) and quantify the interaction between several organisms. This framework uncovered a potential cross-feeding for choline, explaining the predicted mutualism between Lactobacillus rhamnosus GG and the epithelial cell. Finally, we analyzed a five-organism ecosystem, revealing that a minimal microbiota can favor the epithelial cell\'s maintenance.

Fusobacterium nucleatum is an oral commensal bacterium that can colonize extraoral tumor entities, such as colorectal cancer and breast cancer. Recent studies revealed its ability to modulate the immune response in the tumor microenvironment (TME), promoting cancer progression and metastasis. Importantly, F. nucleatum subsp. animalis was shown to bind to Siglec-7 via lipopolysaccharides, leading to a pro-inflammatory profile in human monocyte-derived dendritic cells. In this study, we show that F. nucleatum subsp. nucleatum RadD binds to Siglec-7 on NK cells, thereby inhibiting NK cell-mediated cancer cell killing. We demonstrate that this binding is dependent on arginine residue R124 in Siglec-7. Finally, we determine that this binding is independent of the known interaction of RadD with IgA. Taken together, our findings elucidate the targeting of Siglec-7 by F. nucleatum subsp. nucleatum RadD as a means to modulate the NK cell response and potentially promoting immune evasion and tumor progression.