The microbiome of the pelagic tunicate Dolioletta gegenbauri: a potential link between the grazing and microbial food web

Doliolids often form massive blooms during upwelling conditions in sub-tropical shelves. However, their trophic role, including their nutritious fecal pellets, in pelagic marine food webs remains poorly investigated. In this study, we performed three independent feeding experiments of cultured Dolioletta gegenbauri and used qPCR analysis and 16S rRNA metabarcoding to characterize the microbial community associated with full gut (FG) and empty (EG) doliolids, fresh (FP2Hrs) and senescing (FP24Hrs) fecal pellets, and the surrounding natural seawater (SW). Bacterial abundance (i.e., 16S rRNA gene copies) in EG samples was an order of magnitude lower than in SW and three orders lower than in FP24Hrs. Diversity analyses, based on the 16S rRNA metabarcoding data, supported a richer microbial community in SW, FP2Hrs, FP24Hrs, and FG samples. Furthermore, microbial community structure was determined by sample type, with FG samples appearing more similar to either FP2Hrs or FP24Hrs. These patterns resulted from the higher number of shared ASVs and consequently the contribution of similar major bacterial taxa (e.g., Rhodobacteraceae, Pirellulaceae). These observations support the hypothesis that there are significant ecological and trophic interactions between D. gegenbauri and the ocean microbiome. Predicted gene function recovered many genes related to key processes in the marine environment and supported greater similarity between FP2Hrs, FP24Hrs, and FG samples. These observations suggest that pelagic marine bacteria are utilized by D. gegenbauri to digest captured prey particles, and the subsequent release of fecal pellets supports the rapid proliferation of distinct microbial communities which likely influence key biogeochemical processes in the ocean.

Evaluation and modelling of the performance of an automated SARS-CoV-2 antigen assay according to sample type, target population and epidemic trends

The Lumipulse® G SARS-CoV-2 Ag assay performance was evaluated on prospectively collected saliva and nasopharyngeal swabs (NPS) of recently ill in- and outpatients and according to the estimated viral load. Performances were calculated using RT-PCR positive NPS from patients with symptoms ≤ 7 days and RT-PCR negative NPS as gold standard. In addition, non-selected positive NPS were analyzed to assess the performances on various viral loads. This assay yielded a sensitivity of 93.1% on NPS and 71.4% on saliva for recently ill patients. For NPS with a viral load > 103 RNA copies/mL, sensitivity was 96.4%. A model established on our daily routine showed fluctuations of the performances depending on the epidemic trends but an overall good negative predictive value. Lumipulse® G SARS-CoV-2 assay yielded good performance for an automated antigen detection assay on NPS. Using it for the detection of recently ill patient or to screen high-risk patients could be an interesting alternative to the more expensive RT-PCR.

Comparative analysis of DNA extraction and PCR product purification methods for cervicovaginal microbiome analysis using cpn60 microbial profiling

Background The microbiota of the lower female genital tract plays an important role in women’s health. Microbial profiling using the chaperonin60 (cpn60) universal target (UT) improves resolution of vaginal species associated with negative health outcomes compared to the more commonly used 16S ribosomal DNA target. However, the choice of DNA extraction and PCR product purification methods may bias sequencing-based microbial studies and should be optimized for the sample type and molecular target used. In this study, we compared two commercial DNA extraction kits and two commercial PCR product purification kits for the microbial profiling of cervicovaginal samples using the cpn60 UT. Methods DNA from cervicovaginal secretions and vaginal lavage samples as well as mock community standards were extracted using either the specialized QIAamp DNA Microbiome Kit, or the standard DNeasy Blood & Tissue kit with enzymatic pre-treatment for enhanced lysis of gram-positive bacteria. Extracts were PCR amplified using well-established cpn60 primer sets and conditions. Products were then purified using a column-based method (QIAquick PCR Purification Kit) or a gel-based PCR clean-up method using the QIAEX II Gel Extraction Kit. Purified amplicons were sequenced with the MiSeq platform using standard procedures. The overall quality of each method was evaluated by measuring DNA yield, alpha diversity, and microbial composition. Results DNA extracted from cervicovaginal samples using the DNeasy Blood and Tissue kit, pre-treated with lysozyme and mutanolysin, resulted in increased DNA yield, bacterial diversity, and species representation compared to the QIAamp DNA Microbiome kit. The column-based PCR product purification approach also resulted in greater average DNA yield and wider species representation compared to a gel-based clean-up method. In conclusion, this study presents a fast, effective sample preparation method for high resolution cpn60 based microbial profiling of cervicovaginal samples.

High Mycobacterium tuberculosis Bacillary Loads Detected by Tuberculosis Molecular Bacterial Load Assay in Patient Stool: a Potential Alternative for Nonsputum Diagnosis and Treatment Response Monitoring of Tuberculosis

This paper highlights the value of stool as a sample type for diagnosis of tuberculosis. While other studies have used DNA-based assays like the Xpert MTB/RIF and culture to detect Mycobacterium tuberculosis in stool, this is the first study that has applied TB-MBLA, an RNA-based assay, to quantify TB bacteria in stool.

Multi-Drug and β-Lactam Resistance in Escherichia coli and Food-Borne Pathogens from Animals and Food in Portugal, 2014–2019

Animal and food sources are seen as a potential transmission pathway of antimicrobial resistance (AMR) to humans. The aim of this study is to describe Campylobacter, Salmonella, and commensal Escherichia coli multi-drug resistance (MDR) in the food chain between 2014 and 2019 in Portugal. AMR surveillance data from food-producing animals and food were assessed. MDR relative frequencies were estimated by bacterial genus and year. AMR profiles were created using observations of resistance to antimicrobial classes from each isolate. Antimicrobial susceptibility testing results were clustered using k-modes. Clusters were described by population, AMR classification, β-lactamases, sample stage, sample type, season, and year. Overall, MDR was more prevalent for E. coli, ranging from 74–90% in animal and 94–100% in food samples. MDR was found to be more widespread in resistance profiles that were common among E. coli and Salmonella isolates and in those exclusively observed for E. coli, frequently including (fluoro)quinolones and cephalosporins resistance. β-lactam resistance was observed around 75% to 3rd/4th-generation cephalosporins in E. coli. Clusters suggest an escalating MDR behaviour from farm to post-farm stages in all bacteria and that Salmonella (fluoro)quinolones resistance may be associated with broilers. These findings support policy and decision making to tackle MDR in farm and post-farm stages.

​Faecal Consistency: A Measure of Gastrointestinal Parasitic Infections in Goats

Background: Gastrointestinal (GI) parasitism in goats is a serious and widely distributed problem. Diarrhoea, moderate or severe, though a result of various factors involving feed, fodder, seasons and state of gut physiology of digestion, is a common symptom in goats infested with GI parasites, the nematodes and coccidia. Intensity of diarrhoea corresponds to quantum and type of parasitism. Methods: In the present study, 1451 faecal samples collected from goats of different ages ( less than 3 M, greater than 3-6 M, greater than 6-12 M and greater than 12 M) were categorized as normal, lumpy and diarrheic based on their consistency and were processed for parasitic infections. The GI parasitic load was quantified by faecal eggs/oocysts counting (FEC and FOC) per gram of faeces through the modified Mac-master technique. Identification of parasites was based on the morphology of third-stage larvae procured by coproculture of randomly selected positive samples. FEC/FOC data (strongyle and coccidian), being skewed and uneven, were log-transformed to normalize. The transformed data [loge (100+n)] was analyzed statistically and results were interpreted. Result: Means of FEC and FOC in three type of faecal samples viz. normal, lumpy and diarrheic, were significantly different. Similarly, the effect of age on FEC and FOC was significant. The interaction between animals age × faecal sample type was significant in coccidian and non-significant in strongyle infection. The results were discussed to support the hypothesis that faecal consistency was a measure of coccidian and strongyle worm load in goats and can be a basis of targeted selective treatment.

SARS Antibody Testing in Children: Development of Oral Fluid Assays for IgG Measurements

We report on the first large-scale assessment of the suitability of oral fluids for detection of SARS-CoV-2 antibody obtained from healthy children attending school. The sample type (gingiva-crevicular fluid, which is a transudate of blood but is not saliva) can be self collected.

Islamic Work Ethic

Islamic work ethic (IWE) has been on the rise in the last 10 years and started to attract the attention of researchers. This study examines the development of IWE studies. In this direction, studies with the theme of Islamic work ethic were determined by examining the studies published in the Web of Science database. How IWE research has changed and developed was interpreted by the content analysis method. For that purpose, scientific publications were analyzed in terms of publication year, type of study, research design, sample type, sample size, data collection method, country where the study was carried out, variable types, antecedents and consequences of the IWE by descriptive review model When past studies were examined, it was seen that there was no study examining the literature on IWE in the context of content analysis. This study aims to fill this gap in the literature, to evaluate the situation of the IWE phenomenon in the literature, and to reveal which variables it is associated with.