The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users’ own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org.

Fermented food products are widely consumed for their nutritional and health-promoting properties, earning them a central place in diets around the globe. However, these foods can present a paradox, as they have the potential to harbor not only beneficial probiotics but also antibiotic-resistant (AR) microbes and genes. The impact of AR microbes and genes in fermented foods has far-reaching implications, such as potential effects on human health, repercussions in the food industry, and environmental consequences. An in-depth analysis of AR microbes and genes in fermented foods, including dairy products, fermented fruits and vegetables, meat products, and beverages, would provide insights into the extent and ramifications of the issue with these foods. Therefore, this review systematically presents the status of AR in fermented foods, with a particular focus on AR bacteria and genes within this category of food products. The review also highlights the complexities of AR in fermented foods, emphasizing the role of bacterial adaptation during the fermentation process and the dynamics of bacterial gene transfer. Various factors contributing to AR microbes and genes are brought into focus, including intrinsic resistance among bacteria in fermented foods and the potential risk of contamination with pathogenic bacteria. Moreover, this review presents a range of mitigation strategies, from the development of novel antimicrobials to advances in fermentation technology and regulatory control. This comprehensive perspective on the intricate interplay between AR and fermented food will potentially pave the way for more targeted research and mitigation strategies in this critical area.

Preservation at ultra-low temperatures has been a gold standard for long-term storage of many types of clinical specimens including the SARS-CoV-2 virus. The frozen specimens can be easily transported and tested later. In addition, de-identified frozen remnant samples are resources for many preclinical or clinical studies. It is therefore crucial to understand whether freeze and thaw cycles (FTCs) can adversely affect SARS-CoV-2 test performance when frozen samples are tested. Some early studies suggest that the FTCs increased the cycles threshold (Ct) of RT-PCR indicating the potential degradation of the SARS-CoV-2 nucleic acid after FTCs, while the others did not report any significant changes in the SARS-CoV-2 nucleic acids after the FTCs. Moreover, the impact of FTCs on the performance of the SARS-CoV-2 antigen test is scarcely reported. In this study, we performed paired nucleic acid and rapid antigen tests on the same samples to investigate and directly compare how FTCs affect the performance of two types of tests. Both inactivated viral culture fluid samples and clinical remnant samples were studied. Our results showed that FTCs had minimal negative effects on the performance of the rapid SARS-CoV-2 antigen test, and the test results remained largely consistent throughout the FTCs, whereas the Ct values of RT-PCR increased with the increase of the FTC numbers. In addition, our data also demonstrated that the SARS-CoV-2 is preserved better in VTM than PBS during FTCs in regard to nucleic acid testing.

Abstract:A technique for enhancing decompressed fingerprint image using Wiener2 filter is proposed. First compression is done by sparse representation. Compression of fingerprint is necessary for reducing the memory consumption and efficient transfer of fingerprint images. This is very essential for the application which includes access control and forensics. So the fingerprint image is compressed using sparse representation. In this technique, first dictionary is constructed for patches of fingerprint images. Then a fingerprint is selected and the coefficients are obtained and encoded. Thus the compressed fingerprint is obtained. But when the fingerprint is reconstructed, it is affected by noise. So Wiener2 filter is used to filter the noise in the image. The ridge and bifurcation count is extracted from decompressed and enhanced fingerprints. The experiment result shows that the enhanced fingerprint image preserves more bifurcation than decompressed fingerprint image. The future analysis can be considered for preserving ridges.

Advances in metabolomics research have yielded an avenue for utilizing this laboratory-based modality as a platform for clinical diagnosis, identification of novel biomarkers, and longitudinally monitoring the health status of individuals from normal physiological and pathophysiological perspectives. This chapter provides insight on the application of urinalysis in health and disease from the standpoint of deciphering a larger span of metabolite and biomarker identification using metabolomics, specifically focusing on infectious diseases, oncology, metabolic, and inflammatory diseases in humans.

Among the animal derived food products, contamination of poultry eggs, and egg shell surface is one of the major causes for foodborne salmonellosis in the United States. As a means of reducing the pathogen transfer to the internal egg contents, polysaccharide-based coatings containing antimicrobial phytochemicals could potentially serve as a biocontrol strategy for shelled egg products. The current study investigated the efficacy of four GRAS (Generally Recognized as Safe)-status plant-derived compounds, namely, caproic acid (CAO), caprylic acid (CAY), linalool (LIN) and cuminaldehyde (CUM), as pectin-based coating treatments, individually or in combination, for reducing Salmonella Heidelberg (SH) on shell eggs. A three-strain mixture of SH (~8.0 log CFU in 50 μL inoculum) was spot-inoculated on surface sterilized white-shelled eggs. Eggs were evenly coated with either pectin-based treatments of CAO (1%), CAY (1%), LIN (1%) and CUM (1%), individually, or a combination of 4 phytochemicals (COMB- each phytochemical at 0.5% v/v level of inclusion). The treated eggs were stored at 4°C and SH counts were enumerated on days 0, 1, 3, 5, 7, 14, and 21 of storage. The study was replicated thrice, 3 eggs/treatment/day time point, and the data were analyzed using two-way ANOVA with significance tested at p < 0.05. On day 0, pectin-coated control eggs had ~7.6 log CFU of SH/egg. At the end of refrigerated storage (day 21), pectin-based coating of CAO and CAY at 1% level reduced SH by 2.0–2.5 log CFU/egg (P < 0.05) when compared to controls. In addition, the CUM and LIN based coatings produced 3.0 log and 3.9 log reduction, respectively, in SH counts on eggs by day 21 of storage. Among the treatments with phytochemical combinations, COMB1 [pectin (2%) + Caprylic acid, caproic acid and cuminaldehyde (each at 0.5% level)] was found to be most effective, reducing SH counts to 2.5–3.3 log CFU/egg from day 0 through day 14, and by the end of storage period (day 21), a 3.5 log CFU reduction/egg (p < 0.05) compared to untreated controls. Morphological studies of treated eggs using atomic force microscopy (AFM) have shown that the roughness of eggs can be influenced by a combination of various compounds. Results indicate the potential efficacy of the aforesaid phytochemicals in reducing SH on shell eggs; however, further studies investigating their industrial feasibility and effects on sensory attributes of eggs are warranted.

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Fermented food products are widely consumed for their nutritional and health-promoting properties earning them a central place in diets around the globe. However, these foods can present a paradox, as they have the potential to harbor not only beneficial probiotics but also antibiotic-resistant (AR) microbes and genes. The impact of AR in fermented foods has far-reached implications, such as its potential effects on human health, repercussions in the food industry, and environmental consequences. An in-depth analysis of AR in fermented foods, including dairy products, fermented fruits and vegetables, meat products, and beverages, would provide insights into the extent and ramifications of the issue with these foods. Therefore, this review systematically presents the status of AR in fermented foods, with a particular focus on AR bacteria and genes within this category of food products. The review also highlights the complexities of AR in fermented foods, emphasizing the role of bacterial adaptation during the fermentation process and the dynamics of bacterial gene transfer. Various contributing factors to AR are brought into focus, including intrinsic resistance among bacteria in fermented foods and the potential risk of contamination with pathogenic bacteria. Moreover, this review presents a range of mitigation strategies, from the development of novel antimicrobials to advances in fermentation technology and regulatory control. This comprehensive perspective on the intricate interplay between AR and fermented food will potentially pave the way for more targeted research and mitigation strategies in this critical area.