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Background Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon sequencing for quantification of bacterial spores in a canned food matrix and for monitoring the outgrowth of spoilage microbiota in a ready-to-eat food matrix. Results The detection limit of bar-coded 16S rRNA amplicon sequencing was determined for the number of bacterial spores in a canned food matrix. Analysis of samples from a canned food matrix spiked with a mixture of equinumerous spores from the thermophiles, Geobacillus stearothermophilus and Geobacillus thermoglucosidans, and the mesophiles, Bacillus sporothermodurans, Bacillus cereus, and Bacillus subtilis, led to the detection of these spores with an average limit of 2 × 102 spores ml−1. The data were normalized by setting the number of sequences resulting from DNA of an inactivated bacterial species, present in the matrix at the same concentration in all samples, to a fixed value for quantitative sample-to-sample comparisons. The 16S rRNA amplicon sequencing method was also employed to monitor population dynamics in a ready-to-eat rice meal, incubated over a period of 12 days at 7 °C. The most predominant outgrowth was observed by the genera Leuconostoc, Bacillus, and Paenibacillus. Analysis of meals pre-treated with weak acids showed inhibition of outgrowth of these three genera. The specificity of the amplicon synthesis was improved by the design of oligonucleotides that minimize the amplification of 16S rRNA genes from chloroplasts originating from plant-based material present in the food. Conclusion This study shows that the composition of complex spoilage populations, including bacterial spores, can be monitored in complex food matrices by bar-coded amplicon sequencing in a quantitative manner. In order to allow sample-to-sample comparisons, normalizations based on background DNA are described. This method offers a solution for the identification and quantification of spoilage microbiota, which cannot be cultivated under standard laboratory conditions. The study indicates variable detection limits among species of bacterial spores resulting from differences in DNA extraction efficiencies. Electronic supplementary material The online version of this article (doi:10.1186/s40168-015-0096-3) contains supplementary material, which is available to authorized users.

Infectious disease in the developing world continues to represent one of the greatest challenges facing humanity. Every year over a million children suffer and die from the sequela of enteric infections, and in 2008 was estimated almost 2.7 million (UNAIDS 2009 update) adults and children became infected with human immunodeficiency virus (HIV). While oral rehydration therapy for diarrhea and antiretrovirals (ARV) for HIV are critical, there is a place for adjunctive therapies to improve quality of life. The importance of the human microbiota in retaining health is now recognized, as is the concept of replenishing beneficial microbes through probiotic treatments. Studies have shown that probiotics can reduce the duration of diarrhea, improve gut barrier function, help prevent bacterial vaginosis (BV) and enhance immunity even in HIV-infected subjects. However, many issues remain before the extent of probiotic benefits can be verified, and their application to the developing world realized. This consensus report outlines the potential probiotic, and to a lesser extent prebiotic, applications in resource disadvantaged settings, and recommends steps that could bring tangible relief to millions of people. The challenges to both efficacy and effectiveness studies in these settings include a lack of infrastructure and funding for scientists, students and research projects in developing countries; making available clinically proven probiotic and prebiotic products at affordable prices; and undertaking appropriately designed clinical trials. We present a roadmap on how efficacy studies may be conducted in a resource disadvantaged setting among persons with chronic diarrhea and HIV. These examples and the translation of efficacy into effectiveness are described. © 2011 Landes Bioscience. Chemicals/CAS: glutamine, 56-85-9, 6899-04-3; retinol, 68-26-8, 82445-97-4; zinc, 14378-32-6, 7440-66-6