The consumption of dietary supplements to treat health complications or to improve overall health conditions has become a globally increasing trend that leads to the development of a large number of health-related novel products and expands the associated manufacturing industries around the world. In the current study, we applied selective culturing combined with next-generation sequencing to examine the microbial viability in terms of its culturability on culture medium, composition, and possible contamination in the selected 17 commercial probiotic products sold in the mainland China market. Additionally, the relative abundance of each individual bacterial content was also evaluated by using the generated sequencing reads. The tested probiotic product samples were subjected to Illumina HiSeq-2000 sequencing platform and thoroughly analyzed by the in-house developed bioinformatics pipeline. The comprehensive culturing and sequencing analysis revealed both viability and composition inaccuracy among the several tested probiotic products, however, no contaminant was identified during the analysis. Among the total, five probiotic products (29.41%) were found with an inaccurate or lower colony-forming unit (CFU) counts on culture media while four probiotic products (23.52%) have inaccurately labeled classification. This study provides an ideal qualitative and quantitative assessment approach, which can be used as a diagnostic tool for the accurate assessment of commercial probiotic supplements.

Rice viruses seriously threaten rice cultivation and cause significant economic losses, but they have not yet been systematically identified, with only 20 rice-infecting viruses reported. Here, we perform a large-scale analysis of 17,115 RNA-seq libraries spanning 24 Oryza species across 51 countries. Using de novo assembly and homology-based methods, we identify 810 complete or near-complete viruses, including 276 known viruses and 534 novel viruses. Given the high divergence and atypical genome organizations of novel viruses, more than a half of them are tentatively assigned to 1 new order, 61 new families, and at least 104 new genera. Utilizing homology-independent approaches, we additionally identify 49 divergent RNA-dependent RNA polymerases (RdRPs), which are confirmed by protein structural alignment. Furthermore, we analyze the metadata of related Sequence Read Archive (SRA) libraries and estimated viral abundance in each library, leading to the screening of 427 viruses closely associated with rice plants. Overall, our study vastly expands the viral diversity in rice plants, providing insights for the prevention and control of viral disease.

Kluyveromyces marxianus is a rapidly growing thermotolerant yeast that secretes a variety of lytic enzymes, utilizes different sugars, and produces ethanol. The probiotic potential of this yeast has not been well explored. To evaluate its probiotic potential, the yeast strain Kluyveromyces marxianus DMKU3-1042 was analyzed using next-generation sequencing technology. Analysis of the genomes showed that the yeast isolates had a GC content of 40.10–40.59%. The isolates had many genes related to glycerol and mannose metabolism, as well as genes for acetoin and butanediol metabolism, acetolactate synthase subunits, and lactic acid fermentation. The strain isolates were also found to possess genes for the synthesis of different vitamins and Coenzyme A. Genes related to heat and hyperosmotic shock tolerance, as well as protection against reactive oxygen species were also found. Additionally, the isolates contained genes for the synthesis of lysine, threonine, methionine, and cysteine, as well as genes with anticoagulation and anti-inflammatory properties. Based on our analysis, we concluded that the strain DMKU3-1042 possesses probiotic properties that make it suitable for use in food and feed supplementation.

Viroids and viroid-like exogenous circular RNAs (ex-circRNAs) are small infectious RNA agents capable of autonomous replication within host cells, independent of any helper virus. In this study, we analyzed rRNA-depleted transcriptomic data sets from members of the Vitaceae , Solanaceae , and Rosaceae families to explore the diversity of these subviral elements. Using both homology-based and alignment-free ribozyme detection methods, we recovered 16 known viroids and identified 13 novel viroid-like RNAs from plant metatranscriptomic data sets. Among these, we report two new hammerhead ribozyme-containing viroid-like RNAs—CGHVd-RNA in Physalis peruviana and GPLMVd-RNA in Vitis vinifera —that display distinct secondary structures and limited sequence similarity to known viroids, supporting their classification as new species within the Avsunviroidae family. We also identified a symmetric twister ribozyme-containing ex-circRNA in peach, with validated in vitro self-cleavage activity. Additionally, three ambi-like circular RNAs were detected in grapevine and peach, encoding divergent RNA-dependent RNA polymerases, hairpin (HP), and delta virus ribozymes (DVRz). Finally, a novel Obelisk-like RNA with unique structural features was discovered in the Cape gooseberry. These results reveal the hidden complexity and broad host range of plant-associated viroid-like RNAs and suggest the existence of previously unrecognized subviral lineages with distinct evolutionary origins. IMPORTANCE: This study reveals remarkable diversity in plant-associated subviral RNA populations, identifying 13 novel viroid-like RNAs alongside 16 known viroids. Notable discoveries include new hammerhead ribozyme-containing species-level ex-circRNAs from Cape gooseberry and grapevine, a symmetric twister ribozyme ex-circRNA in peach, and, surprisingly, ambi-like circular RNAs with RNA-dependent RNA polymerases. These findings significantly expand our understanding of the complexity and evolutionary diversity of plant-associated subviral RNAs.