High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome.

Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications in health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve comprehensive understanding of complex microbial communities together with their hosts is therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive responses states among species in Prevotella and Roseburia genus and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated the smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-word situations and promises new perspectives in the understanding of human microbiomes.

Synthesis of Ottonia anisum Extract Mediated ZnO NPs and Their Local Anesthetic, Analgesic and HCl­induced Acute Lung Injury Activities.

In this study, we outlined the green synthesis of Zinc oxide nanoparticles (ZnO NPs) using the plant-mediated method. Employing the nitrate derivative of Zinc and the extract from the native medicinal plant, Ottonia anisum, the nanoparticles were effectively produced. After obtaining a yellow-colored paste, it was meticulously dried, gathered, and set aside for subsequent examination. The UV-visible spectrometry analysis indicated an absorption peak at 320 nm, which is indicative of ZnO NPs. Characterization techniques, such as XRD and HR-TEM, confirmed the existence of agglomerated ZnO NPs with an average diameter of 40 nm. Through EDS analysis, distinct energy signals for both Zinc and Oxygen were observed, confirming their composition. Furthermore, FT-IR spectroscopy highlighted an absorption peak for Zn-O bonding in the range of 400 to 600 cm -1 . Further, we employed three distinct pain models in mice to evaluate the influence of ZnO NPs on the nociceptive threshold. Our findings revealed that, when orally administered, ZnO NPs at concentrations ranging from 5-20 mg/kg exerted a dose-dependent analgesic effect in both the hot-plate and the acetic acid-induced writhing tests. Moreover, when ZnO NPs were administered at doses between 2.5-10 mg/kg, there was a notable reduction in pain responses during both the initial and subsequent phases of the formalin test, but no change in PGE 2 production within the mice's hind paw was found. On the other hand, acute lung injury studies revealed that the administration of ZnO NPs orally 90 minutes prior to HCl instillation decreased the neutrophil infiltration into the lungs in a doseresponsive manner. This reduction in pulmonary inflammation was paralleled by a significant decrease in lung edema, as evidenced by the reduced total protein content in the BALF. Additionally, the ZnO NPs appeared to recalibrate the lung's redox equilibrium following HCl exposure, which was determined through measurements of ROS, malondialdehyde, glutathione, and catalase activity. All these results further indicated the potential of biofabricated ZnO NPs for future applications in analgesics and acute lung injury treatments.

Genomic insights into the evolution of Echinochloa species as weed and orphan crop.

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.