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Abstract Human gut Bacteroides and Parabacteroides species play crucial roles in human health and are known for their capacity to utilize diverse polysaccharides. Understanding how these bacteria utilize medicinal polysaccharides is foundational for developing polysaccharides-based prebiotics and drugs. Here, we systematically mapped the utilization profiles of 20 different medicinal polysaccharides by 28 human gut Bacteroides and Parabacteroides species. The growth profiles exhibited substantial variation across different bacterial species and medicinal polysaccharides. Ginseng polysaccharides promoted the growth of multiple Bacteroides and Parabacteroides species; in contrast, Dendrobium polysaccharides selectively promoted the growth of Bacteroides uniformis. This distinct utilization profile was associated with genomic variation in carbohydrate-active enzymes, rather than monosaccharides composition variation among medicinal polysaccharides. Through comparative transcriptomics and genetical manipulation, we validated that the polysaccharide utilization locus PUL34_Bu enabled Bacteroides uniformis to utilize Dendrobium polysaccharides (i.e. glucomannan). In addition, we found that the GH26 enzyme in PUL34_Bu allowed Bacteroides uniformis to utilize multiple plant-derived mannan. Overall, our results revealed the selective utilization of medicinal polysaccharide by Bacteroides and Parabacteroides species and provided insights into the use of polysaccharides in engineering the human gut microbiome.

Abstract The circadian clock genes are known important for kidney development, maturation and physiological functions. However, whether and how they play a role in renal regeneration remain elusive. Here, by using the single cell RNA-sequencing (scRNA-seq) technology, we investigated the dynamic gene expression profiles and cell states after acute kidney injury (AKI) by gentamicin treatment in zebrafish. The core clock genes such as per1/2 and nr1d1, which encode transcriptional repressors of the circadian system, are strongly induced in the proximal tubule epithelial cells (PTECs). By generating mutant zebrafish lines, we show that per1a and nr1d1 are required for proper renal regeneration, by facilitating the expression of renal progenitor cell (RPC) genes. In per1a and nr1d1 mutants, the expression of RPC genes and the number of RPCs were decreased, resulting in a marked delay in nephron regeneration. lima1a, which encodes a cytoskeleton binding protein that functions to negatively regulate epithelial to mesenchymal transition (EMT), is identified as the direct target of the clock proteins. Down-regulation of lima1a is associated with enhanced EMT, increased expression of cell migration- and RPC markers, and accelerated nephron regeneration. We propose that per1a and nr1d1 are important for the formation of nephrongenic RPCs by repressing lima1a. Our findings using zebrafish provide important insights into the roles of the clock genes in kidney repair.