Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas.

The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.

Entropy Stable DGSEM Schemes of Gauss Points Based on Subcell Limiting.

The discontinuous Galerkin spectral element method (DGSEM) is a compact and high-order method applicable to complex meshes. However, the aliasing errors in simulating under-resolved vortex flows and non-physical oscillations in simulating shock waves may lead to instability of the DGSEM. In this paper, an entropy-stable DGSEM (ESDGSEM) based on subcell limiting is proposed to improve the non-linear stability of the method. First, we discuss the stability and resolution of the entropy-stable DGSEM based on different solution points. Second, a provably entropy-stable DGSEM based on subcell limiting is established on Legendre-Gauss (LG) solution points. Numerical experiments demonstrate that the ESDGSEM-LG scheme is superior in non-linear stability and resolution, and ESDGSEM-LG with subcell limiting is robust in shock-capturing.

Energy Stability Property of the CPR Method Based on Subcell Second-Order CNNW Limiting in Solving Conservation Laws.

This paper studies the energy stability property of the correction procedure via reconstruction (CPR) method with staggered flux points based on second-order subcell limiting. The CPR method with staggered flux points uses the Gauss point as the solution point, dividing flux points based on Gauss weights, with the flux points being one more point than the solution points. For subcell limiting, a shock indicator is used to detect troubled cells where discontinuities may exist. Troubled cells are calculated by the second-order subcell compact nonuniform nonlinear weighted (CNNW2) scheme, which has the same solution points as the CPR method. The smooth cells are calculated by the CPR method. The linear energy stability of the linear CNNW2 scheme is proven theoretically. Through various numerical experiments, we demonstrate that the CNNW2 scheme and CPR method based on subcell linear CNNW2 limiting are energy-stable and that the CPR method based on subcell nonlinear CNNW2 limiting is nonlinearly stable.

Population Genetics Reveals That the Western Tianshan Mountains Populations of Agrilus mali (Coleoptera: Buprestidae) May Have Not been Recently Introduced.

Agrilus mali Matsumura is a wood-boring beetle that aggressively attacks species of the genus Malus, that has recently caused serious damage to the wild apple tree M. sieversii (Lebed.) in the western Tianshan Mountains in Xinjiang. It was first detected there in the early 1990s and spread rapidly, being thus considered a regional invasive pest. To explore the possible outbreak mechanism of the local population and characterize the genetic differentiation of A. mali across different regions of China, we used three mitochondrial genes (COI, COII, and CytB) to investigate the genetic diversity and genetic structure of 17 A. mali populations containing 205 individuals collected from five Chinese provinces. Among them, nine populations were from the western Tianshan Mountains. Ultimately, of the 136 pairwise F st comparisons, 99 showed high genetic differentiation among overall populations, and Tianshan populations exhibited significant differentiation with most of the non-Tianshan populations. Furthermore, A. mali populations represented relatively abundant haplotypes (54 haplotypes). Nine populations from the Tianshan Mountains showed 32 haplotypes (26 of which were unique), displaying relatively high genetic diversity. Additionally, the Mantel test revealed population genetic differentiation among either overall populations or the Tianshan Mountains populations, likely caused by geographical isolation. Phylogenic relationships showed that all populations clustered into three clades, and Tianshan Mountains populations, including CY, occupied one of the three clades. These results suggest that A. mali in the western Tianshan region has possibly been present in the area for a long period, and may not have been introduced recently. Highly frequent gene flows within Tianshan populations are possibly caused by human activities and may enhance the adaptability of A. mali along the western Tianshan Mountains, leading to periodic outbreaks. These findings enhance our understanding of jewel beetle population genetics and provide valuable information for pest management.