The giant panda gut harbors a high diversity of lactic acid bacteria revealed by a novel culturomics pipeline.

Some lactic acid bacteria (LAB) can provide significant health benefits, which are critically important for the conservation of endangered animals, such as giant pandas. However, little is known about the diversity and culturability of LAB in the giant panda gut microbiota. To understand the roles of LAB in giant panda conservation, it is critical to culture bacterial strains of interest. In this study, we established a pipeline to culture bacterial strains using enrichment of target bacteria with different liquid media and growth conditions. Then, the strains were isolated in solid media to study their functions. Using 210 samples from the culture enrichment method and 138 culture-independent samples, we obtained 1120 amplicon sequencing variants (ASVs) belonging to Lactobacillales. Out of the 1120 ASVs, 812 ASVs from the culture enrichment approach were twofold more diverse than 336 ASVs from the culture-independent approach. Many ASVs of interest were not detected in the culture-independent approach. Using this pipeline, we isolated many relevant bacterial strains and established a giant panda gut bacteria strain collection that included strains with low-abundance in culture-independent samples and included most of the giant panda LAB described by other researchers. The strain collection consisted of 60 strains representing 35 species of 12 genera. Thus, our pipeline is powerful and provides guidance in culturing gut microbiota of interest in hosts such as the giant panda.IMPORTANCECultivation is necessary to screen strains to experimentally investigate microbial traits, and to confirm the activities of novel genes through functional characterization studies. In the long-term, such work can aid in the identification of potential health benefits conferred by bacteria and this could aid in the identification of bacterial candidate strains that can be applied as probiotics. In this study, we developed a pipeline with low-cost and user-friendly culture enrichment to reveal the diversity of LAB in giant pandas. We compared the difference between culture-independent and culture enrichment methods, screened strains of interest that produced high concentrations of short-chain fatty acids (SCFAs), and we investigated the catalog of virulence factors, antibiotic resistance, butyrate and lactate synthesis genes of the strains at a genomic level. This study will provide guidance for microbiota cultivation and a foundation for future research aiming to understand the functions of specific strains.

MTP family analysis and association study reveal the role of ZmMTP11 in lead (Pb) accumulation.

The metal tolerance protein (MTP) gene family plays an essential role in the transport of heavy metals, however the function of the MTP family in transporting lead (Pb) was still unclear in plants. In this study, we identified and characterized 12 ZmMTPs in the whole genome of maize. These ZmMTP genes were divided into three subfamilies in evolution, namely Zn-CDF, Zn/Fe-CDF, Mn-CDF subfamilies, which showed diverse expression patterns in different tissues of maize. Using gene-based association analyses, we identified a Pb accumulation-related MTP member in maize, ZmMTP11, which was located in plasma membrane and had the potential of transporting Pb ion. Under the Pb treatment, ZmMTP11 showed a generally decreased expression relative to the normal conditions. Heterologous expressions of ZmMTP11 in yeast, Arabidopsis, and rice demonstrated that ZmMTP11 enhanced Pb accumulation in the cells without affecting yeast and plant growth under Pb stress. Remarkably, the increased Pb concentration in the plant roots did not cause changes in Pb content in the shoots. Our study provides new insights into the genetic improvement of heavy metal tolerance in plants and contributes to bioremediation of Pb-contaminant soils.

Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey.

There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future.

Transcriptome analysis reveals molecular regulation mechanism of Tibet sheep tolerance to high altitude oxygen environment.

As one of the most important livestock breeds on the Qinghai-Tibet Plateau, Tibetan sheep are of great importance to the local economy, agriculture and culture. Its adaptive mechanism in low temperature and low oxygen at highland altitudes has not been reported. In this study, transcriptome sequencing was used to analyze the heart, liver, spleen, lung, kidney, and muscle tissue of sheep at low and highland altitudes. LOC101112291, SELENOW, COL3A1, GPX1, TMSB4X and HSF4 were selected as candidate genes for adapting to plateau characteristics in Tibet Sheep. Besides, glutathione metabolism, arachidonic acid metabolism, nucleotide excision repair, regulation of actin cytoskeleton, protein digestion and absorption, thyroid hormone synthesis, relaxation signaling pathways may play important roles in the adaptation to plateau hypoxia, and cold tolerance. Structural analysis also showed that sequencing genes related to the adaptation mechanism of Tibet sheep to highland altitude. This study will lay a certain foundation for Tibet sheep research.

Tibet sheep are an ancient species in the Qinghai Tibet Plateau. After a long period of domestication. Tibet sheep adapt to the hypoxic environment of the plateau in terms of physiology and morphology. At the same time, Tibet sheep is also one of the major sources of material for herdsmen in tibetan. In this study, six different tissue samples (heart, liver, spleen, lung, kidney, and muscle) of Tibet sheep were analyzed to reveal the underlying mechanisms of different tissues respond to hypothermia condition. The results showed that six key genes and eight important signaling pathways involved in regulating the adaptation of Tibet sheep to the plateau. In addition, there were more alternative splicing (AS) events and single nucleotide polymorphism (SNP) sites in highland altitude Tibet sheep than in lowland altitude sheep, which was also a concern in the highland altitude adaptability of Tibet sheep.