The giant panda gut harbors a high diversity of lactic acid bacteria revealed by a novel culturomics pipeline
Wenping Zhang,
Lijun Zheng,
Junjin Xie,
Xiaoyan Su,
Mingchun Zhang,
He Huang,
Stephan Schmitz-Esser,
Shizhang Du,
Yu Yang,
Jiqin Xie,
Qinrong Zhang,
Shuran Yu,
Qiang Guo,
Hairui Wang,
Liang Zhang,
Kong Yang,
Rong Hou
Affiliations
Wenping Zhang
Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
Lijun Zheng
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Junjin Xie
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Xiaoyan Su
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Mingchun Zhang
China Conservation and Research Center for the Giant Panda, Chengdu, Sichuan, China
He Huang
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Stephan Schmitz-Esser
Department of Animal Science, Iowa State University, Ames, Iowa, USA
Shizhang Du
Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas at Mianyang Teachers' College of Sichuan Province, College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, Sichuan, China
Yu Yang
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Jiqin Xie
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Qinrong Zhang
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Shuran Yu
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Qiang Guo
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Hairui Wang
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Liang Zhang
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
Kong Yang
Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan, China
Rong Hou
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
ABSTRACT 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.
