Table 1_Intestinal microbiome gone native: gut microbiome shift and resistome diversity in first homecoming giant panda family.xlsx

IntroductionThe world-famous giant pandas (Ailuropoda melanoleuca) often travel abroad for public exhibitions and international scientific cooperations. Previous research has reported alternations in the gut microbiome structure and enrichment of gut antibiotic-resistant genes (ARGs) in human international travelers, the latter of which is harmful to native residents and the environment. The microbiome and ARGs of these animal travelers, however, have not yet been investigated, even though they often interact with local keepers, visitors, and other pandas.
MethodsIn this study, we have clarified the dynamic microbiome composition and snapshot of ARGs (resistome) of the first panda family returning from overseas. Fecal samples were gathered for high-throughput sequencing for both amplicon and metagenomics sequencing, which were collected on the first day of their quarantine (Admission stage) and 3 days after the quarantine (Release stage). Feces from two native captive pandas were used as controls.
Results and discussionThe predominant Escherichia–Shigella proportion in the mother and father pandas decreased from 79.02 and 47.46% to 57.03 and 33.77%, while the Streptococcus abundance increased from 0.27 and 12.44% to 29.47 and 54.59%. The main genus of child pandas, Weissella, decreased from 45.24 to 0.02% after quarantine, and the Streptococcus ratio increased from 11.89 to 43.82%. Significant richness and bacterial diversities were found in these samples. The main ARG types are multidrug and polymyxin; the latter being an uncommon ARG in native pandas. Consequently, to protect local ecosystems from the introduction of novel ARGs, waste from translocated giant pandas should be managed under strict biosecurity protocols.

引言：享誉全球的大熊猫（Ailuropoda melanoleuca）常赴海外开展公开展览与国际科研合作。既往研究显示，人类国际旅行者的肠道微生物组结构会发生改变，且肠道抗生素抗性基因（antibiotic-resistant genes, ARGs）丰度升高，后者会对当地居民与生态环境造成危害。然而，尽管这些赴外动物旅行者常与当地饲养员、游客及其他大熊猫发生接触，但其肠道微生物组与抗生素抗性基因的相关研究仍未开展。
方法：本研究明确了首个归国大熊猫家族的肠道微生物组动态组成与抗生素抗性基因（resistome）的全貌。研究人员采集了该家族在检疫首日（入检疫期）与检疫结束3天后（出检疫期）的粪便样本，分别进行扩增子测序与宏基因组测序。同时以2只本地圈养大熊猫的粪便样本作为对照。
结果与讨论：大熊猫父母的优势菌属埃希氏菌-志贺氏菌（Escherichia–Shigella）占比分别从79.02%与47.46%降至57.03%与33.77%，而链球菌属（Streptococcus）的丰度分别从0.27%与12.44%升至29.47%与54.59%。幼崽大熊猫的核心菌属魏斯氏菌属（Weissella）在检疫后占比从45.24%降至0.02%，链球菌属占比则从11.89%升至43.82%。本研究的粪便样本中检测到显著的菌群丰富度与多样性变化。样本中的主要抗生素抗性基因为多药抗性基因与多粘菌素抗性基因，其中多粘菌素抗性基因在本地圈养大熊猫中较为罕见。综上，为避免外来新型抗生素抗性基因入侵本地生态系统，赴外转运大熊猫产生的粪便废弃物应严格按照生物安全规程进行管理。