California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals

Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.全球范围内，秃鹫与神鹰等食腐鸟类的种群数量正经历急剧下降。食腐鸟类拥有独特的消化机制，用以分解其主要食物——不同腐烂程度的动物尸体中携带的大量细菌。基于上述观察，我们对圈养健康加州神鹫（Gymnogyps californianus）的微生物组展开分析，以表征相同饲养条件下的种群微生物群落特征。本研究对圈养鸟类的粪便与泄殖腔样本进行了宏基因组鸟枪法DNA测序分析，利用Sequedex工具包对肽特征标记的鸟枪DNA测序数据进行分类，可同时获得系统发育与功能特征谱，还能对测序读长进行单独注释，用于针对性验证分析。我们检测到此前已在鸟类与肠道微生物组中被报道的细菌类群，包括产气荚膜梭菌（Clostridium perfringens）、痤疮丙酸杆菌（Propionibacterium acnes）、弗氏志贺菌（Shigella flexneri）、坏死梭杆菌（Fusobacterium mortiferum）等致病与条件致病菌，约翰逊乳杆菌（Lactobacillus johnsonii）、瘤胃乳杆菌（Lactobacillus ruminus）、普通拟杆菌（Bacteroides vulgatus）等常见菌群，以及食酸代尔夫特菌（Delftia acidovorans）、嗜麦芽窄食单胞菌（Stenotrophomonas maltophilia）、法尔西棒杆菌（Corynebacterium falsnii）等黏膜相关微生物。基于系统发育标记基因的宏基因组鸟枪读长分类结果与16S rDNA数据分析结果一致，且具备更高的特异性。基于基因组片段的系统发育或功能特征谱对样本进行分类，可将其区分为三类：粪便样本、成熟泄殖腔样本与未成熟泄殖腔样本，其中未成熟个体的微生物多样性约比成熟个体高40%。