利用下一代DNA测序和地理特异性细菌和真菌差异对健康家兔（Oryctolagus cuniculus domesticus）鼻腔微生物群的表征

IF 0.5 4区农林科学 Q4 VETERINARY SCIENCES

Journal of Exotic Pet Medicine Pub Date : 2025-06-01 DOI:10.1053/j.jepm.2025.05.003

Linda J. Siperstein , Janina A. Krumbeck , Kaylie Zapanta , Elizabeth Marie Rush

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引用次数: 0

摘要

家兔（Oryctolagus cuniculus domesticus）的呼吸道感染是兽医从业人员常见但具有挑战性的病例。虽然传统的培养可能只能培养一小部分微生物，但下一代DNA测序（NGS）可以更有效地揭示挑剔或新的生物。本研究旨在表征兔鼻腔微生物组并确定潜在的地理差异。实验动物：来自美国加利福尼亚州（CA, n = 25）和阿拉巴马州（AL, n = 24）的临床健康宠物兔。方法采用双鼻腔拭子法采集标本。利用NGS对细菌和真菌微生物组进行了分析，针对细菌的16S rRNA V1至V3区域和真菌的ITS-2区域。结果共检出186个菌群，其中9个菌群占菌群总数的1%以上。每个样本共检出18个细菌分类群，平均37.5±标准差（SD）（AL组平均36.79±SD 19.8， CA组平均38.20±SD 17.1）。细菌数量最多的分类群为假单胞菌目（平均12.7%±SD 17）、丘莫拉菌（平均11.9%±SD 18）和奈丝菌科（平均8.5%±SD 9）。虽然家兔被认为是健康的，但在49份样品中有37份检测到支原体属的一种（平均4.7%±SD 9）。幽门螺杆菌属（平均3.7%±SD 5.5）和弯曲菌科（平均2.84%±SD 6.1）也存在。真菌mycobiome比bacteriome更加多样化,最丰富的真菌类群是枝孢属属内物种25±SD(平均38.1%),其次是一个物种内的链格孢属属8±SD(平均5.5%),一个物种在Pleosporales秩序±SD 10(平均3.8%),链格孢属infectoria-rosae(平均6.8±3.72% SD), Vishniacozyma victoriae(平均4.4±2.93% SD),和一个物种Microascus (Scopularipsis)属(平均5.1±1.02% SD)。CA组有23个真菌类群较为丰富，AL组有3个较为常见。临床意义本研究结果建立了健康家兔鼻腔微生物组和真菌组，供兽医专业人员使用NGS对上呼吸道体征家兔进行比较。

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Characterization of nasal cavity microbiome from healthy rabbits (Oryctolagus cuniculus domesticus) using next-generation DNA sequencing and geographically specific bacterial and fungal differences

Background

Upper respiratory infections in rabbits (Oryctolagus cuniculus domesticus) present common yet challenging cases for veterinary practitioners. While conventional cultures may only grow a small percentage of microbes, next-generation DNA sequencing (NGS) can be more effective at revealing fastidious or novel organisms. This study aimed to characterize the rabbit nasal cavity microbiome and determine potential geographical differences.

Animals

Clinically healthy pet rabbits from California (CA, n = 25) and Alabama (AL, n = 24), United States.

Methods

Samples were collected via standard protocol of swabbing both nasal cavities. The bacterial and fungal microbiomes were profiled using NGS, targeting the 16S rRNA V1 to V3 region for bacteria and ITS-2 for fungi.

Results

In total, 186 bacterial taxa were detected, 9 representing at least 1% of the microbiome. In each sample, a mean of 37.5 ± standard deviation (SD) of 18 bacterial taxa were detected (mean 36.79 ± SD 19.8 in the AL group, and a mean of 38.20 ± and SD of 17.1 in the CA group). The most abundant bacterial taxa were species within the Pseudomonadales order (mean 12.7% ± SD 17), Moraxella cuniculi (mean 11.9% ± SD 18), and Neisseriaceae sp. (mean 8.5% ± SD 9). Although rabbits were considered healthy, a species within the Mycoplasma genus was detected in 37 out of 49 samples (mean 4.7% ± SD 9). The Helicobacter genus (mean 3.7% ± SD 5.5) and the Campylobacteraceae order (mean 2.84% ± SD 6.1) were also present. The fungal mycobiome was more diverse than the bacteriome, with the most abundant fungal taxa being a species within the Cladosporium genus (mean 38.1% ± SD 25), followed by a species within the Alternaria genus (mean 5.5% ± SD 8), a species within the Pleosporales order (mean 3.8% ± SD 10), Alternaria infectoria-rosae (mean 3.72% ± SD 6.8), Vishniacozyma victoriae (mean 2.93% ± SD 4.4), and a species within the Microascus (Scopularipsis) genus (mean 1.02% ± SD 5.1). Twenty-three fungal taxa were more abundant in the CA group, and 3 species were more common in the AL group.

Clinical Relevance

Findings from this study establish the healthy rabbit nasal cavity microbiome and mycobiome using NGS for veterinary professionals to use a comparison for rabbits with upper respiratory signs.

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来源期刊

Journal of Exotic Pet Medicine 农林科学-兽医学

CiteScore

1.20

自引率

0.00%

发文量

审稿时长

60 days

期刊介绍： The Journal of Exotic Pet Medicine provides clinicians with a convenient, comprehensive, "must have" resource to enhance and elevate their expertise with exotic pet medicine. Each issue contains wide ranging peer-reviewed articles that cover many of the current and novel topics important to clinicians caring for exotic pets. Diagnostic challenges, consensus articles and selected review articles are also included to help keep veterinarians up to date on issues affecting their practice. In addition, the Journal of Exotic Pet Medicine serves as the official publication of both the Association of Exotic Mammal Veterinarians (AEMV) and the European Association of Avian Veterinarians (EAAV). The Journal of Exotic Pet Medicine is the most complete resource for practitioners who treat exotic pets.