Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma, USA.
Present Address: Poultry Research Unit, USDA-Agricultural Research Service, Mississippi State, MS, USA.
Microbiome. 2022 Apr 1;10(1):55. doi: 10.1186/s40168-022-01252-9.
Extensive work has been accomplished to characterize the intestinal bacterial community, known as the microbiota, and its association with host health and disease. However, very little is known about the spatiotemporal development and the origin of a minor intestinal fungal community, known as the mycobiota, in humans and animals, particularly in avian species.
In this study, we comprehensively characterized the biogeography and succession of the gastrointestinal (GI) mycobiota of broiler chickens and further revealed the fungal sources that are responsible for initial and long-term establishment of the mycobiota in the GI tract. Using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes, we detected significant spatial and temporal differences in the mycobiota along the GI tract. In contrary to the microbiota, the mycobiota was more diverse in the upper than the lower GI tract with no apparent trend of succession up to 42 days of age. The intestinal mycobiota was dominated by the phyla Ascomycota and Basidiomycota with Gibberella, Aspergillus, and Candida being the most abundant genera. Although the chicken mycobiota was highly dynamic, Fusarium pseudonygamai was dominant throughout the GI tract regardless of age in this study. The core chicken mycobiome consisted of 26 fungal taxa accounting for greater than 85% of the fungal population in each GI location. However, we observed high variations of the intestinal mycobiota among different studies. We also showed that the total fungal population varied greatly from 1.0 × 10 to 1.1 × 10 /g digesta along the GI tract and only accounted for less than 0.06% of the bacteria in day-42 broilers. Finally, we revealed that the mycobiota from the hatchery environment was responsible for initial colonization in the GI tract of newly hatched chickens, but was quickly replaced by the fungi in the diet within 3 days.
Relative to the intestinal microbiota that consists of trillions of bacteria in hundreds of different species and becomes relatively stabilized as animals age, the chicken intestinal mycobiota is a minor microbial community that is temporally dynamic with limited diversity and no obvious pattern of successive changes. However, similar to the microbiota, the chicken mycobiota is spatially different along the GI tract, although it is more diverse in the upper than the lower GI tract. Dietary fungi are the major source of the intestinal mycobiota in growing chickens. Video abstract.
人们已经对肠道细菌群落（即微生物群）进行了广泛的研究，并了解了其与宿主健康和疾病的关系。然而，人们对人类和动物，特别是禽类中肠道真菌群落（即真菌群）的时空发展和起源知之甚少。
在这项研究中，我们全面描述了肉鸡胃肠道（GI）真菌群的生物地理学和演替，并进一步揭示了导致真菌群在 GI 道中初始和长期定植的真菌来源。我们通过对真菌 rRNA 基因内转录间隔区 2（ITS2）的 Illumina 测序，检测到 GI 道中真菌群在空间和时间上存在显著差异。与微生物群相反，真菌群在上部 GI 道中的多样性高于下部 GI 道，并且在 42 天龄之前没有明显的演替趋势。肠道真菌群以子囊菌门和担子菌门为主，其中镰孢菌属、曲霉属和假丝酵母属最为丰富。尽管鸡真菌群具有高度动态性，但在本研究中，无论年龄大小，Fusarium pseudonygamai 都是整个 GI 道中的优势种。鸡核心真菌群由 26 种真菌组成，占每个 GI 部位真菌群的 85%以上。然而，我们观察到不同研究之间肠道真菌群的高度变异性。我们还表明，总真菌群在 GI 道中从 1.0×10 到 1.1×10 个/g 食糜变化很大，并且在 42 日龄肉鸡中仅占细菌的不到 0.06%。最后，我们揭示了孵化场环境中的真菌群是刚孵化出的小鸡 GI 道初始定植的原因，但在 3 天内就被饲料中的真菌所取代。
与由数以万亿计的细菌组成的肠道微生物群（其在动物年龄增长过程中变得相对稳定，有数百种不同的物种）相比，鸡肠道真菌群是一个较小的微生物群落，其具有时间动态性、多样性有限且没有明显的连续变化模式。然而，与微生物群类似，鸡真菌群在 GI 道上是空间不同的，尽管在上部 GI 道中的多样性高于下部 GI 道。生长鸡的肠道真菌群的主要来源是饮食真菌。
