Lopes Déborah Romaskevis Gomes, La Reau Alex J, Duarte Márcio de Souza, Detmann Edenio, Bento Cláudia Braga Pereira, Mercadante Maria Eugênia Zerlotti, Bonilha Sarah Figueiredo Martins, Suen Garret, Mantovani Hilario Cuquetto
Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Brazil.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.
Front Microbiol. 2019 Jun 25;10:1263. doi: 10.3389/fmicb.2019.01263. eCollection 2019.
The ruminant gastrointestinal tract (GIT) microbiome plays a major role in the health, physiology and production traits of the host. In this work, we characterized the bacterial and fungal microbiota of the rumen, small intestine (SI), cecum and feces of 27 Nelore steers using next-generation sequencing and evaluated biochemical parameters within the GIT segments. We found that only the bacterial microbiota clustered according to each GIT segment. Bacterial diversity and richness as well as volatile fatty acid concentration was lowest in the SI. Taxonomic grouping of bacterial operational taxonomic units (OTUs) revealed that (24.61 ± SD 6.58%) and (20.87 ± SD 4.22%) were the two most abundant taxa across the GIT. For the fungi, the family dominated in all GIT segments, with the genus being the most abundant. Twenty-eight bacterial and six fungal OTUs were shared across all GIT segments in at least 50% of the steers. We also evaluated if the fecal-associated microbiota of steers showing negative and positive residual feed intake (n-RFI and p-RFI, respectively) was associated with their feed efficiency phenotype. Diversity indices for both bacterial and fungal fecal microbiota did not vary between the two feed efficiency groups. Differences in the fecal bacterial composition between high and low feed efficiency steers were primarily assigned to OTUs belonging to the families and and to the genus . The fungal OTUs shared across the GIT did not vary between feed efficiency groups, but 7 and 3 OTUs were found only in steers with positive and negative RFI, respectively. These results provide further insights into the composition of the Nelore GIT microbiota, which could have implications for improving animal health and productivity. Our findings also reveal differences in fecal-associated bacterial OTUs between steers from different feed efficiency groups, suggesting that fecal sampling may represent a non-invasive strategy to link the bovine microbiota with productivity phenotypes.
反刍动物胃肠道（GIT）微生物群在宿主的健康、生理和生产性状中起着重要作用。在本研究中，我们使用下一代测序技术对27头内洛尔阉牛的瘤胃、小肠（SI）、盲肠和粪便中的细菌和真菌微生物群进行了特征分析，并评估了GIT各节段内的生化参数。我们发现，只有细菌微生物群根据每个GIT节段聚类。小肠中的细菌多样性和丰富度以及挥发性脂肪酸浓度最低。细菌操作分类单元（OTU）的分类分组显示，（24.61±标准差6.58%）和（20.87±标准差4.22%）是整个GIT中最丰富的两个分类群。对于真菌，该科在所有GIT节段中占主导地位，属最为丰富。在至少50%的阉牛中，28个细菌OTU和6个真菌OTU在所有GIT节段中都有共享。我们还评估了表现出负和正剩余采食量（分别为n-RFI和p-RFI）的阉牛的粪便相关微生物群是否与其饲料效率表型相关。两个饲料效率组之间的细菌和真菌粪便微生物群的多样性指数没有差异。高饲料效率和低饲料效率阉牛粪便细菌组成的差异主要归因于属于科和科以及属的OTU。GIT中共享的真菌OTU在饲料效率组之间没有差异，但分别仅在具有正RFI和负RFI的阉牛中发现了7个和3个OTU。这些结果为内洛尔GIT微生物群的组成提供了进一步的见解，这可能对改善动物健康和生产力有影响。我们的研究结果还揭示了来自不同饲料效率组的阉牛之间粪便相关细菌OTU的差异，表明粪便采样可能是一种将牛微生物群与生产性状表型联系起来的非侵入性策略。
