Preweaned dairy calves and lactating dairy cows are known reservoirs of antibiotic-resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from preweaned dairy calves and lactating dairy cows on 17 commercial dairy farms (n = 34 samples). Results indicated significant differences in the structures of the microbial communities (analysis of similarities [ANOSIM] R = 0.81, p = 0.001) and resistomes (ANOSIM R = 0.93 to 0.96, p = 0.001) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, whereas Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-(TM7) were more abundant in lactating cow samples. Diverse suites of antibiotic resistance genes (ARGs) were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, ARGs were significantly more abundant in composite fecal samples from calves than those from lactating cows (calf median ARG abundance = 1.8 × 10⁰ ARG/16S ribosomal RNA [rRNA], cow median ARG abundance = 1.7 × 10⁻¹ ARG/16S rRNA) and at the antibiotic resistance class level, the relative abundance of tetracycline, trimethoprim, aminoglycoside, macrolide-lincosamide-streptogramin B, β-lactam, and phenicol resistance genes was significantly higher in calf samples than in cow samples. Results of this study indicate that composite feces from preweaned calves harbor different bacterial communities and resistomes than composite feces from lactating cows, with a greater abundance of resistance genes detected in preweaned calf feces.

中文翻译：

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商业奶牛群中断奶小牛和泌乳奶牛粪便微生物群落和抗性结构的差异。

断奶前的奶牛和泌乳奶牛是已知的抗生素抗性细菌的宿主。为了进一步了解两者之间的抗性组和微生物群落的差异，我们对来自 17 个商业奶牛场（n  = 34 个样本）的断奶前奶牛和泌乳奶牛的粪便复合样本的宏基因组进行了测序。结果表明微生物群落结构（相似性分析 [ANOSIM] R  = 0.81，p  = 0.001）和抗性组（ANOSIM R  = 0.93 至 0.96，p = 0.001) 在两个年龄组之间。Firmicutes、Bacteroidetes、Proteobacteria 和 Actinobacteria 是这些群落的主要成员，但是当比较各组时，Bacteroidetes 和 Verrumicrobia 在小牛粪便复合样本中的含量显着更高，而 Firmicutes、Spirochaetes、Deinococcus-Thermus、Lentisphaerae、Planctomycetes和 Saccharibacteria-(TM7) 在泌乳奶牛样品中更丰富。在所有样品中都鉴定出多种抗生素抗性基因 (ARG)，其中最常检测到的为四环素和氨基糖苷类抗性。比较两组时，小牛复合粪便样本中的 ARG 显着高于泌乳奶牛的复合粪便样本（小牛中值 ARG 丰度 = 1.8 × 10 ⁰ARG/16S 核糖体 RNA [rRNA]，牛中值 ARG 丰度 = 1.7 × 10 ^-1 ARG/16S rRNA) 和在抗生素抗性等级水平，四环素、甲氧苄氨嘧啶、氨基糖苷类、大环内酯-林可酰胺-链球菌素 B、β 的相对丰度-内酰胺和苯酚抗性基因在小牛样品中显着高于在奶牛样品中。这项研究的结果表明，断奶前小牛的复合粪便与泌乳奶牛的复合粪便具有不同的细菌群落和抵抗组，在断奶前的小牛粪便中检测到更多的抗性基因。