The success of poultry litter reuse in U.S. poultry production can be attributed to the efficient treatment methods used by producers during downtimes (the time lapse between consecutive flocks, during which the broiler house is empty). During this period, reused litter may be decaked, tilled/windrowed, or treated with acid-based amendments to reduce ammonia and bacteria levels. Competitive exclusion, pH, and temperature are proposed factors that influence the level of pathogens and the overall litter microbiome during downtimes. We previously reported on the bacterial genetic factors associated with the fitness of two strains of Salmonella enterica serovar Heidelberg (SH) incubated for 14 d in reused litter. Here, we investigated the physicochemical parameters and the microbiome of the litter correlating with SH abundance during this period. We used 16S ribosomal RNA gene sequencing to determine the litter microbiome and whole genome sequencing to characterize bacteria with competitive exclusion potential against SH. The β diversity of the litter microbiome was significantly affected by the duration of incubation, microcosm, and microcosm plus Heidelberg strain combinations. In addition, β diversity was significantly affected by litter parameters, including NH4 , pH, moisture, water activity, and aluminum. The major phyla observed in the reused litter throughout the 14-d incubation experiment were Firmicutes and Actinobacteria, although their abundance differed by microcosm and time. Amplicon-specific variants homologous to the members of the genera Nocardiopsis and Lentibacillus and the family Bacillaceae_2 were found to significantly correlate with the abundance of Salmonella. A consortium of Bacillus subtilis strains isolated from the litter microcosms reduced the growth of SH in vitro.

中文翻译：

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对海德堡沙门氏菌具有竞争性排除潜力的再利用家禽垫料微生物组

美国家禽生产中家禽垫料再利用的成功可归因于生产者在停工期（连续鸡群之间的时间间隔，肉鸡舍是空的）期间使用的有效处理方法。在此期间，可以对重复使用的垫料进行去结块、翻耕/堆放或用酸基改良剂处理以降低氨和细菌水平。竞争排斥、pH 值和温度是影响停机期间病原体水平和整体垫料微生物组的建议因素。我们之前报道了与在重复使用的垫料中孵育 14 天的两种肠道沙门氏菌血清型海德堡 (SH) 菌株的适应性相关的细菌遗传因素。在这里，我们研究了与此期间 SH 丰度相关的垃圾的理化参数和微生物组。我们使用 16S 核糖体 RNA 基因测序来确定垃圾微生物组和全基因组测序来表征对 SH 具有竞争排斥潜力的细菌。垫料微生物组的β多样性受孵化时间、微观世界和微观世界加海德堡菌株组合的显着影响。此外，β多样性受凋落物参数的显着影响，包括NH4、pH、水分、水分活度和铝。在整个 14 天孵化实验中，在重复使用的垫料中观察到的主要门是厚壁菌门和放线菌门，尽管它们的丰度因微观世界和时间而异。发现与 Nocardiopsis 和 Lentibacillus 属以及 Bacillaceae_2 家族成员同源的扩增子特异性变体与沙门氏菌的丰度显着相关。