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Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2021-11-18 , DOI: 10.1016/j.csbj.2021.11.020 Chhedi Lal Gupta 1 , Ran Avidov 2 , Karuppasamy Kattusamy 1 , Ibrahim Saadi 2 , Vempalli Sudharsan Varma 2 , Shlomo E Blum 3 , Yong-Guan Zhu 4, 5 , Xin-Yuan Zhou 4 , Jian-Qiang Su 4 , Yael Laor 2 , Eddie Cytryn 1
Computational and Structural Biotechnology Journal ( IF 4.4 ) Pub Date : 2021-11-18 , DOI: 10.1016/j.csbj.2021.11.020 Chhedi Lal Gupta 1 , Ran Avidov 2 , Karuppasamy Kattusamy 1 , Ibrahim Saadi 2 , Vempalli Sudharsan Varma 2 , Shlomo E Blum 3 , Yong-Guan Zhu 4, 5 , Xin-Yuan Zhou 4 , Jian-Qiang Su 4 , Yael Laor 2 , Eddie Cytryn 1
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Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the , and families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and were abundant. was the most abundant species, and high levels of the opportunistic pathogen were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside ((6′)-Ib(aka A4), A5), tetracycline (G), vancomycin (C), phenicol (R) and MLSB (B) resistance genes. were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen were detected, as was the opportunistic pathogen , which was linked to vancomycin (, ), MLSB () and tetracycline () resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.
中文翻译：
肉鸡垫料堆中微生物组和抗性组的时空动态
农民在不同时期的储存后，将肉鸡垫料施用于土壤中，以丰富有机质并为农作物提供养分。然而，垃圾中经常含有粪便来源的微生物病原体和相关的抗生素抗性基因（ARG），并且可能是农产品微生物污染的来源。我们将尖端的 Loop Genomics 长读长 16S rRNA 扩增子测序平台与针对一组 ARG 的高通量 qPCR 相结合，以评估时间（60 天内的五个时间点）和空间（顶部、中部和底部）。底层）肉鸡垫料堆中的微生物组和抗性组动力学。我们重点关注与食源性疾病相关的 和 科的潜在致病物种。细菌多样性在库存中部显着较低，那里的目标病原体最低且丰富。是最丰富的物种，并且检测到高水平的机会病原体。相关分析显示后者与氨基糖苷类((6′)-Ib(又名A4)、A5)、四环素(G)、万古霉素(C)、苯尼考(R)和MLSB(B)耐药基因显着相关。主要是非致病性的，但检测到极低水平的机会病原体，以及与万古霉素 (, )、MLSB () 和四环素 () 抗性基因相关的机会病原体。总的来说，我们发现库存微生物组和抗性组在很大程度上受到时间波动和空间异质性的影响。这项研究的见解可用于改进库存管理实践，以支持未来可持续的抗菌药物耐药性缓解政策。
更新日期：2021-11-18
中文翻译：
肉鸡垫料堆中微生物组和抗性组的时空动态
农民在不同时期的储存后，将肉鸡垫料施用于土壤中，以丰富有机质并为农作物提供养分。然而，垃圾中经常含有粪便来源的微生物病原体和相关的抗生素抗性基因（ARG），并且可能是农产品微生物污染的来源。我们将尖端的 Loop Genomics 长读长 16S rRNA 扩增子测序平台与针对一组 ARG 的高通量 qPCR 相结合，以评估时间（60 天内的五个时间点）和空间（顶部、中部和底部）。底层）肉鸡垫料堆中的微生物组和抗性组动力学。我们重点关注与食源性疾病相关的 和 科的潜在致病物种。细菌多样性在库存中部显着较低，那里的目标病原体最低且丰富。是最丰富的物种，并且检测到高水平的机会病原体。相关分析显示后者与氨基糖苷类((6′)-Ib(又名A4)、A5)、四环素(G)、万古霉素(C)、苯尼考(R)和MLSB(B)耐药基因显着相关。主要是非致病性的，但检测到极低水平的机会病原体，以及与万古霉素 (, )、MLSB () 和四环素 () 抗性基因相关的机会病原体。总的来说，我们发现库存微生物组和抗性组在很大程度上受到时间波动和空间异质性的影响。这项研究的见解可用于改进库存管理实践，以支持未来可持续的抗菌药物耐药性缓解政策。
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