Coates Jessica, Bostick Kathleen J, Jones Brooke A, Caston Nymeer, Ayalew Mentewab
Microbiology and Molecular Genetics Graduate Program, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30329, USA.
Department of Biology, Spelman College, 350 Spelman Lane, Atlanta, GA, 30314, USA.
Environ Evid. 2022 May 12;11(1):18. doi: 10.1186/s13750-022-00274-y.
Aminoglycosides are potent bactericidal antibiotics naturally produced by soil microorganisms and are commonly used in agriculture. Exposure to these antibiotics has the potential to cause shifts in the microorganisms that impact plant health. The systematic review described in this protocol will compile and synthesize literature on soil and plant root-associated microbiota, with special attention to aminoglycoside exposure. The systematic review should provide insight into how the soil and plant microbiota are impacted by aminoglycoside exposure with specific attention to the changes in the overall species richness and diversity (microbial composition), changes of the resistome (i.e. the changes in the quantification of resistance genes), and maintenance of plant health through suppression of pathogenic bacteria. Moreover, the proposed contribution will provide comprehensive information about data available to guide future primary research studies. This systematic review protocol is based on the question, "What is the impact of aminoglycoside exposure on the soil and plant root-associated microbiota?".
A boolean search of academic databases and specific websites will be used to identify research articles, conference presentations and grey literature meeting the search criteria. All search results will be compiled and duplicates removed before title and abstract screening. Two reviewers will screen all the included titles and abstracts using a set of predefined inclusion criteria. Full-texts of all titles and abstracts meeting the eligibility criteria will be screened independently by two reviewers. Inclusion criteria will describe the eligible soil and plant root-associated microbiome populations of interest and eligible aminoglycosides constituting our exposure. Study validity will be evaluated using the CEE Critical Appraisal Tool Version 0.2 (Prototype) to evaluate the risk of bias in publications. Data from studies with a low risk of bias will be extracted and compiled into a narrative synthesis and summarized into tables and figures. If sufficient evidence is available, findings will be used to perform a meta-analysis.
氨基糖苷类是土壤微生物天然产生的强效杀菌抗生素，常用于农业。接触这些抗生素有可能导致影响植物健康的微生物群落发生变化。本方案中描述的系统评价将汇编和综合关于土壤和植物根系相关微生物群的文献，特别关注氨基糖苷类暴露情况。该系统评价应深入了解氨基糖苷类暴露如何影响土壤和植物微生物群，特别关注整体物种丰富度和多样性（微生物组成）的变化、抗性组的变化（即抗性基因定量的变化）以及通过抑制病原菌来维持植物健康。此外，本研究将提供有关现有数据的全面信息，以指导未来的初步研究。本系统评价方案基于这样一个问题：“氨基糖苷类暴露对土壤和植物根系相关微生物群有何影响？”
将使用学术数据库和特定网站的布尔搜索来识别符合搜索标准的研究文章、会议报告和灰色文献。在进行标题和摘要筛选之前，将汇总所有搜索结果并去除重复项。两名评审员将使用一组预定义的纳入标准筛选所有纳入的标题和摘要。所有符合资格标准的标题和摘要的全文将由两名评审员独立筛选。纳入标准将描述符合条件的感兴趣的土壤和植物根系相关微生物群落以及构成我们暴露源的符合条件的氨基糖苷类。将使用CEE关键评估工具0.2版（原型）评估研究的有效性，以评估出版物中的偏倚风险。将提取低偏倚风险研究的数据并汇编成叙述性综述，并汇总成表格和图表。如果有足够的证据，将使用研究结果进行荟萃分析。
