A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy
A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy
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DOI：
10.1093/femsec/fix136
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发表时间：
2017-11-01
影响因子：
4.2
通讯作者：
Suchodolski, J. S.
中科院分区：
文献类型：
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作者：
AlShawaqfeh, M. K.;Wajid, B.;Suchodolski, J. S.
最近的研究已经确定了与健康犬相比，慢性炎症性肠病（CE）犬中的各种细菌群发生了变化。该研究的目的是使用定量PCR（qPCR）测定来证实大量犬的这些发现，并建立一种数学算法来报告这些微生物群变化作为生态失调指数（DI）。分析了95只健康犬和106只组织学证实CE的犬的粪便DNA。将样本分组为训练集和验证集。评价了各种数学模型和qPCR测定的组合，以找到具有最高区分能力的模型。最终的qPCR板由8个细菌组组成：总细菌、粪杆菌属、粪杆菌属、大肠杆菌属、链球菌属、布劳特氏菌属、梭杆菌属和海氏梭菌。基于qPCR的DI基于最近的质心分类器构建，并以单个数值报告生态失调的程度，该数值测量测试样品的I-2范数与每个类别的平均原型的接近程度。负DI指示正常生态，而正DI指示生态失调。对于阈值为0，基于组合数据集的DI对于分开的健康和CE犬实现了74%的灵敏度和95%的特异性。
Recent studies have identified various bacterial groups that are altered in dogs with chronic inflammatory enteropathies (CE) compared to healthy dogs. The study aim was to use quantitative PCR (qPCR) assays to confirm these findings in a larger number of dogs, and to build a mathematical algorithm to report these microbiota changes as a dysbiosis index (DI). Fecal DNA from 95 healthy dogs and 106 dogs with histologically confirmed CE was analyzed. Samples were grouped into a training set and a validation set. Various mathematical models and combination of qPCR assays were evaluated to find a model with highest discriminatory power. The final qPCR panel consisted of eight bacterial groups: total bacteria, Faecalibacterium, Turicibacter, Escherichia coli, Streptococcus, Blautia, Fusobacterium and Clostridium hiranonis. The qPCR-based DI was built based on the nearest centroid classifier, and reports the degree of dysbiosis in a single numerical value that measures the closeness in the I-2-norm of the test sample to the mean prototype of each class. A negative DI indicates normobiosis, whereas a positive DI indicates dysbiosis. For a threshold of 0, the DI based on the combined dataset achieved 74% sensitivity and 95% specificity to separate healthy and CE dogs.