University of Maryland Eastern Shore, Princess Anne, MD 21853, USA.
EzBiome Inc, Gaithersburg, MD 20878, USA.
J Food Prot. 2023 Nov;86(11):100176. doi: 10.1016/j.jfp.2023.100176. Epub 2023 Oct 5.
Investigating the chicken microbiome is important to establish control measures for pathogens to protect consumers. This study aimed at evaluating the comparative efficiency of human pathogen detection through 16S rRNA sequencing of organic and conventional chickens processed using whole carcass enrichment (WCE) and rinse (WCR) methods. Organic and conventional whole broiler carcasses (n = 31) were vigorously shaken with 500 mL buffered peptone water (BPW). For the rinse method, a 30 mL aliquot was mixed with 30 mL of BPW. The rest of the sample, including the carcass, was used for the enrichment method. All samples were incubated at 37°C for 24 h. The samples were divided into five groups [Negative Control: only BPW without chicken (n = 5), Organic-Rinsed (n = 7), -Enriched (n = 8), Conventional-Rinsed (n = 7), and -Enriched (n = 9)]. Fifty milliliters of each sample were subjected to DNA extraction followed by 16S rRNA sequencing. Proteobacteria and Firmicutes predominated the microbiota of both conventional and organic chickens, followed by low abundances of Bacteroidetes and Fusobacterium. While the abundance of Proteobacteria and Firmicutes remained unchanged in organic chicken irrespective of the methods used, a noticeable shift in the Proteobacteria and Firmicutes ratio (59%:39% in rinsed to 38%:60% in enriched) was observed in conventional chicken. Furthermore, the choice of method did not yield any differences in Abundance-Based Coverage Estimator, and Jackknife, among conventional and organic chickens but resulted in a statistically significant difference in the Shannon, Simpson, Chao1, and phylogenetic diversity indices (p < 0.05). The relative abundance of Salmonella and Campylobacter was less than 0.1%. The results suggested the WCE method provides a broad range of information on the chicken microbiome.
研究鸡的微生物组对于制定控制病原体的措施以保护消费者非常重要。本研究旨在评估通过对使用全尸富集（WCE）和冲洗（WCR）方法处理的有机和常规鸡的 16S rRNA 测序来检测人类病原体的比较效率。将 31 只有机和常规全肉鸡的尸体剧烈摇晃 500ml 缓冲蛋白胨水（BPW）中。对于冲洗方法，将 30ml 等分试样与 30ml BPW 混合。其余的样品，包括尸体，用于富集方法。所有样品均在 37°C 下孵育 24 小时。样品分为五组[阴性对照：仅含 BPW 不含鸡（n=5）、有机冲洗组（n=7）、-富集组（n=8）、常规冲洗组（n=7）和-富集组（n=9）]。对每份 50 毫升样品进行 DNA 提取，然后进行 16S rRNA 测序。两种鸡的微生物群中，变形菌门和厚壁菌门占主导地位，其次是拟杆菌门和梭杆菌门的丰度较低。虽然有机鸡中 Proteobacteria 和 Firmicutes 的丰度不受方法影响，但在常规鸡中观察到 Proteobacteria 和 Firmicutes 比例的明显变化（冲洗中为 59%：39%，富集中为 38%：60%）。此外，方法的选择并未在常规鸡和有机鸡之间的基于丰度的覆盖估计（Abundance-Based Coverage Estimator）和 Jackknife 中产生差异，但在 Shannon、Simpson、Chao1 和系统发育多样性指数（p<0.05）中产生了统计学上的显著差异。沙门氏菌和弯曲杆菌的相对丰度小于 0.1%。结果表明，WCE 方法提供了有关鸡微生物组的广泛信息。
