Elbir Haitham
Camel Research Center, King Faisal University, 400 Al-Ahsa, Hofuf 31982, Saudi Arabia.
Vet Sci. 2024 Dec 17;11(12):661. doi: 10.3390/vetsci11120661.
Currently, bacterial classification at the species level relies on the 95-96% average nucleotide identity (ANI) value that is known to be equivalent to a 70% digital DNA-DNA hybridization (dDDH) value. However, during the routine identification of bacteria in the uteri of camels with a history of conception failure, we found that four out of the seven strains (2298A, 2569A, 2652, 2571B, 1103A, 2571A, and 335C) could not be assigned to any valid species. Furthermore, a 70% dDDH value did not correspond to a 95-96% ANI value in strain 2569A. Thus, we aimed to classify these strains and explain the mechanisms underlying gene repertoire diversity and the disagreement we found between the ANI and dDDH cutoff values. For this study, we extracted information from the genomes of 150 -type species and seven sequenced genomes of uterine isolates. We found that the 96.67% OrthoANI value should be used in place of the generally accepted 95-96% ANI threshold in order to obtain an equivalent 70% dDDH value. Phylogenomic analysis determined the evolutionary position of each uterine strain. Then, strains 2652 and 2571B were classified as based on the ANI value (98.44% and 98.72%) and dDDH value (85.8% and 88.5%). Strain 2569A had a 96.58% ANI and a 69.4% dDDH value and was classified as The strains 335C, 1103A, 2571A, and 2298A were classified as novel based on the ANI value (77.12, 94.01%, 94.26%, and 94.03%) and dDDH value (21.3%, 54.1%, 54.9%, and 51.3%), respectively. Genes for menaquinone biosynthesis and the saturation of chains were detected in uterine strains and their closely related type strains. Gene gain predominates as a source of variation in the gene repertoire. Most of these genes are gained by horizontal gene transfer, driven by genomic islands and prophage. In summary, we refined the ANI cutoff value for an accurate diagnosis of . Moreover, we clarified the mechanism underlying the diversity of the gene repertoire and expanded the number of species isolated from the camel uterus.
目前，物种水平的细菌分类依赖于95 - 96%的平均核苷酸同一性（ANI）值，已知该值等同于70%的数字DNA - DNA杂交（dDDH）值。然而，在对有受孕失败史的骆驼子宫内细菌进行常规鉴定时，我们发现七株菌株（2298A、2569A、2652、2571B、1103A、2571A和335C）中有四株无法归类到任何有效物种。此外，菌株2569A中70%的dDDH值并不对应95 - 96%的ANI值。因此，我们旨在对这些菌株进行分类，并解释基因库多样性背后的机制以及我们在ANI和dDDH截止值之间发现的差异。在本研究中，我们从150个模式物种的基因组和七株子宫分离株的测序基因组中提取信息。我们发现，为了获得等同于70% dDDH值的结果，应使用96.67%的OrthoANI值来取代普遍接受的95 - 96%的ANI阈值。系统发育基因组分析确定了每个子宫菌株的进化位置。然后，根据ANI值（98.44%和98.72%）和dDDH值（85.8%和88.5%），菌株2652和2571B被归类为[具体分类]。菌株2569A的ANI值为96.58%，dDDH值为69.4%，被归类为[具体分类]。根据ANI值（77.12、94.01%、94.26%和94.03%）和dDDH值（21.3%、54.1%、54.9%和51.3%），菌株335C、1103A、2571A和2298A分别被归类为新的[具体分类]。在子宫菌株及其密切相关的模式菌株中检测到了甲萘醌生物合成和链饱和的基因。基因获得是基因库变异的主要来源。这些基因大多是通过由基因组岛和前噬菌体驱动的水平基因转移获得的。总之，我们优化了ANI截止值以进行[具体疾病]的准确诊断。此外，我们阐明了基因库多样性的潜在机制，并增加了从骆驼子宫分离出的[具体细菌]物种数量。
