South Dakota State University, Biology and Microbiology Department, Brookings SD 57007, USA.
Int J Syst Evol Microbiol. 2021 Jan;71(1). doi: 10.1099/ijsem.0.004599. Epub 2020 Dec 3.
A Gram-negative, rod-shaped bacterium, strain DN04, was isolated from the soil of a maize field in North Carolina, USA. Based on the 16S rRNA gene sequence, the most similar species are Sac-22, DCY83, and Sac-41 with a 97.8, 97.6, or 96.9 % sequence similarity, respectively. We compared the biochemical phenotype of DN04 to Sac-22 and 115 and other reference strains from different genera within the Oxalobacteraceae and while the biochemical profile of DN04 is most similar to Sac-22 and other and strains, there are also distinct differences. DN04 can for example utilize turanose, N-acetyl-d-glucosamine, inosine, and l-pyroglutamic acid. The four fatty acids found in the highest percentages were C iso (24.6 %), C isoG (19.4 %), C iso3-OH (16.8 %), and summed feature 3 (C ⍵7c and/or C ⍵6c) (12.5 %). We also applied whole genome sequencing to determine if DN04 is a novel species. The most similar AAI (average amino acid identity) score was 70.8 % ( NZ CP038026), and the most similar ANI (average nucleotide identity) score was 84.8 % ( KCTC 22382), which indicates that DN04 is a novel species. The genome-to-genome-distance calculation (GGDC) revealed a DDH of 28.3 % to KCTC 22382, which is much lower than the new species threshold. Based on the morphological, phenotypic, and genomic differences, we propose sp. nov. as a novel species within the genus (type strain DN04=NRRL B-65552=LMG 31736).
一株革兰氏阴性、杆状细菌，菌株 DN04，从美国北卡罗来纳州一个玉米地的土壤中分离得到。基于 16S rRNA 基因序列，最相似的物种是 Sac-22、DCY83 和 Sac-41，序列相似度分别为 97.8%、97.6%和 96.9%。我们将 DN04 的生化表型与 Sac-22 和 115 以及 Oxalobacteraceae 科内不同属的其他参考菌株进行了比较，尽管 DN04 的生化特征与 Sac-22 和其他菌株最为相似，但也存在明显的差异。例如，DN04 可以利用棉子糖、N-乙酰-d-葡萄糖胺、肌苷和 l-焦谷氨酸。发现的四种脂肪酸含量最高的分别是 C iso（24.6%）、C isoG（19.4%）、C iso3-OH（16.8%）和特征脂肪酸 3（C ⍵7c 和/或 C ⍵6c）（12.5%）。我们还应用全基因组测序来确定 DN04 是否为新物种。最相似的 AAI（平均氨基酸同一性）评分是 70.8%（NZ_CP038026），最相似的 ANI（平均核苷酸同一性）评分是 84.8%（KCTC 22382），这表明 DN04 是一个新物种。基因组到基因组距离计算（GGDC）显示与 KCTC 22382 的 DDH 为 28.3%，远低于新物种的阈值。基于形态、表型和基因组差异，我们提议将其作为属内的一个新种（模式菌株 DN04=NRRL B-65552=LMG 31736）。
