Davies Cary P, Jurkiw Thomas, Haendiges Julie, Reed Elizabeth, Anderson Nathan, Grasso-Kelley Elizabeth, Hoffmann Maria, Zheng Jie
Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, NEA, U.S. Department of Agriculture, Beltsville, MD, United States.
Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States.
Front Microbiol. 2022 Sep 9;13:970135. doi: 10.3389/fmicb.2022.970135. eCollection 2022.
Low moisture foods (LMFs) have traditionally been recognized as safe for consumption, as most bacteria require higher water content to grow. However, outbreaks due to LMF foods are increasing, and the microbial pathogen is frequently implicated. can survive in LMFs for years, but few serovars have been studied, and the mechanisms which underlie this longevity are not well understood. Here, we determine that serovars . Tennessee, . Anatum, and Reading but not . Oranienburg can survive in the ground black pepper for 6 years. Reading was not previously associated with any LMF. Using both Illumina and Pacific Biosciences sequencing technologies, we also document changes in the genomes and methylomes of the surviving serovars over this 6-year period. The three serovars acquired a small number of single nucleotide polymorphisms (SNPs) including seven substitutions (four synonymous, two non-synonymous, and one substitution in a non-coding region), and two insertion-deletions. Nine distinct N6-methyladenine (m6A) methylated motifs across the three serovars were identified including five which were previously known, G ATC, CAG AG, BATGC AT, CRT AYNCTC, and CC ANTGAG, and four novel serovar-specific motifs, GRT ANTTYG, GA ACNGTA, GAA CY, and CAA ANCC. Interestingly, the BATGCAT motif was incompletely methylated (35-64% sites across the genome methylated), suggesting a possible role in gene regulation. Furthermore, the number of methylated BATGC AT motifs increased after storage in ground black pepper for 6 years from 475 to 657 (. Tennessee), 366 to 608 (. Anatum), and 525 to 570 ( Reading), thus warranting further study as an adaptive mechanism. This is the first long-term assessment of genomic changes in in a low moisture environment, and the first study to examine the methylome of any bacteria over a period of years, to our knowledge. These data contribute to our understanding of survival in LMFs, and coupled with further studies, will provide the information necessary to design effective interventions which reduce in LMFs and maintain a healthy, safe food supply.
低水分食品（LMFs）传统上被认为食用安全，因为大多数细菌需要较高的含水量才能生长。然而，由低水分食品引起的疾病暴发正在增加，且微生物病原体常与此有关。[病原体名称]能在低水分食品中存活数年，但很少有血清型被研究过，其这种长寿的潜在机制也未被充分了解。在此，我们确定[病原体名称]的田纳西血清型、阿纳托姆血清型和雷丁血清型，但不包括奥兰延堡血清型，能在磨碎的黑胡椒中存活6年。雷丁血清型以前未与任何低水分食品相关联。使用Illumina和太平洋生物科学公司的测序技术，我们还记录了这三种存活血清型在这6年期间基因组和甲基化组的变化。这三种血清型获得了少量单核苷酸多态性（SNP），包括七个替换（四个同义替换、两个非同义替换和一个非编码区的替换）以及两个插入缺失。在这三种血清型中鉴定出九个不同的N6 - 甲基腺嘌呤（m6A）甲基化基序，包括五个先前已知的基序，即G ATC、CAG AG、BATGC AT、CRT AYNCTC和CC ANTGAG，以及四个新的血清型特异性基序，即GRT ANTTYG、GA ACNGTA、GAA CY和CAA ANCC。有趣的是，BATGCAT基序甲基化不完全（全基因组35 - 64%的位点甲基化），这表明其在基因调控中可能发挥作用。此外，在磨碎的黑胡椒中储存6年后，甲基化的BATGC AT基序数量从475增加到657（田纳西血清型）、从366增加到608（阿纳托姆血清型）以及从525增加到570（雷丁血清型），因此作为一种适应性机制值得进一步研究。据我们所知，这是首次在低水分环境中对[病原体名称]的基因组变化进行长期评估，也是首次在数年时间内研究任何细菌的甲基化组。这些数据有助于我们理解[病原体名称]在低水分食品中的存活情况，并且与进一步的研究相结合，将提供设计有效干预措施所需的信息，以减少低水分食品中的[病原体名称]并维持健康、安全的食品供应。
