Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper.
Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper.
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DOI：
10.3389/fmicb.2022.970135
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发表时间：
2022
影响因子：
5.2
通讯作者：
中科院分区：
文献类型：
--
作者：
低水分食品（LMF）传统上被认为是安全的，因为大多数细菌需要更高的含水量才能生长。然而，由于LMF食品的爆发正在增加，并且微生物病原体肠道沙门氏菌经常涉及。S.肠杆菌可以在LMF中存活多年，但很少有血清型被研究，并且这种长寿的机制还没有很好地理解。在这里，我们确定S。肠道血清型S. Tennessee，S. Anatum和S.阅读而不是S。Oranienburg可以在地面黑胡椒中存活6年。S.阅读之前与任何LMF无关。使用Illumina和Pacific Biosciences测序技术，我们还记录了在这6年期间存活血清型的基因组和甲基化组的变化。这三个血清型获得了少量的单核苷酸多态性（SNP），包括7个取代（4个同义，2个非同义，1个非编码区取代）和2个插入缺失。在三种血清型中鉴定了九种不同的N6-甲基腺嘌呤（m6 A）甲基化基序，包括五种先前已知的基序，Gm 6ATC、CAGm 6AG、BATGCm 6AT、CRTm 6AYN 6CTC和CCm 6AN 7 TGAG，以及四种新的血清型特异性基序，GRTm 6AN 8 TTYG、GAm 6ACN 7 GTA、GAA m6 ACY和CAAm 6ANCC。有趣的是，BATGCAT基序是不完全甲基化的（整个基因组中35-64%的位点甲基化），表明可能在基因调控中起作用。此外，甲基化的BATGCm 6AT基序的数量在储存6年后从475增加到657（S. Tennessee），366 to 608（S. Anatum）和525至570（S.阅读），从而使进一步的学习成为一种适应机制。这是第一次对S.这是在低湿度环境中对enterica进行的第一次研究，并且据我们所知，这是第一次在一段时间内检查任何细菌的甲基化组。这些数据有助于我们对S.肠道沙门氏菌在LMF中的存活率，再加上进一步的研究，将提供必要的信息，以设计有效的干预措施，减少沙门氏菌。肠道菌在LMF和维持健康，安全的食品供应。
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 Salmonella enterica is frequently implicated. S. enterica 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 S. enterica serovars S. Tennessee, S. Anatum, and S. Reading but not S. Oranienburg can survive in the ground black pepper for 6 years. S. 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, Gm6ATC, CAGm6AG, BATGCm6AT, CRTm6AYN6CTC, and CCm6AN7TGAG, and four novel serovar-specific motifs, GRTm6AN8TTYG, GAm6ACN7GTA, GAA m6ACY, and CAAm6ANCC. 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 BATGCm6AT motifs increased after storage in ground black pepper for 6 years from 475 to 657 (S. Tennessee), 366 to 608 (S. Anatum), and 525 to 570 (S. Reading), thus warranting further study as an adaptive mechanism. This is the first long-term assessment of genomic changes in S. enterica 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 S. enterica survival in LMFs, and coupled with further studies, will provide the information necessary to design effective interventions which reduce S. enterica in LMFs and maintain a healthy, safe food supply.
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影响因子：
4.6
作者：
Baert L;Gimonet J;Barretto C;Fournier C;Jagadeesan B
通讯作者：
Jagadeesan B
影响因子：
48
作者：
Flusberg, Benjamin A.;Webster, Dale R.;Lee, Jessica H.;Travers, Kevin J.;Olivares, Eric C.;Clark, Tyson A.;Korlach, Jonas;Turner, Stephen W.
通讯作者：
Turner, Stephen W.
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
2
作者：
Beuchat, Larry R.;Komitopoulou, Evangelia;Ter Kuile, Benno H.
通讯作者：
Ter Kuile, Benno H.
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.