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Microbiology research at the systems biology and bioinformatics - 2019 (SBB-2019) school
BMC Microbiology ( IF 4.0 ) Pub Date : 2020-11-24 , DOI: 10.1186/s12866-020-02038-5
Yuriy L Orlov 1, 2, 3, 4 , Alexander N Ignatov 3, 5 , Elvira R Galieva 2 , Oxana B Dobrovolskaya 3, 4
Affiliation  

This Special Issue of BMC Microbiology “Systems Biology and Bioinformatics” presents the materials discussed at the 11-th Young Scientists School “Systems Biology and Bioinformatics”-2019 (SBB-2019) in Novosibirsk, Russia (http://conf.bionet.nsc.ru/sbb2019/en/). These Young Scientists’ Schools on bioinformatics have been organized every year since 2008 by the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences and Novosibirsk State University [1, 2]. To accompany this Special Issue on microbiology, parallel special journal issues in the fields of genomics, bioinformatics, and medical genomics were published as a part of SBB-2019 series in BioMed Central journals: BMC Genomics, BMC Medical Genomics, BMC Genetics, BMC Medical Genetics, and BMC Bioinformatics (https://bmcbioinformatics.biomedcentral.com/articles/supplements/volume-21-supplement-11). The SBB Schools in Novosibirsk are satellite training meetings for young scientists and PhD students, which are organized either as satellite events for BGRS\SB (Bioinformatics of Genome Regulation and Structure \ Systems Biology) conferences series [3, 4] or as independent events [2, 5]. The Schools were accompanied and complemented by the publication of special journal issues in BMC Microbiology [6] and other BioMed Central journals [3, 4].

This special issue contains the study by S.E. Peltek and co-authors [7] describing microbial life habitats in unique volcano caldera environment.

The caldera of the Uzon Volcano (Kamchatka Peninsula, Russia) is a region with active hydrothermal activity, which contains outlets of unique natural hydrothermal petroleum [8] with distinct microbiota. Hydrothermal petroleum is the oil found in natural outlets within active hydrothermal fields [8, 9]. According to carbon 14C dating, hydrothermal petroleum from various regions of the Earth is modern in geological scale, with the oldest sample being 29,000 years old [10]. The Uzon petroleum is the youngest on Earth, with the initial time estimate at 1000 years, and later found to be only 50 years old [11].

The composition of the Uzon oil was investigated in several studies [12]. Uzon oil has a unique make-up, with low proportion of heavy fractions and relatively high content of saturated hydrocarbons [11]. Correspondingly, the microbial communities of the “oil site” have diverse composition profiles, living at almost boiling temperatures (up to 97 °C), significant oscillations of pH, and high content of sulfides, arsenic, antimony, and mercury in water.

In this journal issue, Peltek et al. [7] analyzed the composition, structure, unique genetic features and the metabolic pathways of the microbial communities at the oil site. The authors present evidence of diverse metabolic pathways of hydrocarbon degradation by microorganisms being operational within the local microbiota. Interestingly, the authors found statistically significant relationships between geochemical parameters, taxonomic composition and the completeness of metabolic pathways [7]. Metabolic pathways of hydrocarbon oxidation were found to prevail in the studied communities, which corroborated the hypothesis on abiogenic synthesis of Uzon hydrothermal petroleum.

In previous research, the majority of the studied oil sites contained representatives of Actinomycetales (Actinobacteria). Typically, the geochemical parameters defined the structure and metabolic potential of microbial communities. This is confirmed by the genome sequence of Anoxybacillus flavithermus KU2–6-11 isolated from hot-spring in Uzon caldera, which was published recently [13]. Other prior work includes the microbial community analysis of the Uzon caldera springs, which was presented earlier at the BMC special journal issues accompanying a previous BGRS conference in 2014 [14]. The same researchgroup, A.V. Bryanskaya et al., published description of environmental factors for the composition of microbial communities of saline lakes in BMC Microbiology special issue [15]. While this journal issue has been in preparation, novel thermophilic Aeribacillus bacteriophage AP45 was isolated from the Kamchatka [16] as well as a thermophilic bacterium Geobacillus icigianus [17].

Going back to the BGRS post-conference issues, we would like to note fundamental systems biology work by late Dr. Vitaly A. Likhoshvai on the mathematical modeling of metabolic systems in Escherichia coli cells, which was published in BMC Microbiology [6]. This research showed that the modeling of relevant environmental factors can increase a heuristic value of a genomic study of the microbial communities. The manuscript by V.A.Likhoshvai, which has been finalized by his co-authors, was published in the parallel BMC Bioinformatics special issue after SBB-2019 School [18]. Here it is also appropriate to refer to the recent publication by V.A. Likhoshvai on dynamical model of non-inherited antibiotic tolerance of microorganisms [19].

We aim to support international exchanges and education in bioinformatics and systems biology in the forms of the Schools for young scientists and make new results open keeping traditions of the BGRS conference series [1, 2, 5, 20].

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We thank Prof. T.V. Tatarinova and A.V. Baranova for the editorial work on SBB-2019 journal issues. We are grateful to Academician N.A. Kolchanov for the organization of the “Systems Biology and Bioinformatics”-2019 School in Novosibirsk, Russia. We thank Dr. O. Tolmachov for the help with the manuscript preparation.

The publication has been prepared with the support of the RUDN University Program 5-100 (Recipients: YO, AI, OD).

About this supplement

This article has been published as part of BMC Microbiology Volume 20 Supplement 2, 2020: Selected Topics in “Systems Biology and Bioinformatics” - 2019: microbiology. The full contents of the supplement are available online at - https://bmcmicrobiol.biomedcentral.com/articles/supplements/volume-20-supplement-2.

Publication of this article was not covered by sponsorship.

Affiliations

  1. The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119146, Moscow, Russia

    Yuriy L. Orlov

  2. Novosibirsk State University, 630090, Novosibirsk, Russia

    Yuriy L. Orlov & Elvira R. Galieva

  3. Agrarian and Technological Institute, Peoples’ Friendship University of Russia (RUDN University), 117198, Moscow, Russia

    Yuriy L. Orlov, Alexander N. Ignatov & Oxana B. Dobrovolskaya

  4. Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia

    Yuriy L. Orlov & Oxana B. Dobrovolskaya

  5. PhytoEngineering R&D Centre, 141880, Moscow Region, Moscow, Russia

    Alexander N. Ignatov

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Contributions

YO is guest editor of SBB-2019 issues. AI, EG and OD are the invited editors and the organizing committee members. All the authors read, revised and approved the final manuscript.

Authors’ information

Yuriy L. Orlov, the conference organizer and guest editor of the SBB-2019 special issues orlov@d-health.institute.

Elvira R. Galieva, organizing committee member.

Alexander N. Ignatov, organizing committee member.

Oxana B. Dobrovolskaya, organizing committee member.

Corresponding author

Correspondence to Yuriy L. Orlov.

Competing interests

The authors declare that they have no competing interests.

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Orlov, Y.L., Ignatov, A.N., Galieva, E.R. et al. Microbiology research at the systems biology and bioinformatics - 2019 (SBB-2019) school. BMC Microbiol 20, 348 (2020). https://doi.org/10.1186/s12866-020-02038-5

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中文翻译：
系统生物学和生物信息学的微生物学研究-2019（SBB-2019）学校

BMC微生物学特刊“系统生物学和生物信息学”介绍了在俄罗斯新西伯利亚的第11届青年科学家学校“系统生物学和生物信息学” -2019（SBB-2019）上讨论的材料（http：//conf.bionet。 nsc.ru/sbb2019/en/）。自2008年以来，这些年轻的生物信息学青年学院每年都由俄罗斯科学院西伯利亚分校的细胞学和遗传学研究所和新西伯利亚国立大学组织[1，2]。为配合本期微生物学专刊，在BioMed Central期刊上将基因组学，生物信息学和医学基因组学领域的平行专刊作为SBB-2019系列的一部分出版：BMC Genomics，BMC Medical Genomics，BMC Genetics，BMC Medical遗传学和BMC生物信息学（https：//bmcbioinformatics.biomedcentral。com / articles / supplements / volume-21-supplement-11）。新西伯利亚的SBB学校是面向年轻科学家和博士生的卫星培训会议，既可以作为BGRS \ SB（基因组调控和结构\系统生物学的生物信息学）会议系列[3，4]的卫星活动，也可以作为独立活动[ 2，5]。在BMC微生物学[6]和其他BioMed Central期刊[3，4]上，特殊学校的出版物得到了学校的伴随和补充。

本期特刊包含SE Peltek及其合作者的研究[7]，该研究描述了火山独特的火山口环境中的微生物生活栖息地。

Uzon火山的火山口（俄罗斯堪察加半岛）是一个热液活动活跃的地区，其中包含独特的天然热液石油[8]和独特的微生物群落。热液石油是在活跃的热液田中的天然出口发现的油[8，9]。根据碳14 C测年，来自地球各个地区的热液石油在地质规模上是现代的，最古老的样品有29,000年的历史[10]。乌宗石油是地球上最年轻的石油，最初的估计时间为1000年，后来发现只有50年[11]。

在几项研究中对乌松油的成分进行了研究[12]。乌宗石油具有独特的组成，重质馏分的比例低​​，饱和烃含量较高[11]。相应地，“油位”的微生物群落具有多种组成特征，几乎处于沸腾温度（最高97°C），pH值明显波动，水中的硫化物，砷，锑和汞含量很高。

在此期刊中，Peltek等人。[7]分析了油位微生物群落的组成，结构，独特的遗传特征和代谢途径。作者提出了微生物在本地微生物群中运行的烃降解的各种代谢途径的证据。有趣的是，作者发现地球化学参数，分类学组成和代谢途径的完整性之间在统计学上具有显着关系[7]。在所研究的社区中发现了碳氢化合物代谢的代谢途径，这证实了乌松热液石油非生物合成的假说。

在先前的研究中，大多数被研究的油位都包含放线菌（放线菌）的代表。通常，地球化学参数定义了微生物群落的结构和代谢潜能。这由黄杆菌无氧杆菌的基因组序列证实KU2-6-11是最近从乌桑破火山口的温泉中分离出来的[13]。其他先前的工作包括对Uzon破火山口弹簧的微生物群落分析，该分析在2014年上一次BGRS会议的伴随BMC特刊上发表过[14]。同一研究小组AV Bryanskaya等人在BMC Microbiology特刊[15]中发表了有关盐湖微生物群落组成的环境因素的描述。在准备本期杂志时，从堪察加[16]以及嗜热细菌igigbacus icigianus [17]中分离出了新型嗜热航空杆菌噬菌体AP45 。

回到BGRS会议后的问题，我们想指出已故的Vitaly A. Likhoshvai博士对大肠杆菌细胞代谢系统的数学建模的基础系统生物学工作，该工作发表在BMC Microbiology [6]中。这项研究表明，相关环境因素的建模可以增加微生物群落基因组研究的启发式价值。VALikhoshvai的手稿已由他的合著者完成，在SBB-2019学校之后在平行的BMC生物信息学特刊上发表[18]。在这里也有必要参考VA Likhoshvai的最新出版物，即关于非遗传的微生物对抗生素的耐受性的动力学模型[19]。

我们旨在以青年科学家学校的形式，支持生物信息学和系统生物学方面的国际交流和教育，并保持BGRS会议系列的传统[1、2、5、20]，从而取得新成果。

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下载参考

我们感谢TV Tatarinova教授和AV Baranova所做的关于SBB-2019期刊问题的编辑工作。我们感谢NA Kolchanov院士在俄罗斯新西伯利亚组织的“系统生物学和生物信息学” -2019年学校的组织工作。我们感谢O. Tolmachov博士为稿件准备工作提供的帮助。

该出版物是在RUDN大学计划5-100（收件人：YO，AI，OD）的支持下编写的。

关于此补品

本文已作为BMC微生物学第20卷增补本2020：《系统生物学和生物信息学》-2019：微生物学中的选定主题的一部分发表。该补充剂的全部内容可在线访问-https://bmcmicrobiol.biomedcentral.com/articles/supplements/volume-20-supplement-2。

这篇文章的发表不包括在赞助范围内。

隶属关系

  1. 俄罗斯联邦卫生部莫斯科国立第一医科大学（谢切诺夫大学）IM舍切诺夫数字健康研究所，119146，俄罗斯莫斯科

    尤里·L·奥尔洛夫（Yuriy L.Orlov）

  2. 新西伯利亚国立大学，630090，俄罗斯新西伯利亚

    Yuriy L.Orlov和Elvira R.Galieva

  3. 俄罗斯人民友谊大学（RUDN大学）农业技术学院，117198，俄罗斯莫斯科

    Yuriy L.Orlov，Alexander N.Ignatov和Oxana B.Dobrovolskaya

  4. SB RAS细胞与遗传研究所，630090，俄罗斯新西伯利亚

    Yuriy L.Orlov和Oxana B.Dobrovolskaya

  5. PhytoEngineering R＆D Center，141880，莫斯科地区，俄罗斯莫斯科

    亚历山大·伊格纳托夫（Alexander N.Ignatov）

s
  1. Yuriy L. Orlov查看作者出版物

    您也可以在PubMed Google学术搜索中搜索该作者 

  2. Alexander N. Ignatov查看作者出版物

    您也可以在PubMed Google学术搜索中搜索该作者 

  3. Elvira R. Galieva查看作者出版物

    您也可以在PubMed Google学术搜索中搜索该作者 

  4. Oxana B. Dobrovolskaya查看作者出版物

    您也可以在PubMed Google学术搜索中搜索该作者 

会费

YO是SBB-2019问题的客座编辑。AI，EG和OD是特邀编辑和组委会成员。所有作者都阅读，修订和批准了最终手稿。

作者信息

会议组织者兼SBB-2019特刊orlov@d-health.institute的客座编辑Yuriy L.Orlov。

Elvira R. Galieva，组委会成员。

亚历山大·伊格纳托夫（Alexander N. Ignatov），组委会成员。

Oxana B. Dobrovolskaya，组委会成员。

通讯作者

与Yuriy L. Orlov的对应。

利益争夺

作者宣称他们没有竞争利益。

发行人须知

对于已发布地图和机构隶属关系中的管辖权主张，Springer Nature保持中立。

开放存取本文是根据知识共享署名4.0国际许可许可的，该许可允许以任何媒介或格式使用，共享，改编，分发和复制，只要您对原始作者和出处提供适当的信誉，链接到知识共享许可，并指出是否进行了更改。本文的图像或其他第三方材料包含在该文章的知识共享许可中，除非在该材料的信用栏中另有说明。如果该材料未包含在该文章的创用CC许可中，并且您的预期用途未得到法律法规的许可或超出了许可的用途，则您需要直接获得版权所有者的许可。要查看此许可证的副本，请访问http://creativecommons.org/licenses/by/4.0/。

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引用本文

Orlov，YL​​，Ignatov，AN，Galieva，ER等。系统生物学和生物信息学-2019（SBB-2019）学校的微生物学研究。BMC微生物学 20， 348（2020）。https://doi.org/10.1186/s12866-020-02038-5

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  • 发表时间：

  • DOI ：https ：//doi.org/10.1186/s12866-020-02038-5
更新日期：2020-11-25
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