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Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N) 斯瓦尔巴特(北纬 79 度)Ny Ålesund 永久冻土活动层中细菌 MAGs 的特定深度分布情况
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-28 DOI: 10.1016/j.syapm.2024.126544
Katie Sipes , Joy Buongiorno , Andrew D. Steen , Andrey A. Abramov , Chukwufumnanya Abuah , Samantha L. Peters , Richard J. Gianonne , Robert L. Hettich , Julia Boike , Sarahi L. Garcia , Tatiana A. Vishnivetskaya , Karen G. Lloyd

Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018–2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from −5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2–4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ∼6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.

北极土壤微生物群落可能会随着温度的升高和气候变化带来的水供应量的增加而发生变化。我们考察了斯瓦尔巴群岛Ny Ålesund的Bayelva监测站2年(2018-2019年)来受永久冻土影响的土壤上层80厘米处的温度和体积液态水含量(VWC)。我们的研究表明,VWC随深度增加而增加,而原地温度在垂直方向较为稳定,季节性温度范围为-5°C至5°C。在2018年4月冷冻时采集的2-4厘米垂直分辨率和2019年9月解冻时采集的10厘米垂直分辨率的原核生物元基因组(MAGs)均已获得。最丰富的 MAGs 是酸性菌群(Acidobacteriota)、放线菌群(Actinomycetota)和绿僵菌群(Chloroflexota)。放线菌群(Actinomycetota)和绿菌群(Chloroflexota)随着深度的增加而增加,而酸性细菌群(Acidobacteriota)类中的Thermoanaerobaculia Gp7-AA8、Blastocatellia UBA7656和Vicinamibacteria Vicinamibacterales则分别出现在6厘米以上、6厘米以下和20厘米以下。所有 MAGs 都有多种碳降解基因,放线菌属(Actinomycetota)和绿僵菌属(Chloroflexota)有自养基因。编码β-葡萄糖苷酶、N-乙酰-β-D-葡萄糖苷酶和木糖苷酶的基因随着深度的增加而增加,表明随着 VWC 越高,有机物降解的潜力越大。酸性菌群主要分布在顶部 6 厘米处,其类别随深度而分离,而放线菌群和绿藻菌群主要分布在 6 厘米以下。这表明酸性菌群适应地表较低的 VWC,而放线菌群和绿僵菌群则在 6 厘米以下持续存在,具有较高的 VWC。这表明,在北极矿质土壤的微生物气候变化响应中,VWC 可能与温度一样重要。在此,我们描述了酸细菌群(Onstottus arcticum、Onstottus frigus 和 Gilichinskyi gelida)和放线菌群(Mayfieldus profundus)中基于 MAG 的 Seqcode 类型物种。
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引用次数: 0
Harmonious naming across nomenclature codes exemplified by the description of bacterial isolates from the mammalian gut 以哺乳动物肠道细菌分离物的描述为例,说明不同命名编码之间的和谐命名。
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-12 DOI: 10.1016/j.syapm.2024.126543
Thomas C.A. Hitch , David Wylensek , Kevin Bisdorf , Eva M. Buhl , Nicole Treichel , Birte Abt , Jörg Overmann , Thomas Clavel

A dual system for naming prokaryotes is currently in place based on the well-established International Code of Nomenclature of Prokaryotes (ICNP) and the newly created Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Whilst recent creation of the SeqCode opened an avenue to accelerate the naming of uncultured taxa, the existence of two codes increases the risk of species being assigned multiple validly published names. In this work we present a workflow that aims to limit conflicts by firstly naming novel cultured taxa under the SeqCode, and secondly under the ICNP, enhancing the traceability of the taxa across the two codes. To exemplify this workflow, we describe four novel taxa isolated from the intestine of pigs: Intestinicryptomonas porci gen. nov., sp. nov. (strain CLA-KB-P66T, genome accession GCA_033971905.1TS) within a novel family, Intestinicryptomonaceae; Grylomicrobium aquisgranensis gen. nov., sp. nov. (CLA-KB-P133T, GCA_033971865.1TS); Absicoccus intestinalis sp. nov. (CLA-KB-P134T, GCA_033971885.1TS); and Mesosutterella porci sp. nov. (oilRF-744- wt-GAM-9T, GCF_022134585.1TS).

目前,原核生物的命名有双重系统,一个是行之有效的《国际原核生物命名法》(ICNP),另一个是新创建的《序列数据描述的原核生物命名法》(SeqCode)。虽然最近创建的 SeqCode 为加快未培养类群的命名开辟了一条途径,但两个代码的存在增加了物种被赋予多个有效已发表名称的风险。在这项工作中,我们提出了一个工作流程,旨在通过首先用 SeqCode 命名新的培养类群,其次用 ICNP 命名新的培养类群来限制冲突,从而提高类群在两种代码之间的可追溯性。为了举例说明这一工作流程,我们介绍了从猪肠中分离出来的四个新分类群:新菌株(菌株 CLA-KB-P66T,基因组登录号 GCA_033971905.1TS);Grylomicrobium aquisgranensis gen、sp.nov.(CLA-KB-P133T,GCA_033971865.1TS);Absicoccus intestinalis sp.nov.(CLA-KB-P134T,GCA_033971885.1TS);以及 Mesosutterella porci sp.nov.(oilRF-744- wt-GAM-9T,GCF_022134585.1TS)。
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引用次数: 0
Atacama desert is a source of new Micromonospora strains: description of Micromonospora sicca sp. nov 阿塔卡马沙漠是新的小孢子菌株的来源:描述了Micromonospora sicca sp.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-03 DOI: 10.1016/j.syapm.2024.126542
Lorena Carro , Patrycja Golińska , Zaki Saati-Santamaría , José M. Igual , Hans-Peter Klenk , Michael Goodfellow

Several strains were isolated from subsurface soil of the Atacama Desert and were previously assigned to the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of isolates 4G51T, 4G53, and 4G57. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, including meso-diaminopimelic acid in the cell wall peptidoglycan, MK-9(H4) as major respiratory quinone, iso-C15:0 and iso-C16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strains 4G51T, 4G53, and 4G57 showed the highest similarity (97.9 %) with the type strain of Micromonospora costi CS1-12T, forming an independent branch in the phylogenetic gene tree. Their independent position was confirmed with genome phylogenies, being most closely related to the type strain of Micromonospora kangleipakensis. Digital DNA-DNA hybridization and average nucleotide identity analyses between the isolates and their closest phylogenomic neighbours confirmed that they should be assigned to a new species within the genus Micromonospora for which the name Micromonospora sicca sp. nov. (4G51T=PCM 3031T=LMG 30756T) is proposed.

一些菌株是从阿塔卡马沙漠的地下土壤中分离出来的,以前被归入小孢子菌属。一项多相研究旨在确定分离物 4G51T、4G53 和 4G57 的分类归属。所有菌株的化学分类学特性都符合其在小孢子属中的分类,包括细胞壁肽聚糖中的中二氨基丙二酸、主要呼吸醌 MK-9(H4)、主要脂肪酸异-C15:0 和异-C16:0 以及主要极性脂质二磷脂酰甘油、磷脂酰乙醇胺和磷脂酰肌醇。菌株 4G51T、4G53 和 4G57 的 16S rRNA 基因序列与成本小孢子菌 CS1-12T 型菌株的相似度最高(97.9%),在系统发生基因树中形成一个独立的分支。它们的独立位置在基因组系统进化中得到了证实,与 Kangleipakensis 小单胞菌的模式菌株关系最为密切。数字 DNA-DNA 杂交和分离物与其最相近的系统发生组之间的平均核苷酸同一性分析证实,这些分离物应归属于小孢子属中的一个新种,其名称为 Micromonospora sicca sp.nov.(4G51T=PCM 3031T=LMG 30756T)。
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引用次数: 0
Ignisphaera cupida sp. nov., a hyperthermophilic hydrolytic archaeon from a hot spring of Uzon (Kamchatka), and emended description of the genus Ignisphaera 来自乌宗(堪察加半岛)温泉的嗜热水解古菌 Ignisphaera cupida sp.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-07-26 DOI: 10.1016/j.syapm.2024.126541
Olga A. Podosokorskaya, Alexander G. Elcheninov, Alexandra A. Klyukina, Alexander Y. Merkel

A novel strictly anaerobic hyperthermophilic archaeon, strain 4213-coT, was isolated from a terrestrial hot spring in the Uzon Caldera, Kamchatka (Russian Federation). Coccoid cells were present singly, in pairs, or aggregates, and occasionally were motile. The strain grew at 75–100 °C and within a pH range of 5.4–8.2 with the optimum at 92 °C and pH 6.4–6.7. Strain 4213-coT was a chemoorganoheterotroph, growing on proteinaceous substrates and mono-, di- and polysaccharides (starch, guar gum, xanthan gum). It did not require sodium chloride for growth. The complete genome of strain 4213-coT was 1.74 Mbp in size; its G+C content was 36.18 %. Genome analysis allowed to identify 25 genes encoding glycosidases involved in polysaccharide hydrolysis as well as genes of ADP-forming acetate-CoA ligase, lactate dehydrogenase and two [NiFe] hydrogenases responsible for acetate, lactate and hydrogen formation during fermentation. Moreover gene cluster encoding archaellum subunits was found. According to the phylogenomic analysis strain 4213-coT formed a species-level phylogenetic lineage within Ignisphaera genus. Our phylogenomic analysis also supports the delineation of the Ignisphaera genus into a separate family Ignisphaeraceae, as recently published. Here we propose a novel species Ignisphaera cupida, sp. nov. with type strain 4213-coT (=JCM 39446T=VKM B-3715T=UQM 41593T). Ecogenomic analysis showed that representatives of the Ignisphaera are thermophilic archaea, the majority of them were found in terrestrial hot springs and deep-sea hydrothermal vents. This study allowed a better understanding of physiology and ecology of Ignisphaeraceae – a rather understudied archaeal group.

从堪察加半岛(俄罗斯联邦)乌孙破火山口的陆地温泉中分离出了一种新的严格厌氧的嗜热古菌--4213-coT 菌株。球状细胞单个、成对或聚集存在,偶尔会运动。该菌株的生长温度为 75-100℃,pH 值范围为 5.4-8.2,最适生长温度为 92℃,pH 值为 6.4-6.7。菌株 4213-coT 是一种化学有机异养生物,可在蛋白质基质和单糖、双糖和多糖(淀粉、瓜尔豆胶、黄原胶)上生长。它的生长不需要氯化钠。菌株 4213-coT 的完整基因组大小为 1.74 Mbp,G+C 含量为 36.18%。通过基因组分析,确定了参与多糖水解的 25 个糖苷酶编码基因、ADP 形成醋酸-CoA 连接酶基因、乳酸脱氢酶基因以及在发酵过程中负责形成醋酸、乳酸和氢气的两个[NiFe]氢酶基因。此外,还发现了编码弓形体亚基的基因簇。根据系统发生组分析,菌株 4213-coT 在 Ignisphaera 属中形成了一个种级系统发生系。我们的系统发生组分析也支持最近发表的将 Ignisphaera 属划分为一个独立的 Ignisphaeraceae 科的观点。在此,我们提出了一个新物种 Ignisphaera cupida,新种,其模式菌株为 4213-coT(=JCM 39446T=VKM B-3715T=UQM 41593T)。生态基因组分析表明,Ignisphaera 的代表是嗜热古细菌,它们中的大多数在陆地温泉和深海热液喷口中被发现。这项研究有助于更好地了解嗜热古细菌的生理学和生态学。
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引用次数: 0
Comparative genomics of the carmine cochineal symbiont Candidatus Dactylopiibacterium carminicum reveals possible protection to the host against viruses via CRISPR/Cas 胭脂鱼共生菌 Candidatus Dactylopiibacterium carminicum 的比较基因组学揭示了通过 CRISPR/Cas 保护宿主免受病毒侵害的可能性。
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-07-20 DOI: 10.1016/j.syapm.2024.126540
Rafael Bustamante-Brito , Arturo Vera-Ponce de León , Mónica Rosenblueth , Esperanza Martínez-Romero

We present new genomes from the bacterial symbiont Candidatus Dactylopiibacterium carminicum obtained from non-domesticated carmine cochineals belonging to the scale insect Dactylopius (Hemiptera: Coccoidea: Dactylopiidae). As Dactylopiibacterium has not yet been cultured in the laboratory, metagenomes and metatranscriptomics have been key in revealing putative symbiont functions. Dactylopiibacterium is a nitrogen-fixing beta-proteobacterium that may be vertically transmitted and shows differential gene expression inside the cochineal depending on the tissue colonized. Here we found that all cochineal species tested had Dactylopiibacterium carminicum which has a highly conserved genome. All Dactylopiibacterium genomes analyzed had genes involved in nitrogen fixation and plant polymer degradation. Dactylopiibacterium genomes resemble those from free-living plant bacteria, some found as endophytes. Notably, we found here a new putative novel function where the bacteria may protect the insect from viruses, since all Dactylopiibacterium genomes contain CRISPRs with a spacer matching nucleopolyhedrovirus that affects insects.

我们展示了从属于鳞翅目昆虫胭脂虫(半翅目:茧科:Dactylopiidae)的非驯化胭脂虫身上获得的细菌共生体胭脂虫细菌(Candidatus Dactylopiibacterium carminicum)的新基因组。由于 Dactylopiibacterium 尚未在实验室中培养,因此元基因组和元转录组学是揭示假定共生功能的关键。Dactylopiibacterium 是一种固氮的 beta 蛋白细菌,可以垂直传播,并根据定殖组织的不同,在褐藻体内表现出不同的基因表达。在这里,我们发现所有被检测的褐藻物种都含有褐藻双歧杆菌,而褐藻双歧杆菌的基因组具有高度保守性。分析的所有 Dactylopiibacterium 基因组都有参与固氮和植物聚合物降解的基因。Dactylopiibacterium 的基因组与自由生活的植物细菌的基因组相似,其中一些是作为内生菌发现的。值得注意的是,我们在这里发现了一种新的推测功能,即细菌可能会保护昆虫免受病毒的侵害,因为所有的双歧杆菌基因组都含有与影响昆虫的核多角体病毒相匹配的CRISPRs。
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引用次数: 0
Phylogenetically diverse bacterial species produce histamine 不同系统发育的细菌物种都会产生组胺。
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-07-17 DOI: 10.1016/j.syapm.2024.126539
Kristen A. Engevik , Amber Hazzard , Brenton Puckett , Kathleen M. Hoch , Sigmund J. Haidacher , Anthony M. Haag , Jennifer K. Spinler , James Versalovic , Melinda A. Engevik , Thomas D. Horvath

Histamine is an important biogenic amine known to impact a variety of patho-physiological processes ranging from allergic reactions, gut-mediated anti-inflammatory responses, and neurotransmitter activity. Histamine is found both endogenously within specialized host cells and exogenously in microbes. Exogenous histamine is produced through the decarboxylation of the amino acid L-histidine by bacterial-derived histidine decarboxylase enzymes. To investigate how widespread histamine production is across bacterial species, we examined 102,018 annotated genomes in the Integrated Microbial Genomes Database and identified 3,679 bacterial genomes (3.6 %) which possess the enzymatic machinery to generate histamine. These bacteria belonged to 10 phyla: Bacillota, Bacteroidota, Actinomycetota, Pseudomonadota, Lentisphaerota, Fusobacteriota, Armatimonadota, Cyanobacteriota, Thermodesulfobacteriota, and Verrucomicrobiota. The majority of the identified bacteria were terrestrial or aquatic in origin, although several bacteria originated in the human gut microbiota. We used liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted metabolomics to confirm our genome discoveries correlated with L-histidine-to-histamine conversion in a chemically defined bacterial growth medium by a cohort of select environmental and human gut bacteria. We found that environmental microbes Vibrio harveyi, Pseudomonas fluorescens and Streptomyces griseus generated considerable levels of histamine (788 – 8,730 ng/mL). Interestingly, we found higher concentrations of histamine produced by gut-associated Fusobacterium varium, Clostridium perfringens, Limosilactobacillus reuteri and Morganella morganii (8,510––82,400 ng/mL). This work expands our knowledge of histamine production by diverse microbes.

组胺是一种重要的生物胺,已知会影响过敏反应、肠道介导的抗炎反应和神经递质活动等多种病理生理过程。组胺既存在于特化的宿主细胞内源性,也存在于微生物的外源性。外源性组胺是通过源于细菌的组氨酸脱羧酶将氨基酸 L-组氨酸脱羧而产生的。为了研究组胺的产生在细菌物种中的广泛程度,我们研究了综合微生物基因组数据库(Integrated Microbial Genomes Database)中的102,018个注释基因组,发现3,679个细菌基因组(3.6%)拥有产生组胺的酶机制。这些细菌属于 10 个门类:这些细菌属于 10 个门类:芽孢杆菌门、类杆菌门、放线菌门、假单胞菌门、扁桃体杆菌门、镰刀菌门、臂杆菌门、蓝藻菌门、热硫化杆菌门和疣菌门。虽然有几种细菌来源于人类肠道微生物群,但大多数被鉴定的细菌来源于陆生或水生生物。我们使用基于液相色谱-串联质谱(LC-MS/MS)的靶向代谢组学来证实我们的基因组发现与精选的环境细菌和人类肠道细菌在化学定义的细菌生长培养基中将左旋组氨酸转化为组胺有关。我们发现,环境微生物哈维弧菌、荧光假单胞菌和灰葡萄孢链霉菌产生了相当高水平的组胺(788 - 8730 纳克/毫升)。有趣的是,我们发现肠道相关的变异镰刀菌、产气荚膜梭菌、Limosilactobacillus reuteri和摩根菌产生的组胺浓度更高(8510-82400纳克/毫升)。这项研究拓展了我们对多种微生物产生组胺的认识。
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引用次数: 0
Streptococcus suis subsp. hashimotonensis subsp. nov.: Lancefield group A antigen–positive organisms isolated from human clinical specimens and wild boar oral cavity samples Streptococcus suis subsp:从人类临床标本和野猪口腔样本中分离出的兰斯菲尔德A组抗原阳性菌
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-07-11 DOI: 10.1016/j.syapm.2024.126538
Yuki Hasegawa , Toyokazu Akita , Tomokazu Kuchibiro , Tohru Miyoshi-Akiyama , Junko Tomida , Ryo Kutsuna , Ryota Mori , Miki Okuno , Yoshitoshi Ogura , Yoshiaki Kawamura

Three Streptococcus suis-like strains positive for Lancefield antigen group A were isolated from human boar bite wounds and the oral cavities of boars in Hashimoto City, Wakayama Prefecture, Japan, and their taxonomic positions were investigated. Application of the VITEK2 system identified all three isolates as S. suis with > 94 % probability. The isolates were assigned to S. suis based on the results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis (Biotyper score of 2.382) but were differentiated according to the characteristic signal peaks (4709 m/z and 9420 m/z) that were not present for S. suis. Sequence analysis of the 16S rRNA and sodA genes determined that the isolates were similar to S. suis; however, these genes appeared on a phylogenetic sub-branch. Phylogenetic analysis of the whole chromosomal DNA showed that the isolate formed a cluster with S. suis but with clear divergence. The average nucleotide index using BLAST between the clinical isolate (PAGU 2482) and a closely related reference strain of S. suis was 94.75 %, which was not clearly conclusive; however, digital DNA-DNA hybridization showed a value of 61.2 %. Biochemical reactions, including those with acid phosphatase, α-chymotrypsin, and tagatose (acidification), distinguished our isolates from S. suis. Thus, based on phylogenetic, genomic, and phenotypic characteristics and MALDI-TOF-MS signal patterns, we propose that the isolate with Lancefield group A positive characteristics be designated as a novel subspecies, Streptococcus suis subsp. hashimotonensis subsp. nov., with the type strain PAGU 2482T (GTC 18290T = CCUG 77434T).

从日本和歌山县桥本市的人被野猪咬伤的伤口和野猪的口腔中分离出了三株对兰斯菲尔德抗原 A 群呈阳性的猪链球菌样菌株,并对它们的分类位置进行了研究。应用 VITEK2 系统将所有三个分离物鉴定为猪链球菌的概率为 > 94 %。根据基质辅助激光解吸/电离飞行时间质谱(MALDI-TOF-MS)分析的结果(Biotyper 得分为 2.382),这些分离物被归类为 S. suis,但根据 S. suis 不存在的特征信号峰(4709 m/z 和 9420 m/z)进行了区分。16S rRNA 和 sodA 基因的序列分析表明,这些分离物与猪痢疾杆菌相似;但是,这些基因出现在一个系统发育子分支上。对整个染色体 DNA 的系统进化分析表明,该分离物与 S. suis 形成了一个群集,但有明显的差异。使用 BLAST 对临床分离株(PAGU 2482)和与之密切相关的猪链球菌参考株之间的核苷酸平均指数进行了分析,结果为 94.75%,这并不能明确得出结论;然而,数字 DNA-DNA 杂交的结果显示该值为 61.2%。生化反应,包括酸性磷酸酶、α-糜蛋白酶和塔格糖(酸化)反应,将我们的分离物与猪链球菌区分开来。因此,根据系统发育、基因组和表型特征以及 MALDI-TOF-MS 信号模式,我们建议将具有 Lancefield A 组阳性特征的分离物定为一个新亚种,即猪链球菌 hashimotonensis 亚种,模式菌株为 PAGU 2482T (GTC 18290T = CCUG 77434T)。
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引用次数: 0
Classification of a novel Serratia species, isolated from a wound swab in North Rhine-Westphalia: Proposal of Serratia sarumanii sp. nov 从北莱茵-威斯特法伦州的伤口拭子中分离出的新型沙雷氏菌的分类:提出新的沙雷氏菌(Serratia sarumanii sp.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-06-29 DOI: 10.1016/j.syapm.2024.126527
Levin Joe Klages , Olaf Kaup , Tobias Busche , Jörn Kalinowski , Christian Rückert-Reed

Novel, white-pigmented, Gram-negative bacterial strains (K-M0706T, K-M0228, K-M0252, K-M0260) were isolated from clinical samples. With a similarity of up to 69.7 % to Serratia nevei S15T and up to 63.8 % to Serratia marcescens ATCC 13880T, as determined by digital DNA-DNA hybridization, the strains were assigned as novel species of the genus Serratia. The species can easily be differentiated from the red colored Serratia marcescens sensu stricto by its white phenotype. Discrimination between this strain and Serratia nevei is possible due to alpha-glucosidase activity and O/129-resistance, as shown for strain K-M0706T. The major fatty acids were determined as myristate, palmitate, cis–9,10-methylenehexadecanoate, linoleate, and (all cis-9,10)-methyleneoctadecanoate. These phenotypical and genomic data support the assignment of a novel species within the genus Serratia, named S. sarumanii due to its pathogenicity and white phenotype, with strain K-M0706T as the type strain.

从临床样本中分离出了新的白色色素革兰氏阴性细菌菌株(K-M0706T、K-M0228、K-M0252、K-M0260)。经数字 DNA-DNA 杂交测定,这些菌株与 Serratia nevei S15T 的相似度高达 69.7%,与 Serratia marcescens ATCC 13880T 的相似度高达 63.8%,因此被认定为 Serratia 属的新种。该菌株的白色表型很容易与红色的严格意义上的 Serratia marcescens 区分开来。如菌株 K-M0706T 所示,该菌株具有α-葡萄糖苷酶活性和对 O/129 的抗性,因此可以将其与新韦氏沙雷氏菌区分开来。主要脂肪酸被确定为肉豆蔻酸、棕榈酸、顺式-9,10-亚甲基十六烷酸、亚油酸和(所有顺式-9,10)亚甲基十八烷酸。这些表型和基因组数据支持在沙雷氏菌属中划分出一个新物种,因其致病性和白色表型而被命名为沙雷氏菌(S. sarumanii),菌株 K-M0706T 为模式菌株。
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引用次数: 0
Rosettibacter primus gen. nov., sp. nov., and Rosettibacter firmus sp. nov., facultatively anaerobic moderately thermophilic bacteria of the class Ignavibacteria from hot springs of North Ossetia Rosettibacter primus gen.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-06-28 DOI: 10.1016/j.syapm.2024.126528
Olga A. Podosokorskaya, Nika F. Petrova, Ekaterina N. Tikhonova, Alexandra A. Klyukina, Alexander G. Elcheninov

A novel facultatively anaerobic moderately thermophilic bacteria, strains 4137-MeT and 4148-MeT, were isolated from hot springs of Karmadon and Ursdon, respectively (North Ossetia, Russian Federation). Gram-negative, motile rods were present singly, in pairs, rosettes, and aggregates, or formed biofilms. Both strains grew optimally at 50–55 °C, pH 7.0 and did not require sodium chloride or yeast extract for growth. They were chemoorganoheterotrophs, growing on mono-, di- and polysaccharides (cellulose, starch, xylan, lichenan, galactan, xyloglucan, mannan, xanthan gum, guar gum) as well as proteinaceous substrates (gelatin, peptone, beef and yeast extract). Growth under anaerobic conditions was observed in presence and absence of external electron acceptors. Sulfur, thiosulfate, arsenate, Fe-citrate, and ferrihydrite were reduced with acetate, starch, or yeast extract as electron donors. The respiratory quinone was MK-7. Major cellular fatty acids of both strains were iso-C15:0, anteiso-C17:0, C15:0, iso-C16:0 and additionally iso-C17:0 for strain 4137-MeT. The size of the genome and genomic DNA G + C content of strain 4137-MeT were 3.24 Mb. and 29.9 %, respectively; for strain 4148-MeT – 3.33 Mb and 30.7 %. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strains 4137-MeT and 4148-MeT represented a distinct lineage of the family Melioribacteraceae within the class Ignavibacteria. Based on phylogenetic analysis and phenotypic features, the novel isolates were assigned to a novel genus, for which the name Rosettibacter gen. nov. is proposed. Strain 4148-MeT represents its type species Rosettibacter primus sp. nov., while strain 4137-MeT represents a new species Rosettibacter firmus sp. nov.

一种新型兼性厌氧中度嗜热细菌--菌株 4137-MeT 和 4148-MeT--分别从卡尔马东和乌尔斯顿(俄罗斯联邦北奥塞梯)的温泉中分离出来。这两种菌株均为革兰氏阴性,可运动,以单个、成对、莲座状和聚集状存在,或形成生物膜。这两种菌株在 50-55 °C、pH 值为 7.0 的条件下生长最佳,生长不需要氯化钠或酵母提取物。它们是化学有机异养生物,可在单糖、双糖和多糖(纤维素、淀粉、木聚糖、地衣聚糖、半乳聚糖、木聚糖、甘露聚糖、黄原胶、瓜尔胶)以及蛋白质基质(明胶、蛋白胨、牛肉和酵母提取物)上生长。在有和没有外部电子受体的情况下,都能观察到厌氧条件下的生长情况。以醋酸盐、淀粉或酵母提取物为电子供体还原了硫、硫代硫酸盐、砷酸盐、柠檬酸铁和亚铁。呼吸醌为 MK-7。两种菌株的主要细胞脂肪酸均为异-C15:0、前-C17:0、C15:0、异-C16:0,4137-MeT 菌株的主要细胞脂肪酸为异-C17:0。菌株 4137-MeT 的基因组大小和基因组 DNA G + C 含量分别为 3.24 Mb 和 29.9 %;菌株 4148-MeT 的基因组大小和基因组 DNA G + C 含量分别为 3.33 Mb 和 30.7 %。根据 16S rRNA 基因序列和保守蛋白序列的系统发育,4137-MeT 和 4148-MeT 菌株代表了伊格纳维氏菌(Ignavibacteria)中美利奥氏菌科(Melioribacteraceae)的一个独特品系。根据系统进化分析和表型特征,这两个新分离株被归入一个新属,命名为 Rosettibacter gen.菌株 4148-MeT 代表其模式种 Rosettibacter primus sp.
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引用次数: 0
Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode 根据 SeqCode 描述 Asgardarchaeum abyssi gen.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-06-15 DOI: 10.1016/j.syapm.2024.126525
Daniel Tamarit , Stephan Köstlbacher , Kathryn E. Appler , Kassiani Panagiotou , Valerie De Anda , Christian Rinke , Brett J. Baker , Thijs J.G. Ettema

Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest archaeal relatives of eukaryotes. Despite their prevalence in the scientific literature, the name Asgardarchaeota lacks nomenclatural validation. Here, we describe a novel high-quality metagenome-assembled genome (MAG), AB3033_2TS, proposed to serve as the nomenclatural type for the species Asgardarchaeum abyssiTS according to the rules of the SeqCode. Based on protein content and compositional features, we infer that A. abyssi AB3033_2TS is an acetogenic chemoheterotroph, possibly a facultative lithoautotroph, and is adapted to a thermophilic lifestyle. Utilizing genomes from Asgard archaea, TACK, and Euryarchaea, we perform phylogenomic reconstructions using the GTDB archaeal marker genes, the current reference set for taxonomic classification. Calibrating relative evolutionary divergence (RED) values for Asgardarchaeota using established Thermoproteota lineages in the GTDB r207 reference tree, we establish a robust classification and propose Asgardarchaeum as the type genus for the family Asgardarchaeaceae (fam. nov)., the order Asgardarchaeales (ord. nov.), the class Asgardarchaeia (class. nov.), and the phylum Asgardarchaeota (phyl. nov.). This effort aims to preserve taxonomic congruence in the scientific literature.

阿斯加德古菌群(Asgardarchaeota)通常被称为阿斯加德古菌,是一个候选的门级古菌支系,包括真核生物的近缘古菌。尽管它们在科学文献中很常见,但阿斯加德古菌群(Asgardarchaeota)这一名称缺乏命名学上的验证。这里,我们描述了一个新的高质量元基因组组装基因组(MAG)--AB3033_2TS,建议根据 SeqCode 规则将其作为 Asgardarchaeum abyssiTS 这一物种的命名类型。根据蛋白质含量和组成特征,我们推断阿贝斯藻 AB3033_2TS 是一种产乙酸的化合自养型生物,可能是一种面性自养型生物,并适应嗜热的生活方式。我们利用来自阿斯加德古菌、TACK 和 Euryarchaea 的基因组,使用 GTDB 古菌标记基因(目前的分类参考集)进行了系统发生组重建。通过使用 GTDB r207 参考树中已建立的热蛋白类系校准 Asgardarchaeota 的相对进化差异(RED)值,我们建立了一个稳健的分类,并提议将 Asgardarchaeum 作为 Asgardarchaeaceae 科(新科)、Asgardarchaeales 目(新目)、Asgardarchaeia 类(新类)和 Asgardarchaeota 门(新门)的模式属。这项工作旨在保持科学文献中分类学的一致性。
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引用次数: 0
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Systematic and applied microbiology
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