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Corrigendum to “Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili” [Syst. Appl. Microbiol. 45(5) (2022) 126344] 两个新型戊糖发酵和 GABA 产物的特征:Levilactobacillus tujiorum sp:从固态发酵的辣椒中分离出的 Levilactobacillus tujiorum sp.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 DOI: 10.1016/j.syapm.2024.126558
Chun Tao Gu
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引用次数: 0
Inconsistent identification of Apilactobacillus kunkeei-related strains obtained by well-developed overall genome-related indices 通过完善的整体基因组相关指数获得的昆明杏杆菌相关菌株的鉴定结果不一致。
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-01 DOI: 10.1016/j.syapm.2024.126559
Shintaro Maeno , Akihito Endo
During a decade, overall genome related indices, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), have been used as standards for the classification and identification of bacteria. On the other hand, a former study suggested that ANI-based classification is difficult for fructophilic lactic acid bacterium Apilactobacillus kunkeei. In the present study, the classification of Apilactobacillus spp., including A. kunkeei, was evaluated by multiple genome-based analyses. ANIb-based classification appropriately identified strains of Apilactobacillus spp., except for A. kunkeei-related strains. A number of strain pairings in A. kunkeei-related strains showed ANIb values around the threshold value of 95 %, based on which they were unable to be identified. On the other hand, dDDH provided clearer identification results for A. kunkeei-related strains but segmentalized them into a number of groups, while the validity of this segmentation was unclear. Certain strains shared similarities over the threshold with multiple species-level taxonomic groups in ANIb and dDDH. GTDB-Tk classifies the A. kunkeei-related strains into six species-level taxonomic groups without marked confusion, while the classification results differed from those obtained by ANIb and dDDH. The present study highlighted the inconsistent identification of A. kunkeei-related strains by the well-developed overall genome related indices, which would be a significant concern for bacterial taxonomy. Moreover, the rule adopted in GTDB-Tk, i.e., the classification of strains to taxa containing type strains showing the highest similarity, is recommended for introduction into ANIb- and GGDC-based classifications.
近十年来,包括平均核苷酸同一性(ANI)和数字 DNA-DNA 杂交(dDDH)在内的整体基因组相关指数一直被用作细菌分类和鉴定的标准。另一方面,以前的一项研究表明,基于 ANI 的分类对于嗜果乳酸菌 Apilactobacillus kunkeei 来说是困难的。在本研究中,通过基于基因组的多重分析,对包括昆凯嗜酸乳杆菌(A. kunkeei)在内的嗜酸乳杆菌属的分类进行了评估。除了与A. kunkeei相关的菌株外,基于ANIb的分类能正确识别Apilactobacillus属的菌株。与 A. kunkeei 相关菌株中的一些菌株配对显示 ANIb 值接近 95 % 的阈值,因此无法对其进行鉴定。另一方面,dDDH 为 A. kunkeei-相关菌株提供了更清晰的鉴定结果,但将其细分为若干组,而这种细分的有效性尚不明确。在 ANIb 和 dDDH 中,某些菌株与多个物种级分类群的相似性超过了阈值。GTDB-Tk 将与 A. kunkeei 相关的菌株分为 6 个种级分类群,没有出现明显的混淆,而分类结果与 ANIb 和 dDDH 的结果不同。本研究凸显了用完善的整体基因组相关指数鉴定 A. kunkeei 相关菌株的不一致性,这将是细菌分类学的一个重要问题。此外,建议在基于 ANIb 和 GGDC 的分类中引入 GTDB-Tk 所采用的规则,即把菌株分类到包含相似度最高的类型菌株的类群中。
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引用次数: 0
Helicobacter cappadocius sp. nov., from lizards: The first psychrotrophic Helicobacter species 来自蜥蜴的卡帕多慈氏螺旋杆菌新种(Helicobacter cappadocius sp:第一个精神滋养型螺旋杆菌物种
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-14 DOI: 10.1016/j.syapm.2024.126557
Fuat Aydin , Serdal Tarhane , Emre Karakaya , Seçil Abay , Tuba Kayman , Özgür Güran , Emin Bozkurt , Nazan Üzüm , Aziz Avci , Kurtuluş Olgun , Daniel Jablonski , Cansu Güran , İzzet Burçin Saticioğlu
It was aimed to determine the prevalence of Helicobacter in some reptilian and amphibian species in Türkiye and to describe the bacteria. For this purpose, 73 cloacal swab samples were used as material. The description of the isolates was performed by detailed phenotypic tests, whole genome analyses, and MALDI-TOF MS. As a result of the phenotypic analysis, two helical, curved Gram-negative, motile isolates were recovered. It was determined through the analysis of 16S rRNA gene sequences that two isolates belonged to the genus Helicobacter. These isolates were found to be in a distinct group from other Helicobacter species. However, the 16S rRNA sequence did not match any identified species, with the closest match being Helicobacter mustelae strain R85-13-6T, which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75T and faydin-H76 had a 99.3 % identity level for their 16S rRNA genes. After conducting dDDH and ANI analyses, it was found that strains faydin-H75T and their close neighbors H.anseris ATCC BAA-1299T shared 13.5 % and 68.8 % similarity, respectively. The genome size of the strains was 1.7 Mb while G + C contents were 33.5 %. Metagenomic analyses using IMNGS and Protologger tools revealed the presence of faydin-H75T in various lizard species with high similarity, confirming its broad distribution and host specificity. The results indicated that these two strains represent a novel species, for which we propose the name Helicobacter cappadocius with faydin-H75T (=NCTC014972 = LMG 33382 = DSM117062) as the respective type strain. The current novel species is the first Helicobacter species to exhibit a psychrotrophic feature.
该研究旨在确定图尔基耶一些爬行动物和两栖动物中螺旋杆菌的流行情况,并对这些细菌进行描述。为此,研究人员使用了 73 份泄殖腔拭子样本作为材料。通过详细的表型测试、全基因组分析和 MALDI-TOF MS 对分离菌进行了描述。表型分析的结果是,发现了两种螺旋形、弯曲的革兰氏阴性、能动的分离物。通过分析 16S rRNA 基因序列,确定这两个分离物属于螺旋杆菌属。这些分离物被发现与其他螺旋杆菌属属不同。不过,16S rRNA 序列与任何已确定的物种都不匹配,最接近的匹配是芥子螺旋杆菌菌株 R85-13-6T,其同一性水平为 96.2%。此外,研究还发现 faydin-H75T 和 faydin-H76 菌株的 16S rRNA 基因具有 99.3 % 的同一性。在进行 dDDH 和 ANI 分析后,发现 faydin-H75T 菌株与近邻 H.anseris ATCC BAA-1299T 菌株的相似度分别为 13.5 % 和 68.8 %。菌株的基因组大小为 1.7 Mb,G + C 含量为 33.5%。利用 IMNGS 和 Protologger 工具进行的元基因组分析表明,faydin-H75T 在多种蜥蜴物种中都存在,且相似度很高,这证实了它的广泛分布和宿主特异性。结果表明,这两株菌株代表了一个新物种,我们建议将其命名为卡帕多西螺旋杆菌,并以 faydin-H75T (=NCTC014972 = LMG 33382 = DSM117062)作为各自的模式菌株。当前的新物种是第一个表现出精神营养特征的螺旋杆菌物种。
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引用次数: 0
Limosilactobacillus allomucosae sp. nov., a novel species isolated from wild boar faecal samples as a potential probiotic for domestic pigs 从野猪粪便样本中分离出的新物种 Limosilactobacillus allomucosae sp.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-25 DOI: 10.1016/j.syapm.2024.126556
Binbin Chen, Shaktheeshwari Silvaraju, Sharifah Nora Ahmad Almunawar, Yu Chyuan Heng, Jolie Kar Yi Lee, Sandra Kittelmann
Six strains, WILCCON 0050, WILCCON 0051, WILCCON 0052, WILCCON 0053, WILCCON 0054, WILCCON 0055T, were isolated from four different faecal samples of wild boars on Pulau Ubin, Singapore, Singapore. Based on core genome phylogenetic analysis, the six strains formed a distinct clade within the genus Limosilactobacillus (Lm.), with the most closely related type strain being Lm. mucosae DSM 13345T. The minimum ANI, dDDH, and AAI values within these six strains were 97.8%, 78.8%, and 98.6%, respectively. In contrast, the ANI, dDDH, and AAI values with Lm. mucosae DSM 13345T were lower, ranging between 94.8–95.1%, 57.1–59.0%, and 95.9–97.0%, respectively. While ANI and AAI were close to the thresholds of 95% and 97% for bacterial species delineation, respectively, dDDH was significantly lower than the threshold value of 70%. Based on our phylogenomic, phenotypic and chemotaxonomic analyses, we propose a novel species with the name Limosilactobacillus allomucosae sp. nov., with WILCCON 0055T (DSM 117632T = LMG 33563T) as the designated type strain. In vitro investigations revealed the strains’ ability to break down raffinose-family oligosaccharides, and to utilize prebiotics such as xylo-oligosaccharides and galacturonic acid, thereby enhancing fibre digestion and nutrient absorption. Moreover, strong auto-aggregation properties, as well as resistance to low pH and porcine bile were observed, suggesting their potential survival and persistence during passage through the gut. The high bile tolerance of these strains appears to be attributed to their ability to deconjugate a wide range of conjugated bile compounds. In silico analysis indicated a strong potential for mucin-binding activity, which aids their colonization in the gut. These characteristics indicate the potential suitability of strains of Lm. allomucosae as probiotics for domestic pigs.
从新加坡乌滨岛(Pulau Ubin)四种不同的野猪粪便样本中分离出六株菌株,分别为 WILCCON 0050、WILCCON 0051、WILCCON 0052、WILCCON 0053、WILCCON 0054 和 WILCCON 0055T。根据核心基因组系统进化分析,这六株菌株在Limosilactobacillus(Lm.)属中形成了一个独特的支系,与之关系最密切的模式菌株是Lm.mucosae DSM 13345T。这六个菌株的最小 ANI、dDDH 和 AAI 值分别为 97.8%、78.8% 和 98.6%。相比之下,Lm. mucosae DSM 13345T 的 ANI、dDDH 和 AAI 值较低,分别为 94.8-95.1%、57.1-59.0% 和 95.9-97.0%。虽然 ANI 和 AAI 分别接近 95% 和 97% 的细菌物种划分阈值,但 dDDH 明显低于 70% 的阈值。根据系统发生组学、表型学和化学分类学分析,我们提出了一个新物种,命名为全口低硅乳酸杆菌(Limosilactobacillus allomucosae sp.nov.),WILCCON 0055T (DSM 117632T = LMG 33563T)为指定的模式菌株。体外研究显示,这些菌株能够分解棉子糖族低聚糖,并利用益生元(如木寡糖和半乳糖醛酸),从而促进纤维消化和营养吸收。此外,还观察到这些菌株具有很强的自动聚集特性,以及对低 pH 值和猪胆汁的耐受性,这表明它们在通过肠道时具有存活和持久的潜力。这些菌株对胆汁的高度耐受性似乎归因于它们对多种共轭胆汁化合物的解结合能力。硅学分析表明,这些菌株具有很强的粘蛋白结合活性,这有助于它们在肠道中定植。这些特征表明,异粘酵母菌株可能适合作为家猪的益生菌。
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引用次数: 0
Acidimicrobiia, the actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential 酸性微生物,沿海海洋沉积物中的放线菌群:丰度、分类和基因组潜力。
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-24 DOI: 10.1016/j.syapm.2024.126555
Sebastián Silva-Solar, Tomeu Viver, Yueqing Wang, Luis H. Orellana, Katrin Knittel, Rudolf Amann
Microbial communities in marine sediments represent some of the densest and most diverse biological communities known, with up to a billion cells and thousands of species per milliliter. Among this taxonomic diversity, the class Acidimicrobiia, within the phylum Actinomycetota, stands out for its consistent presence, yet its limited taxonomic understanding obscures its ecological role. We used metagenome-assembled genomes from a 5-year Arctic fjord sampling campaign and compared them to publicly available Acidimicrobiia genomes using 16S rRNA gene and whole-genome phylogenies, alongside gene prediction and annotation to study their taxonomy and genomic potential. Overall, we provide a taxonomic overview of the class Acidimicrobiia and show its significant prevalence in Isfjorden and Helgoland coastal sediments, representing over 90% of Actinomycetota 16S rRNA gene sequences, and 3–7% of Bacteria. We propose Benthobacter isfjordensis gen. nov., sp. nov., Hadalibacter litoralis gen. nov., sp. nov., and two new species from Ilumatobacter, following SeqCode guidelines. In addition, we report the first in situ quantification of the family Ilumatobacteraceae, revealing its substantial presence (1–6%) in coastal sediments. This work highlights the need of refining the taxonomy of Acidimicrobiia to better understand their ecological contributions.
海洋沉积物中的微生物群落是已知密度最高、种类最丰富的生物群落,每毫升中含有多达十亿个细胞和数千个物种。在这种分类多样性中,放线菌门(Actinomycetota)中的酸性微生物(Acidimicrobiia)类因其持续存在而脱颖而出,但对其分类的有限了解却掩盖了其生态作用。我们使用了为期 5 年的北极峡湾采样活动中的元基因组组装基因组,并使用 16S rRNA 基因和全基因组系统进化、基因预测和注释将其与公开的 Acidimicrobiia 基因组进行了比较,以研究其分类学和基因组潜力。总之,我们对酸性微生物类进行了分类概述,并显示了其在伊斯菲尤登和赫尔戈兰沿海沉积物中的显著分布,占放线菌16S rRNA基因序列的90%以上,占细菌的3-7%。根据 SeqCode 准则,我们提出了 Benthobacter isfjordensis gen.此外,我们还首次报告了 Ilumatobacteraceae 科的原位定量,揭示了其在沿海沉积物中的大量存在(1-6%)。这项工作强调了完善酸性微生物分类的必要性,以便更好地了解它们对生态的贡献。
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引用次数: 0
Options and considerations for validation of prokaryotic names under the SeqCode 根据 SeqCode 验证原核生物名称的选项和注意事项
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-19 DOI: 10.1016/j.syapm.2024.126554
Stephanus N. Venter , Luis M. Rodriguez-R , Maria Chuvochina , Marike Palmer , Philip Hugenholtz , Emma T. Steenkamp

Stable taxon names for Bacteria and Archaea are essential for capturing and documenting prokaryotic diversity. They are also crucial for scientific communication, effective accumulation of biological data related to the taxon names and for developing a comprehensive understanding of prokaryotic evolution. However, after more than a hundred years, taxonomists have succeeded in valid publication of only around 30 000 species names, based mostly on pure cultures under the International Code of Nomenclature of Prokaryotes (ICNP), out of the millions estimated to reside in the biosphere. The vast majority of prokaryotic species have not been cultured and are becoming increasingly known to us via culture-independent sequence-based approaches. Until recently, such taxa could only be addressed nomenclaturally via provisional names such as Candidatus or alphanumeric identifiers. Here, we present options and considerations to facilitate validation of names for these taxa using the recently established Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Community engagement and participation of relevant taxon specialists are critical and encouraged for the success of endeavours to formally name the uncultured majority.

细菌和古细菌的稳定分类名称对于捕捉和记录原核生物的多样性至关重要。它们对于科学交流、有效积累与分类名称相关的生物数据以及全面了解原核生物进化也至关重要。然而,一百多年过去了,在生物圈中估计存在的数百万个物种中,分类学家根据《国际原核生物命名法》(ICNP),主要以纯培养物为基础,只成功地公布了约 3 万个物种名称。绝大多数原核生物物种都没有经过培养,我们越来越多地通过与培养无关的基于序列的方法来了解它们。直到最近,我们还只能通过 "类群"(Candidatus)等临时名称或字母数字标识符对这些类群进行命名。在此,我们提出了一些方案和注意事项,以方便利用最近制定的《序列数据描述的原核生物命名代码》(SeqCode)来验证这些类群的名称。社区参与和相关分类群专家的参与对于正式命名大多数未培养生物的努力取得成功至关重要,我们对此表示鼓励。
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引用次数: 0
Description of three new Pseudomonas species isolated from aquarium fish: Pseudomonas auratipiscis sp. nov., Pseudomonas carassii sp. nov. and Pseudomonas ulcerans sp. nov 描述从水族鱼类中分离出的三种新假单胞菌:Pseudomonas auratipiscis sp.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-19 DOI: 10.1016/j.syapm.2024.126552
Muhammed Duman , Jorge Lalucat , Izzet Burcin Saticioglu , Magdalena Mulet , Margarita Gomila , Soner Altun , Nihed Ajmi , Elena García-Valdés
Pseudomonas species constitute a significant group of pathogens in aquarium fish and frequently cause haemorrhagic septicaemia. This study conducted a taxonomic characterization of Pseudomonas isolates from aquarium fish exhibiting deep ulceration and general disease signs. A polyphasic approach was employed to ascertain the taxonomic affiliation of the strains. The overall genome relatedness indices of digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genus Pseudomonas were found to be below the established thresholds of 70 and 95–96%, respectively. Whole-genome based phylogenetic analysis revealed that strains 119PT and 120P were closely related to P. arcuscaelestis. Strain 137PT was related to P. peradeniyensis, while strains 147PT and 148P were closely related to P. japonica. The morphological, physiological, and biochemical characteristics of the strains and the genome relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as three novel species. Genome analyses of the strains were also conducted to determine their biosynthesis-related gene clusters, virulence features and ecological distribution patterns. Based on polyphasic characterization, the strains 119PT, 120P, 137PT, 147PT, and 148P are novel species within the genus Pseudomonas, for which the following names are proposed: Pseudomonas auratipiscis sp. nov., with the strain 119PT as the type strain (=DSM 117162 T, =LMG 33381T); Pseudomonas carassii sp. nov., with the strain 137PT as the type strain (=DSM 117060T, =LMG 33378T); and Pseudomonas ulcerans sp. nov. 147PT, as the type strain (=DSM 117163T, =LMG 33377T).
假单胞菌是水族鱼类的重要病原体之一,经常引起出血性败血症。本研究对从表现出深度溃疡和一般疾病症状的水族鱼中分离出的假单胞菌进行了分类鉴定。采用多相法来确定菌株的分类归属。发现这些菌株与假单胞菌属其他成员之间的数字 DNA-DNA 杂交(dDDH)和平均核苷酸同一性(ANI)的整体基因组亲缘关系指数分别低于 70% 和 95-96% 的既定阈值。基于全基因组的系统发育分析表明,菌株 119PT 和 120P 与 P. arcuscaelestis 关系密切。菌株 137PT 与 P. peradeniyensis 关系密切,而菌株 147PT 和 148P 与 P. japonica 关系密切。这些菌株的形态、生理和生化特征以及 dDDH 和 ANI 的基因组亲缘关系指数低于既定阈值,证实了这些菌株被划分为三个新物种。此外,还对菌株进行了基因组分析,以确定其生物合成相关基因簇、毒力特征和生态分布模式。根据多相特征,119PT、120P、137PT、147PT 和 148P 株系是假单胞菌属中的新物种,现将其命名如下:以 119PT 株为模式菌株(=DSM 117162 T,=LMG 33381T);以 137PT 株为模式菌株(=DSM 117060T,=LMG 33378T);以 147PT 株为模式菌株(=DSM 117163T,=LMG 33377T)。
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引用次数: 0
Halorubrum miltondacostae sp. nov., a potential polyhydroxyalkanoate producer isolated from an inland solar saltern in Rio Maior, Portugal Halorubrum miltondacostae sp.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-17 DOI: 10.1016/j.syapm.2024.126553
Luciana Albuquerque , Tomeu Viver , Cristina Barroso , Ricardo Claudino , Mariana Galvan , Gabriela Simões , Alexandre Lobo-da-Cunha , Conceição Egas

One hundred and sixty-three extreme halophiles were recovered from a single sample collected from an inland solar saltern in Rio Maior. Based on random amplified polymorphic DNA (RAPD) profiles and partial 16S rRNA gene sequencing 125 isolates were identified as members of the Archaea domain within the genus Halorubrum. Two strains, RMP-11T and RMP-47, showed 99.1 % sequence similarity with the species Halorubrum californiense based on phylogenetic analysis of the 16S rRNA gene sequence. However, phylogenetic analysis based on five housekeeping genes, atpB, EF-2, glnA, ppsA and rpoB’, showed Halorubrum coriense as the closest related species with 96.7 % similarity. The average nucleotide identity (ANI) of strains RMP-11T, RMP-47 and species Hrr. coriense were within the range of 90.0–90.5 %, supporting that strains RMP-11T and RMP-47 represent a novel species of the genus Halorubrum. These strains formed red-pigmented colonies that were able to grow in a temperature range of 25–50 °C. Polyhydroxyalkanoate (PHA) granules were detected in both strains. The polar lipid profile was identical to the neutrophilic species of the genus Halorubrum. The Rio Maior sample from which both strains were isolated was metagenome sequenced. We identified five metagenome-assembled genomes representing novel Halorubrum species but distinct from the species represented by strains RMP-11T and RMP-47. Based on phylogenetic, phylogenomic, comparative genomics, physiological and chemotaxonomic parameters, we describe a new species of the genus Halorubrum represented by strains RMP-11T (=CECT 30760T = DSM 115521T) and RMP-47 (=CECT 30761 = DSM 115541) for which we propose the name Halorubrum miltondacostae sp. nov.

从里约马约尔内陆日晒盐场采集的单一样本中分离出 163 个极端嗜卤菌。根据随机扩增多态脱氧核糖核酸(RAPD)图谱和部分 16S rRNA 基因测序,125 个分离物被确定为卤虫属中的古生菌。根据 16S rRNA 基因序列的系统进化分析,两株菌株 RMP-11T 和 RMP-47 与 Halorubrum californiense 的序列相似度为 99.1%。然而,基于五个看家基因(atpB、EF-2、glnA、ppsA 和 rpoB')的系统进化分析表明,Halorubrum coriense 是与之亲缘关系最近的物种,相似度为 96.7%。RMP-11T、RMP-47和Hrr. coriense的平均核苷酸同一性(ANI)在90.0%-90.5%之间,证明RMP-11T和RMP-47菌株代表了卤虫属的一个新种。这些菌株形成的红色色素菌落能够在 25-50 °C 的温度范围内生长。两株菌株中都检测到了聚羟基烷酸(PHA)颗粒。极性脂质特征与 Halorubrum 属的嗜中性物种相同。对分离出这两种菌株的 Rio Maior 样品进行了元基因组测序。我们确定了五个元基因组,它们代表了 Halorubrum 的新物种,但与 RMP-11T 和 RMP-47 菌株所代表的物种不同。根据系统发生学、系统基因组学、比较基因组学、生理学和化学趋向学参数,我们描述了以菌株 RMP-11T (=CECT 30760T = DSM 115521T)和 RMP-47 (=CECT 30761 = DSM 115541)为代表的 Halorubrum 属新物种,并将其命名为 Halorubrum miltondacostae sp.
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引用次数: 0
Evidence for the occurrence of Acinetobacter faecalis in cattle feces and its emended description 牛粪便中存在粪杆菌的证据及其修订描述。
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.syapm.2024.126545
Martina Kyselková , Kyriaki Xanthopoulou , Violetta Shestivska , Petra Španělová , Martina Maixnerová , Paul G. Higgins , Alexandr Nemec

This study provides an emended description of Acinetobacter faecalis, a species previously described based on a single isolate (YIM 103518T) from elephant feces in China. Our emended description is based on 15 novel isolates conspecific with the A. faecalis type strain, obtained from eight cattle farms in the Czech Republic. The A. faecalis strains have relatively small genomes (≈2.5−2.7 Mbp), with a GC content of 36.3−36.7 mol%. Core genome-based phylogenetic analysis showed that the 15 strains, together with the type strain of A. faecalis, form a distinct and internally coherent phylogroup within the genus. Pairwise genomic ANIb values for the 16 A. faecalis strains were 97.32−99.04 %, while ANIb values between the genomes of the 16 strains and those of the other Acinetobacter spp. were ≤ 86.2 %. Analysis of whole-cell MALDI-TOF mass spectra supported the distinctness and cohesiveness of the taxon. The A. faecalis strains could be differentiated from the other validly named Acinetobacter spp. by the absence of hemolytic activity along with their ability to grow at 37 °C and on L-aspartate, ethanol, and L-glutamate but not at 41 °C or on adipate or 2,3-butanediol. Reduced susceptibility to sulfamethoxazole, trimethoprim and/or streptomycin was shown in eight strains, along with the presence of corresponding antibiotic resistance genes. In conclusion, this study provides a comprehensive description of A. faecalis and demonstrates its occurrence in cattle feces. Though the ecological role of A. faecalis remains unknown, our results show its ability to acquire antibiotic resistance genes, likely as an adaptation to antibiotic selection pressure in livestock farms.

本研究对粪链球菌(Acinetobacter faecalis)进行了修订描述,该菌种以前是根据从中国大象粪便中分离到的一个菌株(YIM 103518T)描述的。我们的修订描述是基于从捷克共和国的 8 个养牛场分离到的 15 株与粪链球菌模式菌株同种的新菌株。粪链球菌菌株的基因组相对较小(≈2.5-2.7 Mbp),GC 含量为 36.3-36.7 mol%。基于核心基因组的系统发育分析表明,这 15 株菌株与粪链球菌的模式菌株一起,构成了该属中一个独特且内部连贯的系统群。16 株粪链球菌的成对基因组 ANIb 值为 97.32-99.04%,而这 16 株菌株的基因组与其他醋酸杆菌属菌株的基因组之间的 ANIb 值≤ 86.2%。全细胞 MALDI-TOF 质谱分析证实了该类群的独特性和内聚性。粪肠球菌菌株与其他有效命名的醋肽杆菌属菌株的区别在于,粪肠球菌菌株没有溶血活性,能在 37 °C、L-天门冬氨酸、乙醇和 L-谷氨酸条件下生长,但不能在 41 °C、己二酸或 2,3-丁二醇条件下生长。有 8 株菌株对磺胺甲噁唑、三甲双嘧啶和/或链霉素的敏感性降低,并存在相应的抗生素耐药基因。总之,本研究全面描述了粪酵母菌,并证明其存在于牛粪便中。虽然粪绿假丝酵母菌的生态作用尚不清楚,但我们的研究结果表明,它有能力获得抗生素耐药基因,这很可能是为了适应畜牧场的抗生素选择压力。
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引用次数: 0
Corrigendum to “Natronospira bacteriovora sp. nov., and Natronospira elongata sp. nov., extremely salt-tolerant predatory proteolytic bacteria from soda lakes and proposal to classify the genus Natronospira into Natronospiraceae fam. nov., and Natronospirales ord. nov., within the class Gammaproteobacteria” [Syst. Appl. Microbiol. 47 (2024) 126519] 对 "Natronospira bacteriovora sp. nov., and Natronospira elongata sp. nov., extremely salt-tolerant predatory proteolytic bacteria from soda lakes and proposal to classify the genus Natronospira into Natronospiraceae fam. nov., and Natronospirales ord. nov., within the class Gammaproteobacteria "的更正 [Syst.
IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-01 DOI: 10.1016/j.syapm.2024.126526
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引用次数: 0
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Systematic and applied microbiology
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