Systematic and applied microbiology最新文献_第2页

Methyloraptor flagellatus gen. Nov., sp. nov., novel Ancalomicrobiaceae-affiliated facultatively methylotrophic bacteria that feed on methanotrophs of the genus Methylococcus Methyloraptor flagellatus gen.Nov.，sp. nov.，以甲烷球菌属养甲烷菌为食的隶属于 Ancalomicrobiaceae 的新型兼性滋养甲基细菌

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2024-11-22 DOI: 10.1016/j.syapm.2024.126565

Victoria A. Saltykova , Olga V. Danilova , Igor Y. Oshkin , Svetlana E. Belova , Natalia E. Suzina , Nikolai V. Pimenov , Svetlana N. Dedysh

A morphologically conspicuous microbial association was detected in a bioreactor running in a continuous mode with methanotrophic bacteria of the genus Methylococcus and natural gas as a growth substrate. The association consisted of spherical Methylococcus cells colonized by elongated rods, which produced rosette-like aggregates and inhibited the cultivation process. An isolate of these bacteria, strain S20^T, was obtained and identified as belonging to the alphaproteobacterial family Ancalomicrobiaceae but displaying only a distant relationship (93.9–95.1 % 16S rRNA gene sequence similarity) to characterized members of this family. Strain S20^T was represented by aerobic, motile, facultatively methylotrophic bacteria, which grew between 10 and 45 °C (optimum 30–35 °C) in a pH range of 4.5–8.5 (optimum pH 6.0). These bacteria were capable of attaching to Methylococcus cells and breaking the integrity of methanotroph cell walls, presumably to feed on methanol. The same interaction was observed with Methylomonas species. The finished genome sequence of strain S20^T consisted of a 5.0 Mb chromosome and one plasmid, 0.26 Mb in size; the DNA G + C content was 68.4 %. The genome encoded 3 rRNA operons and ~ 4400 proteins including MxaFI- and XoxF-like methanol dehydrogenases, all enzymes of the serine pathway as well as a complete chemotaxis pathway, a unipolar polysaccharide adhesin, and a wide range of peptidases. The genome sequence displayed 67.20–69.56 % average amino acid identity to those of earlier described Ancalomicrobiaceae species. We propose to classify these bacteria as representing a novel genus and species, Methyloraptor flagellatus gen. Nov., sp. nov., with the type strain S20^T (=KCTC 8649^T = VKM B-3853^T).

在一个以甲烷球菌属的甲烷营养细菌为生长基质、以连续模式运行的生物反应器中，发现了一种形态明显的微生物联合体。这种联合体由球形的甲基球菌细胞和拉长的杆状菌组成，拉长的杆状菌产生莲座状聚集，抑制了培养过程。从这些细菌中分离出的菌株 S20T，经鉴定属于α-蛋白细菌科 Ancalomicrobiaceae，但与该科的特征成员仅有很远的关系（16S rRNA 基因序列相似度为 93.9-95.1 %）。菌株 S20T 由需氧、运动、兼性甲基营养细菌组成，生长温度为 10 至 45 °C（最适温度为 30 至 35 °C），pH 值范围为 4.5 至 8.5（最适 pH 值为 6.0）。这些细菌能够附着在甲基球菌细胞上，破坏甲烷营养细胞壁的完整性，可能是为了吸食甲醇。与甲基单胞菌也观察到了同样的相互作用。菌株 S20T 的完整基因组序列包括一条 5.0 Mb 的染色体和一条 0.26 Mb 的质粒；DNA G + C 含量为 68.4%。基因组编码 3 个 rRNA 操作子和约 4400 个蛋白质，包括 MxaFI 和 XoxF 类甲醇脱氢酶、丝氨酸途径的所有酶以及完整的趋化途径、单极多糖粘附素和多种肽酶。其基因组序列与早先描述的 Ancalomicrobiaceae 物种的平均氨基酸相同度为 67.20-69.56%。我们建议将这些细菌归为一个新属和新种，即 Methyloraptor flagellatus gen.新种，模式菌株为 S20T（=KCTC 8649T = VKM B-3853T）。

{"title":"Methyloraptor flagellatus gen. Nov., sp. nov., novel Ancalomicrobiaceae-affiliated facultatively methylotrophic bacteria that feed on methanotrophs of the genus Methylococcus","authors":"Victoria A. Saltykova , Olga V. Danilova , Igor Y. Oshkin , Svetlana E. Belova , Natalia E. Suzina , Nikolai V. Pimenov , Svetlana N. Dedysh","doi":"10.1016/j.syapm.2024.126565","DOIUrl":"10.1016/j.syapm.2024.126565","url":null,"abstract":"<div><div>A morphologically conspicuous microbial association was detected in a bioreactor running in a continuous mode with methanotrophic bacteria of the genus Methylococcus and natural gas as a growth substrate. The association consisted of spherical Methylococcus cells colonized by elongated rods, which produced rosette-like aggregates and inhibited the cultivation process. An isolate of these bacteria, strain S20T, was obtained and identified as belonging to the alphaproteobacterial family Ancalomicrobiaceae but displaying only a distant relationship (93.9–95.1 % 16S rRNA gene sequence similarity) to characterized members of this family. Strain S20T was represented by aerobic, motile, facultatively methylotrophic bacteria, which grew between 10 and 45 °C (optimum 30–35 °C) in a pH range of 4.5–8.5 (optimum pH 6.0). These bacteria were capable of attaching to Methylococcus cells and breaking the integrity of methanotroph cell walls, presumably to feed on methanol. The same interaction was observed with Methylomonas species. The finished genome sequence of strain S20T consisted of a 5.0 Mb chromosome and one plasmid, 0.26 Mb in size; the DNA G + C content was 68.4 %. The genome encoded 3 rRNA operons and ~ 4400 proteins including MxaFI- and XoxF-like methanol dehydrogenases, all enzymes of the serine pathway as well as a complete chemotaxis pathway, a unipolar polysaccharide adhesin, and a wide range of peptidases. The genome sequence displayed 67.20–69.56 % average amino acid identity to those of earlier described Ancalomicrobiaceae species. We propose to classify these bacteria as representing a novel genus and species, Methyloraptor flagellatus gen. Nov., sp. nov., with the type strain S20T (=KCTC 8649T = VKM B-3853T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126565"},"PeriodicalIF":3.3,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Parafrigoribacterium soli sp. nov. and Parafrigoribacterium humi sp. nov., two novel siderophore-synthesizing species isolated from black soil 从黑土中分离的两个新的铁载体合成种——土壤副嗜酸杆菌和腐殖质副嗜酸杆菌

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2024-11-21 DOI: 10.1016/j.syapm.2024.126564

Yu-Ting OuYang , Le-Bin Chen , Jian-Yu Jiao , Zi-Xuan Hu , Jiong-Shan Wang , Tian-Hang Yang , Jun Xiao , Ting-Ting She , Pin-Jiao Jin , Shuang Wang , Lan Liu , Wen-Jun Li

Two siderophore-synthesizing species SYSU BS000078^T and SYSU BS000231^T were isolated from the black soil collected from fields located in Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that these two strains showed the highest sequence similarity to Parafrigoribacterium mesophilum KCTC 19311^T (98.61 % and 98.68 %, respectively). The average nucleotide identity (ANI) values between the two strains and other members of the genus Parafrigoribacterium were lower than 95 %, recommended for distinguishing novel prokaryotic species. Cells of strains SYSU BS000078^T and SYSU BS000231^T were aerobic, motile, Gram-stain-positive and non-spore-forming rods. The colonies of these two strains exhibited a cream pigment, with tidy edges and smooth surfaces. Growth was observed within the temperature range of 4–37 °C (optimal growth at 28 °C) and pH range of 6.0–8.0 (optimal growth at pH 7.0). The predominant polar lipids detected in these two strains included diphosphatidylglycerol and phosphatidylglycerol. The predominant respiratory quinones was MK-9. The major cellular fatty acids (>10 %) were iso-C_16:0, anteiso-C_15:0, and anteiso-C_17:0. The genome size and G + C content of strain SYSU BS000078^T were determined to be 2.89 Mbp and 66.5 %, respectively. Meanwhile, SYSU BS000231^T exhibited a genome size of 2.81 Mbp, accompanied by a G + C content of 65.8 %. Based on the phenotypic, physiological, genotypic, and phylogenetic data, these two strains represent two novel species of the genus Parafrigoribacterium, which are proposed as Parafrigoribacterium soli sp. nov. SYSU BS000078^T (=GDMCC 1.4599^T = KCTC 59245^T), and Parafrigoribacterium humi sp. nov. SYSU BS000231^T (=GDMCC 1.3816^T = KCTC 59001^T).

从黑龙江省黑土中分离到两个铁载体合成物种SYSU BS000078T和SYSU BS000231T。基于16S rRNA基因序列的系统发育分析结果表明，这两株菌株与中嗜副干酪菌KCTC 19311T的序列相似性最高（分别为98.61%和98.68%）。这两株菌株与副fririgoribacterium属其他成员的平均核苷酸同源性（ANI）值均低于95%，推荐用于区分新的原核物种。菌株SYSU BS000078T和SYSU BS000231T细胞为好氧、运动、革兰氏染色阳性、非孢子形成棒。这两个菌株的菌落呈奶油色，边缘整齐，表面光滑。生长温度范围为4-37℃（28℃最适生长），pH范围为6.0-8.0 （pH 7.0最适生长）。在这两个菌株中检测到的主要极性脂质为二磷脂酰甘油和磷脂酰甘油。主要呼吸醌类为MK-9。主要细胞脂肪酸为iso-C16:0、anteiso-C15:0和anteiso-C17:0（占10%）。菌株SYSU BS000078T的基因组大小和G + C含量分别为2.89 Mbp和66.5%。同时，SYSU BS000231T的基因组大小为2.81 Mbp， G + C含量为65.8%。根据表型、生理、基因型和系统发育数据，这两株菌株代表了副冷僵菌属的两个新种，分别为：Parafrigoribacterium soli sp. nov. SYSU BS000078T （=GDMCC 1.4599T = KCTC 59245T）和Parafrigoribacterium humi sp. nov. SYSU BS000231T （=GDMCC 1.3816T = KCTC 59001T）。

{"title":"Parafrigoribacterium soli sp. nov. and Parafrigoribacterium humi sp. nov., two novel siderophore-synthesizing species isolated from black soil","authors":"Yu-Ting OuYang , Le-Bin Chen , Jian-Yu Jiao , Zi-Xuan Hu , Jiong-Shan Wang , Tian-Hang Yang , Jun Xiao , Ting-Ting She , Pin-Jiao Jin , Shuang Wang , Lan Liu , Wen-Jun Li","doi":"10.1016/j.syapm.2024.126564","DOIUrl":"10.1016/j.syapm.2024.126564","url":null,"abstract":"<div><div>Two siderophore-synthesizing species SYSU BS000078T and SYSU BS000231T were isolated from the black soil collected from fields located in Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that these two strains showed the highest sequence similarity to Parafrigoribacterium mesophilum KCTC 19311T (98.61 % and 98.68 %, respectively). The average nucleotide identity (ANI) values between the two strains and other members of the genus Parafrigoribacterium were lower than 95 %, recommended for distinguishing novel prokaryotic species. Cells of strains SYSU BS000078T and SYSU BS000231T were aerobic, motile, Gram-stain-positive and non-spore-forming rods. The colonies of these two strains exhibited a cream pigment, with tidy edges and smooth surfaces. Growth was observed within the temperature range of 4–37 °C (optimal growth at 28 °C) and pH range of 6.0–8.0 (optimal growth at pH 7.0). The predominant polar lipids detected in these two strains included diphosphatidylglycerol and phosphatidylglycerol. The predominant respiratory quinones was MK-9. The major cellular fatty acids (>10 %) were iso-C16:0, anteiso-C15:0, and anteiso-C17:0. The genome size and G + C content of strain SYSU BS000078T were determined to be 2.89 Mbp and 66.5 %, respectively. Meanwhile, SYSU BS000231T exhibited a genome size of 2.81 Mbp, accompanied by a G + C content of 65.8 %. Based on the phenotypic, physiological, genotypic, and phylogenetic data, these two strains represent two novel species of the genus Parafrigoribacterium, which are proposed as Parafrigoribacterium soli sp. nov. SYSU BS000078T (=GDMCC 1.4599T = KCTC 59245T), and Parafrigoribacterium humi sp. nov. SYSU BS000231T (=GDMCC 1.3816T = KCTC 59001T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126564"},"PeriodicalIF":3.3,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142744184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Describing five new strains in the family Woeseiaceae and emended description of the order Woeseiales with genomic features related to environmental adaptation 描述禾本科（Woeseiaceae）的五个新菌株，并根据与环境适应性相关的基因组特征修订禾本科（Woeseiales）的描述

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2024-11-20 DOI: 10.1016/j.syapm.2024.126563

Feng-Bai Lian , Bing-Jun Zhou , Zi-Yang Zhou , Alejandro P. Rooney , Zhen-Xing Xu , Zong-Jun Du

The family Woeseiaceae, also known as the JTB255 bacterial group, are ubiquitous and abundant core members of microbial communities in marine surface sediments. However, to date, only one Woeseiaceae strain isolated from marine sediments has been described, and the phylogeny and environmental adaptation mechanisms of this group have been little explored. Here, we isolated five novel Woeseiaceae strains from the marine solar saltern in Weihai, China. Multiple genomic, physiological, and chemotaxonomic characteristics supported that these five isolates represent three novel species within a novel genus, for which Lentisalinibacter gen. nov. and three species Lentisalinibacter sediminis sp. nov., Lentisalinibacter salinarum sp. nov. and Lentisalinibacter orientalis sp. nov. are proposed. Moreover, phylogenetic analysis based on the 16S rRNA genes and genome sequences revealed that Woeseiaceae is most closely related to Steroidobacterales. Further comparative genomics analysis indicated the separate evolution of Woeseiaceae and Steroidobacterales, supporting the emended description of the order Woeseiales. Woeseiales representitives showed facultatively anaerobic characteristics and small genome sizes in contrast to their phylogenetic relatives. They primarily inhabit surface marine sediment environments using multiple metabolic and ecological strategies to adapt to the changing microenvironments. Our results demonstrate the novel representatives of Woeseiales and their environmental adaptation mechanisms in marine environments.

Woeseiaceae 科，又称 JTB255 细菌群，是海洋表层沉积物中微生物群落中无处不在的丰富核心成员。然而，迄今为止，仅有一株从海洋沉积物中分离出的 Woeseiaceae 菌株被描述过，对该菌群的系统发育和环境适应机制的探索也很少。在此，我们从中国威海的海洋日晒盐场中分离出了五株新的 Woeseiaceae 菌株。通过基因组学、生理学和化学分类学等多方面的特征，我们认为这五个分离株代表了一个新属中的三个新种，并提出了新种Lentisalinibacter gen.和三个新种Lentisalinibacter sediminis sp.nov.、Lentisalinibacter salinarum sp.nov.和Lentisalinibacter orientalis sp.nov.。此外，基于 16S rRNA 基因和基因组序列的系统进化分析表明，Woeseiaceae 与 Steroidobacterales 的亲缘关系最为密切。进一步的比较基因组学分析表明，Woeseiaceae 和 Steroidobacterales 是分开进化的，支持对 Woeseiales 目进行修正描述。与它们的系统发育近亲相比，Woeseiales 的代表物种表现出兼性厌氧特征和较小的基因组规模。它们主要栖息在表层海洋沉积物环境中，利用多种代谢和生态策略来适应不断变化的微环境。我们的研究结果展示了 Woeseiales 的新代表及其在海洋环境中的环境适应机制。

{"title":"Describing five new strains in the family Woeseiaceae and emended description of the order Woeseiales with genomic features related to environmental adaptation","authors":"Feng-Bai Lian , Bing-Jun Zhou , Zi-Yang Zhou , Alejandro P. Rooney , Zhen-Xing Xu , Zong-Jun Du","doi":"10.1016/j.syapm.2024.126563","DOIUrl":"10.1016/j.syapm.2024.126563","url":null,"abstract":"<div><div>The family Woeseiaceae, also known as the JTB255 bacterial group, are ubiquitous and abundant core members of microbial communities in marine surface sediments. However, to date, only one Woeseiaceae strain isolated from marine sediments has been described, and the phylogeny and environmental adaptation mechanisms of this group have been little explored. Here, we isolated five novel Woeseiaceae strains from the marine solar saltern in Weihai, China. Multiple genomic, physiological, and chemotaxonomic characteristics supported that these five isolates represent three novel species within a novel genus, for which Lentisalinibacter gen. nov. and three species Lentisalinibacter sediminis sp. nov., Lentisalinibacter salinarum sp. nov. and Lentisalinibacter orientalis sp. nov. are proposed. Moreover, phylogenetic analysis based on the 16S rRNA genes and genome sequences revealed that Woeseiaceae is most closely related to Steroidobacterales. Further comparative genomics analysis indicated the separate evolution of Woeseiaceae and Steroidobacterales, supporting the emended description of the order Woeseiales. Woeseiales representitives showed facultatively anaerobic characteristics and small genome sizes in contrast to their phylogenetic relatives. They primarily inhabit surface marine sediment environments using multiple metabolic and ecological strategies to adapt to the changing microenvironments. Our results demonstrate the novel representatives of Woeseiales and their environmental adaptation mechanisms in marine environments.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126563"},"PeriodicalIF":3.3,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Thermodesulfovibrio autotrophicus sp. nov., the first autotrophic representative of the widespread sulfate-reducing genus Thermodesulfovibrio, and Thermodesulfovibrio obliviosus sp. nov. that has lost this ability 自养型热去硫弧菌新种（Thermodesulfovibrio autotrophicus sp.nov.）是广泛存在的硫酸盐还原型热去硫弧菌属的第一个自养型代表，而遗忘型热去硫弧菌新种（Thermodesulfovibrio obliviosus sp.nov.）则丧失了这种能力。

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2024-11-01 DOI: 10.1016/j.syapm.2024.126561

Anastasia I. Maltseva , Alexander G. Elcheninov , Alexandra A. Klyukina , Nikolay V. Pimenov , Andrei A. Novikov , Alexander V. Lebedinsky , Evgenii N. Frolov

Representatives of the genus Thermodesulfovibrio are widespread thermophilic sulfate-reducing bacteria. The genus currently includes five species with validly published names. Two new Thermodesulfovibrio strains, 3907-1M ^T and 3462-1^T, were isolated with molecular hydrogen as an electron donor, sulfate as an electron acceptor and acetate as the carbon source from hot springs of Kunashir Island and Kamchatka Peninsula. Similar to other Thermodesulfovibrio species, the new isolates grew by reduction of sulfate, thiosulfate or Fe (III) with a limited range of electron donors, such as hydrogen (in the presence of acetate), formate (in the presence of acetate), pyruvate and lactate. Surprisingly, strain 3907-1M^T proved to be capable of autotrophic growth as well. Up to now, the genus Thermodesulfovibrio was represented by heterotrophic species only. Genome analysis revealed the presence of a gene cluster encoding enzymes of form III RubisCO-mediated transaldolase variant of the Calvin cycle in both strains, but genes encoding ribulose-1,5-bisphosphate carboxylase and phosphoribulokinase in the genome of the strain 3462-1^T contained internal stop codons in their sequences. On the basis of phylogenomic analysis, as well as distinct phenotypic and genomic properties, strain 3907-1M^T (=DSM 112797^T =JCM 39445^T =VKM B-3594^T =UQM 41601^T) is proposed to be classified as Thermodesulfovibrio autotrophicus sp. nov., and strain 3462-1^T (=JCM 39444^T =VKM B-3714^T =UQM 41602^T) – as Thermodesulfovibrio obliviosus sp. nov. Our results demonstrate a chemolithoautotrophic lifestyle in Thermodesulfovibrio representatives, suggesting greater ecological flexibility of this genus than previously assumed.

嗜热硫酸还原菌属的代表是广泛存在的嗜热硫酸还原菌。该属目前包括五个已公布有效名称的物种。从库纳希尔岛和堪察加半岛的温泉中分离出了两株以分子氢为电子供体、以硫酸盐为电子受体、以醋酸盐为碳源的新热解硫弧菌菌株 3907-1M T 和 3462-1T。与其他热硫化弧菌相似，新分离菌株的生长也是通过还原硫酸盐、硫代硫酸盐或铁（III）与有限范围的电子供体，如氢（在醋酸盐存在的情况下）、甲酸盐（在醋酸盐存在的情况下）、丙酮酸盐和乳酸盐。令人惊讶的是，菌株 3907-1MT 还能自养生长。到目前为止，Thermodesulfovibrio 属只有异养物种。基因组分析表明，两株菌株中都存在编码卡尔文循环中形式 III RubisCO 介导的反醛酸酶变体的基因簇，但 3462-1T 菌株基因组中编码核酮糖-1,5-二磷酸羧化酶和磷酸核糖激酶的基因序列中含有内部终止密码子。根据系统发生组分析以及不同的表型和基因组特性，建议将菌株 3907-1MT （=DSM 112797T =JCM 39445T =VKM B-3594T =UQM 41601T）归类为自养型热硫弧菌（Thermodesulfovibrio autotrophicus sp、和菌株 3462-1T（=JCM 39444T =VKM B-3714T =UQM 41602T）--归类为新产热硫弧菌（Thermodesulfovibrio obliviosus sp.我们的研究结果表明，Thermodesulfovibrio 代表了一种化学溶解自养型的生活方式，这表明该属的生态灵活性比以前假设的要大。

{"title":"Thermodesulfovibrio autotrophicus sp. nov., the first autotrophic representative of the widespread sulfate-reducing genus Thermodesulfovibrio, and Thermodesulfovibrio obliviosus sp. nov. that has lost this ability","authors":"Anastasia I. Maltseva , Alexander G. Elcheninov , Alexandra A. Klyukina , Nikolay V. Pimenov , Andrei A. Novikov , Alexander V. Lebedinsky , Evgenii N. Frolov","doi":"10.1016/j.syapm.2024.126561","DOIUrl":"10.1016/j.syapm.2024.126561","url":null,"abstract":"<div><div>Representatives of the genus Thermodesulfovibrio are widespread thermophilic sulfate-reducing bacteria. The genus currently includes five species with validly published names. Two new Thermodesulfovibrio strains, 3907-1M T and 3462-1T, were isolated with molecular hydrogen as an electron donor, sulfate as an electron acceptor and acetate as the carbon source from hot springs of Kunashir Island and Kamchatka Peninsula. Similar to other Thermodesulfovibrio species, the new isolates grew by reduction of sulfate, thiosulfate or Fe (III) with a limited range of electron donors, such as hydrogen (in the presence of acetate), formate (in the presence of acetate), pyruvate and lactate. Surprisingly, strain 3907-1MT proved to be capable of autotrophic growth as well. Up to now, the genus Thermodesulfovibrio was represented by heterotrophic species only. Genome analysis revealed the presence of a gene cluster encoding enzymes of form III RubisCO-mediated transaldolase variant of the Calvin cycle in both strains, but genes encoding ribulose-1,5-bisphosphate carboxylase and phosphoribulokinase in the genome of the strain 3462-1T contained internal stop codons in their sequences. On the basis of phylogenomic analysis, as well as distinct phenotypic and genomic properties, strain 3907-1MT (=DSM 112797T =JCM 39445T =VKM B-3594T =UQM 41601T) is proposed to be classified as Thermodesulfovibrio autotrophicus sp. nov., and strain 3462-1T (=JCM 39444T =VKM B-3714T =UQM 41602T) – as Thermodesulfovibrio obliviosus sp. nov. Our results demonstrate a chemolithoautotrophic lifestyle in Thermodesulfovibrio representatives, suggesting greater ecological flexibility of this genus than previously assumed.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126561"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proposal of Acinetobacter thermotolerans sp. nov. to accommodate bovine feces-dwelling bacteria growing at 47 °C 提出新的耐高温杆菌（Acinetobacter thermotolerans sp.nov.），以适应在 47 °C 下生长的牛粪便栖息细菌。

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology

Pub Date : 2024-11-01 DOI: 10.1016/j.syapm.2024.126560

Violetta Shestivska , Petra Španělová , Marcela Krůtová , Martina Maixnerová , Priscila Thiago Dobbler , Tomáš Větrovský , Alexandr Nemec , Martina Kyselková

This study aimed to determine the taxonomic status of a new group of bovine strains of the genus Acinetobacter characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and rpoB gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome de novo sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known Acinetobacter species were < 83%. Each of the 12 genomes consisted of a circular chromosome (3.05−3.28 Mb) and 1−6 extrachromosomal elements (1.43−122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37–46 °C differed from that of Acinetobacter baumannii. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of strA/strB, tet(Y), and sul2 genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name Acinetobacter thermotolerans sp. nov. The type strain is ANC 7454^T (= CCM 9356^T = CCUG 77195^T = CNCTC 8200^T).

本研究旨在确定牛杆菌属新菌株的分类地位，这些菌株的特点是能在 44 °C以上的温度下生长，实属罕见。最初，根据初步的全细胞 MALDI-TOF MS 鉴定和 rpoB 基因测序，从 2022 年捷克 11 个农场收集的牛粪便中分离出 24 株菌株，代表了一个暂定的新物种。我们对包含组内多样性的 12 个菌株进行了详细研究，包括全基因组从头测序。基于核心基因组的系统发育分析表明，这 12 株菌株在该属中形成了一个独特的支系。该支系内基于 BLAST 的基因组平均核苷酸同一性（ANIb）值≥ 98.2%，而该支系与已知醋酸杆菌物种之间的 ANIb 值为 T（= CCM 9356T = CCUG 77195T = CNCTC 8200T）。

{"title":"Proposal of Acinetobacter thermotolerans sp. nov. to accommodate bovine feces-dwelling bacteria growing at 47 °C","authors":"Violetta Shestivska , Petra Španělová , Marcela Krůtová , Martina Maixnerová , Priscila Thiago Dobbler , Tomáš Větrovský , Alexandr Nemec , Martina Kyselková","doi":"10.1016/j.syapm.2024.126560","DOIUrl":"10.1016/j.syapm.2024.126560","url":null,"abstract":"<div><div>This study aimed to determine the taxonomic status of a new group of bovine strains of the genus Acinetobacter characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and rpoB gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome de novo sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known Acinetobacter species were < 83%. Each of the 12 genomes consisted of a circular chromosome (3.05−3.28 Mb) and 1−6 extrachromosomal elements (1.43−122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37–46 °C differed from that of Acinetobacter baumannii. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of strA/strB, tet(Y), and sul2 genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name Acinetobacter thermotolerans sp. nov. The type strain is ANC 7454T (= CCM 9356T = CCUG 77195T = CNCTC 8200T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126560"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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

Systematic and applied microbiology

Pub Date : 2024-11-01 DOI: 10.1016/j.syapm.2024.126558

Chun Tao Gu

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

Systematic and 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。

{"title":"Inconsistent identification of Apilactobacillus kunkeei-related strains obtained by well-developed overall genome-related indices","authors":"Shintaro Maeno , Akihito Endo","doi":"10.1016/j.syapm.2024.126559","DOIUrl":"10.1016/j.syapm.2024.126559","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126559"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Systematic and 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 R85-13-6^T, which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75^T 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-H75^T and their close neighbors H.anseris ATCC BAA-1299^T 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-H75^T 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-H75^T (=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。

{"title":"Helicobacter cappadocius sp. nov., from lizards: The first psychrotrophic Helicobacter species","authors":"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","doi":"10.1016/j.syapm.2024.126557","DOIUrl":"10.1016/j.syapm.2024.126557","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126557"},"PeriodicalIF":3.3,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142441607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Systematic and 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 0055^T, 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 13345^T. 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 13345^T 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 0055^T (DSM 117632^T = LMG 33563^T) 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。

{"title":"Limosilactobacillus allomucosae sp. nov., a novel species isolated from wild boar faecal samples as a potential probiotic for domestic pigs","authors":"Binbin Chen, Shaktheeshwari Silvaraju, Sharifah Nora Ahmad Almunawar, Yu Chyuan Heng, Jolie Kar Yi Lee, Sandra Kittelmann","doi":"10.1016/j.syapm.2024.126556","DOIUrl":"10.1016/j.syapm.2024.126556","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126556"},"PeriodicalIF":3.3,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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

Systematic and 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。

{"title":"Acidimicrobiia, the actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential","authors":"Sebastián Silva-Solar, Tomeu Viver, Yueqing Wang, Luis H. Orellana, Katrin Knittel, Rudolf Amann","doi":"10.1016/j.syapm.2024.126555","DOIUrl":"10.1016/j.syapm.2024.126555","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126555"},"PeriodicalIF":3.3,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142354249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0