Systematic and applied microbiology最新文献

{"title":"Assessment of cluster analysis of elastic light scatter profiles for the identification of foodborne Bacteria","authors":"Sana Bari ,&nbsp;Yuwei Zhang ,&nbsp;Valery Patsekin ,&nbsp;J. Paul Robinson ,&nbsp;Bartek Rajwa ,&nbsp;Andrew Gehring ,&nbsp;James Lindsay ,&nbsp;Don Kulasiri ,&nbsp;Stephen L.W. On","doi":"10.1016/j.syapm.2025.126641","DOIUrl":"10.1016/j.syapm.2025.126641","url":null,"abstract":"<div><div>Elastic Light Scatter (ELS) profiling is a novel approach for simultaneous detection and identification of bacteria cultured on solid agar media. The profiles comprise a range of different scatter features that can be used jointly or individually as a basis for comparison. We examined the utility of cluster analysis of ELS profiles for classification and identification of bacteria of relevance to foods. A total of 1562 colonies from 48 strains, representing 17 different species distributed among four genera, were examined. Each of three scatter-derived features (Zernike moments, pseudo-Zernike moments, proprietary Patsekin elements) were used individually and in combination for the cluster analysis. Of these, a combination of Patsekin elements and pseudo-Zernike moments yielded clusters that best reflected the known taxonomic relationships among the strains examined. Evidence of Genus-level markers of colony architecture was seen and there was a general agreement of clustering at the species level. Nonetheless, some individual colonies did not cluster with the majority of others from the same taxon, which could reflect an aberrant ELS phenotype, or known challenges in depicting strain relationships using cluster analytical methods. However, when compared with UMAP data processing, relationships between individual colonies were more easily discerned by inspecting the dendrogram. Cluster analysis of ELS profiles is a useful adjunctive tool for the classification and identification of bacteria and results may also be helpful in informing the development and improvement of other data analytical tools for ELS profile analysis.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 5","pages":"Article 126641"},"PeriodicalIF":3.3,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144686304","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}

{"title":"Astrobacterium formosum gen. nov., sp. nov., a novel psychrotolerant rosette-forming bacterium from a laboratory psychrophilic EGSB bioreactor","authors":"V.V. Potokina ,&nbsp;S.N. Parshina ,&nbsp;A.Y. Merkel ,&nbsp;A.G. Elcheninov ,&nbsp;A.V. Vishnyakova ,&nbsp;A.N. Avtukh ,&nbsp;N.A. Kostrikina ,&nbsp;V.M. Tereshina ,&nbsp;Y.V. Litti","doi":"10.1016/j.syapm.2025.126640","DOIUrl":"10.1016/j.syapm.2025.126640","url":null,"abstract":"<div><div>A new psychrotolerant, facultative anaerobic bacterium, strain Astr-EGSB^T, was isolated from a syntrophic propionate-oxidizing consortium obtained from a low-temperature expanded granular sludge bed (EGSB) bioreactor fed with a mixture of volatile fatty acids. The cells of this strain were Gram-negative and non-spore-forming rods (0.5<strong>·</strong>0.8–1.5<strong>·</strong>9 μm), grew either as individual cells or formed rosettes of various sizes, resembling stars. Bacteria reproduced by budding, and each cell has a sticky, non-reproductive pole that allows them to attach to other cells, forming rosette-like clusters. This strain could grow between 5 and 40 °C, with pH ranging from 4.5 to 7.5 and NaCl concentration of 0 to 2 %. It could degrade a variety of carbon substrates, including sugars, alcohols, casamine acids and several organic acids, but could not grow under photoautotrophic conditions. During glucose fermentation, the products include lactate, acetate, isobutyrate, CO₂, and traces of succinate. Major cellular fatty acids were C_18:1ω9c and C_19:0 cyclo <em>ω</em>9c, menaquinone МХ-10(H10). Main polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Sequence comparison of the 16S rRNA gene revealed that strain Astr-EGSB^T was related to <em>Pseudorhodoplanes sinuspersici</em> RIPI 110^T with a similarity of 95.0 %. Based on phylogenomic analysis using 120 marker genes, strain Astr-EGSB^T belongs to the distinct genus-level phylogenetic lineage that is most related to the genus <em>Rhodoplanes</em>. The G + C content of genomic DNA was 65.8 mol%. Based on genomic and physiological characteristics of strain Astr-EGSB^T, a new genus and a new species, <em>Astrobacterium formosum</em> gen. Nov., sp. nov., is proposed, with Astr-EGSB^T as the type strain.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 5","pages":"Article 126640"},"PeriodicalIF":3.3,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633497","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}

{"title":"Pyranulibacter aquaticus gen. nov., sp. nov., the first nitrate-reducing representative of the class Ignavibacteria from an Iturup well","authors":"Olga A. Podosokorskaya ,&nbsp;Alexander Y. Merkel ,&nbsp;Andrei A. Novikov ,&nbsp;Alexandra A. Klyukina ,&nbsp;Alexander G. Elcheninov","doi":"10.1016/j.syapm.2025.126639","DOIUrl":"10.1016/j.syapm.2025.126639","url":null,"abstract":"<div><div>A novel facultatively anaerobic moderately thermophilic bacterium, strain 4301-Me^T was isolated from the well 13k on the Iturup Island (Kuril Islands, Russian Federation). Gram-stain-negative, motile rods were present singly, in pairs, rosettes, and aggregates, or formed biofilms. The strain grew optimally at 50–55 °C, pH 6.7–7.0 and 0.2–0.4 % NaCl. It did not require yeast extract for growth and utilized mono-, di- and polysaccharides (cellulose, starch, xanthan gum, locust bean gum, glucomannan, lichenan, amorphous chitin) as well as proteinaceous substrates (gelatin, peptone, beef and yeast extract). Growth under anaerobic conditions was observed in the presence and absence of external electron acceptors. Sulfur, thiosulfate, nitrate, arsenate, Fe-citrate, and ferrihydrite were reduced with acetate, or yeast extract as electron donors. The respiratory quinone was MK-7. Major cellular fatty acids were iso-C_15:0, iso-C_16:0, anteiso-C_15:0, 3OH-C_14:0, 3OH-C_13:0. The size of the genome and genomic DNA G + C content of strain 4301-Me^T were 3.34 Mb and 33 %, respectively. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strain 4301-Me^T represented a distinct lineage of the family <em>Melioribacteraceae</em> within the class <em>Ignavibacteria</em>. Based on phylogenomic analysis and phenotypic features, the novel isolate was assigned to a novel genus, for which the name <em>Pyranulibacter</em> gen. nov. is proposed. Strain 4301-Me^T represents its type species <em>Pyranulibacter aquaticus</em> sp. nov. (=CGMCC 1.18061^T = B-3822^T = BIM B-2047^T = UQM 41592^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 5","pages":"Article 126639"},"PeriodicalIF":3.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144623499","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}

{"title":"Genomic and phylogenetic re-assessment of the genus Stenotrophomonas: Description of Stenotrophomonas thermophila sp. nov., and the proposal of Parastenotrophomonas gen. Nov., Pseudostenotrophomonas gen. Nov., Pedostenotrophomonas gen. Nov., and Allostenotrophomonas gen. Nov.","authors":"Amandine Chauviat,&nbsp;Danis Abrouk,&nbsp;Elisabeth Brothier,&nbsp;Daniel Muller,&nbsp;Thibault Meyer ,&nbsp;Sabine Favre-Bonté","doi":"10.1016/j.syapm.2025.126630","DOIUrl":"10.1016/j.syapm.2025.126630","url":null,"abstract":"<div><div>The <em>Stenotrophomonas maltophilia</em> species complex (Smc) currently comprises 19 genomospecies, known for their ecological versatility and role as opportunistic human pathogens. However, significant genomic variability among strains has complicated their classification, and only a few species within the Smc have been validly described. Despite successive taxonomic revisions, there remains no consensus on the naming of many genomospecies, largely due to the phenotypic heterogeneity across the complex.</div><div>In this study, we performed a comprehensive genomic and phylogenetic re-assessment to clarify the boundaries of the <em>Stenotrophomonas</em> genus and its species complex. Using whole-genome phylogeny and Overall Genome-Related Indices (OGRIs) such as digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANIb and ANIm), and Average Amino Acid Identity (AAI), we established precise cutoffs for defining the genus and the Smc. Our analysis led to the formal revision of the <em>Stenotrophomonas</em> genus, resulting in the delineation of four novel bacterial genera: <em>Allostenotrophomonas</em> gen. Nov., <em>Pedostenotrophomonas</em> gen. Nov., <em>Parastenotrophomonas</em> gen. Nov., and <em>Pseudostenotrophomonas</em> gen. Nov. Additionally, we standardized the nomenclature within the Smc by identifying reference strains for each genomospecies. Among these, we describe a novel species, <em>Stenotrophomonas thermophila</em> sp. nov. (type strain BurA1^T = LMG 33562^T = EML 1882^T). This study provides a robust framework for future taxonomic and ecological studies within the <em>Stenotrophomonas</em> genus.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126630"},"PeriodicalIF":3.3,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144338327","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}

{"title":"Polyphasic taxonomic description of Streptomyces tritrimontium sp. nov., actinomycetes isolated from moonmilk in Szczelina Chochołowska cave of Tatra Mountains in Poland and emended descriptions of Streptomyces manipurensis Nimaichand et al. 2021 and Streptomyces nojiriensis Ishida et al. 1967","authors":"Patrycja Bielańska ,&nbsp;Patrycja Golińska ,&nbsp;Elaine Romines ,&nbsp;Łukasz Rąbalski ,&nbsp;Grzegorz Węgrzyn","doi":"10.1016/j.syapm.2025.126627","DOIUrl":"10.1016/j.syapm.2025.126627","url":null,"abstract":"<div><div>In the present study the taxonomic position of two streptomycete strains, isolated from moonmilk in Szczelina Chochołowska cave located in Tatra Mountains in Poland, was established using a polyphasic taxonomic approach. Strains 2.9^T and 4.24 have morphological characteristics and chemotaxonomic properties consistent with their classification in the genus <em>Streptomyces</em>. They are Gram-stain-positive filamentous bacteria which formed an extensively branched substrate mycelium and straight long chains of smooth surfaced spores. They contain <em>LL</em>-diaminopimelic acid, glucose and ribose in whole-organism hydrolysates, produce major proportions of straight, iso- and <em>anteiso</em>- fatty acids, hexa- and octa‑hydrogenated menaquinones with nine isoprene units and have a polar lipid pattern with phosphatidylethanolamine (diagnostic lipid). Strains 2.9^T and 4.24 formed a distinct clade within the <em>Streptomyces</em> 16S rRNA gene tree sharing 100 % sequence similarity with <em>Streptomyces stoeckheimensis</em> DSM 116496ᵀ. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values calculated from the whole genome sequences of strains 2.9^T and 4.24 and their closely related phylogenomic neighbour were found to be 90.4 and 36.3 %, respectively, indicating that they belong to different genomic species. Consequently, based on the genomic, phylogenetic and associated phenotypic data it is proposed that strains 2.9^T and 4.24 be assigned to the genus <em>Streptomyces</em> as <em>Streptomyces tritrimontium</em> sp. nov. with strain 2.9^T (DSM 119353^T = PCM 3548^T) as the type strain.</div><div>The genomes of strains 2.9^T and 4.24 contain relatively high number of biosynthetic gene clusters (28 and 27, respectively), some of which were discontinuously distributed, indicating ones predicted to express for novel specialized metabolites.</div><div>Data acquired in the present study have also been used to emend the descriptions of <em>Streptomyces manipurensis</em> and <em>Streptomyces nojiriensis</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126627"},"PeriodicalIF":3.3,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144280462","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}

{"title":"Revisiting carbon monoxide metabolism in the Moorella genus and isolation of a novel Moorella species","authors":"Anastasia Galani ,&nbsp;Melissa Antony Venancius ,&nbsp;Ben Tumulero ,&nbsp;Detmer Sipkema ,&nbsp;Diana Z. Sousa","doi":"10.1016/j.syapm.2025.126628","DOIUrl":"10.1016/j.syapm.2025.126628","url":null,"abstract":"<div><div>Thermophilic acetogens hold great potential for syngas fermentation, as they efficiently convert CO and H₂/CO₂ into added-value chemical building blocks. Among these, <em>Moorella</em> species are the most studied, known for their versatility by growing autotrophically on C1 gaseous compounds and heterotrophically on sugars and organic acids. In this study, we isolated two novel thermophilic CO-utilising acetogens belonging to the genus <em>Moorella</em>: strain AZ13.I, representing a novel species, and strain AZ24.1, which is closely related to <em>M. humiferrea</em>. We further investigated CO metabolism in this genus and found that all <em>Moorella</em> species isolated to date can utilise CO, contradicting earlier reports suggesting that the type strains of <em>M. humiferrea</em> (DSM 23265^T) and <em>M. mulderi</em> (DSM 14911^T) were incapable of metabolising this substrate. Finally, based on genomic analyses at the genus level, we suggest that CO metabolism is a universal trait across all <em>Moorella</em> species.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126628"},"PeriodicalIF":3.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144297924","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}

{"title":"Liberiplasma polymorphum gen. nov., sp. nov., a novel cell-wall-less free-living anaerobe, isolated from a terrestrial mud volcano, and proposal of Liberiplasmataceae fam. nov. and Liberiplasmatales ord. nov","authors":"M.A. Khomyakova ,&nbsp;A.Y. Merkel ,&nbsp;A.A. Novikov ,&nbsp;A.I. Slobodkin","doi":"10.1016/j.syapm.2025.126629","DOIUrl":"10.1016/j.syapm.2025.126629","url":null,"abstract":"<div><div>A novel anaerobic free-living bacterium (strain C05PYG^T) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells were pleomorphic but mainly consisted of small, cell wall-less, non-motile cocci, 0.40–0.46 μm in diameter. The temperature range for growth was 5–37 °C (optimum at 30 °C). The pH range for growth was 7.5–10.0, with an optimum at pH 8.0–9.0. It was a chemoorganoheterotroph, fermenting mono-, di- and polysaccharides (dextrin, starch), proteinaceous substrates and organic acids (lactate and pyruvate). Yeast extract was essential for growth. Strain C05PYG^T possessed an ability to degrade extraneous DNA. Major cellular fatty acids were C_16:0 and i-C_17:0; major dimethyl acetals were C_14:0 DMA and i-C_15:0 DMA. The genome of strain C05PYG^T had a size of 2.0 Mb with a DNA G + C content of 33.0 % (WGS). Phylogenetic analysis based on 120 marker genes placed strain C05PYG^T in a separate order adjacent to the order <em>Acholeplasmatales</em> within the class <em>Mollicutes</em>, hitherto referred to as “<em>Izemoplasmatales</em>”, which contains no representatives with validly published names. We propose to assign strain C05PYG^T to a novel species of a novel genus, <em>Liberiplasma polymorphum</em> gen. nov., sp. nov.; the type strain is C05PYG^T (=VKM B-3767^T = BIM B-2060^T = UQM 41800^T). This genus is placed in a novel family, <em>Liberiplasmataceae</em> fam. nov. within the novel order <em>Liberiplasmatales</em> ord. nov<em>.,</em> class <em>Mollicutes</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126629"},"PeriodicalIF":3.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144261618","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}

{"title":"Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella","authors":"Juliana Botero ,&nbsp;Nikolas Basler ,&nbsp;Margo Cnockaert ,&nbsp;Charlotte Peeters ,&nbsp;Maria Schreiber ,&nbsp;Manja Marz ,&nbsp;Dirk C. de Graaf ,&nbsp;Jelle Matthijnssens ,&nbsp;Peter Vandamme","doi":"10.1016/j.syapm.2025.126625","DOIUrl":"10.1016/j.syapm.2025.126625","url":null,"abstract":"<div><div>We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 <em>Bartonella</em> isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as <em>Bartonella apihabitans</em> and three as <em>Bartonella choladocola</em> was straightforward, the identification of 25 <em>Bartonella apis</em>-like isolates was challenging. A taxonomic and functional analysis of four <em>B. apis</em>-like genomes and of publicly available <em>B. apis</em> genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of <em>B. apis</em> and <em>B. apis</em>-like genomes. Different phylogenomic analyses showed that <em>B. apis</em> and <em>B. apis</em>-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as <em>B. apis</em>. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of <em>Bartonella</em> species which differed not only in phylogenomic position and ecology, but also in genome size and genomic percentage G + C content, and in many metabolic capabilities. We propose to reclassify the single species of the <em>Bartonella tamiae</em> clade into the novel genus <em>Attibartonella</em> gen. nov., with <em>Attibartonella tamiae</em> comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated <em>Bartonella</em> clade into the novel genus <em>Ditibartonella</em> gen. nov., with <em>Ditibartonella apis</em> comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional <em>Ditibartonella</em> species in honey bee samples, highlighted an evolutionary adaptation of <em>Ditibartonella</em> bacteria to bee hosts and suggested shared transmission routes.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126625"},"PeriodicalIF":3.3,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144271231","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}

{"title":"Characterization of Sphingomicrobium aquimarinum sp. nov. and Sphingomicrobium maritimum sp. nov. highlights astaxanthin-producing bacteria in the family Sphingomonadaceae","authors":"Dao-Feng Zhang ,&nbsp;Hong-Chuan Wang ,&nbsp;Shi Shi ,&nbsp;Tian-Pu Li ,&nbsp;Dan-Yuan Guo ,&nbsp;Zi-Wen Yang ,&nbsp;Yang Yuan ,&nbsp;Jianke Huang ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2025.126624","DOIUrl":"10.1016/j.syapm.2025.126624","url":null,"abstract":"<div><div>Bacteria are considered as better models for industrial production of astaxanthin (AXT) because of their fast growth and convenience for the downstream extraction. Nevertheless, few bacterial species of native AXT producers are explored to date. In this study, bacterial strains XHP0235^T (=GDMCC 1.3093^T = MCCC 1K07532^T = JCM 35574^T) and XHP0239^T (=GDMCC 1.3086^T = MCCC 1K07530^T = JCM 35575^T) were isolated from coastal seawater of China. Polyphasic taxonomy suggested that strains XHP0235^T and XHP0239^T were closely related to <em>Sphingomicrobium aestuariivivum</em> AH-M8^T, <em>S. arenosum</em> CAU 1457^T, and <em>S. astaxanthinifaciens</em> CC-AMO-30B^T, and should be recognized as two novel species of the genus <em>Sphingomicrobium</em>, for which the names <em>Sphingomicrobium aquimarinum</em> sp. nov. and <em>Sphingomicrobium maritimum</em> sp. nov. are proposed, respectively. Comparative genomic analysis revealed the complete AXT pathway (genes <em>crtB</em>, <em>crtI</em>, <em>crtY</em>, <em>crtZ</em>, and <em>crtW</em>) present in strains XHP0235^T, XHP0239^T and the three relative strains, and the carotenoid-targeted metabolome analysis confirmed the productions of AXT and other carotenoids. Inspired by these findings, the AXT pathway was further explored in the family <em>Sphingomonadaceae</em>, and 45 (18.8 %) out of the 240 type strains was identified to harbor all the five genes for AXT synthesis, of which the gene arrangement can be classified as seven types. The flanking gene contents were extremely variable with a concerted evolutionary history of the AXT genes. However, the AXT pathway is still predictable if an isolate is closely related to a known AXT-pathway-positive strain (evolutionary distance &lt;0.14). This study significantly enlarged the diversity of AXT-producing bacteria with highlighting such species in the family <em>Sphingomonadaceae</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126624"},"PeriodicalIF":3.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230869","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}

{"title":"Cellulosispirillum alkaliphilum, gen. nov., sp. nov., an obligately anaerobic cellulotrophic member of the phylum Fibrobacterota from soda lakes","authors":"Dimitry Y. Sorokin ,&nbsp;Alexander Y. Merkel ,&nbsp;Tatjana V. Khizhniak","doi":"10.1016/j.syapm.2025.126623","DOIUrl":"10.1016/j.syapm.2025.126623","url":null,"abstract":"<div><div>Intensive microbiology studies of the past several decades of soda lakes, uncovered a rich functional diversity of haloalkaliphilic microbes driving carbon, nitrogen and sulfur cycles in these unique double-extreme habitats. One of the unexpected finding was a discovery there of aerobic extremely halophilic cellulotrophic natronoarchaea. Yet, little is still known about the identity of the soda lake bacteria able to use native cellulose as growth substrate, except for a single case of an anaerobic clostridium. In this work we present results of phenotypic and functional genomic analysis of an anaerobic bacterium, strain ANBcel5^T, enriched from hypersaline Siberian soda lakes with amorphous cellulose as growth substrate. Phylogenetic analysis placed the isolate into the family <em>Chitinispirillaceae</em> in the phylum <em>Fibrobacterota</em> as a new genus and species lineage with the 16S rRNA gene identity and Relative Evolutionary Divergence (RED) to its only known species <em>Chitinispirillum alkaliphilum</em> ACht6–1^T of 95.2 % and 0.847, respectively. In contrast, despite obvious morphological resemblance to ACht6–1^T, strain ANBcel5^T is a narrow cellulose-utilizing fermentative anaerobe fermenting cellulose and cellobiose to acetate, H₂ and succinate. It is a moderately salt-tolerant obligate alkaliphile growing optimally at 0.6 M total Na⁺ as carbonates and pH 9.5. Functional genome analysis of the isolate revealed the presence of multiple genes encoding extracellular endocellulases from the GH families 5 and 9, three sodium-translocating membrane complexes and osmolytes <em>Nε</em>-acetyl-β-lysine and glycine betaine biosynthesis. The bacterium is proposed to be classified as <em>Cellulosispirillum alkaliphilum</em> gen. nov., sp. nov. (DSM 113825 = UQM 41584).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 4","pages":"Article 126623"},"PeriodicalIF":3.3,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144222371","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}