Archives of Microbiology

A hydrogenotrophic methanogen, designated strain ACI-7T, was isolated from an alkaline, saline wetland located in eastern Nebraska, USA. Cells were identified as non-motile rods (0.9-4.2 m in length and 0.2-0.4 {micro}m in diameter) that occurred singly, in chains, and as long filaments and twisted aggregates. Strain ACI-7T utilized H2 + CO2 or formate as methanogenic substrates and required growth factors present in yeast extract for continuous cultivation. The strain grew at 20-45{degrees}C (optimum, 40{degrees}C), at pH 6.5-8.5 (optimum, pH 7.3) and with 0-2.5% NaCl (optimum, 0-1%). The genomic G+C content of ACI-7T was 31.79 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated strain ACI-7T was affiliated with the genus Methanobacterium, most closely related to Methanobacterium oryzae FPiT (97.1% sequence similarity) and Methanobacterium veterum MK4T (96.9% sequence similarity). Overall genome relatedness indices for strain ACI-7T compared to other Methanobacterium species ranged from 68.45-78.17% for average nucleotide identity and 18.9-25.7% for digital DNA-DNA hybridization. Morphological, physiological, and genomic characteristics indicate that strain ACI-7T represents a novel species, for which the name Methanobacterium nebraskense sp. nov. is proposed. The type strain is ACI-7T (=DSM 118696T=ATCC TSD-487T).

The family Natrialbaceae is a member of the class Halobacteria of the archaeal phylum Euryarchaeota. Seventeen genera with validly or effectively published names are currently included within this family. In this study, using pairwise average nucleotide identity and average amino acid identity comparisons in conjunction with phylogenetic analysis, it has been shown that the family Natrialbaceae is highly diverse and contains several potentially novel species and genera that are yet to be fully characterized. The deduced proteome sequence-based phylogenetic tree, constructed using the alignment- and parameter-free method CVTree3, contained six major clades, with Salinarchaeum sp. Harcht-Bsk1 being the only representative within clade 1. Furthermore, Haloterrigena daqingensis was found to be closely related to Natronorubrum sediminis, and it is proposed that these archaea together represent a novel genus. Interestingly, Haloterrigena jeotgali, Haloterrigena thermotolerans, and Natrinema pellirubrum were found to be very closely related to each other, and it is proposed that they be merged into a single species. Notably, the type genus Natrialba itself appeared to be heterogenous and contains species that could be broadly classified among two genera. Likewise, the genus Natrinema is also heterogenous and contains species that could be classified among six genera. Altogether, 19 novel genera have been proposed to be created, and four haloalkaliphilic archaea hitherto recognized only using genus names are confirmed to represent novel species.

This study describes a novel bacterium, Chryseobacterium strain PS-8, isolated from the skin of freshwater pufferfish (Tetraodon cutcutia). Cells are Gram-negative. The genome size is 4.72 Mb, and the G+C content is 36.4%. The in silico DDH homology, ANI, and AAI were below the cutoff value, 70% and 95% to 96%, respectively, as required for novel species delineation. The phylogenomic analysis using core and non-recombinant core genes, the strain PS-8 showed clustering with Chryseobacterium gambrini DSM 18014T. Generally, Chryseobacterium species are considered opportunistic pathogens. Prediction of the virulence genes revealed genes for adherence, biofilm and stability (glf, lpxD, clpE, cps0, clpE, IlpA), proliferation (tufA, cap8E, galE, kfic, bioB, clpP, kdtB, csgD, carB), resistance to immune response (htpB, katA, wbtl, sodB, kpsF), and host-defense evasion system (kpst, clpE, kfic, ybtQ, cap8G, clpP). The cladogram based upon the virulence genes showed a similar phylogeny amongst the Chryseobacterium species. Additionally, secondary metabolites producing gene clusters were identified, including microviridin, resorcinol and polyene, terpene, etc. Our study showed that strain PS-8 constitute a novel species for which Chryseobacterium indicum sp. nov. is proposed. The type strain is PS-8T (= TBRC 15233T = NBRC 115235T).

The linear genome of genus Streptomyces members has the potential to encode diverse and novel biosynthetic gene clusters of invaluable antimicrobial and therapeutic significance. The use of limited taxonomic markers makes the precise identification of these miracle microbes very challenging. In the ongoing omics era, genome sequencing and in-silico analysis of these potential antibiotic producers provide deeper insights into their taxonomy, functional capabilities, and potential for antibiotic production. Here this study presents a multifaceted approach for proper taxonomic identification and genomic and bioinformatic analysis of five bioactive Streptomyces species collected from different sampling sites in the high-altitude oligotrophic North-Western Himalaya, Kashmir, India. We used polyphasic taxonomic classification approaches, such as phylogenetic markers (16S rDNA and gyrase B), average nucleotide identity (ANI) estimation, and digital DNA-DNA hybridization (dDDH), which revealed accurate taxonomic placement of five Streptomyces species, named as, Streptomyces violarus ASQP_29, S. rhizosphaerihabitans ASQP_78, S. fulvoviolaceus ASQP_80, S. mirabilis ASQP_98, and S. thajiwasiensis ASQP_92. Amongst these, one notable finding is the discovery of a novel species proposed as Streptomyces thajiwasiensis sp. nov. ASQP_92. In addition, our study presents the first genome announcement report and analysis for S. rhizosphaerihabitans ASQP_78. Genomic annotation highlighted the presence of an exceptionally high number of poorly characterized genes and hypothetical proteins, indicating their potential for undiscovered biotechnological applications. Clusters of orthologous groups (COG) and gene ontology (GO) analysis provided insights into their varied functional roles in metabolism, signaling, information storage and secondary metabolite biosynthesis. Domain-based functional characterization further detailed their involvement in various biological processes particularly in antibiotic biosynthesis, transport, and resistance. Biosynthetic gene clusters (BGC) analysis demonstrated their diverse metabolite biosynthetic capabilities and identified both unique and conserved BGCs emphasizing the species-specific roles in bioactive metabolite production and the potential of orphan BGCs in novel drug discovery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/596145v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@15ac69corg.highwire.dtl.DTLVardef@a52f89org.highwire.dtl.DTLVardef@d3f8d6org.highwire.dtl.DTLVardef@75cce7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Genomic analysis and taxonomic affiliations of five bioactive Streptomyces species isolated from high altitudes of the North Western Himalaya C_FIG

The utilization of microbial resources requires their relevant reproducible characteristics, and genome analysis plays a crucial role in discovering valuable strains for future applications. In this study, we analyzed potential carbon-fixing microorganisms via Calvin-Benson-Bassham (CBB) cycle using 6,262 bacterial and 487 archaeal genomes from available cultures in Japan Collection of Microorganisms (JCM), one of the well-established culture collections today. A total of 306 strains (147 genera, eight phyla) carried CBB cycle genes and a literal survey showed that 74 genera had reported evidence of their autotrophic growth, although 73 lacked supporting information. Phylogenetic analysis of RubisCO large subunit (RbcL) identified diverse forms (IA, IB, IC, IE, I+, II, and III) with distinct metabolic associations: form IA associated with sulfur oxidation and form IC with hydrogen oxidation. Genome-based metabolic predictions suggested potential carbon fixation in numerous strains lacking experimental evidence. Our analyses showed members of Actinomycetota harboring form IE RubisCO tend to associate with hydrogen oxidation possibly using oxygen or nitrate as an electron acceptor. Additionally, 12 strains in Pseudomonadota contained pufL and pufM genes, suggesting possible phototrophic capabilities, although some failed to predict their electron donors and they possibly use CBB cycle to regulate intracellular redox balance under photoheterotrophic growth. Our findings highlight unrecognized autotrophic potentials in JCM strains and expand our knowledge of carbon fixation diversity. Future experimental validation will deepen our understanding of these microbes roles in the global carbon cycle, with potential applications in carbon sequestration and environmental sustainability.

Syngas fermentation by carbon monoxide (CO)-utilising acetogens offers a sustainable route for converting gasified waste materials into value-added chemicals. In this study, we isolated a novel thermophilic CO-utilising bacterium, strain AZ2, from marine hydrothermal sediment collected on the island of Sao Miguel, Azores, Portugal. Strain AZ2 is an obligately anaerobic, spore-forming bacterium. Average nucleotide identity (ANI; 78.4-86.7%) and digital DNA-DNA hybridization (dDDH; 23.4-32.5 %) analyses indicate that strain AZ2 represents a novel species within a previously uncharacterised lineage represented by the GTDB placeholder genus UBA2545 in the Neomoorellaceae family. Strain AZ2 was able to grow fermentatively on CO, producing acetate. We further demonstrated that its closest isolated relatives - Thermanaeromonas toyohensis, T. burensis, and Thermanaeromonas sp. strain 9S - are capable of growing on CO, producing either acetate or hydrogen gas (H2). Additionally, we unveiled the genomic potential for CO utilisation within other members of the GTDB placeholder class DSM-521 (previously Moorellia) to which our isolate belongs, expanding the list of possible thermophilic CO-utilising acetogens. We propose that strain AZ2T represents the type strain of a novel genus and species, named Thermobium azorense gen. nov., sp. nov. (= DSM 121889T = JCM 39698T).

Microbacterium fakhimi sp. nov. has been isolated from a contaminated algal culture (Chlamydomonas reinhardtii). Its genome has been fully sequenced (3,753,259 base pairs) and a tentative annotation is provided (3,704 genes). Both, genome information and growth tests suggest that M. fakhimi sp. nov. is auxotroph for biotin and thiamine and unable to use sulfate as sulfur (S) source. S-reduced forms, such as methionine and cysteine can support M. fakhimi sp. nov. growth. The potential biotechnological interest of this bacteria is discussed here and in a related research paper (Fakhimi et al., 2023b).

Polyhydroxyalkanoates (PHAs) have emerged as an ecologically friendly alternative to conventional polyesters. In this study, we present a comprehensive analysis of the genomic and phenotypic characteristics of three non-model thermophilic bacteria known for their ability to produce PHAs: Schlegelella aquatica LMG 23380T, Caldimonas thermodepolymerans DSM 15264, and C. thermodepolymerans LMG 21645 accompanied by a comparison with the type strain C. thermodepolymerans DSM 15344T. We have assembled the first complete genomes of these three bacteria and performed the structural and functional annotation. This analysis has provided valuable insights into the biosynthesis of PHAs and has allowed us to propose a comprehensive scheme for the carbohydrate metabolism in the studied bacteria. Through phylogenomic analysis, we have confirmed the synonymity between Caldimonas and Schlegelella genera, and further demonstrated that S. aquatica and S. koreensis, currently classified as orphan species, belong to the Caldimonas genus. SummaryThe genomic and phenotypic analysis of Schlegelella aquatica LMG 23380T and Caldimonas thermodepolymerans DSM 15264 and LMG 21645 sheds light on the production of sustainable polyesters known as polyhydroxyalkanoates (PHAs). The genome assembly and functional annotation highlight key genes related to PHA production and other important traits. Notably, C. thermodepolymerans stands out with its unique xyl operon, making it a highly promising candidate for biotechnological PHA production from xylose-rich lignocellulosic resources. The study emphasizes the importance of a polyphasic approach combining genotypic and phenotypic analyses in prokaryotic taxonomy, emphasizing the need for exploration in the genomic era. By uncovering the key traits of these bacteria, this research opens new horizons towards sustainable production of environmentally friendly polyesters.

Stenotrophomonas goyi sp. nov. has been isolated from a contaminated algal culture (Chlamydomonas reinhardtii). Its genome has been fully sequenced (4,487,389 base pairs) and a tentative annotation is provided (4,147 genes). The genome information suggests that S. goyi sp. nov. is unable to use sulfate and nitrate as sulfur and nitrogen sources, respectively. Growth tests have confirmed the dependence of the sulfur-containing amino acids methionine and cysteine. The potential biotechnological interest of this bacteria is discussed here and in a related research paper (Fakhimi et al., 2023b).

Streptomyces species are ubiquitous bacteria renowned for their prolific production of pharmaceuticals and therapeutic agents. In this study, we explored the draft genome of a novel Streptomyces species, Streptomyces sp. IICT-RSP475, isolated from Talakona, Tirupati, using next-generation sequencing and bioinformatics tools. The draft genome of Streptomyces sp. IICT-RSP475 consists of 4,550,481 base pairs (bp) with a high GC content of >70%. Genome analysis identified 18 biosynthetic gene clusters (BGCs) responsible for the production of ribosomally synthesized and post-translationally modified peptides (RiPPs), polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and other secondary metabolites, including hydrogen cyanide, terpenes, and N1-siderophores. Notably, genome mining using the antiSMASH tool uncovered two novel BGCs classified as RiPP-like clusters. These clusters exhibited unique genetic architectures with previously uncharacterized biosynthetic genes, suggesting the presence of novel bioactive metabolites. Ribotyping analysis, further supported by TYGS (Type Strain Genome Server) and ribosomal MLST (Multilocus Sequence Typing), confirmed the classification of this strain as a novel Streptomyces species. These findings highlight the genomic potential of Streptomyces sp. IICT-RSP475 and warrant further investigation into the expression, structural elucidation, and functional characterization of its novel therapeutic metabolites.

Bacterial symbionts in corals and coral-associated zooxanthellae are attracting increasing attention as potential probiotics. Some members of the family Flavobacteriaceae are zooxanthellae-associated bacteria, which are known to protect zooxanthellae from stresses such as heat and light by producing carotenoids that reduce reactive oxygen species production. This study characterized two Flavobacteriaceae bacteria, Muricauda sp. strains ORYM1 (NBRC115792) and ORYM2 (NBRC115793), isolated from the reef-building coral Galaxea fascicularis and its surrounding seawater in Okinawa, Japan, respectively. The Muricauda sp. strain ORYM2 was isolated from subtropical seawater, and carotenoid production was assessed using ORYM2 as well as ORYM1, which was previously isolated from G. fascicularis. De novo genome sequencing revealed that both strains contain complete sets of zeaxanthin biosynthesis genes, similar to those found in other Muricauda spp. Thin-layer chromatography and high-performance liquid chromatography analyses demonstrated that ORYM1 and ORYM2 produce several carotenoids. The bacterial strains and carotenoids identified in this study provide insights into the biological roles of zooxanthellae-associated bacteria in protecting zooxanthellae and reef-building corals from environmental stresses. Statements and declarationsCompeting interests: The authors declare no competing interests.

Iron is a key micronutrient that constrains microbial growth and productivity in many aquatic and terrestrial environments due to its limited bioavailability. Microorganisms evolved sophisticated acquisition strategies, including the production of siderophores, high-affinity iron-chelating molecules that facilitate iron solubilisation and uptake. Cyanobacteria, photosynthetic prokaryotes and major contributors to global primary production, also depend on iron as a cofactor to their core metabolic enzymes. However, very few cyanobacterial siderophores were described so far, and cyanobacteria remain an underxplored source of possibly novel siderophores. Here we report a novel cyanobacterial siderophore, cyanochelin C, that employs two {beta}-hydroxyaspartate residues for iron chelation. We provide extensive nuclear magnetic resonance (NMR) and mass spectrometry (MS) evidence on the molecular structure and identify the corresponding biosynthetic gene cluster (BGC). Bioinformatic analysis of the BGC further revealed the presence of an acylase CcsQ clustering with a broader cyanobacteria-specific family of acylases associated with predicted siderophore-encoding BGCs. Discovery of cyanochelin C and its deacylation by CcsQ expands the known structural diversity of cyanobacterial siderophores and improves the understanding of important enzymatic reactions.

A facultatively anaerobic, hydrogen-oxidizing, thermophilic bacterium (strain KUI-RBT) was isolated from a geothermal spring biofilm in Rotorua, New Zealand. Strain KUI-RBT is a motile, straight rod, measuring approximately 0.7 {micro}m by 1.0 to 1.5 {micro}m with a diderm cell wall. Growth of KUI-RBT occurred from 39 to 74 {degrees}C (Topt 64.5 {degrees}C), pH 5.0 to 7.5 (pHopt 6.5), and 0 to 1% (w/v) NaCl (NaClopt 0.4-0.7%, w/v). KUI-RBT utilizes carbon dioxide and various organic carbon substrates as carbon sources and hydrogen as an electron donor. KUI-RBT can use oxygen (0-21%, v/v), elemental sulfur, thiosulfate, sulfite, nitrate, arsenate, and selenate as terminal electron acceptors. Major fatty acids of strain KUI-RBT include C20:1, C18:1, and C18:0 and the primary quinone is MTK-7. The whole genome G+C content is 34.23 mol%. Phylogenetic analyses indicate KUI-RBT to be a member of the family Hydrogenothermaceae, with Sulfurihydrogenibium azorense Az-Fu1T its closest characterised relative (94.51% 16S rRNA gene sequence similarity, 78.01% whole genome ANI, 61.34% whole genome AAI). Based on phylogenetic and phenotypic analyses, we propose KUI-RBT represents a novel genus and species within the family Hydrogenothermaceae, for which we propose the name Reysenbachia aerophila gen. nov., sp. nov. The type strain is KUI-RBT (=KCTC accession =JCM accession). The GenBank accession number for the 16S rRNA gene sequence of strain KUI-RBT is PZ052650. The GenBank accession number for the whole genome of strain KUI-RBT is JBVODP000000000.

Cyanobacteria play an important role in primary production and nitrogen fixation. Although Cyanobacteria are well-known diazotrophic organisms, their role in other steps Nitrogen Cycle is obscure. Screening of Cyanobacterial genomes from cultured and unculturable species can help identify potentially novel functions. In this study, we assembled Cyanobacterial genomes from metagenomic data generated from environmental DNA isolated from a brackish water lagoon (Chilika, India). We annotated these Cyanobacterial metagenome-assembled genomes (MAG) for all the encoded functions using KEGG Orthology. We found two high-quality Cyanobacterial MAGs containing the nirBD gene and nifH and nifD genes involved in the nitrogen cycle. nirBD encodes for the Dissimilatory Nitrate Reduction to Ammonium (DNRA) activity, a function previously not ascribed to Cyanobacteria. We validated the presence of NirBD in publicly available isolate genomes of Cyanobacteria and examined its evolution in the phylum by phylogenetic reconciliation of species and gene trees. Our analysis revealed that both horizontal gene transfers and speciation events contributed to the dispersal of the nirBD gene in Cyanobacteria. We observed that mostly filamentous Cyanobacteria served as ancestral donors in horizontal gene transfer events. Further, we found that the nirBD gene is under a purifying selection pressure in Cyanobacteria. This study demonstrates the genomic potential and evolution of DNRA activity in Cyanobacteria for the utilisation of nitrate in the ecosystem which can help these organisms to cope with extreme environmental conditions. It expands our overall comprehension of the contribution of Cyanobacteria in the biogeochemical cycling in aquatic ecosystems.

Sphingomonadaceae has a large number of strains that can biodegrade hepatotoxins or environmental pollutants. The latest research reported that certain strains can also produce lutein. Based on the third-generation sequencing technology, we analyzed the whole genome sequence and compared related functional genes of two strains of Sphingomonadaceae isolated from different habitats. The genome of Sphingopyxis USTB-05 was 4,679,489 bp and contained 4312 protein coding genes. The 4,239,716 bp nuclear genome of Sphingomonas morindae NBD5, harboring 3882 protein coding genes, has two sets of chromosomes. Both strains had lutein synthesis metabolism pathway sharing identical synthetic genes of crtB, crtE, crtI, crtQ, crtL, crtR, atoB, dxs, dxr, ispD, ispE, ispDF, gcpE, ispG, ispH, ispA, ispB and ispU. Sphingopyxis USTB-05 had hepatotoxins microcystins and nodularin metabolic pathways related to 16 genes (ald, ansA, gdhA, crnA, phy, ocd, hypdh, spuC, nspC, speE, murI, murD, murC, hmgL, bioA and glsA), while these genes were not found in Sphingomonas morindae NBD5. The unique protein sequences of strain NBD5 and strain USTB-05 were 155 and 199, respectively. The analysis of whole genome of the two Sphingomonadaceae strains provides insights into prokaryote evolution, the new pathway for lutein production and the new genes for environmental pollutant biodegradation. IMPORTANCEUnderstanding the functional genes related to the special functions of strains is essential for humans to utilize microbial resources. The ability of Sphingopyxis USTB-05 to degrade hepatotoxins microcystins and nodularin has been studied in depth, however the complete metabolic process still needs further elucidation. Sphingomonas morindae NBD5 can produce lutein, and it is necessary to determine whether there is a new pathway of lutein. In this study, the whole genome sequencing of Sphingopyxis USTB-05 and Sphingomonas morindae NBD5 were performed for the first time. Lutein synthesis metabolic pathways and synthetic genes were discovered in Sphingomonadaceae. We predicted the existence of new lutein synthesis pathways and revealed most of the genes of the new synthesis pathways. A comparative analysis of the functional genes of the two strains revealed that Sphingopyxis USTB-05 contains a large number of functional genes related to the biodegradation of hepatotoxins or hexachlorocyclohexane. Among them, the functional genes related to the biodegradation and metabolism of hexachlorocyclohexane had not been previously reported. These findings lay the foundation for the biosynthesis of lutein using Sphingomonas morindae NBD5 or Sphingopyxis USTB-05 and the application of Sphingopyxis USTB-05 for the biodegradation of hepatotoxins microcystins and nodularin or environmental pollutants.

From Brazilian limestone caves, we isolated 29 bacteria utilizing phenol (23 bacteria), toluene (all bacteria), and/or benzene (all bacteria) as sole carbon sources. One isolate showed phosphate solubilization, while lipase/esterase activity occurred in two isolates; no amylase activity was detected, but 16 isolates ([~]55%) exhibited protease activity. Among them, Nocardioides sp. SF1 was selected for whole-genome sequencing due to its aromatic compound tolerance and protease activity. Additionally, catechol cleavage assays yielded unexpected purple pigmentation, suggesting non-canonical aromatic metabolism. Its high-quality draft genome (4.25 Mbp, 16 contigs, N50 of 887 kb) lacks canonical phenol hydroxylase but encodes alternative oxidation systems, phenylacetyl-CoA pathway, besides, desferrioxamine siderophore, biosurfactants, and phosphate solubilization, key adaptations for oligotrophic caves and biotechnologically interesting activities. Whole-genome comparisons (TYGS/GGDC, OrthoANI and k-mer) suggest potential new species. Lacks acquired antimicrobial resistance genes (ResFinder) and pathogenicity potential (PathogenFinder). Nocardioides sp. SF1 emerges as a non-pathogenic candidate for aromatic bioremediation and plant growth promotion in contaminated, nutrient-poor environments, highlighting cave actinobacterias unexplored biotechnological potential.

A novel, autotrophic, mesophilic bacterium, strain RS19-109T, was isolated from sulfidic stream sediments in the Frasassi Caves, Italy. The cells of this strain grew chemolithoautotrophically under anaerobic conditions while disproportionating elemental sulfur (S0) and thiosulfate, but not sulfite with bicarbonate/CO2 as a carbon source. Autotrophic growth was also observed with molecular hydrogen as an electron donor, and S0, sulfate, thiosulfate, nitrate, and ferric iron as electron acceptors. Oxygen was not used as an electron acceptor and sulfide was not used as an electron donor. Weak growth was observed with sulfate as an electron acceptor and organic carbon as electron donors and carbon sources. The strain also showed weak growth by fermentation of tryptone. Strain RS19-109T was found to be phylogenetically distinct based on 16S rRNA gene sequence similarity (89.2%) to its closest relative, Desulfurivibrio alkaliphilus AHT2T. The draft genome sequence for strain RS19-109T had average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization values of 72.2%, 63.0%, and 18.3%, respectively, compared with the genome sequence of D. alkaliphilus AHT2T. On the basis of its physiological and genomic properties, strain RS19-109T is proposed as the type strain of a novel species of a novel genus, Thiovibrio frasassiensis gen. nov., sp. nov. A novel family, Thiovibrionaceae fam. nov., is proposed to accommodate Thiovibrio within the order Desulfobulbales.

ASS1 was isolated as a motile Stenotrophomonas strain from crude oil-contaminated soils in Tabasco, Mexico. We characterized this strain using physiological and biochemical traits. ASS1 grew at temperature 25-37 (optimally at 37 {degrees} C) and at pH 6 to 8 (optimally at pH 7 to 8). The assembled genome has a total length of 4.56MB with a G + C content of 66.6%. The 16S rRNA gene sequence analysis confirmed that this strain belongs to the genus Stenotrophomonas. Based on the 16S rRNA analysis, Stenotrophomonas geniculata ATCC 19374 is the closest species, and it shares 99.86% similarity with ASS1. Similarly, a phylogenomic tree based on core genome sequence revealed that the closest species to ASS1 is Stenotrophomonas geniculata ATCC 19374. The major fatty acids in ASS1 are C16:0, antesio C15:0, iso C12:0, iso C15:0, iso C17:0 and C18:0. The genome of ASS1 consists of 4,373,402 bp. The Average Nucleotide Identity (ANI) values for ASS1 which it shared with its closest phylogenetic neighbors, are Stenotrophomonas geniculata ATCC 19374 = JCM 13324 [T] 92.66 %, Stenotrophomonas maltophilia 13637[T] 92.15%, Stenotrophomonas maltophilia K279a 92.13% Stenotrophomonas maltophilia R551-3 92.15% Stenotrophomonas maltophilia MTCC 434 [T] 92.08% and Pseudomonas hibisicicola ATCC [T] 91.66%. ASS1 possesses genes that are essential for the degradation of Polycyclic Aromatic hydrocarbon. Genes such as 1, 2 dihydroxyl 1, 2 dihydronaphthalene dehydrogenase; MG068 17425, homologous to 2 hydroxyl chromene 2 carboxylate isomerases; MG 18055, homologous to salicylaldehyde dehydrogenase and MG068 20095, homologous to naphthalene 1, 2 dioxygenases were identified in ASS1. The dDDH value between ASS1 and its closest neighbor Stenotrophomonas geniculata ATCC 19374 = JCM 13324 [T] is 50%, which is the highest for all the typed species and as such we proposed that ASS1 is a novel species with the name Stenotrophomonas oleivorans sp. nov. sp. nov. and ASS1T as the typed strain

Steroid hormones (androgens and estrogens) are crucial for development, reproduction, and communication of multicellular eukaryotes. The ubiquitous distribution and persistence of steroid hormones in our ecosystems have become an environmental issue due to the adverse effects on wildlife and humans upon long-term exposure. Microbial degradation is critical for the removal of steroid hormones from ecosystems. The aerobic degradation pathways for androgens and estrogens and the anaerobic degradation pathway for androgen have been studied into some details; however, the mechanism for anaerobic estrogen degradation remains completely unknown. Here, we presented the circular genomes of D. oestradiolicum DSM 16959 and Denitratisoma sp. strain DHT3, two betaproteobacteria capable of anaerobic estrogen degradation. We identified the genes involved in steroid transformation and in the anaerobic 2,3-seco pathway in both genomes. Additionally, the comparative genomic analysis revealed that genes exclusively represented in estrogen-degrading anaerobes might play a role in anaerobic estrogen catabolism.

The tumor-associated microbiome is a key player in cancer development, progression, prognosis, and therapeutic response. Notably, distinct microbial signatures have been identified across cancer types. Small cell lung carcinoma (SCLC) accounts for approximately 15% of all lung cancer, yet its microbiome remains unclear. Analyzing the bacteriome composition in tissue from ten SCLC cases and in 10 cases of a heterogenous lung pathology group, we found a distinct microbial signature associated with SCLC with significantly lower diversity and higher dissimilarity, characterized by a higher relative abundance of Firmicutes and Bacteroidota, and a markedly different set of dominant genera (Pseudomonas, Streptococcus and Haemophilus) resulting in an increased Proteobacteria-to-Actinobacteria ratio. Unexpectedly, mycobiome analysis comparing pooled samples of these SCLC cases with ten pooled lung adenocarcinoma (LUAD) cases revealed that the fungal genus Taphrina was uniquely represented in SCLC. Strikingly, mycobiome individual analysis of twenty-one additional SCLC cases compared with 10 LUAD cases showed an increased prevalence of Taphrina sp. in SLCL tissue. Overall, the results suggest that SCLC microbiome is distinct from other lung pathologies and uncovers a novel link between the biotrophic plant pathogenic Taphrina and human cancer.