Here, we report draft genome sequences of two bacterial type strains isolated from cows, Pseudobutyrivibrio xylanivorans DSM 14809T and [Clostridium] fimetarium DSM 9179T. The P. xylanivorans DSM 14809T genome is 3.4 Mbp with 3,147 predicted genes, while the C. fimetarium DSM 9179T genome is 4.6 Mbp with 4,215 predicted genes.

We report the genome sequence of Clostridium tetanomorphum DSM 4474T isolated from a septic wound. In addition to its potential as a human pathogen, this species may be useful in biofuel production due to its ability to synthesize butanol without the byproduct acetone. The genome is 4,374,054 bp.

Ruminiclostridium sufflavum DSM 19573T and Anaerosphaera aminiphila DSM 21120T were first isolated from a methanogenic bioreactor treating cattle waste in Hokkaido, Japan. The R. sufflavum draft genome sequence is 4.4 Mb with 3,773 predicted genes, and the A. aminiphila draft genome sequence is 2.0 Mb with 1,962 predicted genes.

Strain MCT is a strictly anaerobic, homoacetogenic bacterium with the ability to utilize methyl chloride as the sole energy source. It was tentatively assigned to the genus Acetobacterium as 'Acetobacterium dehalogenans'. Due to sequence ambiguities, it was not possible to determine the 16S rRNA gene sequence of this strain by direct sequencing of a PCR-amplified DNA segment. Whole-genome sequencing revealed significant heterogeneity amongst the five rRNA operons detected in this strain, with maximum sequence differences between the individual 16S rRNA genes exceeding 1.4%, compared to <0.8% in related species. Genome comparisons identified strain MCT as most closely related to Acetobacterium malicum MuME1T, with a digital DNA-DNA hybridization value of 71.9% and an average nucleotide identity score of 96.59%, indicating that the strains belong to the same species. Both strains share the ability to utilize malate, a key feature of A. malicum, but differ in the utilization of methanol and glucose. Chemotaxonomic analyses also revealed distinct fatty acid and polar lipid patterns. Based on these findings, we propose the classification of strain 'Acetobacterium dehalogenans' MCT (=DSM 11527T=NBRC 117038T) as A. malicum subsp. dehalogenans subsp. nov. This automatically establishes A. malicum subsp. malicum subsp. nov., with MuME1T (=DSM 4132T=ATCC 51201T) as the type strain.

Here, we report the draft genome sequences of two Butyrivibrio-type strains isolated from rumen fluid. The genome sequence of Butyrivibrio hungatei DSM 14810 was 3.3 Mb with 3,093 predicted genes, while the Butyrivibrio fibrisolvens DSM 3071 genome sequence was 4.8 Mb with 4,132 predicted genes.

The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.

Abstract Ki.ri.ti.ma.ti.el.la.ce'ae. N.L. fem. dim. n. Kiritimatiella , type genus of the family; L. fem. pl. n. suff. – aceae , ending to denote a family; N.L. fem. pl. n. Kiritimatiellaceae , the Kiritimatiella family. Kiritimatiellota / Kiritimatiellia / Kiritimatiellales / Kiritimatiellaceae To date, there is only one cultivated strain in the family Kiritimatiellaceae , the type strain of Kiritimatiella glycovorans (Spring et al., 2016). Microorganisms assigned to this family are generally free‐living, nonmotile, non‐spore‐forming, coccoid bacteria adapted to anoxic aquatic niches characterized by hypersaline conditions. Other features include cell division by binary fission, a Gram‐negative type cell wall containing peptidoglycan, no intracellular membranes, and an anaerobic metabolism based on the fermentation of carbohydrates. The main nongaseous fermentation products are ethanol and acetate. Transparent exopolymers are formed and probably protect cells from desiccation in hypersaline environments. Cellular fatty acid patterns are dominated by straight‐chain (C 18:0 ) and iso‐branched fatty acids (iso‐C 14:0 ). The major polar lipid was identified as phosphatidylglycerol (PG) besides minor amounts of an unidentified phospholipid, two distinct glycolipids, an aminolipid and small amounts of phosphoglycolipids. The genome size of the only described type strain of this family is 2.9 Mb. DNA G + C content (mol%) : 63 (genome analysis). Type genus : Kiritimatiella Spring et al. 2016, VL174.

Abstract Ki.ri.ti.ma.ti.el.la'les. N.L. fem. dim. n. Kiritimatiella , type genus of the order; L. fem. pl. n. suff. – ales, ending to denote an order; N.L. fem. pl. n. Kiritimatiellales , the Kiritimatiella order. Kiritimatiellota / Kiritimatiellia / Kiritimatiellales The order Kiritimatiellales as defined in the chapter on the class Kiritimatiellia encompasses all cultivated members of the phylum Kiritimatiellota , which are represented by the species Kiritimatiella glycovorans , Pontiella desulfatans , P. sulfatireligans , and Tichowtungia aerotolerans . Microorganisms assigned to this order are generally free‐living, nonmotile, non‐spore‐forming, coccoid bacteria adapted to anoxic aquatic niches often characterized by marine or hypersaline salinity. Further features common to all strains include cell division by binary fission, a cell wall of the Gram‐negative type that contains peptidoglycan, absence of intracellular membranes, and an anaerobic metabolism based on the fermentation of carbohydrates. Transparent exopolymers are produced by pure cultures of the known strains. A specialization in the degradation of complex polysaccharides can be assumed for most strains, since the corresponding genomes contain a large number of genes encoding glycoside hydrolases and sulfatases. Cellular fatty acid patterns of axenic cultures are dominated by straight‐chain (C 18:0 ) and iso‐branched fatty acids (iso‐C 14:0 , iso‐C 18:0 ). The major polar lipids were identified as phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). The genome sizes among described representatives of this order range from 2.9 to 8.7 Mb. DNA G + C content (mol%) : 53–63 (genome analyses, n = 4). Type genus : Kiritimatiella Spring et al. 2016, VL174.

We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life. MediaDive is designed to enable broad range applications from every-day-use in research and diagnostic laboratories to knowledge-driven support of new media design and artificial intelligence-driven data mining. It offers a number of intuitive search functions and comparison tools, for example to identify media for related taxonomic groups and to integrate strain-specific modifications. Besides classical PDF archiving and printing, the state-of-the-art website allows paperless use of media recipes on mobile devices for convenient wet-lab use. In addition, data can be retrieved using a RESTful web service for large-scale data analyses. An internal editor interface ensures continuous extension and curation of media by cultivation experts from the Leibniz Institute DSMZ, which is interlinked with the growing microbial collections at DSMZ. External user engagement is covered by a dedicated media builder tool. The standardized and programmatically accessible data will foster new approaches for the design of cultivation media to target the vast majority of uncultured microorganisms.

A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2T could be affiliated with the phylum Synergistota . Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2T (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2T (=DSM 107166T=NBRC 114655T) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.

Abstract Ki.ri.ti.ma.ti.el'li.a. N.L. fem. dim. n. Kiritimatiella , type genus of the type order of the class; N.L. neut. pl. n. suff. – ia, ending to denote a class; N.L. neut. pl. n. Kiritimatiellia , the class of the order Kiritimatiellales . Kiritimatiellota / Kiritimatiellia emend . The effectively published synonym Kiritimatiellae (sic) Spring et al. 2016 was corrected to Kiritimatiellia by Spring et al. (2022) in Göker (2022). At the time of writing, the class Kiritimatiellia encompasses all cultivated representatives of the phylum Kiritimatiellota . Members of this taxon are in general free‐living, nonmotile, non‐spore‐forming, coccoid bacteria adapted to anoxic niches found in aquatic environments or the intestines of animals. Further features common to all strains include cell division by binary fission, a cell wall of the Gram‐negative type that contains peptidoglycan, no intracellular membranes, and an anaerobic metabolism based on the fermentation of carbohydrates. Transparent exopolymers are produced by pure cultures of the known strains. A specialization in the degradation of complex polysaccharides can be assumed for most strains, since the corresponding genomes contain a large number of genes encoding glycoside hydrolases and sulfatases. Cellular fatty acid patterns of axenic cultures are dominated by straight‐chain (C 18:0 ) and iso‐branched fatty acids (iso‐C 12:0 , iso‐C 14:0 ). The major polar lipids are identified as phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). The genome sizes among described representatives of this phylum range from 2.9 to 8.6 Mb. DNA G + C content (mol%) : 53–63 (genome analyses, n = 4). Type order : Kiritimatiellales Spring et al. 2016, VL174.

Abstract Ki.ri.ti.ma.ti.el.lo'ta. N.L. fem. dim. n. Kiritimatiella , type genus of the phylum; N.L. neut. pl. n. suff. ‐ ota , ending to denote a phylum; N.L. neut. pl. n. Kiritimatiellota , the Kiritimatiella phylum. Analysis of environmental 16S rRNA gene sequences suggests that members of this phylum prefer animal intestines and anoxic aquatic niches ranging in salinity from hypersaline to freshwater. These data further indicate that most members of the Kiritimatiellota are mesophilic and neutrophilic, being adapted to moderate habitats. Cells of cultivated strains divide by binary fission, do not form intracellular membranes, are spherical, nonmotile, and non‐spore‐forming. They have a cell wall of the Gram‐negative type that contains peptidoglycan and an outer membrane. Strains available in pure culture produce transparent exopolymers during growth. Based on the habitat preference, it can be concluded that most representatives are anaerobic bacteria with a fermentative and saccharolytic type of metabolism. In sequenced genomes of some representatives, extraordinarily high numbers of genes encoding putative glycoside hydrolases and sulfatases were detected, which may be necessary for the degradation of complex sulfated polysaccharides typically occurring in the animal intestine or marine environments (Spring et al., 2016; van Vliet et al., 2020). Cellular fatty acid patterns of axenic cultures were dominated by straight‐chain (C 18:0 ) and iso ‐branched fatty acids ( iso ‐C 12:0 , iso ‐C 14:0 ). The major polar lipids were identified as phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). In some strains, respiratory lipoquinones (menaquinones MK‐6 – MK‐9) were detected. The genome sizes among described representatives of this phylum range from 2.9 to 8.6 Mb. DNA G + C content (mol%) : 53–63 (genome analyses). Type genus : Kiritimatiella Spring et al. 2016, VL174.

Strain L21-Ace-BEST, isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the class Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl-CoA:acetate-CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H-2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and dimethyl sulfoxide, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over-reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium.

Abstract Se.di.men.ti.sphae'ra. L. neut. n. sedimentum sediment; L. fem. n. sphaera a sphere; N.L. fem. n. Sedimentisphaera , a spherical bacterium from sediment. Planctomycetes / Phycisphaerae / Sedimentisphaerales / Sedimentisphaeraceae / Sedimentisphaera Free‐living, unpigmented, nonmotile, and non‐spore‐forming coccoid cells that divide by binary fission. Intracellular membranes are not formed. Gram‐negative type of cell wall with a peptidoglycan layer. Dominating cellular fatty acids are anteiso‐C 15:0 and anteiso‐C 13:0 . Unsaturated cellular fatty acids, respiratory lipoquinones, or cytochromes are not present. The polar lipid composition is dominated by phosphatidylglycerol and several distinct glycolipids. Tests for catalase and oxidase are negative. Nitrate is not reduced. Obligately anaerobic and moderately halophilic, mesophilic, and neutrophilic. Vitamins required for growth. Strictly fermentative metabolism with sugars as preferred substrates. Medium viscosity increases during growth due to the production of extracellular polymeric substances. Oxygen can be tolerated up to 0.5% (v/v) in the gas atmosphere but does not stimulate growth. Susceptible to the antibiotics chloramphenicol and tetracycline, but resistant to rifampicin. Members of the class Phycisphaerae , order Phycisphaerales , family Sedimentisphaeraceae . Known habitats are hypersaline sediments and microbial mats in salt lakes and evaporation ponds. DNA G + C content (mol%) : 46.2–46.4 (genome analyses). Type species : Sedimentisphaera salicampi Spring et al. 2018, VL184.

AbstractSa.li.ni.spi'ra. L. neut. n.salinumsalt‐cellar; L. fem. n.spiracoil, spire; N.L. fem. n.Salinispiraa saline spiral.Spirochaetes / Spirochaetia / Spirochaetales / Spirochaetaceae / SalinispiraThe genusSalinispiraaccommodates spirochetes from anoxic hypersaline environments and is represented by one species and strain. Cells of the nomenclatural type,Salinispira pacificaL21‐RPul‐D2T, have a helical shape and a size of 0.2–0.25 × 8–9 μm, stain Gram‐negative, are motile, and produce an orange carotenoid‐like pigment. Spherical bodies can be formed during stationary phase. Optimal conditions for growth are 35°C, a salinity of 5% NaCl, and a pH around 7.0. Preferred substrates for growth are carbohydrates and a few carboxylic acids. Obligate fermentative metabolism with the production of ethanol, acetate, lactate, hydrogen, and carbon dioxide during growth on glucose. Oxygen in the gas phase is tolerated but does not stimulate growth. Major cellular fatty acids are C14:0, iso‐C15:0, C16:0, and C18:0. Polar lipids are dominated by an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid, and two unidentified glycolipids. No detectable lipoquinones or cytochromes. The genome ofSalinispira pacificaL21‐RPul‐D2Tcomprises one circular chromosome with a size of 3.78 Mb that contains 3,450 protein‐coding genes and 50 RNA genes, including two operons of ribosomal RNA genes.DNA G + C content (mol%): 51.9 (genome analysis).Type species:Salinispira pacificaBen Hania et al. 2015, VL163.

A novel obligately anaerobic spirochete strain K2T was isolated from bottom marine sediments at Crater Bay of Yankicha Island (Kuril Islands, Russia). Strain K2T had helical shape and Gram-negatively stained. The optimal growth conditions were as follows: the optimum temperature was 28-30 °C with range 5-34 °C; optimal pH at 7.0-7.5 with range of 6.8-8.5; NaCl optimum at 3-3.5 % (w/v) and range of 1-7 % (w/v). Strain K2T was catalase- and oxidase-negative. Glucose fermentation products were acetate, lactate, ethanol, CO2, H2. The major fatty acids were C14 : 0, iso-C13 : 0, iso-C15:0, C14 : 0 DMA, iso-C15 : 0 DMA. The G+C content of genomic DNA was 43.2 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain K2T belonged to the genus Oceanispirochaeta of the family Spirochaetaceae. The 16S rRNA gene sequence similarity of strain K2T and O. litoralis DSM 2029T and O. sediminicola DSM 104770T was 96 and 94 %, respectively. Based on the results of our study, we propose the name Oceanispirochaeta crateris sp. nov.; type strain K2T (=DSM 16308T=VKM B-3266T). Also, the taxonomic status of Spirochaeta perfilevii was revised: 16S rRNA genes sequence showed less than 89 % similarity to nearest phylogenetic neighbours. Therefore, we proposed to separate this species into a novel genus Thiospirochaeta - T. perfilievii gen. nov., comb. nov.

Abstract Ther.mo.ha.lo.bac.te.ra.ce'ae. N.L. masc. n. Thermohalobacter , type genus of the family; suff. ‐aceae , ending to denote a family; N.L. fem. pl. n. Thermohalobacteraceae , the Thermohalobacter family. Firmicutes / Clostridia / Tissierellales / Thermohalobacteraceae fam. nov. Free‐living bacteria that mainly occur in anoxic saline environments. Cells are not pigmented and have a Gram‐positive type of cell wall. Gram‐stain reaction can be negative or positive. Typically slender rod‐shaped cells that are motile by flagella. Several strains form heat‐resistant spores. Mainly euryhaline, moderately thermophilic and halophilic. Members of the family are strictly anaerobic bacteria that utilize carbohydrates or peptides by fermentation. Cellular fatty acid patterns are dominated by iso ‐C 15:0 and iso ‐C 15:0 DMA. The family currently accommodates members of the genera Thermohalobacter , Caldisalinibacter , Caloranaerobacter , Brassicibacter , Sporosalibacterium , and Clostridiisalibacter , which were previously affiliated with the family Clostridiaceae . The affiliation of novel species to this family depends on the phylogenetic position, which should be determined on the basis of comparative sequence analyses of 16S rRNA genes or genomes. DNA G + C content (mol%): 28–33. Type genus: Thermohalobacter Cayol et al. 2000.

Abstract Se.di.men.ti.sphae.ra.ce'ae. N.L. fem. n. Sedimentisphaera , type genus of the family; suff. –aceae , ending to denote a family; N.L. fem. pl. n. Sedimentisphaeraceae , the Sedimentisphaera family. Planctomycetes / Phycisphaerae / Sedimentisphaerales / Sedimentisphaeraceae Cells are Gram‐negative, free‐living, unpigmented, nonmotile, and non‐spore‐forming irregular cocci that divide by binary fission. Intracellular membranes are not formed. Most strains are resistant against rifampicin and kanamycin A but susceptible to chloramphenicol. Vitamins required for growth. Tests for catalase and oxidase are negative. Nitrate is not reduced. Members of the family are anaerobic and utilize carbohydrates by fermentation. The family encompasses mainly bacteria found in anoxic hypersaline environments. The affiliation of novel species to this family mainly depends on the phylogenetic position, which should be determined on the basis of comparative sequence analyses of 16S rRNA genes or genomes. DNA G + C content (mol%) : 46–47 (genome analyses). Type genus : Sedimentisphaera Spring et al. 2018, VL184.