Description of Ancylobacter oerskovii sp. nov. and two additional strains of Ancylobacter polymorphus

Ancylobacter radicis sp. nov., a novel aerobic methylotrophic bacteria associated with plants

The two novel bacterial strains, designated as VT^T and ML, were isolated from roots of cinquefoil (Potentilla sp.) and leaves of meadow-grass (Poa sp.) on the flooded bank of lake, respectively. These isolates were Gram-negative, non-spore-forming, non-motile, rod-shaped cells, utilized methanol, methylamine, and polycarbon compounds as carbon and energy sources. In the whole-cell fatty acid pattern of strains prevailed C_18:1ω7c and C_19:0cyc. Based on the phylogenetic analysis of 16S rRNA gene sequences, strains VT^T and ML were closely related to the representatives of the genus Ancylobacter (98.3-98.5%). The assembled genome of strain VT^T has a total length of 4.22 Mbp, and a G + C content is 67.3%. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain VT^T and closely related type strains of genus Ancylobacter were 78.0-80.6%, 73.8-78.3% and 22.1-24.0%, respectively, that clearly lower than proposed thresholds for species. On the basis of the phylogenetic, phenotypic, and chemotaxonomic analysis, isolates VT^T and ML represent a novel species of the genus Ancylobacter, for which the name Ancylobacter radicis sp. nov. is proposed. The type strain is VT^T (= VKM B-3255^T = CCUG 72400^T). In addition, novel strains were able to dissolve insoluble phosphates, to produce siderophores and plant hormones (auxin biosynthesis). According to genome analysis genes involved in the biosynthesis of siderophores, polyhydroxybutyrate, exopolysaccharides and phosphorus metabolism, as well as the genes involved in the assimilation of C₁-compounds (natural products of plant metabolism) were found in the genome of type strain VT^T.

Ancylobacter mangrovi sp. nov., a novel endophytic bacterium isolated form mangrove plant☆

Two novel strains GSK1Z-4-2^T and MQZ15Z-1 were isolated from branches of mangrove plants collected from Guangxi Zhuang Autonomous Region, China. Both strains were Gram-negative, aerobic, non-flagellated and non-spore-forming bacteria. The comparison of 16S rRNA gene sequences initially indicated that the two strains were assigned to the genus Ancylobacter with sharing the highest similarity to Ancylobacter pratisalsi DSM 102029^T (97.3%). The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strains GSK1Z-4-2^T and MQZ15Z-1 were 99.9%, 97.4% and 77.4%, respectively, which revealed that the two strains belonged to the same species. Phylogenetic analyses based on 16S rRNA gene sequences and the core proteome showed that the two strains formed a well-supported cluster with A. pratisalsi DSM 102029^T. Moreover, the ANI and isDDH values between strain GSK1Z-4-2^T and A. pratisalsi DSM 102029^T were 83.0% and 25.8%, respectively, demonstrating that strain GSK1Z-4-2^T was a previously undescribed species. Meanwhile, strains GSK1Z-4-2^T and MQZ15Z-1 exhibited most of chemotaxonomic and phenotypic features consistent with the description of the genus Ancylobacter. Based on the polyphasic data, strains GSK1Z-4-2^T and MQZ15Z-1 should represent a novel species of the genus Ancylobacter, for which the name Ancylobacter mangrovi sp. nov. is proposed. The type strain is GSK1Z-4-2^T (=MCCC 1K07181^T = JCM 34924^T).

Ancylobacter moscoviensis sp. nov., novel facultatively methylotrophic bacteria from activated sludge and the reclassification of Starkeya novella (Starkey 1934) Kelly et al. 2000 as Ancylobacter novellus comb. nov., Starkeya koreensis Im et al. 2006 as Ancylobacter koreensis comb.nov., Angulomicrobium tetraedrale Vasil'eva et al. 1986 as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme Fritz et al. 2004 as Ancylobacter amanitiformis comb. nov., and Methylorhabdus multivorans Doronina et al. 1996 as Ancylobacter multivorans comb. nov., and emended description of the genus Ancylobacter

Three novel facultatively methylotrophic bacteria, strains 3C^T, 1A, 8P, were isolated from activated sludges. The isolates were aerobic, Gram-stain-negative, non-motile, non-spore forming rods multiplying by binary fission. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethylethanolamine, phosphatidylmonomethylethanolamine, and diphosphatidylglycerol. The major fatty acids of cells were С_18:1ω7c, C_19:0ω8c cyclo and C_16:0. Levels of 16S rRNA gene similarity indicates that the closely relatives are representatives of the genera Starkeya, Ancylobacter, Angulomicrobium and Methylorhabdus (96.4-99.4%). Genomic comparisons of 3C^T and its closest relatives, S. novella DSM 506^T and S. koreensis Jip08^T, shared 87.3 and 86.8% nucleotide identity and 28.3 and 26.8% digital DNA-DNA hybridization values, respectively. The average amino acid identities between the strain 3C^T and representatives of Starkeya, Ancylobacter and Angulomicrobium were in the range of 75.6-84.3%, which combines these strains into a single genus and gives rise to their reclassification. Based on polyphasic analyses, the strains 3C^T, 1A, 8P represents a novel species of the genus Ancylobacter, for which the name Ancylobacter moscoviensis sp. nov. is proposed. The type strain is 3C^T (= VKM B-3218^T = KCTC 62336^T). Furthermore, we also suggested the reclassification of Starkeya novella as Ancylobacter novellus comb. nov., Starkeya koreensis as Ancylobacter koreensis comb. nov., Angulomicrobium tetraedrale as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme as Ancylobacter amanitiformis comb. nov. and Methylorhabdus multivorans as Ancylobacter multivorans comb. nov. with the emended description of the genus Ancylobacter.

Ancylobacter gelatini sp. nov., isolated from beach sediment of Zhairuo Island, China

A Gram-negative, aerobic, non-motile, oxidase-positive, catalase-positive, methyl red-positive, and lipase-negative bacterium, designated A5.8^T, was isolated from beach sediment of Zhairuo Island located in the East China Sea. Growth occurred at 10-40 °C (optimum, 30 °C), pH 5.5-9.5 (optimum, 7.5), and 0-2% NaCl (optimum, 1.5%). Based on 16S rRNA gene sequence analysis, strain A5.8^T belongs to the genus Ancylobacter, sharing the highest similarity with Ancylobacter aquaticus JCM 20518^T (98.0%). Its polar lipids mainly consist of phosphatidylethanolamine (PE) and phosphatidylcholine (PC). The predominant fatty acids are summed feature 8 (C_18:1ω7c and/or C_18:1ω6c, 91.0%), and the major respiratory quinone is Q-10. The DNA G + C content is 67.2 mol%. Based on above analysis, as well as digital DNA-DNA hybridization (22.5-22.9%) and average nucleotide identity (83.0-83.6%) of strain A5.8^T with reference type strains of the genus Ancylobacter, strain A5.8^T was suggested to represent a novel species of the genus Ancylobacter, for which the name Ancylobacter gelatini sp. nov. is proposed. The type strain is A5.8^T (= MCCC 1K07167^T = LMG 32566^T).

Ancylobacter sonchi sp. nov., a novel methylotrophic bacterium frоm roots of Sonchus arvensis L

An aerobic facultatively methylotrophic bacterium was isolated from roots of Sonchus arvensis L. and designated strain Osot^T The cells of this strain were Gram-stain-negative, asporogenous, motile short rods multiplying by binary fisson. They utilized methanol, methylamines and a variety of polycarbon compounds as the carbon and energy sources. Methanol was assimilated after sequential oxidation to formaldehyde and CO2 via the ribulose bisphosphate pathway. The organism grew optimally at 22-29 °C and pH 7.5-8.0. The dominant phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). The major cellular fatty acids of strain Osot^T cells grown in R2A medium were C18 : 1ω7c (49.0 %), C19 : 0ω8c cyclo (38.3 %) and C16 : 0 (8.4 %). The major ubiquinone was Q-10. The DNA G+C content of strain Osot^T was 66.1 mol% (Tm). On the basis of 16S rRNA gene sequence analysis strain Osot^T is phylogenetically related to the members of genus Ancylobacter (97.1-98.8 % sequence similarity). Based on 16S rRNA gene sequence analysis and DNA-DNA relatedness (27-29 %) with type strains of the genus Ancylobacter, the novel isolate is classified as a new species of this genus and named Ancylobacter sonchi sp. nov.; the type strain is Osot^T (=VKM B-3145^T=JCM 32039^T).

Ancylobacter pratisalsi sp. nov. with plant growth promotion abilities from the rhizosphere of Plantago winteri Wirtg

A Gram-negative bacterium, designated E130^T, was isolated from rhizospheric soil of Plantago winteri Wirtg. from a natural salt meadow as part of an investigation on rhizospheric bacteria from salt-resistant plant species and evaluation of their plant growth-promoting abilities. Cells were rods, non-motile, aerobic, and oxidase and catalase positive, grew in a temperature range of between 4 and 37 °C, and in the presence of 0.5-5 % NaCl (w/v). Based on 16S rRNA gene sequence analysis, strain E130^T is affiliated within the genus Ancylobacter, sharing the highest similarity with Ancylobacter rudongensis DSM 17131^T (97.6 %), Ancylobacter defluvii CCUG 63806^T (97.5 %) and Ancylobacter dichloromethanicus DSM 21507^T (97.4 %). The DNA G+C content of strain E130^T was 65.1 mol%. Its respiratory quinones were Q-9 and Q-10 and its major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified phospholipid. Major fatty acids of the strains E130^T were C12 : 0, C16 : 0, C18 : 1ω7c and C19 : 0cycloω8c. The DNA-DNA relatedness of E130^T to A. rudongensis DSM 17131^T, A. defluvii CCUG 63806^T and A. dichloromethanicus DSM 21507^T was 29.2, 21.2 and 32.2 % respectively. On the basis of our polyphasic taxonomic study the new isolate represents a novel species, for which the name Ancylobacter pratisalsi sp. nov. is proposed. The type strain is E130^T (LMG 29367^T=DSM 102029^T).

The first 1000 cultured species of the human gastrointestinal microbiota

The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.

Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.

Azorhizobium oxalatiphilum sp. nov., and emended description of the genus Azorhizobium

A Gram-negative, motile, non-spore-forming rod, designated NS12T, was isolated from macerated petioles of Rumex sp. after enrichment with oxalate. On the basis of 16S rRNA gene sequence similarity, strain NS12T was phylogenetically related to the genera Azorhizobium and Xanthobacter in the class Alphaproteobacteria . Strain NS12T was most closely related to Azorhizobium doebereinerae BR 5401T and Azorhizobium caulinodans ORS 571T (98.3 and 97.3 % 16S rRNA gene sequence similarity, respectively). Membership of the genus Xanthobacter was excluded by phenotypic characterization. The whole-cell fatty acid compositions of the isolate was typical of members of the genus Azorhizobium with C18 : 1ω7c, cyclo-C19 : 0ω8c, 11-methyl-C18 : 1ω7c and C16 : 0 as the main components. The results of DNA–DNA hybridization and physiological tests allowed the genotypic and phenotypic differentiation of strain NS12T from the two members of the genus Azorhizobium . Therefore it is concluded that the isolate represents a novel species of the genus Azorhizobium , for which the name Azorhizobium oxalatiphilum sp. nov. is proposed. The type strain is NS12T ( = DSM 18749T = CCM 7897T). The description of the genus Azorhizobium is also emended.

Ancylobacter dichloromethanicus sp. nov.--a new aerobic facultatively methylotrophic bacterium utilizing dichloromethane

A novel aerobic facultative methylotroph was isolated from contaminated soil. The organism (strain DM16) is a Gram-negative asporogenous non-motile curved rod multiplying by binary fission. Cells are neutrophilic and mesophilic. This strain utilized dichloromethane, methanol, formate and formaldehyde along with a variety of polycarbon compounds. Strain DM16 employs the ribulosebisphosphate pathway for C1 assimilation. The DNA G+C content is 64.5 mol%. The major ubiquinone is Q-10. The dominant cellular fatty acids are 18:1omega7c (58.6%), cyclo-19:0omega8c (34.8%) and 16:0 (3.2%). Sequencing of the 16S rRNA gene and DNA-DNA hybridization experiments clearly indicated that this methylotroph should be classified as a new species within genus Ancylobacter--Ancylobacter dichloromethanicus sp. nov. with the type strain DM16T (DSM 21507T = VKM B-2484T).