Добірка наукової літератури з теми "Oxalobacteraceae"

A taxonomic study was performed on strain YIM 31775T, which was isolated from a soil sample collected from Yunnan Province, China. The isolate was chemo-organotrophic, aerobic and Gram-negative. Cells were short rods and motile, with one or more polar flagella. Growth temperature and pH ranged from 4 to 55 °C and 6·5 to 12·0, respectively; the optimum growth temperature and pH were 28–37 °C and 7·0–9·0, respectively. Q-8 was the predominant respiratory lipoquinone. The major fatty acids were C16 : 1 ω7c (42·4 %) and C16 : 0 (28·1 %). The DNA G+C content was 62·4±0·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 31775T should be placed within the family ‘Oxalobacteraceae’, in which it formed a distinct lineage. Based on the high 16S rRNA gene sequence divergence and phenotypic characteristics, it is proposed that strain YIM 31775T should be classified as representing a novel member of the family ‘Oxalobacteraceae’, for which the name Naxibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain is YIM 31775T (=CCTCC AA 204003T=KCTC 12194T).

Strains Cr9-30T and Cr9-12 were isolated from alpine glacier cryoconite. Both strains were Gram-negative-staining, non-motile, rod-shaped and psychrophilic, showing good growth over the temperature range 1–20 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that the two strains formed a distinct branch within the family Oxalobacteraceae and were most closely related to members of the genus Collimonas. The 16S rRNA gene sequence similarity between strains Cr9-30T and Cr9-12 was 99.0 %. The two strains showed highest 16S rRNA gene sequence pairwise similarity with Collimonas pratensis LMG 23965T (96.6 and 96.1 % for strains Cr9-30T and Cr9-12, respectively), Collimonas arenae LMG 23964T (96.5 and 96.3 %, respectively) and Collimonas fungivorans LMG 21973T (96.4 and 96.2 %, respectively). The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The DNA G+C content of strain Cr9-30T was 51.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strains Cr9-30T and Cr9-12 represent a novel species in a new genus of the family Oxalobacteraceae, for which the name Glaciimonas immobilis gen. nov., sp. nov. is proposed. The type strain of Glaciimonas immobilis is Cr9-30T ( = DSM 23240T = LMG 25547T).

Emerging evidences link gut microbiota to colorectal cancer (CRC) initiation and development. However, the CRC stage- and spatial-specific bacterial taxa were less investigated, especially in a Chinese cohort, leading to our incomplete understanding of the functional roles of gut microbiota in promoting CRC progression and recurrence. Here, we report the composition and structure of gut microbiota across CRC stages I, II and III, by analyzing the gut mucosal microbiomes of 75 triplet-paired samples collected from on-tumor, adjacent-tumor and off-tumor sites and 26 healthy controls. We observed tumor-specific pattern of mucosal microbiome profiles as CRC progressed and identified ten bacterial taxa with high abundances (>1%) as potential biomarkers for tumor initiation and development. Peptostreptococcus and Parvimonas can serve as biomarkers for CRC stage I. Fusobacterium, Streptococcus, Parvimonas, Burkholderiales, Caulobacteraceae, Delftia and Oxalobacteraceae can serve as biomarkers for CRC stage II, while Fusobacterium, Burkholderiales, Caulobacteraceae, Oxalobacteraceae, Faecalibacterium and Sutterella can serve as biomarkers for CRC stage III. These biomarkers classified CRC stages I, II and III distinguished from each other with an area under the receiver-operating curve (AUC) > 0.5. Moreover, co-occurrence and co-excluding network analysis of these genera showed strong correlations in CRC stage I, which were subsequently reduced in CRC stages II and III. Our findings provide a reference index for stage-specific CRC diagnosis and suggest stage-specific roles of Peptostreptococcus, Fusobacterium, Streptococcus and Parvimonas in driving CRC progression.

A novel psychrotolerant, Gram-negative, shiny white, curved-rod-shaped, facultatively anaerobic bacterium PB1T was isolated from a soil sample collected from a glacier forefield of the Larsemann Hills, East Antarctica. Isolate PB1T has catalase and low urease activity and hydrolyses gelatin and starch. Strain PB1T is able to grow between −5 °C and 30 °C with optimum growth at 14–20 °C. Glycerol, dl-arabinose, d-xylose, d-galactose, d-fructose, d-lyxose, d-fucose and potassium gluconate are used as sole carbon sources. The major quinone is ubiquinone Q-8. The major fatty acids (>10 %) for PB1T are C16 : 0 (19.1 %), C16 : 1ω7cis (44.6 %) and C18 : 1ω7cis (16.2 %). The major polyamines are putrescine [54.9 µmol (g dry weight)−1] and 2-hydroxy putrescine [18.5 µmol (g dry weight)−1]. DNA G+C content is 62.5 mol%. Strain PB1T is phylogenetically related to species of the genus Herbaspirillum , with highest 16S rRNA gene sequence similarities to Herbaspirillum canariense (97.3 %), Herbaspirillum aurantiacum (97.2 %), Herbaspirillum soli (97.2 %) and Herbaspirillum frisingense (97.0 %). The DNA–DNA relatedness values were below 30 % between PB1T and the type strains of Herbaspirillum canariense , Herbaspirillum aurantiacum and Herbaspirillum soli . The different geographical origin of strain PB1T from its closest phylogenetic relatives resulted in different phenotypic and genotypic specifications, whereby strain PBT represents a novel species of the genus Herbaspirillum , for which the name Herbaspirillum psychrotolerans is proposed. The type strain is PB1T (DSM 26001T = LMG 27282T).

Preplant soil fumigation with metam sodium is used worldwide to control soilborne diseases. The development of accelerated degradation of pesticides in soil, including metam sodium, results in reduced pesticide efficacy. Therefore, we studied microbial involvement in accelerated degradation of methyl isothiocyanate (MITC) following repeated soil applications of the parent compound, metam sodium. MITC degradation was reduced in soil with a history of metam sodium applications following sterilization, indicating the key role of microorganisms in accelerated degradation. Accelerated degradation of MITC was induced by inoculation of soil with no previous application of metam sodium with soil with a history of metam sodium applications. We developed a method to extract the active microbial fraction responsible for MITC degradation from soil with a history of metam sodium applications. This concentrated soil extract induced accelerated degradation of MITC when added to two different soils with no previous application of metam sodium. An extensive shift in total bacterial community composition in concentrated soil extracts occurred after a single metam sodium application. Two Oxalobacteraceae strains, MDB3 and MDB10, isolated from Rehovot soil following triple application of metam sodium rapidly degraded MITC in soil with no previous application of metam sodium. Polymerase chain reaction–denaturing gradient gel electrophoresis analysis of bacterial community composition showed relative enrichment of MDB3 following metam sodium application, suggesting its potential in situ involvement in accelerated degradation development in Rehovot soil. Responses of resident Oxalobacteraceae community members to metam sodium applications differed between Rehovot and En Tamar soils. Isolate MDB10 did not induce accelerated degradation of MITC in En Tamar soil and, with the slow dissipation of MITC, soil suppressiveness of accelerated degradation is suggested. The isolation and identification of MITC-degrading bacteria might be helpful in developing tools for managing accelerated degradation.

A strain S307 that can oxidize selectively (S)- 1-phenylethanol to acetophenone and a strain IS 118 that can asymmetric reduce acetophenone to (R)- 1-phenylethanol were isolated from soil. S307 was identified as a species of Undibacterium belonging to the family Oxalobacteraceae of the Betaproteobacteria. S307. IS 118 was identified as Asperillus tamarii. The oxidation of (R, S)-1- phenylethanol with Undibacterium sp. S307 followed by the reduction of the oxidation mixture with Asperillus tamarii IS 118 to afford (R)-1-phenylethanol was described. The effects of redox-coupling patterns on the product of (R)-1-phenylethanol were investigated. After redox-coupling deracemization, the yield and ee of (R)-1-phenylethanol were 87% and 99% respectively.

Dans les régions tempérées, les minéraux et les roches représentent la source principale de cations nutritifs des sols des écosystèmes à faible intrants telles que les forêts. Dans de tels environnements pauvres en nutriments, l’accès et le recyclage des cations nutritifs sont des processus clés pour la croissance et la productivité des arbres. Cependant, ces cations nutritifs ne sont pas directement accessibles aux racines des arbres car piégés dans les minéraux et roches des sols. En conséquence, le processus d’altération des minéraux joue un rôle essentiel car il contribue à restaurer la fertilité des sols et à fournir des nutriments inorganiques nécessaires à la croissance des arbres. L’altération des minéraux peut être dûe à des processus abiotiques (pH, érosion…) ou des processus biotiques (plantes, champignons, bactéries…). Parmi les acteurs biotiques, les bactéries sont capables d’altérer les minéraux par différents mécanismes comme la production de protons (acidolyse) ou la production de molécules chélatrices (complexolyse). Néanmoins, les gènes et protéines impliqués dans l’altération des minéraux par les bactéries sont mal connus. Dans le cadre de cette thèse, la souche bactérienne Collimonas pratensis PMB3(1) a été utilisée comme modèle pour identifier les gènes de l’altération. Cette souche a été isolée de la mycorhizosphère du chêne et est particulièrement efficace pour altérer les minéraux. Dans cette thèse l’analyse du génome de la souche PMB3(1) a mis en évidence l’absence certains gènes décrits dans l’altération (comme les glucose déshydrogénases PQQ dépendantes) et a souligné la nécessité de développer deux approches complémentaires : avec et sans a priori. (i) La démarche sans a priori a été développée via la création d’une banque de mutants aléatoires. Le criblage de cette banque de mutants sur des biotests mimant l’altération des minéraux a permis de sélectionner 3 mutants impactés dans leur capacité à altérer les minéraux. La caractérisation de ces mutants a révélé des mutations dans différents gènes impliqués dans la synthèse d’une glucose/méthanol/choline oxidoréductase (GMC). La comparaison de composés chimiques présents dans le surnageant de la souche sauvage et des mutants a révélé que cette GMC était responsable de la métabolisation du glucose en gluconate et de la production de protons, conduisant à une acidification du milieu et à une acidolyse des minéraux. (ii) La démarche avec a priori a été réalisée par la création d’un mutant ciblé au niveau du gène mbaA codant pour un NRPS (Non-Ribosomal Peptide Synthetase) responsable de la synthèse de sidérophore. L’utilisation conjointe de méthodes de chromatographie et de spectrométrie de masse a permis de caractériser chimiquement ce sidérophore, qui a été identifié comme étant une malléobactine. La comparaison de la souche sauvage et du mutant a révélé que la production de la malléobactine est impliquée dans l’altération de l’hématite par complexolyse et ce dans un milieu avec un fort pouvoir tampon. Les tests d’altération réalisés avec différents types de minéraux en présence de deux sources de carbones (glucose ou mannitol) et deux milieux ayant un pouvoir tampon différent ont révélé que la souche PMB3(1) était efficace pour altérer tous les minéraux testés. De plus, la source de carbone et le tampon du milieu avaient une forte influence sur l’efficacité des agents altérants. Enfin, des résultats préliminaires ont été obtenus sur la régulation des gènes et protéines en fonction de la disponibilité en nutriments inorganiques et de la présence du minéral par des techniques de transcriptomique et protéomique. Pour conclure, cette thèse a permis de (i) découvrir de nouveaux gènes liés à l’altération des minéraux par les bactéries, (ii) mettre en évidence l’influence des facteurs environnementaux dans l’efficacité des mécanismes d’altération utilisés par les bactéries
In temperate regions, minerals and rocks represent one of the main sources of nutritive cations in the soil of low-input ecosystems such as forests. In such nutrient-poor and non-amended environments, the access and the recycling of nutritive cations are key processes for tree growth and productivity. However, these nutritive cations are almost inaccessible to the tree roots as they are entrapped into organic matter or into soil minerals and rocks. Consequently, the mineral weathering process is essential, as it allows the restauration of soil fertility and provides the inorganic nutrients for tree growth. Mineral weathering can be attributed to abiotic (temperature, pH, erosion…) or biotic (plants, fungi, bacteria…) processes. Among the biotic processes, bacteria are able to weather minerals by different mechanisms such as the production of protons (acidolysis) or the production of chelating molecules (complexolysis). However, genes and proteins involved in mineral weathering by bacteria are not yet elucidated. As part of this thesis, a bacterial Collimonas pratensis strain PMB3(1) was used as a model to identify genes involved in mineral weathering. This strain was isolated from oak mycorrhizosphere and is efficient in weathering minerals. In this thesis, the analysis of the genome of the strain PMB3(1) evidenced the absence of certain genes described in mineral weathering (such as PQQ-dependent glucose dehydrogenases) and highlighted the need to develop two complementary approaches: with and without a priori. (i) The without a priori approach, has been developed with the building of a mutant library with the insertion of a plasposon pOT-182. The screening of this mutant library on biotests miming mineral weathering allowed the selection of three mutants impacted in their mineral weathering ability. The characterisation of these mutants revealed mutations in different genes involved in a glucose/methanol/choline oxidoreductase (GMC) synthesis. Comparisons between wild type and mutants chemical compounds in the culture supernatants showed that this GMC was able to converts glucose to gluconate and produce protons, leading to the acidification of the medium and minerals acidolysis. (ii) The with a priori approach was the building of a mbaA mutant coding for a NRPS (non-ribosomal peptide synthetase) responsible of siderophore biosynthesis. The combined use of chromatography (HPLC) and mass spectrometry (LC-ESI-MS and MS/MS) methods allowed to chemically characterize the siderophore as malleobactin X. Comparisons between wild ype and mbaA mutant strains revealed that the production of malleobactin was involved in mineral weathering by complexolysis in a strong buffered medium. Weathering tests performed with different mineral types in presence of two carbon sources (glucose or mannitol) and two media with different buffering capacities showed that the strain PMB3(1) was efficient to weather all tested minerals and that weathering molecules (GMC and malleobactin) had a similar effect whatever the mineral type. Furthermore, the carbon source and the buffering capacity had a strong influence on weathering molecules efficiency. Finally, preliminary results have been obtained on the regulation of genes and proteins according to inorganic nutrients availability and the presence of minerals by transcriptomic and proteomic technics. To conclude, this thesis (i) allowed the discovery of new genes involved in mineral weathering by bacteria, (ii) evidenced the influence of environmental factors in efficiency of molecular mechanisms involved in mineral weathering and used by bacteria

Background: Recent studies had explored that gut microbiota was associated with neurodegenerative diseases (including Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS)) through the gut-brain axis, among which metabolic pathways played an important role. However, the underlying causality remained unclear. Objective: Our study aimed to evaluate potential causal relationships between gut microbiota, metabolites, and neurodegenerative diseases through Mendelian randomization (MR) approach. Methods: We selected genetic variants associated with gut microbiota traits (N = 18,340) and gut microbiota-derived metabolites (N = 7,824) from genome-wide association studies. Summary statistics of neurodegenerative diseases were obtained from IGAP (AD, 17,008 cases; 37,154 controls), IPDGC (PD, 37,688 cases; 141,779 controls), and IALSC (ALS, 20,806 cases; 59,804 controls) respectively. Results: Greater abundance of Ruminococcus (OR, 1.245; 95%CI, 1.103–1.405; p = 0.0004) was found significantly related to higher risk of ALS. Besides, our study found suggestive associations of Actinobacteria, Lactobacillaceae, Faecalibacterium, Ruminiclostridium, and Lachnoclostridium with AD, of Lentisphaerae, Lentisphaeria, Oxalobacteraceae, Victivallales, Bacillales, Eubacteriumhalliigroup, Anaerostipes, and Clostridiumsensustricto1 with PD, and of Lachnospira, Fusicatenibacter, Catenibacterium, and Ruminococcusgnavusgroup with ALS. Our study also revealed suggestive associations between 12 gut microbiome-dependent metabolites and neurodegenerative diseases. Glutamine was related to lower risk of AD. For the serotonin pathway, serotonin was found as a protective factor of PD, while kynurenine as a risk factor for ALS. Conclusion: Our study firstly applied a two-sample MR approach to detect causal relationships among gut microbiota, gut metabolites, and neurodegenerative diseases. Our findings may provide new targets for treatments and may offer valuable insights for further studies on the underlying mechanisms.