Browsing by Subject "BACTERIUM"

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  • Aserse, Aregu Amsalu; Woyke, Tanja; Kyrpides, Nikos C.; Whitman, William B.; Lindstrom, Kristina (2017)
    The type strain of the prospective Bradyrhizobium shewense sp. nov. ERR11(T), was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain Bradyrhizobium yuanmingense CCBAU 10071(T), was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11(T) and CCBAU 10071(T) were sequenced by DOE-JGI and deposited at the DOE-JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11(T) is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein-coding and 86 RNA genes. The CCBAU 10071(T) genome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of Bradyrhizobium diazoefficiens USDA110(T). The genes encoding for nodulation and nitrogen fixation in ERR11(T) showed high sequence similarity with homologous genes found in the draft genome of peanut-nodulating Bradyrhizobium arachidis LMG 26795(T). The nodulation genes nolYAnodD2D1YABCSUIJ-nolO-nodZ of ERR11(T) and CCBAU 10071(T) are organized in a similar way to the homologous genes identified in the genomes of USDA110(T), Bradyrhizobium ottawaense USDA 4 and Bradyrhizobium liaoningense CCBAU 05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11(T) also contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the B. ottawaense branch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11(T) and closely related sequences revealed that strains belonging to B. ottawaense branch (USDA4 and CCBAU15615), were the closest strains to the strain ERR11(T) with 95.2% ANI. Type strain ERR11(T) showed the highest DDH predicted value with CCBAU15615 (58.5%), followed by USDA 4 (53.1%). Nevertheless, the ANI and DDH values obtained between ERR11(T) and CCBAU 15615 or USDA 4 were below the cutoff values (ANI = 96.5%; DDH = 70%) for strains belonging to the same species, suggesting that ERR11(T) is a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of B. shewense sp. nov. with strain ERR11(T) (HAMBI 3532(T)= LMG 30162(T)) as the type strain.
  • van der Ark, Kees C. H.; Nugroho, Avis Dwi Wahyu; Berton-Carabin, Claire; Wang, Che; Belzer, Clara; de Vos, Willem M.; Schroen, Karin (2017)
    There is considerable attention for developing Akkermansia muciniphila as a new therapeutic microbe since it has shown to prevent diet-induced obesity and type 2 diabetes in mice. However, A. muciniphila is sensitive to gastric conditions such as low pH and oxygen. Therefore, we explored the possibility of encapsulating A. muciniphila in a water-in-oil-in-water (W/O/W) double emulsion, to allow for protection during gastric passage and subsequent release in the small intestine. The bacteria were efficiently encapsulated in the inner emulsion droplets and remained entrapped during in vitro gastric digestion. The cells were then released in the simulated intestinal phase of the in vitro system. The viability of encapsulated cells was found to be higher when compared to cells dispersed in buffer, that had been subjected to similar mechanical process as the one conducted to prepare the emulsion systems. Surprisingly, the viability of the processed cells was even higher than that of the cells dispersed in buffer without processing, likely due to shear-induced stress tolerance. To conclude, encapsulation in a double emulsion seems to be a. promising strategy to protect A. muciniphila during gastric passage in oral formulations.
  • Karcher, Nicolai; Nigro, Eleonora; Puncochar, Michal; Blanco-Miguez, Aitor; Ciciani, Matteo; Manghi, Paolo; Zolfo, Moreno; Cumbo, Fabio; Manara, Serena; Golzato, Davide; Cereseto, Anna; Arumugam, Manimozhiyan; Bui, Thi Phuong Nam; Tytgat, Hanne L. P.; Valles-Colomer, Mireia; de Vos, Willem M.; Segata, Nicola (2021)
    Background Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored. Results We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. Conclusions We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria.
  • Jayachandra, Yaradoddi A.; Sulochana, M. B.; Merja, Kontro H.; Parameshwar, A. B.; Dayanand, Agsar (2020)
    Many halophiles were considered to be extremophiles due to their inborn industrial potentials and tolerance to hostile environmental conditions. The isolated halophilic bacteria described in the present study are not only grown at environmentally adverse conditions, also they can be able to produce bioactive molecules. Among the isolated strains, Oceanobacillus iheyensis strain JAS12 and Salinicoccus roseus strain JS20 are known for the unique biotechnological applications. The isolate Oceanobacillus sp. grows well at 35-55 degrees C (optimum 45 degrees C) and pH 6 to 12 (maximum growth at pH 8), interestingly the strain could hydrolyze casein, starch and gelatin. The G+C content was 40.2 mol % and the major fatty acids are iso-15:0: 30.52%, primary-C15: 0 (29.29 %), iso-14:0 (16.15%) anteiso-C17: 0 (4.03%). Another isolate was Salinicoccus sp. JS20 The DNA G+C content was 50.4 mol % and the major fatty acids are anteiso-C15: 0 (26.23%), iso15:0, (17.62%)Y, 16:0 (11.5%), anteiso-C17: 0 (7.7 %), iso- C16: 0 (10.20 %), iso-17:0: (5.43%) and iso-C14: 0 (3.97 %). These isolates are also producers of many extracellular enzymes such as protease, amylase, inulinases, gelatinase and beta-fructofurinosidase above the optimal conditions. Oceanobacillus sp. JAS12 16S rRNA gene sequence similarity is 99% similar to the reported genera. Salinicoccus sp. JS20 indicated 96% 16S rRNA sequence similarity with near species Salinicoccus genus, thus, they were found to be novel concerning to their genetic makeup and biochemical features.
  • Miettinen, Hanna; Bomberg, Malin; Bes, René; Tiljander, Mia; Vikman, Minna (2022)
    Bentonite is one of the materials used to construct engineered barriers in high-level radioactive nuclear waste geological disposal with its many advantageous features such as low hydraulic conductivity, self-sealing ability, durability, adsorption and immobilization of metals and radionuclides and reduction of microbial activity. Many of these properties are linked with the bentonite swelling capability. Transformations of indigenous microorganism communities from Wyoming-type bentonite and the Finnish repository site groundwater and their effects on the bentonite structural iron over five years were studied in repository relevant anoxic and oxic slurry conditions. Active sulfate reduction (0.06 nmol mL-1 day-1) was detected in the anoxic microcosm waters after a year, however after two years sulfate reduction was not active anymore. Microbial numbers determined by quantitative PCR in the bentonite slurry of both experiment types supported the finding of decrease of overall microbial activity after a year of incubation that was not maintained anymore by the dissolving organic carbon from the bentonite. Regular electron donor additions (final concentration of 2 mM for formate and acetate each, three times per year) activated the microbiome resulting in increasing numbers of bacterial 16S rRNA gene copies and sulfate reducers (dsrB gene copies) as well as detection of sulfide in the water phase of both experiment types. After 4.9 years the structural iron in the fine portion of the montmorillonite had become completely reduced in all microbial microcosms and minor smectite illitization was detected especially in anoxic microcosms. Dominating bacterial groups at the end of the experiment were mainly known sulfur/sulfate and iron reducers. Archaea and fungi constituted a minor part of the microbiomes. In originally oxic microcosms, the bacterial 16S RNA and dsrB gene copy numbers were lower than in the anoxic experiment but started to significantly increase after the electron donor additions. Microorganisms originating from the repository environment could reduce the bentonite structural iron in a few years to an extent likely to affect the bentonite swelling ability if sufficient amounts of suitable electron donors are available in localized areas where bentonite is not at high density and pressure in the geological disposal.
  • Shetty, Sudarshan A.; Boeren, Sjef; Bui, Thi P. N.; Smidt, Hauke; de Vos, Willem M. (2020)
    Thed- andl-forms of lactate are important fermentation metabolites produced by intestinal bacteria but are found to negatively affect mucosal barrier function and human health. Both enantiomers of lactate can be converted with acetate into the presumed beneficial butyrate by a phylogenetically related group of anaerobes, includingAnaerobutyricumandAnaerostipesspp. This is a low energy yielding process with a partially unknown pathway inAnaerobutyricumandAnaerostipesspp. and hence, we sought to address this via a comparative genomics, proteomics and physiology approach. We compared growth ofAnaerobutyricum soehngeniion lactate with that on sucrose and sorbitol. Comparative proteomics revealed complete pathway of butyrate formation from sucrose, sorbitol and lactate. Notably, a gene cluster,lctABCDEFwas abundantly expressed when grown on lactate. This gene cluster encodes a lactate dehydrogenase (lctD), electron transport proteins A and B (lctCB), nickel-dependent racemase (lctE), lactate permease (lctF) and short-chain acyl-CoA dehydrogenase (lctG). Investigation of available genomes of intestinal bacteria revealed this new gene cluster to be highly conserved in onlyAnaerobutyricumandAnaerostipesspp. Present study demonstrates thatA. soehngeniiand several relatedAnaerobutyricumandAnaerostipesspp. are highly adapted for a lifestyle involving lactate plus acetate utilization in the human intestinal tract.