scholarly journals A New Fungal Isolate, Penidiella sp. Strain T9, Accumulates the Rare Earth Element Dysprosium

2015 ◽  
Vol 81 (9) ◽  
pp. 3062-3068 ◽  
Author(s):  
Takumi Horiike ◽  
Mitsuo Yamashita
Keyword(s):  
Rare Earth ◽  
Mine Drainage ◽  
Liquid Waste ◽  
Morphological Characterization ◽  
Rrna Gene ◽  
Content Type ◽  
Cell Pellet ◽  
Acidic Conditions ◽  
High Concentrations ◽  
Rrna Gene Sequencing

ABSTRACTWith an aim to develop a highly efficient method for the recovery of rare earth elements (REEs) by using microorganisms, we attempted to isolate dysprosium (Dy)-accumulating microorganisms that grow under acidic conditions from environmental samples containing high concentrations of heavy metals. One acidophilic strain, T9, which was isolated from an abandoned mine, decreased the concentration of Dy in medium that contained 100 mg/liter Dy to 53 mg/liter Dy after 3 days of cultivation at pH 2.5. The Dy content in the cell pellet of the T9 strain was 910 μg/mg of dry cells. The T9 strain also accumulated other REEs. Based on the results of 28S-D1/D2 rRNA gene sequencing and morphological characterization, we designated this fungal strainPenidiellasp. T9. Bioaccumulation of Dy was observed on the cell surface of the T9 strain by elemental mapping using scanning electron microscopy-energy dispersive X-ray spectroscopy. Our results indicate thatPenidiellasp. T9 has the potential to recover REEs such as Dy from mine drainage and industrial liquid waste under acidic conditions.

scholarly journals Longitudinal Analysis of the Prevalence, Maintenance, and IgA Response to Species of the Order Bacteroidales in the Human Gut

2011 ◽  
Vol 79 (5) ◽  
pp. 2012-2020 ◽  
Author(s):  
Naamah Levy Zitomersky ◽  
Michael J. Coyne ◽  
Laurie E. Comstock
Keyword(s):  
Longitudinal Analysis ◽  
Phase Variation ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Human Intestinal Microbiota ◽  
Iga Response ◽  
High Concentrations ◽  
Rrna Gene Sequencing ◽  
Arbitrarily Primed Pcr

ABSTRACTBacteroidalesspecies are the most abundant Gram-negative bacteria of the human intestinal microbiota. These bacteria evolved to synthesize numerous capsular polysaccharides (PS) that are subject to phase variation. InBacteroides fragilis, PS synthesis is regulated so that only one of the eight PS biosynthesis loci is transcribed at a time in each bacterium. To determine if the bacteria evolved this unusual property to evade a host IgA response, we directly studied the human fecal ecosystem. We performed a longitudinal analysis of the abundantBacteroidalesspecies from 15 healthy adults at four intervals over a year. For this study, we used bacterial culture to perform analyses not accurate with DNA-based methods, including quantification of total viableBacteroidalesbacteria, strain maintenance, and IgA responses. AbundantBacteroidalesisolates were identified to the species level using multiplex PCR and 16S rRNA gene sequencing. Arbitrarily primed PCR was used for strain typing. IgA responses to endogenous strains carried over the year were analyzed, and the orientations of the invertible PS locus promoters from the ecosystem were quantified. Subjects consistently harbored from 5 × 108to 8 × 1010Bacteroidalesbacteria/g of feces. Within the cohort, 20 differentBacteroidalesspecies were detected at high concentrations.Bacteroides uniformiswas the most prevalent; however, abundantBacteroidalesspecies varied between subjects. Strains could be maintained over the year within the ecosystem at high density. IgA responses were often not induced and did not correlate with the elimination of a strain or major changes in the orientations of the capsular PS locus promoters.

scholarly journals Citroniella saccharovorans gen. nov. sp. nov., a member of the family Peptoniphilaceae isolated from a human fecal sample from a coastal traditional community member

2019 ◽  
Vol 69 (4) ◽  
pp. 1142-1148 ◽  
Author(s):  
Nisha B. Patel ◽  
Alexandra J. Obregón-Tito ◽  
Raul Y. Tito ◽  
Omar Trujillo-Villaroel ◽  
Luis Marin-Reyes ◽  
...  
Keyword(s):  
Fecal Sample ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
The Family ◽  
Diamino Acid ◽  
Rrna Gene Sequencing

A novel Gram-stain-positive, non-motile, non-spore-forming coccus-shaped obligately anaerobic bacterium was recovered from a fecal sample obtained from an individual from a traditional community located on the southern coast of Peru. The results of analysis based on 16S rRNA gene sequencing indicated the novel bacterium to be phylogenetically distinct from other genera of members of the Peptoniphilaceae family, sharing a loose affinity with the genera Ezakiella , Finegoldia , Gallicola and Parvimonas . The major cellular fatty acids of the novel isolate were determined to be C16:0, C17:1ω8c, and C18:1ω9c. The DNA G+C content was 29.9 mol%. End products of metabolism from peptone yeast glucose broth (PYG) were determined to be acetate and methyl succinate. The diagnostic diamino acid present in the cell wall was lysine. On the basis of the phenotypic, chemotaxonomic and phylogenetic results the organism is a member of a novel genus belonging to the family Peptoniphilaceae for which the name Citroniella saccharovorans gen nov. sp. nov., is proposed. The type strain is M6.X9T (DSM 29873T=CCUG 66799T).

scholarly journals Impact of Oral Fidaxomicin Administration on the Intestinal Microbiota and Susceptibility to Clostridium difficile Colonization in Mice

2018 ◽  
Vol 62 (5) ◽  
Author(s):  
N. J. Ajami ◽  
J. L. Cope ◽  
M. C. Wong ◽  
J. F. Petrosino ◽  
L. Chesnel
Keyword(s):  
Clostridium Difficile ◽  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Colonization Resistance ◽  
Content Type ◽  
Rrna Gene Sequencing ◽  
Hospital Acquired ◽  
Predetermined Time

ABSTRACT Clostridium difficile infection (CDI), a common cause of hospital-acquired infections, typically occurs after disruption of the normal gut microbiome by broad-spectrum antibiotics. Fidaxomicin is a narrow-spectrum antibiotic that demonstrates a reduced impact on the normal gut microbiota and is approved for the treatment of CDI. To further explore the benefits of this property, we used a murine model to examine the effects of fidaxomicin versus vancomycin on gut microbiota and susceptibility to C. difficile colonization while tracking microbiota recovery over time. Mice were exposed to fidaxomicin or vancomycin by oral gavage for 3 days and subsequently challenged with C. difficile spores at predetermined time points up to 21 days postexposure to antibiotics. Fecal samples were subsequently collected for analysis. Twenty-four hours postchallenge, mice were euthanized and the colon contents harvested. The microbiota was characterized using 16S rRNA gene sequencing. All fidaxomicin-exposed mice (except for one at day 8) were resistant to C. difficile colonization. However, 9 of 15 vancomycin-exposed mice were susceptible to C. difficile colonization until day 12. All vancomycin-exposed mice recovered colonization resistance by day 16. Bacterial diversity was similar prior to antibiotic exposure in both arms and decreased substantially after exposure. A shift in taxonomic structure and composition occurred after both exposures; however, the shift was greater in vancomycin-exposed than in fidaxomicin-exposed mice. In summary, compared with vancomycin, fidaxomicin exposure had less impact on microbiota composition, promoted faster microbial recovery, and had less impact on the loss of C. difficile colonization resistance.

scholarly journals Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Shinya Kageyama ◽  
Mikari Asakawa ◽  
Toru Takeshita ◽  
Yukari Ihara ◽  
Shunsuke Kanno ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Bacterial Diversity ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Bacterial Composition ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

scholarly journals Whole-Genome Sequencing ofAggregatibacterSpecies Isolated from Human Clinical Specimens and Description ofAggregatibacter kilianiisp. nov.

2018 ◽  
Vol 56 (7) ◽  
Author(s):  
May Murra ◽  
Lisbeth Lützen ◽  
Aynur Barut ◽  
Reinhard Zbinden ◽  
Marianne Lund ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Clinical Specimens ◽  
Phylogenetic Cluster ◽  
Invasive Infections ◽  
Rrna Gene Sequencing

ABSTRACTAggregatibacterspecies are commensal bacteria of human mucosal surfaces that are sometimes involved in serious invasive infections. During the investigation of strains cultured from various clinical specimens, we encountered a coherent group of 10 isolates that could not be allocated to any validly named species by phenotype, mass spectrometry, or partial 16S rRNA gene sequencing. Whole-genome sequencing revealed a phylogenetic cluster related to but separate fromAggregatibacter aphrophilus. The meanin silicoDNA hybridization value for strains of the new cluster versusA. aphrophiluswas 56% (range, 53.7 to 58.0%), whereas the average nucleotide identity was 94.4% (range, 93.9 to 94.8%). The new cluster exhibited aggregative properties typical of the genusAggregatibacter. Key phenotypic tests for discrimination of the new cluster from validly namedAggregatibacterspecies are alanine-phenylalanine-proline arylamidase,N-acetylglucosamine, and β-galactosidase. The nameAggregatibacter kilianiiis proposed, with PN_528 (CCUG 70536Tor DSM 105094T) as the type strain.

scholarly journals Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

2014 ◽  
Vol 80 (12) ◽  
pp. 3677-3686 ◽  
Author(s):  
Jun Liu ◽  
Zheng-Shuang Hua ◽  
Lin-Xing Chen ◽  
Jia-Liang Kuang ◽  
Sheng-Jin Li ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Community Composition ◽  
Environmental Conditions ◽  
Mine Tailings ◽  
Large Scale ◽  
Hot Springs ◽  
Mine Drainage ◽  
Rrna Gene ◽  
Content Type ◽  
Geochemical Parameters

ABSTRACTRecent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within theAlphaproteobacteria,Deltaproteobacteria, andFirmicuteswere attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

scholarly journals Cloacibacillus sp., a Potential Human Pathogen Associated with Bacteremia in Quebec and New Brunswick

2015 ◽  
Vol 53 (10) ◽  
pp. 3380-3383 ◽  
Author(s):  
M.-C. Domingo ◽  
C. Yansouni ◽  
C. Gaudreau ◽  
F. Lamothe ◽  
S. Lévesque ◽  
...  
Keyword(s):  
16S Rrna ◽  
New Brunswick ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Human Pathogen ◽  
Emerging Pathogens ◽  
Content Type ◽  
Rrna Gene Sequencing ◽  
Anaerobic Infections

Bacteremia due toCloacibacillusspecies is poorly described. We present three cases involving eitherCloacibacillusevryensisorCloacibacillusporcorum. The isolates were identified by 16S rRNA gene sequencing and were susceptible to antibiotics commonly used for anaerobic infections. The clinical significance of these organisms as potential emerging pathogens is discussed.

Emendation of the description of the species Corynebacterium propinquum to include strains which produce urease

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2146-2154 ◽  
Author(s):  
Kathryn Bernard ◽  
Ana Luisa Pacheco ◽  
Ian Cunningham ◽  
Navdeep Gill ◽  
Tamara Burdz ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Single Test ◽  
Content Type ◽  
Link Type ◽  
Corynebacterium Pseudodiphtheriticum ◽  
Rrna Gene Sequencing

Corynebacterium propinquum is a Gram-positive rod occasionally recovered from clinical infections which, according to 16S rRNA gene sequencing, is most closely related (>99 % sequence similarity) to Corynebacterium pseudodiphtheriticum . The two species are very similar biochemically, commonly differentiated by a single test, the detection of urease, where strains of C. propinquum are described as being urease-non-producing and strains of C. pseudodiphtheriticum are described as urease-producing. In this study, historical and contemporary strains of C. propinquum and C. pseudodiphtheriticum from this laboratory were definitively characterized, which included use of rpoB sequencing. Urease-producing strains of C. propinquum as well as typical urease-non-producing isolates were identified after rpoB sequencing, with six of these being originally identified as C. pseudodiphtheriticum . Based on these observations, we propose emendation of the description of C. propinquum to include strains which produce urease. MALDI-TOF analysis may be a useful tool to differentiate these taxa. Existing commercial databases should be updated to include urease-positive strains of C. propinquum .

scholarly journals Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1486-1490 ◽  
Author(s):  
Dominique Clermont ◽  
Laurence Motreff ◽  
Virginie Passet ◽  
José-Carlos Fernandez ◽  
Chantal Bizet ◽  
...  
Keyword(s):  
Type Species ◽  
16S Rrna Gene Sequencing ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Rrna Gene Sequencing

Strains originating from various sources and classified as members of the genus Citrobacter within the family Enterobacteriaceae were characterized by sequencing internal portions of genes rpoB, fusA, pyrG and leuS, 16S rRNA gene sequencing, average nucleotide identity (ANI) of genomic sequences and biochemical tests. Phylogenetic analysis based on the four housekeeping genes showed that the 11 species of the genus Citrobacter with validly published names are well demarcated. Strains CIP 55.13T and CIP 55.9 formed a distinct branch associated with Citrobacter youngae . The ANI between CIP 55.9 and CIP 55.13T was 99.19 %, whereas it was 94.75 % between CIP 55.13T and strain CIP 105016T of the species C. youngae , the most closely related species. Biochemical characteristics consolidated the fact that the two isolates represent a separate species, for which the name Citrobacter pasteurii sp. nov. is proposed. The type strain is CIP 55.13T ( = DSM 28879T = Na 1aT).

Chryseobacterium panacisoli sp. nov., isolated from ginseng-cultivation soil with ginsenoside-converting activity

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Dong Ho Keum ◽  
Jun Mo Yeon ◽  
Chan-Seok Yun ◽  
Soon Youl Lee ◽  
Wan-Taek Im
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Active Components ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing ◽  
Ginseng Cultivation

A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped and yellow-pigmented bacterium, designated strain Gsoil 183T, was isolated from ginseng-cultivation soil sampled in Pocheon Province, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 183T grew at 10–37 °C and at pH 5.0–9.0 on tryptic soy agar. Strain Gsoil 183T had β-glucosidase activity, which was responsible for its ability to convert ginsenoside Rb1 (one of the dominant active components of ginseng) to F2. Based on 16S rRNA gene sequencing, strain Gsoil 183T clustered with species of the genus Chryseobacterium and appeared to be closely related to Chryseobacterium sediminis LMG 28695T (99.1 % sequence similarity), Chryseobacterium lactis NCTC 11390T (98.6%), Chryseobacterium rhizoplanae LMG 28481T (98.6%), Chryseobacterium oncorhynchi CCUG 60105T (98.5%), Chryseobacterium viscerum CCUG 60103T (98.4%) and Chryseobacterium joostei DSM 16927T (98.3%). Menaquinone MK-6 was the predominant respiratory quinone and the major fatty acids were iso-C15 : 0, iso-C17 : 0-3OH and summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c). The polar lipids were phosphatidylethanolamine, six unidentified glycolipids, five unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 36.6 mol%. Digital DNA–DNA hybridization between strain Gsoil 183T and the type strains of C. sediminis , C. lactis , C. rhizoplanae , C. oncorhynchi , C. viscerum and C. joostei resulted in values below 70 %. Strain Gsoil 183T could be differentiated genotypically and phenotypically from the recognized species of the genus Chryseobacterium . The isolate therefore represents a novel species, for which the name Chryseobacterium panacisoli sp. nov. is proposed, with the type strain Gsoil 183T (=KACC 15033T=LMG 23397T)

Sign in / Sign up

Export Citation Format

Share Document