Characterization of Ferroplasma Isolates and Ferroplasma acidarmanus sp. nov., Extreme Acidophiles from Acid Mine Drainage and Industrial Bioleaching Environments

ABSTRACT Three recently isolated extremely acidophilic archaeal strains have been shown to be phylogenetically similar to Ferroplasma acidiphilum YT by 16S rRNA gene sequencing. All four Ferroplasma isolates were capable of growing chemoorganotrophically on yeast extract or a range of sugars and chemomixotrophically on ferrous iron and yeast extract or sugars, and isolate “Ferroplasma acidarmanus” Fer1T required much higher levels of organic carbon. All four isolates were facultative anaerobes, coupling chemoorganotrophic growth on yeast extract to the reduction of ferric iron. The temperature optima for the four isolates were between 35 and 42°C and the pH optima were 1.0 to 1.7, and “F. acidarmanus” Fer1T was capable of growing at pH 0. The optimum yeast extract concentration for “F. acidarmanus” Fer1T was higher than that for the other three isolates. Phenotypic results suggested that isolate “F. acidarmanus” Fer1T is of a different species than the other three strains, and 16S rRNA sequence data, DNA-DNA similarity values, and two-dimensional polyacrylamide gel electrophoresis protein profiles clearly showed that strains DR1, MT17, and YT group as a single species. “F. acidarmanus” Fer1T groups separately, and we propose the new species “F. acidarmanus” Fer1T sp. nov.

Download Full-text

A rare case of equine Haemotropic Mycoplasma infection in Nigeria

Nigerian Veterinary Journal ◽

10.4314/nvj.v41i3.8 ◽

2021 ◽

Vol 41 (3) ◽

pp. 274-286

Author(s):

A.N Happi ◽

P.E Oluniyi

Keyword(s):

16S Rrna ◽

Bacterial Infections ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Clinical Findings ◽

Epidemiological Surveillance ◽

Response To Treatment ◽

Molecular Evidence ◽

Rrna Gene ◽

16S Rrna Sequence

Equine haemotropic mycoplasmosis (EHM) is a condition rarely reported worldwide. A horse presented with unspecific clinical findings and non-response to treatment to the common and endemic haemoparasitic and bacterial infections, warranted a thorough molecular investigation of suspected haemoparasitic infection given the fluctuating parasitaemia and the low sensitivity and specificity of Light Microscopy (LM) detection of haemoparasitic infections. Blood collected from an adult horse, domiciled at the University of Ibadan Veterinary Teaching Hospital, Ibadan, Nigeria was screened by LM and PCR techniques for haemo-parasites. The 16S rRNA gene of pan-Hemoplasma spp was targeted amplified and sequenced using Sanger automatic sequencing techniques. This case shows the very first molecular evidence of EHM in Africa and Nigeria, and the third case in the World. Microscopic examination of the horse’s blood smear presented with signs of lethargy, inactivity, anorexia and moderate emaciation, showed numerous coccoid-shaped epierythrocytic parasites. Subsequent 16S rRNA sequence data and phylogenetic analyses confirmed the presence of a haemotropic mycoplasma (‘Candidatus M. haemocervae’–like) in the horse. The hemoplasma sequence obtained falls in the same clade with some Candidatus Mycoplasma haemocervae sequences with which it shared more than 98.7% homology. This finding suggests that horses in this geographical region may also be suffering from EHM and calls for the need of epidemiological surveillance of equine hemoplasmosis with emphasis on their clinical, economic, performance and zoonotic implications in the sub-region. Keywords: Nigeria, Horse, Haemotropic mycoplasma, ‘Candidatus M. haemocervae’–like

Download Full-text

Phylogenetic Affinity of a Wide, Vacuolate, Nitrate-AccumulatingBeggiatoa sp. from Monterey Canyon, California, withThioploca spp

Applied and Environmental Microbiology ◽

10.1128/aem.65.1.270-277.1999 ◽

1999 ◽

Vol 65 (1) ◽

pp. 270-277 ◽

Cited By ~ 41

Author(s):

Azeem Ahmad ◽

James P. Barry ◽

Douglas C. Nelson

Keyword(s):

16S Rrna ◽

Fluorescent In Situ Hybridization ◽

Sequence Data ◽

Rrna Gene ◽

Polymorphism Analysis ◽

Cold Seeps ◽

16S Rrna Sequence ◽

Species Cluster ◽

Physiological Adaptations

ABSTRACT Environmentally dominant members of the genus Beggiatoaand Thioploca spp. are united by unique morphological and physiological adaptations (S. C. McHatton, J. P. Barry, H. W. Jannasch, and D. C. Nelson, Appl. Environ. Microbiol. 62:954–958, 1996). These adaptations include the presence of very wide filaments (width, 12 to 160 μm), the presence of a central vacuole comprising roughly 80% of the cellular biovolume, and the capacity to internally concentrate nitrate at levels ranging from 150 to 500 mM. Until recently, the genera Beggiatoa andThioploca were recognized and differentiated on the basis of morphology alone; they were distinguished by the fact that numerousThioploca filaments are contained within a common polysaccharide sheath, while Beggiatoa filaments occur singly. Vacuolate Beggiatoa or Thioploca spp. can dominate a variety of marine sediments, seeps, and vents, and it has been proposed (H. Fossing, V. A. Gallardo, B. B. Jorgensen, M. Huttel, L. P. Nielsen, H. Schulz, D. E. Canfield, S. Forster, R. N. Glud, J. K. Gundersen, J. Kuver, N. B. Ramsing, A. Teske, B. Thamdrup, and O. Ulloa, Nature [London] 374:713–715, 1995) that members of the genusThioploca are responsible for a significant portion of total marine denitrification. In order to investigate the phylogeny of an environmentally dominant Beggiatoa sp., we analyzed complete 16S rRNA gene sequence data obtained from a natural population found in Monterey Canyon cold seeps. Restriction fragment length polymorphism analysis of a clone library revealed a dominant clone, which gave rise to a putative Monterey Beggiatoa 16S rRNA sequence. Fluorescent in situ hybridization with a sequence-specific probe confirmed that this sequence originated from wideBeggiatoa filaments (width, 65 to 85 μm). A phylogenetic tree based on evolutionary distances indicated that the MontereyBeggiatoa sp. falls in the gamma subdivision of the classProteobacteria and is most closely related to the genusThioploca. This vacuolate Beggiatoa—Thioplocacluster and a more distantly related freshwater Beggiatoaspecies cluster form a distinct phylogenetic group.

Download Full-text

Phaeodactylibacter luteus sp. nov., isolated from the oleaginous microalga Picochlorum sp.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000321 ◽

2015 ◽

Vol 65 (Pt_8) ◽

pp. 2666-2670 ◽

Cited By ~ 12

Author(s):

Xueqian Lei ◽

Yi Li ◽

Guanghua Wang ◽

Yao Chen ◽

Qiliang Lai ◽

...

Keyword(s):

16S Rrna ◽

Sequence Data ◽

Sequence Similarity ◽

16S Rrna Gene Sequencing ◽

Biodiesel Production ◽

Rrna Gene ◽

16S Rrna Sequence ◽

Respiratory Quinone ◽

Gram Staining ◽

Rrna Gene Sequencing

A Gram-staining-negative, orange-pigmented, non-motile, aerobic bacterial strain, designated GYP20T, was isolated from a culture of the alga Picochlorum sp., a promising feedstock for biodiesel production, which was isolated from the India Ocean. Growth was observed at temperatures from 20 to 37 °C, salinities from 0 to 3 % and pH from 5 to 9.Mg 2+ and Ca2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain was a member of the genus Phaeodactylibacter, which belongs to the family Saprospiraceae. Strain GYP20T was most closely related to Phaeodactylibacter xiamenensis KD52T (95.5 % sequence similarity). The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3. The predominant respiratory quinone was menaquinone-7 (MK-7). The polar lipids of strain GYP20T were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, four unidentified glycolipids, two unidentified phospholipids and three unidentified aminolipids. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence data, the novel strain most appropriately belongs to the genus Phaeodactylibacter, but can readily be distinguished from Phaeodactylibacter xiamenensis GYP20T. The name Phaeodactylibacter luteus sp. nov. is proposed with the type strain GYP20T ( = MCCC 1F01222T = KCTC 42180T).

Download Full-text

Evaluation of recA Sequences for Identification of Mycobacterium Species

Journal of Clinical Microbiology ◽

10.1128/jcm.38.8.2846-2852.2000 ◽

2000 ◽

Vol 38 (8) ◽

pp. 2846-2852 ◽

Cited By ~ 56

Author(s):

Kym S. Blackwood ◽

Cheng He ◽

James Gunton ◽

Christine Y. Turenne ◽

Joyce Wolfe ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Sequence Similarity ◽

Gene Sequencing ◽

Genetic Identification ◽

Rrna Gene ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Accurate Identification

16S rRNA sequence data have been used to provide a molecular basis for an accurate system for identification of members of the genusMycobacterium. Previous studies have shown thatMycobacterium species demonstrate high levels (>94%) of 16S rRNA sequence similarity and that this method cannot differentiate between all species, i.e., M. gastri and M. kansasii. In the present study, we have used the recAgene as an alternative sequencing target in order to complement 16S rRNA sequence-based genetic identification. The recA genes of 30 Mycobacterium species were amplified by PCR, sequenced, and compared with the published recA sequences of M. tuberculosis, M. smegmatis, and M. leprae available from GenBank. By recA sequencing the species showed a lower degree of interspecies similarity than they did by 16S rRNA gene sequence analysis, ranging from 96.2% betweenM. gastri and M. kansasii to 75.7% betweenM. aurum and M. leprae. Exceptions to this were members of the M. tuberculosis complex, which were identical. Two strains of each of 27 species were tested, and the intraspecies similarity ranged from 98.7 to 100%. In addition, we identified new Mycobacterium species that contain a protein intron in their recA genes, similar to M. tuberculosis and M. leprae. We propose thatrecA gene sequencing offers a complementary method to 16S rRNA gene sequencing for the accurate identification of theMycobacterium species.

Download Full-text

Three Cases of Anaerobiospirillum succiniciproducens Bacteremia Confirmed by 16S rRNA Gene Sequencing

Journal of Clinical Microbiology ◽

10.1128/jcm.36.5.1209-1213.1998 ◽

1998 ◽

Vol 36 (5) ◽

pp. 1209-1213 ◽

Cited By ~ 27

Author(s):

Wee Tee ◽

Tony M. Korman ◽

Mary Jo Waters ◽

Andrew Macphee ◽

Adam Jenney ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Sequence Data ◽

Infected Individual ◽

The Other ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Anaerobiospirillum Succiniciproducens

We describe three cases of Anaerobiospirillum succiniciproducens bacteremia from Australia. We believe one of these cases represents the first report of A. succiniciproducens bacteremia in a human immunodeficiency virus (HIV)-infected individual. The other two patients had an underlying disorder (one patient had bleeding esophageal varices complicating alcohol liver disease and one patient had non-Hodgkin’s lymphoma). A motile, gram-negative, spiral anaerobe was isolated by culturing blood from all patients. Electron microscopy showed a curved bacterium with bipolar tufts of flagella resembling Anaerobiospirillumspp. Sequencing of the 16S rRNA genes of the isolates revealed no close relatives (organisms likely to be in the same genus) in the sequence databases, nor were any sequence data available for A. succiniciproducens. This report presents for the first time the 16S rRNA gene sequence of the type strain of A. succiniciproducens, strain ATCC 29305. Two of the three clinical isolates have sequences identical to that of the type strain, while the sequence of the other strain differs from that of the type strain at 4 nucleotides.

Download Full-text

Anaerosporobacter mobilis gen. nov., sp. nov., isolated from forest soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63283-0 ◽

2007 ◽

Vol 57 (8) ◽

pp. 1784-1787 ◽

Cited By ~ 25

Author(s):

Hyunyoung Jeong ◽

Young Woon Lim ◽

Hana Yi ◽

Yuji Sekiguchi ◽

Yoichi Kamagata ◽

...

Keyword(s):

16S Rrna ◽

Forest Soil ◽

Sequence Data ◽

Sequence Similarity ◽

Rrna Gene ◽

Strictly Anaerobic ◽

Phenotypic Characteristics ◽

16S Rrna Sequence ◽

Bacterium Strain ◽

Low Levels

A strictly anaerobic, Gram-positive, endospore-forming bacterium, strain HY-37-4T, was isolated from a forest-soil sample collected in Jeju, Republic of Korea. The cells were motile rods with peritrichous flagella. Strain HY-37-4T fermented various carbohydrates and the end products from glucose were formate, acetate and H2. The major cellular fatty acids were C16 : 0, C16 : 0 3-OH and iso-C17 : 1 I/anteiso B. The G+C content of the DNA was 41 mol%. A phylogenetic analysis based on 16S rRNA sequence data indicated that the forest isolate was most closely related to Clostridium herbivorans, Clostridium populeti, Clostridium polysaccharolyticum and Eubacterium xylanophilum, which belong to Clostridium cluster XIVa. However, the low levels of 16S rRNA gene sequence similarity (92.3–93.9 %) with respect to these taxa indicate that strain HY-37-4T represents a novel species. Several phenotypic characteristics readily allowed the isolate to be distinguished from other phylogenetically related taxa. On the basis of the polyphasic evidence, strain HY-37-4T represents a novel taxon, for which the name Anaerosporobacter mobilis gen. nov., sp. nov. is proposed. The type strain is HY-37-4T (=IMSNU 40011T=KCTC 5027T=DSM 15930T).

Download Full-text

Strong influence of vertebrate host phylogeny on gut archaeal diversity

10.1101/2020.11.10.376293 ◽

2020 ◽

Author(s):

Nicholas D. Youngblut ◽

Georg H. Reischer ◽

Silke Dauser ◽

Chris Walzer ◽

Gabrielle Stalder ◽

...

Keyword(s):

16S Rrna ◽

Sequence Data ◽

Gas Production ◽

Rrna Gene ◽

Archaeal Diversity ◽

16S Rrna Sequence ◽

Waste Products ◽

Bacterial Fermentation ◽

Host Phylogeny ◽

Host Associations

AbstractCommonly used 16S rRNA gene primers miss much of the archaeal diversity present in the vertebrate gut, leaving open the question of which archaea are host associated, the specificities of such associations, and the major factors influencing archaeal diversity. We applied 16S rRNA amplicon sequencing with Archaea-targeting primers to a dataset of 311 fecal/gut samples spanning 5 taxonomic classes (Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii) and obtained from mainly wild individuals (76% were wild). We obtained sufficient archaeal sequence data from 185 samples comprising 110 species that span all 5 classes. We provide evidence for novel Archaea-host associations, including Bathyarchaeia and Methanothermobacter — the latter of which was prevalent among Aves and enriched in higher body temperatures. Host phylogeny more strongly explained archaeal diversity than diet, while specific taxa were associated with each factor. Co-phylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last command ancestors of mammals and all host species. Archaea-Bacteria interactions seem to have a limited effect on archaeal diversity. These findings substantially expand on the paradigm of Archaea-vertebrate associations and the factors that explain those associations.SignificanceArchaea play key roles in the vertebrate gut such as promoting bacterial fermentation via consumption of waste products. Moreover, gut-inhabiting methanogenic Archaea in livestock are a substantial source of greenhouse gas production. Still, much is not known of the archaeal diversity in most vertebrates, especially since 16S rRNA sequence surveys often miss much of the archaeal diversity that is present. By applying Archaea-targeted gut microbiome sequencing to a large collection of diverse vertebrates, we reveal new Archaea-host associations such as a high prevalence of Methanothermobacter in birds. We also show that host evolutionary history explains archaeal diversity better than diet, and certain genera in one particular class of Archaea (Methanobacteria) were likely pervasive in the ancestral vertebrate gut.

Download Full-text

An experimental intraradicular biofilm model in the pig for evaluating irrigation techniques

BMC Oral Health ◽

10.1186/s12903-021-01536-w ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Toshinori Tanaka ◽

Yoshio Yahata ◽

Keisuke Handa ◽

Suresh V. Venkataiah ◽

Mary M. Njuguna ◽

...

Keyword(s):

16S Rrna ◽

Root Canal ◽

Apical Periodontitis ◽

Exposure Model ◽

Rrna Gene ◽

16S Rrna Sequence ◽

Bacterial Phyla ◽

Biofilm Model ◽

Biofilm Removal

Abstract Background We established an in vivo intraradicular biofilm model of apical periodontitis in pigs in which we compared the efficacy of different irrigant activation techniques for biofilm removal. Methods Twenty roots from the deciduous mandibular second premolar of 5 male pigs were used. After pulpectomy, canals were left open for 2 weeks and then sealed for 4 weeks to enable the development of an intracanal biofilm. The intraradicular biofilms was evaluated using SEM and bacterial 16S rRNA gene-sequencing. To investigate the efficacy of biofilm removal, root canal irrigations were performed using conventional needle, passive ultrasonic, subsonic, or laser-activated irrigation. Real-time PCR was conducted to quantitate the remaining biofilm components. Statistical analysis was performed using ANOVA followed by a Tukey kramer post-hoc test with α = 0.05. Results The pulp exposure model was effective in inducing apical periodontitis and SEM analysis revealed a multi-layer biofilm formation inside the root canal. 16S rRNA sequence analysis identified Firmicutes, Bacteroidetes, and Fusobacteria as the predominant bacterial phyla components, which is similar to the microbiome profile seen in humans. None of the tested irrigation techniques completely eradicated the biofilm components from the root canal, but the subsonic and laser-activated irrigation methods produced the lowest bacterial counts (p < 0.05). Conclusions An experimental intraradicular biofilm model has been successfully established in pigs. Within the limitations of the study, subsonic or laser-activated irrigation demonstrated the best biofilm removal results in the pig system.

Download Full-text

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.01541-09 ◽

2009 ◽

Vol 75 (23) ◽

pp. 7537-7541 ◽

Cited By ~ 11597

Author(s):

Patrick D. Schloss ◽

Sarah L. Westcott ◽

Thomas Ryabin ◽

Justine R. Hall ◽

Martin Hartmann ◽

...

Keyword(s):

16S Rrna ◽

Software Package ◽

Sequence Data ◽

Rrna Gene ◽

Sequencing Data ◽

Laptop Computer ◽

Operational Taxonomic Units ◽

Β Diversity ◽

Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Download Full-text

Extremely Acidophilic Protists from Acid Mine Drainage Host Rickettsiales-Lineage Endosymbionts That Have Intervening Sequences in Their 16S rRNA Genes

Applied and Environmental Microbiology ◽

10.1128/aem.69.9.5512-5518.2003 ◽

2003 ◽

Vol 69 (9) ◽

pp. 5512-5518 ◽

Cited By ~ 78

Author(s):

Brett J. Baker ◽

Philip Hugenholtz ◽

Scott C. Dawson ◽

Jillian F. Banfield

Keyword(s):

Acid Mine Drainage ◽

16S Rrna ◽

16S Rrna Gene ◽

Mine Drainage ◽

Close Association ◽

Variable Region ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Acid Mine

ABSTRACT During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria. The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba. Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage samples, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage samples contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region V1 of their 16S rRNA genes. The IVS does not match any sequence in current databases, but the predicted secondary structure forms well-defined stem loops. IVSs are uncommon in rRNA genes and appear to be confined to bacteria living in close association with eukaryotes. Based on the phylogenetic novelty of the endosymbiont sequences and initial culture-independent characterization, we propose the name “Candidatus Captivus acidiprotistae.” To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat.

Download Full-text