scholarly journals The Role of Host Phylogeny Varies in Shaping Microbial Diversity in the Hindguts of Lower Termites

2014 ◽  
Vol 81 (3) ◽  
pp. 1059-1070 ◽  
Author(s):  
Vera Tai ◽  
Erick R. James ◽  
Christine A. Nalepa ◽  
Rudolf H. Scheffrahn ◽  
Steve J. Perlman ◽  
...  
Keyword(s):  
Community Composition ◽  
Bacterial Community Composition ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Microbial Composition ◽  
Variable Regions ◽  
Content Type ◽  
Symbiotic Associations ◽  
Host Phylogeny

ABSTRACTThe hindguts of lower termites andCryptocercuscockroaches are home to a distinct community of archaea, bacteria, and protists (primarily parabasalids and some oxymonads). Within a host species, the composition of these hindgut communities appears relatively stable, but the evolutionary and ecological factors structuring community composition and stability are poorly understood, as are differential impacts of these factors on protists, bacteria, and archaea. We analyzed the microbial composition of parabasalids and bacteria in the hindguts ofCryptocercus punctulatusand 23 species spanning 4 families of lower termites by pyrosequencing variable regions of the small-subunit rRNA gene. Especially for the parabasalids, these data revealed undiscovered taxa and provided a phylogenetic basis for a more accurate understanding of diversity, diversification, and community composition. The composition of the parabasalid communities was found to be strongly structured by the phylogeny of their hosts, indicating the importance of historical effects, although exceptions were also identified. Particularly, spirotrichonymphids and trichonymphids likely were transferred between host lineages. In contrast, host phylogeny was not sufficient to explain the majority of bacterial community composition, but the compositions of theBacteroidetes,Elusimicrobia,Tenericutes,Spirochaetes, andSynergisteswere structured by host phylogeny perhaps due to their symbiotic associations with protists. All together, historical effects probably resulting from vertical inheritance have had a prominent role in structuring the hindgut communities, especially of the parabasalids, but dispersal and environmental acquisition have played a larger role in community composition than previously expected.

scholarly journals Regulation of Plasmodium yoelii Oocyst Development by Strain- and Stage-Specific Small-Subunit rRNA

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Yanwei Qi ◽  
Feng Zhu ◽  
Richard T. Eastman ◽  
Young Fu ◽  
Martine Zilversmit ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Small Subunit ◽  
Plasmodium Yoelii ◽  
Rrna Genes ◽  
Parasite Development ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Malaria Parasites ◽  
Content Type ◽  
Small Subunit Rrna Gene

ABSTRACT One unique feature of malaria parasites is the differential transcription of structurally distinct rRNA (rRNA) genes at different developmental stages: the A-type genes are transcribed mainly in asexual stages, whereas the S-type genes are expressed mostly in sexual or mosquito stages. Conclusive functional evidence of different rRNAs in regulating stage-specific parasite development, however, is still absent. Here we performed genetic crosses of Plasmodium yoelii parasites with one parent having an oocyst development defect (ODD) phenotype and another producing normal oocysts to identify the gene(s) contributing to the ODD. The parent with ODD—characterized as having small oocysts and lacking infective sporozoites—was obtained after introduction of a plasmid with a green fluorescent protein gene into the parasite genome and subsequent passages in mice. Quantitative trait locus analysis of genome-wide microsatellite genotypes of 48 progeny from the crosses linked an ~200-kb segment on chromosome 6 containing one of the S-type genes (D-type small subunit rRNA gene [D-ssu]) to the ODD. Fine mapping of the plasmid integration site, gene expression pattern, and gene knockout experiments demonstrated that disruption of the D-ssu gene caused the ODD phenotype. Interestingly, introduction of the D-ssu gene into the same parasite strain (self), but not into a different subspecies, significantly affected or completely ablated oocyst development, suggesting a stage- and subspecies (strain)-specific regulation of oocyst development by D-ssu. This study demonstrates that P. yoelii D-ssu is essential for normal oocyst and sporozoite development and that variation in the D-ssu sequence can have dramatic effects on parasite development. IMPORTANCE Malaria parasites are the only known organisms that express structurally distinct rRNA genes at different developmental stages. The differential expression of these genes suggests that they play unique roles during the complex life cycle of the parasites. Conclusive functional proof of different rRNAs in regulating parasite development, however, is still absent or controversial. Here we functionally demonstrate for the first time that a stage-specifically expressed D-type small-subunit rRNA gene (D-ssu) is essential for oocyst development of the malaria parasite Plasmodium yoelii in the mosquito. This study also shows that variations in D-ssu sequence and/or the timing of transcription may have profound effects on parasite oocyst development. The results show that in addition to protein translation, rRNAs of malaria parasites also regulate parasite development and differentiation in a strain-specific manner, which can be explored for controlling parasite transmission.

scholarly journals Description of Pelistega indica sp. nov., isolated from human gut

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1389-1394 ◽  
Author(s):  
Om Prakash ◽  
Hitendra Munot ◽  
Yogesh Nimonkar ◽  
Madhu Sharma ◽  
Shreyas Kumbhare ◽  
...  
Keyword(s):  
Similarity Search ◽  
Type Species ◽  
Sequence Similarity ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Healthy Human ◽  
Content Type ◽  
Link Type ◽  
Polyphasic Characterization

A Gram-stain-negative, motile, non-spore-forming, coccoid bacterium was isolated from a stool sample of a healthy human subject and formed cream colour colonies on tryptic soy agar. Almost full-length (1500 bp) small subunit rRNA (16S rRNA) gene sequences were generated and a similarity search was conducted by blast. The results of the similarity search indicated that the bacterium belongs to the class Betaproteobacteria , family Alcaligenaceae . It showed maximum sequence similarity (96.5 %) with Pelistega europaea CCUG 39967T followed by Advenella mimigardefordensis DSM 17166T (96.1 %) and Taylorella asinigenitalis LMG 19572T (95.3 %). The DNA G+C content of strain HM-7T was 42 mol%. Strain HM-7T contained C14 : 0, C16 : 0, C16 : 0 3-OH and C18 : 0 as the dominant fatty acids. Morphological, physiological and biochemical data also indicated that strain HM-7T represents a member of the genus Pelistega , but at the same time distinguished it from Pelistega europaea CCUG 39967T, the only species of the genus with a validly published name. Based on polyphasic characterization we conclude that the bacterium represents a novel species of the genus Pelistega and propose the name Pelistega indica sp. nov., with strain HM-7T ( = MCC 2185T = DSM 27484T) as the type strain of the species.

scholarly journals Vaginal bacterial community composition and concentrations of estradiol at the time of artificial insemination in Brangus heifers

2020 ◽  
Vol 98 (6) ◽  
Author(s):  
Riley D Messman ◽  
Zully E Contreras-Correa ◽  
Henry A Paz ◽  
George Perry ◽  
Caleb O Lemley
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Artificial Insemination ◽  
Beta Diversity ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Species Level ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Vaginal Tract

Abstract The knowledge surrounding the bovine vaginal microbiota and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal bacterial community and estradiol concentrations at the time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-d Co-Synch + controlled internal drug release estrus synchronization protocol. At AI, a double-guarded uterine culture swab was used to sample the anterior vaginal tract. Immediately after swabbing the vaginal tract, blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) vs. nonpregnant (n = 49) between 41 and 57 d post-AI. Additionally, heifers were classified into low (1.1 to 2.5 pg/mL; n = 21), medium (2.6 to 6.7 pg/mL; n = 30), and high (7.2 to 17.6 pg/mL; n = 27) concentration of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4 region from the 16S rRNA gene using the Illumina Miseq platform. Alpha diversity was compared via ANOVA and beta diversity was compared via PERMANOVA. There were no differences in the Shannon diversity index (alpha diversity; P = 0.336) or Bray–Curtis dissimilarity (beta diversity; P = 0.744) of pregnant vs. nonpregnant heifers. Overall, bacterial community composition in heifers with high, medium, or low concentrations of estradiol did not differ (P = 0.512). While no overall compositional differences were observed, species-level differences were present within pregnancy status and estradiol concentration groups. The implications of these species-level differences are unknown, but these differences could alter the vaginal environment thereby influencing fertility and vaginal health. Therefore, species-level changes could provide better insight rather than overall microbial composition in relation to an animal’s reproductive health.

scholarly journals Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

2015 ◽  
Vol 81 (14) ◽  
pp. 4697-4710 ◽  
Author(s):  
Kelsea A. Jewell ◽  
Caroline A. McCormick ◽  
Christine L. Odt ◽  
Paul J. Weimer ◽  
Garret Suen
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Milk Production ◽  
Feed Efficiency ◽  
Production Efficiency ◽  
Bacterial Community Composition ◽  
Feed Consumption ◽  
Rrna Gene ◽  
Content Type ◽  
Bacterial Microbiota

ABSTRACTFourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows wereBacteroidetes(49.42%),Firmicutes(39.32%),Proteobacteria(5.67%), andTenericutes(2.17%), and the most abundant genera includedPrevotella(40.15%),Butyrivibrio(2.38%),Ruminococcus(2.35%),Coprococcus(2.29%), andSucciniclasticum(2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles.

scholarly journals Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake

2014 ◽  
Vol 80 (21) ◽  
pp. 6807-6818 ◽  
Author(s):  
Esther A. Gies ◽  
Kishori M. Konwar ◽  
J. Thomas Beatty ◽  
Steven J. Hallam
Keyword(s):  
Single Cell ◽  
Niche Partitioning ◽  
454 Sequencing ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Metabolic Potential ◽  
Content Type ◽  
Lake Ecosystems ◽  
Pathway Reconstruction

ABSTRACTDespite recent advances in metagenomic and single-cell genomic sequencing to investigate uncultivated microbial diversity and metabolic potential, fundamental questions related to population structure, interactions, and biogeochemical roles of candidate divisions remain. Numerous molecular surveys suggest that stratified ecosystems manifesting anoxic, sulfidic, and/or methane-rich conditions are enriched in these enigmatic microbes. Here we describe diversity, abundance, and cooccurrence patterns of uncultivated microbial communities inhabiting the permanently stratified waters of meromictic Sakinaw Lake, British Columbia, Canada, using 454 sequencing of the small-subunit rRNA gene with three-domain resolution. Operational taxonomic units (OTUs) were affiliated with 64 phyla, including more than 25 candidate divisions. Pronounced trends in community structure were observed for all three domains with eukaryotic sequences vanishing almost completely below the mixolimnion, followed by a rapid and sustained increase in methanogen-affiliated (∼10%) and unassigned (∼60%) archaeal sequences as well as bacterial OTUs affiliated withChloroflexi(∼22%) and candidate divisions (∼28%). Network analysis revealed highly correlated, depth-dependent cooccurrence patterns betweenChloroflexi, candidate divisions WWE1, OP9/JS1, OP8, and OD1, methanogens, and unassigned archaeal OTUs indicating niche partitioning and putative syntrophic growth modes. Indeed, pathway reconstruction using recently published Sakinaw Lake single-cell genomes affiliated with OP9/JS1 and OP8 revealed complete coverage of the Wood-Ljungdahl pathway with potential to drive syntrophic acetate oxidation to hydrogen and carbon dioxide under methanogenic conditions. Taken together, these observations point to previously unrecognized syntrophic networks in meromictic lake ecosystems with the potential to inform design and operation of anaerobic methanogenic bioreactors.

Desulfotomaculum peckii sp. nov., a moderately thermophilic member of the genus Desulfotomaculum , isolated from an upflow anaerobic filter treating abattoir wastewaters

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2082-2087 ◽  
Author(s):  
Linda Jabari ◽  
Hana Gannoun ◽  
Jean-Luc Cayol ◽  
Moktar Hamdi ◽  
Bernard Ollivier ◽  
...  
Keyword(s):  
Type Species ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Terminal Electron Acceptor ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Sulfate Reducing ◽  
Link Type ◽  
Nitrate And Nitrite

A novel anaerobic thermophilic sulfate-reducing bacterium designated strain LINDBHT1T was isolated from an anaerobic digester treating abattoir wastewaters in Tunisia. Strain LINDBHT1T grew at temperatures between 50 and 65 °C (optimum 55–60 °C), and at pH between 5.9 and 9.2 (optimum pH 6.0–6.8). Strain LINDBHT1T required salt for growth (1–40 g NaCl l−1), with an optimum of 20–30 g l−1. In the presence of sulfate as terminal electron acceptor, strain LINDBHT1T used H2/CO2, propanol, butanol and ethanol as carbon and energy sources but fumarate, formate, lactate and pyruvate were not utilized. Butanol was converted to butyrate, while propanol and ethanol were oxidized to propionate and acetate, respectively. Sulfate, sulfite and thiosulfate were utilized as terminal electron acceptors but elemental sulfur, iron (III), fumarate, nitrate and nitrite were not used. The G+C content of the genomic DNA was 44.4 mol%. Phylogenetic analysis of the small-subunit rRNA gene sequence indicated that strain LINDBHT1T was affiliated to the genus Desulfotomaculum with the type strains of Desulfotomaculum halophilum and Desulfotomaculum alkaliphilum as its closest phylogenetic relatives (about 89 % similarity). This strain represents a novel species of the genus Desulfotomaculum , Desulfotomaculum peckii sp. nov.; the type strain is LINDBHT1T ( = DSM 23769T = JCM 17209T).

scholarly journals Respiratory Microbiota Dynamics following Streptococcus pneumoniae Acquisition in Young and Elderly Mice

2014 ◽  
Vol 82 (4) ◽  
pp. 1725-1731 ◽  
Author(s):  
Cassandra L. Krone ◽  
Giske Biesbroek ◽  
Krzysztof Trzciński ◽  
Elisabeth A. M. Sanders ◽  
Debby Bogaert
Keyword(s):  
Streptococcus Pneumoniae ◽  
Young Adult ◽  
Hypervariable Region ◽  
Small Subunit ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Small Subunit Rrna ◽  
Content Type ◽  
Portal Of Entry ◽  
The Impact

ABSTRACTThe upper respiratory tract (URT) is a distinct microbial niche of low-density bacterial communities and, also, a portal of entry for many potential pathogens, includingStreptococcus pneumoniae. Thus far, animal models have been used to study the dynamics of and interactions between limited numbers of different species in the URT. Here, we applied a deep sequencing approach to explore, for the first time, the impact ofS. pneumoniaeacquisition on URT microbiota in a mouse model, as well as potential age-dependent effects. Young-adult and elderly mice were inoculated intranasally withS. pneumoniae, and nasal lavage samples were collected for up to 28 days postcolonization. Bacterial DNA extracted from lavage samples was subjected to barcoded pyrosequencing of the V5-to-V7 hypervariable region of the small-subunit rRNA gene. We observed highly diverse microbial profiles, with the presence overall of 15 phyla and approximately 645 operational taxonomic units (OTUs). We noted differences in the composition of microbiota between young and elderly mice, with a significantly higher abundance ofBacteroidetesin the young mice. The introduction ofS. pneumoniaeinto the URT led to a temporary dominance of pneumococci in the microbiota of all mice, accompanied by a significant decrease in microbial diversity. As mice gradually cleared the colonization, the diversity returned to baseline levels. Diversification was accompanied by an early expansion ofBacteroidetes,Staphylococcusspp., andLachnospiraceae. Moreover, theBacteroidetesexpansion was significantly greater in young-adult than in elderly mice. In conclusion, we observed differences in URT microbiota composition between naive young-adult and elderly mice that were associated with differences in pneumococcal clearance over time.

Mesotoga infera sp. nov., a mesophilic member of the order Thermotogales , isolated from an underground gas storage aquifer

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3003-3008 ◽  
Author(s):  
Wajdi Ben Hania ◽  
Anne Postec ◽  
Thomas Aüllo ◽  
Anthony Ranchou-Peyruse ◽  
Gaël Erauso ◽  
...  
Keyword(s):  
Type Species ◽  
Elemental Sulfur ◽  
Gas Storage ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Underground Gas Storage ◽  
Terminal Electron Acceptor ◽  
Content Type ◽  
Link Type

Strain VNs100T, a novel mesophilic, anaerobic, rod-coccoid-shaped bacterium, having a sheath-like outer structure (toga), was isolated from a water sample collected in the area of an underground gas storage aquifer. It was non-motile with cells appearing singly (2–4 µm long×1–2 µm wide), in pairs or as long chains and stained Gram-negative. Strain VNs100T was heterotrophic, able to use arabinose, cellobiose, fructose, galactose, glucose, lactose, lactate, mannose, maltose, raffinose, ribose, sucrose and xylose as energy sources only in the presence of elemental sulfur as terminal electron acceptor. Acetate, CO2 and sulfide were the end products of sugar metabolism. Hydrogen was not detected. Elemental sulfur, but not thiosulfate, sulfate or sulfite, were reduced to sulfide. Strain VNs100T grew at temperatures between 30 and 50 °C (optimum 45 °C), at pH values between 6.2 and 7.9 (optimum 7.3–7.5) and at NaCl concentrations between 0 and 15 g l−1 (optimum 2 g l−1). The DNA G+C content was 47.5 mol%. The main cellular fatty acid was C16 : 0. Phylogenetic analysis of the small subunit rRNA gene sequence indicated that strain VNs100T had as its closest relatives ‘ Mesotoga sulfurireducens’ (97.1 % similarity) and Mesotoga prima (similarity of 97.1 % and 97.7 % with each of its two genes, respectively) within the order Thermotogales . Hybridization between strain VNS100T and ‘M. sulfurireducens’ and between strain VNS100T and M. prima showed 12.9 % and 20.6 % relatedness, respectively. Based on phenotypic, phylogenetic and taxonomic characteristics, strain VNs100T is proposed as a representative of a novel species of the genus Mesotoga in the family Thermotogaceae , order Thermotogales . The name Mesotoga infera sp. nov. is proposed. The type strain is VNs100T ( = DSM 25546T = JCM 18154T).

scholarly journals Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6768
Author(s):  
Matheus A.P. Cipriano ◽  
Afnan K.A. Suleiman ◽  
Adriana P.D. da Silveira ◽  
Janaína B. do Carmo ◽  
Eiko E. Kuramae
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Microbial Community Composition ◽  
Nitrous Oxide Emissions ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Microbial Composition

The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on16S rRNAsequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar toLysinibacillus, encode fornirKgene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.

Phenotypic effects of targeted mutations in the small subunit rRNA gene of Tetrahymena thermophila

1993 ◽  
Vol 13 (8) ◽  
pp. 4814-4825
Author(s):  
R Sweeney ◽  
L Chen ◽  
M C Yao
Keyword(s):  
Tertiary Structure ◽  
Tetrahymena Thermophila ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Variable Regions ◽  
Small Subunit Rrna Gene

Tetrahymena thermophila is an ideal organism with which to study functional aspects of the rRNAs in vivo since the somatic rRNA genes of T. thermophila can be totally replaced by cloned copies introduced via microinjection. In this study, we made small insertions into seven sites within the small subunit rRNA gene and observed their phenotypic effects on transformed cells. Two mutated genes coding for rRNA (rDNAs), both of which bear insertions in highly conserved sequences, failed to transform and are therefore believed to produce nonfunctional rRNAs. Three other altered rDNAs produce functional rRNAs that can substitute for most or all of the cellular rRNA. Two of these bear insertions in highly variable regions, and, surprisingly, the other has an insertion in a region that is well conserved for both sequence and secondary structure among eucaryotes. In addition, two other insertions appear to destabilize rRNAs that contain them. Our findings make predictions concerning the positions of some of these sites within the tertiary structure of the small ribosomal subunit and thus serve as an in vivo test of the existing tertiary structure models for the small subunit rRNA. Our results are in good agreement with expectations based on sequence comparison and in vitro work.

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