scholarly journals Overestimation of the Abundance of Sulfate-Reducing Bacteria in Human Feces by Quantitative PCR Targeting the Desulfovibrio 16S rRNA Gene

2011 ◽  
Vol 77 (10) ◽  
pp. 3544-3546 ◽  
Author(s):  
C. T. Christophersen ◽  
M. Morrison ◽  
M. A. Conlon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Quantitative Pcr ◽  
Sulfate Reducing Bacteria ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Gene Assay ◽  
Reducing Bacteria ◽  
Pcr Targeting ◽  
The 16S Rrna Gene

ABSTRACTThe dominant genus of sulfate-reducing bacteria (SRB) in humans isDesulfovibrio, and quantitative PCR (QPCR) targeting the 16S rRNA gene is often used in assays. We show that the 16S rRNA gene assay overestimated SRB abundance in feces from 24 adults compared to QPCR assays using primers targeting two genes involved in SRB energy metabolism.

scholarly journals Production of biogas: relationship between methanogenic and sulfate-reducing microorganisms

2017 ◽  
Vol 12 (1) ◽  
pp. 82-91 ◽  
Author(s):  
Ivan Kushkevych ◽  
Monika Vítězová ◽  
Tomáš Vítěz ◽  
Milan Bartoš
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Biogas Production ◽  
Sulfate Reducing Bacteria ◽  
Quantitative Composition ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Relationship Of ◽  
Reducing Bacteria

AbstractThe production of high-quality methane depends on many factors, including temperature, pH, substrate, composition and relationship of the microorganisms. The qualitative and quantitative composition of methanogenic and sulfate-reducing microorganisms and their relationship in the experimental bioreactors has never been studied. The aim of this research was to characterize, for the first time, the diversity of the methanogenic microorganisms and sulfate-reducing bacteria, and study their relationship and biogas production in experimental bioreactors. Amplification of 16S rRNA gene fragments was carried out. Purified amplicons were paired-end sequenced on an Illumina Mi-Seq platform. The dominant morphotypes of these microorganisms in the bioreactor were homologous (99%) by the sequences of 16S rRNA gene to theMethanosarcina,Thermogymnomonas,Methanoculleusgenera andArchaeondeposited in GenBank. Three dominant genera of sulfate-reducing bacteria,Desulfomicrobium,DesulfobulbusandDesulfovibrio, were detected in the bioreactor. The phylogenetic trees showing their genetic relationship were constructed. The diversity and number of the genera, production of methane, hydrogen sulfide and hydrogen in the bioreactor was investigated. This research is important for understanding the relationship between methanogenic microbial populations and other bacterial physiological groups, their substrate competition and, in turn, can be helpful for controlling methanogenesis in bioreactors.

scholarly journals A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jaeho Song ◽  
Juchan Hwang ◽  
Ilnam Kang ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Novel Species ◽  
Sulfate Reducing Bacteria ◽  
Rrna Gene ◽  
Novel Genus ◽  
Sulfate Reducing ◽  
Tidal Flat Sediments ◽  
Reducing Bacteria

AbstractTidal-flat sediments harbor a diverse array of sulfate-reducing bacteria. To isolate novel sulfate-reducing bacteria and determine their abundance, a tidal-flat sediment sample collected off Ganghwa Island (Korea) was investigated using cultivation-based and culture-independent approaches. Two Gram-stain-negative, strictly anaerobic, rod-shaped, sulfate-reducing bacteria, designated IMCC35004T and IMCC35005T, were isolated from the sample. The two strains reduced sulfate, sulfite, elemental sulfur, thiosulfate, Fe(III) citrate, and Mn(IV) oxide by utilizing several carbon sources, including acetate. The 16S rRNA gene amplicon sequencing revealed that the tidal-flat sediment contained diverse members of the phylum Desulfobacterota, and the phylotypes related to IMCC35004T and IMCC35005T were < 1%. The two strains shared 97.6% similarity in 16S rRNA gene sequence and were closely related to Desulfopila aestuarii DSM 18488T (96.1–96.5%). The average nucleotide identity, level of digital DNA–DNA hybridization, average amino acid identity, and percentages of conserved proteins determined analyzing the whole-genome sequences, as well as the chemotaxonomic data showed that the two strains belong to two novel species of a novel genus. Additionally, genes related to dissimilatory sulfate reduction were detected in the genomes of the two strains. Unlike the genera Desulfopila and Desulfotalea, IMCC35004T and IMCC35005T contained menaquinone-5 as the major respiratory quinone. Collectively, IMCC35004T and IMCC35005T were concluded to represent two novel species of a novel genus within the family Desulfocapsaceae, for which the names Desulfosediminicola ganghwensis gen. nov., sp. nov. (IMCC35004T = KCTC 15826T = NBRC 114003T) and Desulfosediminicola flagellatus sp. nov. (IMCC35005T = KCTC 15827T = NBRC 114004T) are proposed.

scholarly journals Chromium Precipitation Activity and Molecular Characterization of Sulfate-Reducing Bacteria

2019 ◽  
Vol 4 (1) ◽  
pp. 15
Author(s):  
Dwiana Muflihah Yulianti ◽  
Endah Retnaningrum ◽  
Wahyu Wilopo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sulfate Reducing Bacteria ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Sulfate Reducing ◽  
Sulfate Reducing Bioreactor ◽  
Reducing Bacteria

Chromium is one of the metals used in many areas of industry., However, chromium is toxic to organisms when present in large quantities in the environment. One of the method for treatment of hazardous waste containing chromium in the aquatic environment can be removed by bioremediation using sulfate-reducing bacteria (SRB). Therefore, the purpose of this research were to analyze the chromium precipitation activity of sulfate-reducing bacteria isolated from sulfate reducing bioreactor and its molecular identification using 16S rRNA gene sequences. The result observed that the isolate of sulfate-reducing bacteria (KGP1 strain) has chromium tolerancy ability up to 5 ppm. It also showed that the strain KGP1 could precipitate chromium up to 0.141 ppm (79 %) on 5 days incubation. Based on 16S rRNA gene sequences, this strain identified as Desulfovibrio aerotolerans.

Microbial Diversity in Acidic Anaerobic Sediments at the Geothermal Caviahue-Copahue System, Argentina

2013 ◽  
Vol 825 ◽  
pp. 7-10 ◽  
Author(s):  
Graciana Willis ◽  
Sabrina Hedrich ◽  
Ivan Nancucheo ◽  
D. Barrie Johnson ◽  
Edgardo R. Donati
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hot Spring ◽  
Rrna Gene ◽  
Sulfate Reducer ◽  
Sulfate Reducing ◽  
Culture Independent ◽  
Cultivation Techniques ◽  
Reducing Bacteria ◽  
The 16S Rrna Gene

In this work we have examined the bacterial diversity from the hot spring sediment Agua del Limón (AL1) present at the geothermal Caviahue-Copahue system using a combination of molecular and cultivation techniques, with particular emphasis on indigenous anaerobic prokaryotes. Microorganisms involved in the iron (Acidithiobacillus ferrooxidansandLeptospirillumspp.) and sulphur (Acidithiobacillusspp., Thermotogales-like bacteria,Thiomonassp., andDesulfurellasp.) cycles were identified in the clone library. Although no obvious sulfate-reducing bacteria were detected by culture-independent techniques, several isolates related to the mesophilic, spore-forming sulfate-reducer"Desulfobacillus acidavidus"strain CL4 were isolated at 30°C and 40°C. The 16S rRNA gene of another isolate showed 94% similarity toDesulfotomaculum thermobenzoicum. Sulfate-reducing enrichment cultures of the Copahue samples were also dominated by"Dsb. acidavidus"CL4.

scholarly journals Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1913 ◽  
Author(s):  
Elizabeth Trembath-Reichert ◽  
David H. Case ◽  
Victoria J. Orphan
Keyword(s):  
Network Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sulfate Reducing Bacteria ◽  
Gene Clone ◽  
Rrna Gene ◽  
Methane Seep ◽  
Sulfate Reducing ◽  
Card Fish ◽  
Reducing Bacteria

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1,Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involvingEpsilon-,Delta-, andGammaproteobacteriain methane seep ecosystems.

scholarly journals Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1902-1907 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Meromictic Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
The Novel ◽  
Sulfate Reducing ◽  
The Family ◽  
The 16S Rrna Gene

A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0–4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0–7.5 and the optimum temperature was 42–45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91  % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).

scholarly journals Desulfovibrio arcticus sp. nov., a psychrotolerant sulfate-reducing bacterium from a cryopeg

2012 ◽  
Vol 62 (1) ◽  
pp. 33-37 ◽  
Author(s):  
Svetlana A. Pecheritsyna ◽  
Elizaveta M. Rivkina ◽  
Vladimir N. Akimov ◽  
Viktoria A. Shcherbakova
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Barents Sea ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sulfate Reducing ◽  
The 16S Rrna Gene

A psychrotolerant sulfate-reducing bacterium, designated B15T, was isolated from supercooled water brine from within permafrost of the Varandey Peninsula, on the southern coast of the Barents Sea. Cells were Gram-negative, motile vibrions (3.0–4.0×0.4–0.5 µm) with a single polar flagellum. The isolate was positive for desulfoviridin as a bisulfite reductase. Strain B15T grew at −2 to 28 °C (optimum 24 °C) and with 0–2.0 % NaCl (optimum 0.2 %). The isolate used H2 plus acetate, formate, ethanol, lactate, pyruvate and choline as electron donors and used sulfate, sulfite, thiosulfate, elemental sulfur, DMSO and Fe3+ as electron acceptors. Pyruvate and lactate were not fermented in the absence of sulfate. The G+C content of genomic DNA was 55.2 mol%. Analysis of the 16S rRNA gene sequence showed that the isolate belonged to the genus Desulfovibrio. Its closest relatives were Desulfovibrio idahonensis CY1T (98.8 % 16S rRNA gene sequence similarity) and Desulfovibrio mexicanus Lup1T (96.5 %). On the basis of genotypic, phenotypic and phylogenetic characteristics, the isolate represents a novel species, for which the name Desulfovibrio arcticus sp. nov. is proposed; the type strain is B15T ( = VKM B-2367T = DSM 21064T).

scholarly journals Quantification of Expression of Staphylococcus epidermidis Housekeeping Genes with Taqman Quantitative PCR during In Vitro Growth and under Different Conditions

2001 ◽  
Vol 183 (24) ◽  
pp. 7094-7101 ◽  
Author(s):  
S. J. Vandecasteele ◽  
W. E. Peetermans ◽  
R. Merckx ◽  
J. Van Eldere
Keyword(s):  
Gene Expression ◽  
Heat Shock ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Quantitative Pcr ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
In Vitro Growth ◽  
The 16S Rrna Gene

ABSTRACT The aims of the present study were (i) to develop and test a sensitive and reproducible method for the study of gene expression in staphylococci and (ii) to study the expression of five housekeeping genes which are involved in nucleic acid metabolism (gmk, guanylate kinase; the dihydrofolate reductase [DHFR] gene), glucose metabolism (tpi, triosephosphate isomerase), and protein metabolism (the 16S rRNA gene;hsp-60, heat-shock protein 60) during in vitro exponential and stationary growth. A modified method for instant mRNA isolation was combined with gene quantification via Taqman real-time quantitative PCR. The detection limit of our method was 10 copies of RNA. The average intersample variability was 16%. A 10-fold increase in the expression of the hsp-60 gene was induced by exposure to a 10°C heat shock (37 to 47°C) for 10 min. During in vitro growth, the expression of all five housekeeping genes showed rapid up-regulation after inoculation of the bacteria in brain heart infusion medum and started to decline during the mid-exponential-growth phase. Maximal gene expression was 110- to 300-fold higher than gene expression during stationary phase. This indicates that housekeeping metabolism is a very dynamic process that is extremely capable of adapting to different growth conditions. Expression of the 16S rRNA gene decreases significantly earlier than that of other housekeeping genes. This confirms earlier findings forEscherichia coli that a decline in bacterial ribosomal content (measured by 16S rRNA gene expression) precedes the decline in protein synthesis (measured by mRNA expression).

scholarly journals Accuracy of Conventional PCR Targeting the 16S rRNA Gene with the Ot-16sRF1 and Ot-16sRR1 Primers for Diagnosis of Scrub Typhus: a Case-Control Study: TABLE 1

2015 ◽  
Vol 54 (1) ◽  
pp. 178-179 ◽  
Author(s):  
Choon-Mee Kim ◽  
Min Keun Cho ◽  
Dong-Min Kim ◽  
Na-Ra Yun ◽  
Seok Won Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Scrub Typhus ◽  
Rrna Gene ◽  
Conventional Pcr ◽  
Content Type ◽  
Increased Sensitivity ◽  
Good Diagnostic Accuracy ◽  
Pcr Targeting ◽  
The 16S Rrna Gene

We retrospectively evaluated the accuracy of conventional PCR targeting the 16S rRNA gene (16S C-PCR) using the Ot-16sRF1/Ot-16sRR1 primers for diagnosing scrub typhus. The diagnosis ofOrientia tsutsugamushiinfection by 16S C-PCR presented an increased sensitivity of 87.0% and specificity of 100% compared with those obtained with other targets and is thus a simple and clinically useful method with good diagnostic accuracy.

scholarly journals Chlamydiales and hemotropic mycoplasma in captive and free-living bats

2020 ◽  
Author(s):  
Janine Fritschi ◽  
Hanna Marti ◽  
Helena M.B. Seth-Smith ◽  
Sébastien Aeby ◽  
Gilbert Greub ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Real Time ◽  
Real Time Pcr ◽  
Rrna Gene ◽  
Free Living ◽  
Hemotropic Mycoplasma ◽  
Total Prevalence ◽  
Pcr Targeting ◽  
The 16S Rrna Gene

Abstract Background: Bats are hosts for a variety of microorganisms, however, little is known about the presence of Chlamydiales and hemotropic mycoplasma. This study investigated 475 free-living and captive bats from Switzerland, Germany and Costa Rica for the occurrence of Chlamydiales and hemotropic mycoplasma.Results: Screening for Chlamydiales was performed using a Chlamydiaceae-specific real-time PCR targeting the 23S rRNA gene and a pan-Chlamydiales PCR targeting the 16S rRNA gene resulting in a total prevalence of 31.4%. For sequencing, a PCR with the specifically designed inner primers panFseq and panRseq was performed, and criteria published by Pillonel et al. were used to classify the 19 obtained sequences, resulting in the formation of two groups. Groups one and two shared sequence identities to Chlamydiaceae and to Chlamydia-like organisms, including Rhabdochlamydiaceae and unclassified Chlamydiales from environmental samples, respectively.Analysis for the presence of hemotropic mycoplasma was performed using a universal SYBR Green hemoplasma screening real-time PCR targeting the 16S rRNA gene, real-time PCRs specific for M. haemofelis-like and 'Candidatus M. haemominutum'-like organisms and two conventional PCRs targeting an 871-bp and 1030-bp region of the 16S rRNA gene resulting in a total prevalence of 0.7%. Sequencing and phylogenetic analysis of the 871-bp and 1030-bp region of the 16S rRNA gene were used to classify positive specimens and infer their phylogenetic relationships. Three sequences with identities to other unidentified mycoplasma found in vampire bats and Chilean bats were obtained.Conclusions: Bats can harbor Chlamydiales and hemotropic mycoplasma and the newly described sequences in this study indicate that the diversity of these bacteria in bats is much larger than thought before. Both, Chlamydiales and hemotropic mycoplasmas are not restricted to certain bat species or countries and free-living as well as captive bats can be colonized. In conclusion, bats represent another potential host or vector for novel, previously unidentified, Chlamydiales and hemotropic mycoplasma.

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