Group‐specific primer and probe sets to detect methanogenic communities using quantitative real‐time polymerase chain reaction

Yu, Youngseob; Lee, Changsoo; Kim, Jaai; Hwang, Seokhwan

doi:10.1002/bit.20347

Cited by 1,350 publications

(767 citation statements)

References 36 publications

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“…The V3 and V4 region of the 16S rRNA gene was amplified using forward primer PRK341 and reverse primer PRK806 [20], with further processing for Illumina sequencing as previously described [19]. Finally, quantification of butyric acid in cecum content was performed by GC [21].…”

Section: Methodsmentioning

confidence: 99%

Cecal microbiota association with tumor load in a colorectal cancer mouse model

Bråten

Södring

Paulsen

et al. 2017

Microbial Ecology in Health and Disease

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Background: Colorectal cancer (CRC) is one of the most common cancer types worldwide. The role of the intestinal microbiota in CRC, however, is not well established. In particular, the co-variation between age, tumor progression and microbiota remains largely unknown.Objective and design: We therefore used a recently developed A/J Min/+ mouse model resembling human CRC to investigate how microbial composition in cecum correlates with tumor progression, butyrate and age.Results: We found that the association between the gut microbiota and tumor load was stronger, by far, than the association with both butyrate and age. The strongest direct tumor association was found for mucosal bacteria, with nearly 60% of the significantly correlating operational taxonomic units being correlated with CRC tumor load alone.Conclusion: We favor a systemic association between tumor load and microbiota, since the correlations are associated with tumor load in gut segments other than the cecum (both small and large intestine).

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Section: Methodsmentioning

confidence: 99%

Cecal microbiota association with tumor load in a colorectal cancer mouse model

Bråten

Södring

Paulsen

et al. 2017

Microbial Ecology in Health and Disease

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“…Methanomicrobiales (MMB), Methanosarcinaceae (Msc) and Methanosaetaceae (Mst) were previously described by Yu et al (2005). The reaction mixture of 20µL was prepared by means of the …”

Section: S5 Real-time Pcr Analysismentioning

confidence: 99%

Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion

et al. 2014

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Anaerobic digestion (AD) is a well-established technology for energy recovery from organic waste streams. Several studies noted that inserting a bioelectrochemical system (BES) inside an anaerobic digester can increase biogas output, however the mechanism behind this was not explored and primary controls were not executed. Here, we evaluated whether a BES could stabilize AD of molasses. Lab-scale digesters were operated in the presence or absence of electrodes, in open (no applied potential) and closed circuit conditions. In the control reactors without electrodes methane production decreased to 50% of the initial rate, while it remained stable in the reactors with electrodes, indicating a stabilizing effect. After 91 days of operation, the now colonized electrodes were introduced in the failing AD reactors to evaluate their remediating capacity. This resulted in an immediate increase in CH 4 production and VFA removal. Although a current was generated in the BES operated in closed circuit, no direct effect of applied potential nor current was observed. A high abundance of Methanosaeta was detected on the electrodes, however irrespective of the applied cell potential. This study demonstrated that, in addition to other studies reporting only an increase in methane production, a BES can also remediate AD systems that exhibited process failure. However, the lack of difference between current driven and open circuit systems indicates that the key impact is through biomass retention, rather than electrochemical interaction with the electrodes.

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“…Real-time qPCR was performed using Power SYBR® Green PCR Master Mix (Life Technologies). For the total Eubacteria quantification the primers 338F and 805R (Yu et al 2005) were used for the 16S rRNA gene fragment, and cloned 16S rRNA gene from Escherichia coli (JM109) as a standard. Total SRB were quantified using the primers DSR1F (Wagner et al 1998) and DSR500R (Wilms et al 2007) for amplifying the dsrA operon, and cloned dsrAB genes from Desulfotomaculum geothermicum (DSMZ 3669) as a standard.…”

Section: Quantification Of Total Bacterial 16s Rrna Genes and Dsra Gementioning

confidence: 99%

Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer

et al. 2013

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The microbial diversity of a deep saline aquifer used for geothermal heat storage in the North German Basin was investigated. Genetic fingerprinting analyses revealed distinct microbial communities in fluids produced from the cold and warm side of the aquifer. Direct cell counting and quantification of 16S rRNA genes and dissimilatory sulfite reductase (dsrA) genes by real-time PCR proved different population sizes in fluids, showing higher abundance of bacteria and sulfate reducing bacteria (SRB) in cold fluids compared with warm fluids. The operation-dependent temperature increase at the warm well probably enhanced organic matter availability, favoring the growth of fermentative bacteria and SRB in the topside facility after the reduction of fluid temperature. In the cold well, SRB predominated and probably accounted for corrosion damage to the submersible well pump, and iron sulfide precipitates in the near wellbore area and topside facility filters. This corresponded to lower sulfate content in fluids produced from the cold well as well as higher content of hydrogen gas that was probably released from corrosion, and maybe favored growth of hydrogenotrophic SRB. This study reflects the high influence of microbial populations for geothermal plant operation, because microbiologically induced precipitative and corrosive processes adversely affect plant reliability.2

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Group‐specific primer and probe sets to detect methanogenic communities using quantitative real‐time polymerase chain reaction

Cited by 1,350 publications

References 36 publications

Cecal microbiota association with tumor load in a colorectal cancer mouse model

Cecal microbiota association with tumor load in a colorectal cancer mouse model

Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion

Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer

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